TY - JOUR TI - Symmetrical dinuclear complexes with high DNA affinity based on Ru(dpq)2(phen)2+ AU - Aldrich-Wright, J. AU - Brodie, C. AU - Glazer, E.C. AU - Luedtke, N.W. AU - Elson-Schwab, L. AU - Tor, Y. T2 - Chemical Communications DA - 2004/// PY - 2004/// VL - 10 IS - 8 SP - 1018-1019 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-2442536689&partnerID=MN8TOARS ER - TY - CONF TI - Analysis of Derivatized Biogenic Aldehydes by HPLC Tandem Mass Spectrometry AU - Williams, T.Islam AU - Lovell, M.A. AU - Lynn, B.C. T2 - American Society for Mass Spectrometry C2 - 2004/// CY - Nashville, TN DA - 2004/// PY - 2004/// ER - TY - CHAP TI - Solid State Devices AU - Martin, James T2 - Chemistry: foundations and applications A2 - Lagowski, J.J. A2 - Banks, A.J. A2 - Holme, T. A2 - Silber, H. PY - 2004/// VL - 4 SP - 142–148 PB - Macmillan ER - TY - RPRT TI - Templated Compositions of Inorganic Liquids and Glasses AU - Martin, James DA - 2004/9/14/ PY - 2004/9/14/ M1 - 6,790,382 M3 - U.S. Patent SN - 6,790,382 ER - TY - CONF TI - Amorphous Materials Engineering in Metal-Halide Networks AU - Martin, James T2 - 106th Annual Meeting of The American Ceramic Society C2 - 2004/// CY - Indianapolis, IN DA - 2004/// PY - 2004/// PB - American Ceramic Society ER - TY - SOUND TI - Flexible Crystals and Structured Amorphous Materials AU - Martin, James DA - 2004/// PY - 2004/// ER - TY - CONF TI - On the Mechanism of Metal-Halide Network Formation and Crystal Growth AU - Martin, James T2 - Second American Conference on Neutron Scattering C2 - 2004/6/6/ CY - Baltimore, MD DA - 2004/6/6/ PY - 2004/6/6/ ER - TY - CONF TI - Olefin vs. Carbonyl Reactivity with Copper(I)/Lewis Acid Frameworks AU - Martin, James AU - Capracotta, Michael D. T2 - Gordon Research Conference, Conference on Solid-State Chemistry C2 - 2004/7/25/ CY - Colby-Sawyer College, New Hampshire DA - 2004/7/25/ PY - 2004/7/25/ ER - TY - CONF TI - Scanned Probe Lithography Patterns to Probe Intermolecular Interactions AU - Gorman, C.B. C2 - 2004/// C3 - PMSE preprints DA - 2004/// PB - American Chemical Society ER - TY - CONF TI - Patterning Self-assembled Monolayers Using a Scanning Probe: Technique and Utility AU - Gorman, C.B. C2 - 2004/// C3 - Proceedings of the “Foundations of Nanoscience: Self-Assembled Architectures and Devices” DA - 2004/// SP - 329–333 ER - TY - CHAP TI - Dendritic Encapsulation AU - Cameron, C.S. AU - Gorman, C.B. T2 - Encyclopedia of Nanoscience and Nanotechnology A2 - Nalwa, H. PY - 2004/// VL - 2 SP - 327–335 PB - American Scientific Publishers ER - TY - CHAP TI - Monolayer-Based Scanning Probe Lithography AU - Fuierer, R.R. AU - Gorman, C.B. T2 - Encyclopedia of Nanoscience and Nanotechnology A2 - Nalwa, H. PY - 2004/// VL - 5 SP - 851–859 PB - American Scientific Publishers ER - TY - JOUR TI - PhotochemCAD 2. A Refined Program with Accompanying Spectral Database for Photochemical Calculations AU - Dixon, James M. AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - Photochemistry and Photobiology AB - The PhotochemCAD program has been revised extensively. Calculations can be performed using eight modules (oscillator strength, transition dipole moment and natural radiative lifetime, Förster energy transfer, multicomponent analysis, blackbody radiator, artificial spectrum creation, transmission calculation, and analysis of energy transfer among linear multichromophore arrays). The user interface has been streamlined to facilitate visual display, operation of the various modules, input of user data via a wizard and output of spectra and calculations. The database of absorption and fluorescence spectra has been expanded to 150 photochemically relevant compounds. A database of solar spectra has been added. The program runs under Windows and is equipped with extensive literature references and help features, including a tutorial section with video files. DA - 2004/// PY - 2004/// DO - 10.1562/2004-11-06-tsn-361 ER - TY - JOUR TI - Solution structure and dynamics of Nereis sarcoplasmic calcium binding protein AU - Rabah, G. AU - Popescu, R. AU - Cox, J.A. AU - Engelborghs, Y. AU - Craescu, C.T. DA - 2004/9// PY - 2004/9// DO - 10.2210/pdb1q80/pdb ER - TY - JOUR TI - Can Embedded Annotations Help High School Students Perform Problem Solving Tasks Using A Web-Based Historical Document? AU - Lee, John K. AU - Calandra, Brendan T2 - Journal of Research on Technology in Education AB - Two versions of a Web site on the United States Constitution were used by students in separate high school history classes to solve problems that emerged from four constitutional scenarios. One site contained embedded conceptual scaffolding devices in the form of textual annotations; the other did not. The results of our study demonstrated the situational importance of the annotations as well as the need for instructional Web designers to make their design intentions transparent. A holistic approach to examining annotational content is recommended in which teachers and designers consider how Web-based annotational content might function in instructional settings. An initial topology is also proposed for the annotations on the Web site used in this study. DA - 2004/9// PY - 2004/9// DO - 10.1080/15391523.2004.10782426 VL - 37 IS - 1 SP - 65-84 J2 - Journal of Research on Technology in Education LA - en OP - SN - 1539-1523 1945-0818 UR - http://dx.doi.org/10.1080/15391523.2004.10782426 DB - Crossref ER - TY - JOUR TI - Social Studies Teachers' Use of Classroom-Based and Web-Based Historical Primary Sources AU - Hicks, David AU - Doolittle, Peter AU - Lee, John K. T2 - Theory & Research in Social Education AB - Abstract A limited body of research examines the extent to which social studies teachers are actually utilizing primary sources that are accessible in traditional classroom-based formats versus web-based formats. This paper initiates an exploration of this gap in the literature by reporting on the result of a survey of secondary social studies teachers, all members of the National Council for the Social Studies, that examines the extent to which these social studies teachers are using classroom and web-based primary sources. In particular we ask: To what extent has the availability of web-based primary sources impacted social studies teachers' use of primary sources in the classroom? In order to investigate the above question successfully, we examine the following supporting questions: How are social studies teachers using classroom-based primary sources? How are social studies teachers using web-based primary sources? While the study reveals teachers' understandings of the potential for using primary sources to support historical inquiry and the potential of the web for providing access to previously inaccessible primary sources, the teachers' actual use of both classroom-based and web-based primary sources seems limited. DA - 2004/4// PY - 2004/4// DO - 10.1080/00933104.2004.10473253 VL - 32 IS - 2 SP - 213-247 J2 - Theory & Research in Social Education LA - en OP - SN - 0093-3104 2163-1654 UR - http://dx.doi.org/10.1080/00933104.2004.10473253 DB - Crossref ER - TY - JOUR TI - Lighting Up Biochemiluminescence by the Surface Self-Assembly of DNA-Hemin Complexes AU - Xiao, Yi AU - Pavlov, Valeri AU - Gill, Ron AU - Bourenko, Tatyana AU - Willner, Itamar T2 - ChemBioChem AB - Illuminating DNA: The assembly of two tailored nucleic acids (colored blue and brown in the scheme) in the presence of hemin yields a G-quadruplex that exhibits peroxidase-like activity and catalyzes the generation of chemiluminescence in the presence of H2O2 and luminol. The DNAzyme is employed for the analysis of DNA (green) in solution and on surfaces. DA - 2004/2/26/ PY - 2004/2/26/ DO - 10.1002/cbic.200300794 VL - 5 IS - 3 SP - 374-379 J2 - ChemBioChem LA - en OP - SN - 1439-4227 UR - http://dx.doi.org/10.1002/cbic.200300794 DB - Crossref KW - biocatalysis KW - DNA KW - hemin KW - luminescence KW - monolayers KW - self-assembly ER - TY - JOUR TI - Amplified Chemiluminescence Surface Detection of DNA and Telomerase Activity Using Catalytic Nucleic Acid Labels AU - Pavlov, Valeri AU - Xiao, Yi AU - Gill, Ron AU - Dishon, Arnon AU - Kotler, Moshe AU - Willner, Itamar T2 - Analytical Chemistry AB - A G-rich nucleic acid sequence binds hemin and yields a biocatalytic complex (DNAzyme) of peroxidase activity, namely, the biocatalyzed generation of chemiluminescence in the presence of H2O2 and luminol. The DNAzyme is used as a label for the amplified detection of DNA, or for the analysis of telomerase activity in cancer cells, using chemiluminescence as an output signal. In one configuration, the analyzed DNA is hybridized with a primer nucleic acid that is associated with a Au surface, and the DNAzyme label is hybridized with the surface-confined analyte DNA. The DNA is analyzed with a detection limit of ∼1 × 10-9 M. In the second system, telomerase from HeLa cancer cells induces telomerization of a primer associated with a Au surface and the complementary DNAzyme units are hybridized with the telomere to yield the chemiluminescence. The detection limit of the system corresponds to 1000 HeLa cells in the analyzed sample. DA - 2004/4// PY - 2004/4// DO - 10.1021/ac035219l VL - 76 IS - 7 SP - 2152-2156 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac035219l DB - Crossref ER - TY - JOUR TI - Catalytic Beacons for the Detection of DNA and Telomerase Activity AU - Xiao, Yi AU - Pavlov, Valeri AU - Niazov, Tamara AU - Dishon, Arnon AU - Kotler, Moshe AU - Willner, Itamar T2 - Journal of the American Chemical Society AB - ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCatalytic Beacons for the Detection of DNA and Telomerase ActivityYi Xiao, Valeri Pavlov, Tamara Niazov, Arnon Dishon, Moshe Kotler, and Itamar WillnerView Author Information The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel, and Department of Pathology, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel Cite this: J. Am. Chem. Soc. 2004, 126, 24, 7430–7431Publication Date (Web):May 28, 2004Publication History Received21 December 2003Published online28 May 2004Published inissue 23 June 2004https://doi.org/10.1021/ja031875rCopyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views4911Altmetric-Citations374LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (72 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Absorption,Genetics,Hybridization,Nucleic acids,Peptides and proteins Get e-Alerts DA - 2004/6// PY - 2004/6// DO - 10.1021/ja031875r VL - 126 IS - 24 SP - 7430-7431 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja031875r DB - Crossref ER - TY - JOUR TI - DNAzyme-Functionalized Au Nanoparticles for the Amplified Detection of DNA or Telomerase Activity AU - Niazov, Tamara AU - Pavlov, Valeri AU - Xiao, Yi AU - Gill, Ron AU - Willner, Itamar T2 - Nano Letters AB - DNAzyme-functionalized Au−NPs act as catalytic labels for the amplified detection of DNA and telomerase activity on nucleic acid-functionalized gold surface. The DNAzyme stimulates, in the presence of hemin, H2O2, and luminol, the generation of chemiluminescence. For DNA analysis, a nucleic acid unit complementary to the analyzed DNA is tethered to the DNAzyme structure associated with the Au−NPs. For telomerase activity, a nucleic acid complementary to the telomer repeat units generated on the surface is tethered to the DNAzyme structure associated with the Au−NPs. The detection limit for the detection of DNA is 1 × 10-10 M. The method enables the detection of telomerase activity originating from 1000 HeLa cells. DA - 2004/7/30/ PY - 2004/7/30/ DO - 10.1021/nl0491428 VL - 4 IS - 9 SP - 1683-1687 J2 - Nano Lett. LA - en OP - SN - 1530-6984 1530-6992 UR - http://dx.doi.org/10.1021/nl0491428 DB - Crossref ER - TY - JOUR TI - Electrical contacting of glucose oxidase by DNA-templated polyaniline wires on surfaces AU - Shi, Lixin AU - Xiao, Yi AU - Willner, Itamar T2 - Electrochemistry Communications AB - Poly(aniline–aniline boronic acid) wires are generated on ds-DNA templates, and the resulting wires exhibit redox functions at neutral pH aqueous solutions. The association of flavin adenine dinucleotide (FAD) to the boronic acid ligand followed by the reconstitution of apo-glucose oxidase on the cofactor units yield an integrated enzyme-electrode where the biocatalyst reveals direct electrical contact with the electrode. DA - 2004/10// PY - 2004/10// DO - 10.1016/j.elecom.2004.08.004 VL - 6 IS - 10 SP - 1057-1060 J2 - Electrochemistry Communications LA - en OP - SN - 1388-2481 UR - http://dx.doi.org/10.1016/j.elecom.2004.08.004 DB - Crossref KW - poly(aniline-aniline boronic acid) wires KW - DNA template KW - apo-glucose oxidase KW - reconstitution KW - biosensor ER - TY - JOUR TI - Catalytic Growth of Au Nanoparticles by NAD(P)H Cofactors: Optical Sensors for NAD(P)+-Dependent Biocatalyzed Transformations AU - Xiao, Yi AU - Pavlov, Valeri AU - Levine, Semion AU - Niazov, Tamara AU - Markovitch, Gil AU - Willner, Itamar T2 - Angewandte Chemie International Edition AB - Gold-plated gold: NAD(P)H cofactors mediate the catalytic growth of Au nanoparticles in the presence of AuCl4− and CTAB (cetyltrimethylammonium bromide; see picture). The process allows for the optical detection of the cofactors and the analysis of NAD(P)+-dependent biocatalyzed transformations in solutions and on surfaces. DA - 2004/8/27/ PY - 2004/8/27/ DO - 10.1002/anie.200460608 VL - 43 IS - 34 SP - 4519-4522 J2 - Angew. Chem. Int. Ed. LA - en OP - SN - 1433-7851 1521-3773 UR - http://dx.doi.org/10.1002/anie.200460608 DB - Crossref KW - biosensors KW - cofactors KW - enzymes KW - gold KW - nanostructures ER - TY - JOUR TI - Aptamer-Functionalized Au Nanoparticles for the Amplified Optical Detection of Thrombin AU - Pavlov, Valeri AU - Xiao, Yi AU - Shlyahovsky, Bella AU - Willner, Itamar T2 - Journal of the American Chemical Society AB - ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAptamer-Functionalized Au Nanoparticles for the Amplified Optical Detection of ThrombinValeri Pavlov, Yi Xiao, Bella Shlyahovsky, and Itamar WillnerView Author Information Institute of Chemistry, The Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel Cite this: J. Am. Chem. Soc. 2004, 126, 38, 11768–11769Publication Date (Web):September 3, 2004Publication History Received23 May 2004Published online3 September 2004Published inissue 1 September 2004https://doi.org/10.1021/ja046970uCopyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views9032Altmetric-Citations601LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (65 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Absorption,Gold,Metal nanoparticles,Peptides and proteins,Plasmons Get e-Alerts DA - 2004/9// PY - 2004/9// DO - 10.1021/ja046970u VL - 126 IS - 38 SP - 11768-11769 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja046970u DB - Crossref ER - TY - CHAP TI - Chemical bonding and electronic structure of high-k transition metal dielectrics: applications to interfacial band offset energies and electronically active defects AU - Lucovsky, Gerald AU - Whitten, Jerry L T2 - High-k Gate Dielectrics A2 - Houssa, Michel PY - 2004/11/26/ DO - 10.1887/0750309067/b1246c10 PB - CRC Press SN - 0750309067 UR - http://dx.doi.org/10.1887/0750309067/b1246c10 ER - TY - CONF TI - Accurate and Expedited Diagnosis of Amyloidotic Transthyretin Neuropathy: Proteomic and Genomic Approach AU - Klein, C.J. AU - Kim, C.H. AU - Dyck, P.J. AU - Zeldenrust, S.R. AU - Bergen, H.R. AU - O'Brien, J.F. AU - Nepomuceno, A.I. AU - Butz, M.L. AU - Thibodeau, S.I. AU - Muddiman, D.C. AU - Dyck, P.J. T2 - American Neurological Association, 129th Annual Meeting C2 - 2004/// C3 - Annals of Neurology CY - Toronto, Ontario, Canada DA - 2004/// PY - 2004/10/3/ VL - 56 SP - 29 M1 - S8 ER - TY - CHAP TI - Inorganic Chemistry AU - Maggard, P T2 - Chemistry: Foundations and Applications A2 - Lagowski, J.J. PY - 2004/// VL - 2 PB - Macmillan Reference USA SN - 9780028657233 ER - TY - CONF TI - New Valence Tautomeric Molecules and Materials AU - Schultz, D T2 - International Conference on Molecular Magnetism C2 - 2004/// CY - Tsukuba, Japan DA - 2004/// PY - 2004/10/12/ ER - TY - CONF TI - Exchange Coupling in Paramagnetic Ligands AU - Schultz, D T2 - 2nd Russian Conference on High-Spin Molecules C2 - 2004/// DA - 2004/// PY - 2004/5/16/ ER - TY - JOUR TI - Detection of Genetic Variants of Transthyretin by Liquid Chromatography–Dual Electrospray Ionization Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry AU - Nepomuceno, Angelito I AU - Mason, Christopher J AU - Muddiman, David C AU - Bergen, H Robert, III AU - Zeldenrust, Steven R T2 - Clinical Chemistry AB - One of the numerous proteins causing amyloidosis is transthyretin (TTR), a protein usually responsible for the transport of thyroxine and retinol-binding protein. Variants within TTR cause it to aggregate and form insoluble fibers that accumulate in tissue, leading to organ dysfunction.TTR was immunoprecipitated from serum by use of a polyclonal antibody and subsequently reduced with tris(2-carboxyethyl)phosphine. The purified TTR was then analyzed by fast-gradient liquid chromatography-dual-electrospray ionization Fourier-transform ion-cyclotron-resonance (FT-ICR) mass spectrometry. DNA sequencing was performed on all samples used in this study.Because of the inherent limitations in achieving high mass measurement accuracy based on the most abundant isotopic mass, we applied a fitting procedure that allowed determination of monoisotopic mass. Wild-type TTR (mean molecular mass, 13,761 Da) and its associated variant forms could be distinguished because of the high molecular mass accuracy afforded by FT-ICR (< or = 3 ppm) except for instances involving isobaric species or when isotopic distributions overlapped significantly. The [M + 11 H+]11+ charge state for all samples was used to determine the mass accuracies for both wild-type and variant forms of the protein. We correctly assigned seven of seven TTR variants. Moreover, using a combination of proteomic and genomic technologies, we discovered and characterized a previously unreported cis double mutation with a mass only 2 Da different from wild-type TTR. Furthermore, DNA sequencing of the TTR gene for all individuals in this study completely agreed with the intact protein measurements.FT-ICR mass spectrometry has sufficient mass accuracy to identify genetic variants of immunoaffinity-purified TTR. We believe that 91% of known TTR variants could be detected by this technique. DA - 2004/9/1/ PY - 2004/9/1/ DO - 10.1373/clinchem.2004.033274 VL - 50 IS - 9 SP - 1535-1543 LA - en OP - SN - 0009-9147 1530-8561 UR - http://dx.doi.org/10.1373/clinchem.2004.033274 DB - Crossref ER - TY - JOUR TI - Identification of Transthyretin Variants by Sequential Proteomic and Genomic Analysis AU - Bergen, H Robert, III AU - Zeldenrust, Steven R AU - Butz, Malinda L AU - Snow, Denise S AU - Dyck, Peter J AU - Dyck, P James B AU - Klein, Christopher J AU - O’Brien, John F AU - Thibodeau, Stephen N AU - Muddiman, David C T2 - Clinical Chemistry AB - Abstract Background: Transthyretin-associated hereditary amyloidosis (ATTR) is an inherited disease in which variants in the primary structure of transthyretin (TTR; prealbumin) lead to the extracellular polymerization of insoluble protein fibrils, causing organ failure and ultimately death when major organs are involved. We have developed an integrated approach to molecular diagnosis with initial analysis of intact plasma TTR by electrospray ionization mass spectrometry (MS) and referral of positive samples for DNA sequence analysis and real-time PCR to confirm the common Gly6Ser polymorphism. Methods: Samples from 6 patients previously diagnosed with ATTR and from 25 controls with (n = 15) or without (n = 10) polyneuropathy were analyzed in a blinded fashion for the presence of variant TTR. TTR protein was extracted with an immunoaffinity resin from 20 μL of archived plasma samples. The purified TTR was reduced with tris(2-carboxyethyl)phosphine and analyzed by MS. The appearance of two peaks (or a single peak shifted in mass indicative of a homozygous variant), including the wild-type mass of 13 761 Da, was indicative of the presence of a variant, and the individual was referred for DNA sequence analysis. Results: MS analysis of intact reduced TTR correctly identified each of six samples known to contain variant TTR. These results were corroborated by subsequent DNA sequence analysis. Additionally, all Gly6Ser polymorphisms were correctly called based on the +30 mass shift and an equal relative abundance of the +30 polymorphism relative to wild-type TTR. No false-positive results were seen. Conclusions: This referral method eliminates the necessity of sequencing most samples and allows screening for the familial forms of amyloidosis in a broad patient population in a timely fashion. This method correctly identified all previously known variants and also identified a novel variant, Val94Ala. DA - 2004/9/1/ PY - 2004/9/1/ DO - 10.1373/clinchem.2004.033266 VL - 50 IS - 9 SP - 1544-1552 LA - en OP - SN - 0009-9147 1530-8561 UR - http://dx.doi.org/10.1373/clinchem.2004.033266 DB - Crossref ER - TY - JOUR TI - Walk-off ring-down spectroscopy: attaining ultrafast resolution by converting time into space AU - Rypkema, H. A. AU - Martin, M. R. AU - Zare, R. N. T2 - Molecular Physics AB - Abstract A new technique for monitoring time-resolved phenomena is demonstrated by which a probe beam is directed into an optical cavity. Spatially separated output pulses are produced by directing the incident beam into the cavity in such a way that it walks in a direction transverse to the optical axis as it propagates between the two mirrors. This effect may be achieved either by a plane-parallel resonator oriented at a nonzero angle of incidence or by a wedge cavity, for which one of the mirrors is set at an angular offset. The spatially resolved output train may then be related to the time-dependent attributes of the resonator and the molecules it encloses. Time resolution is controlled by the separation of the mirrors, wedge geometry, and the angle of incidence. A time resolution of better than 4 ps is achieved using a 500 µm mirror separation and a 20° angle of incidence. DA - 2004/8// PY - 2004/8// DO - 10.1080/00268970410001725819 VL - 102 IS - 14-15 SP - 1501-1508 J2 - Molecular Physics LA - en OP - SN - 0026-8976 1362-3028 UR - http://dx.doi.org/10.1080/00268970410001725819 DB - Crossref ER - TY - CHAP TI - The Modulation of Vesicular Volume and its Effect on Neurotransmitter Secretion through the Fusion Pore in PC12 Cells AU - Sombers, L.A. AU - Hanchar, H.J. AU - Colliver, T.L. AU - Wittenberg, N. AU - Cans, A. AU - Arbault, S. AU - Amatore, C. AU - Ewing, A.G T2 - Cell Biology of the Chromaffin Cell A2 - Borges, Ricardo A2 - Gandia, Luis PY - 2004/// SP - 43–46 PB - Instituto Teófilo Hernando ER - TY - JOUR TI - Discovery of Ovarian Cancer Biomarkers in Serum Using NanoLC Electrospray Ionization TOF and FT-ICR Mass Spectrometry AU - Bergen, H. Robert AU - Vasmatzis, George AU - Cliby, William A. AU - Johnson, Kenneth L. AU - Oberg, Ann L. AU - Muddiman, David C. T2 - Disease Markers AB - Treatment of cancer patients is greatly facilitated by detection of the cancer prior to metastasis. One of the obstacles to early cancer detection is the lack of availability of biomarkers with sufficient specificity. With modern differential proteomic techniques, the potential exists to identify high specificity cancer biomarkers. We have delineated a set of protocols for the isolation and identification of serum biomarkers for ovarian cancer that exist in the low molecular weight serum fraction. After isolation of the low molecular weight fraction by ultrafiltration, the potential biomarkers are separated by reversed phase nano liquid chromatography. Detection via TOF or FT-ICR yields a data set for each sample. We compared stage III/IV ovarian cancer serum with postmenopausal age-matched controls. Using bioinformatics tools developed at Mayo, we normalized each sample for intensity and chromatographic alignment. Normalized data sets are subsequently compared and potential biomarkers identified. Several candidate biomarkers were found. One of these contains the sequence of fibrinopeptide-A known to be elevated in many types of cancer including ovarian cancer. The protocols utilized will be examined and would be applicable to a wide variety of cancers or disease states. DA - 2004/// PY - 2004/// DO - 10.1155/2004/797204 VL - 19 IS - 4-5 SP - 239-249 J2 - Disease Markers LA - en OP - SN - 0278-0240 1875-8630 UR - http://dx.doi.org/10.1155/2004/797204 DB - Crossref ER - TY - JOUR TI - Identification and Characterization of Novel, Naturally Processed Measles Virus Class II HLA-DRB1 Peptides AU - Ovsyannikova, Inna G. AU - Johnson, Kenneth L. AU - Muddiman, David C. AU - Vierkant, Robert A. AU - Poland, Gregory A. T2 - Journal of Virology AB - ABSTRACT Previously, we identified a naturally processed and presented measles virus (MV) 19-amino-acid peptide, ASDVETAEGGEIHELLRLQ (MV-P), derived from the phosphoprotein and eluted from the human leukocyte antigen (HLA) class II molecule by using mass spectrometry. We report here the identification of a 14-amino-acid peptide, SAGKVSSTLASELG, derived from the MV nucleoprotein (MV-N) bound to HLA-DRB1*0301. Peripheral blood mononuclear cells (PBMC) from 281 previously vaccinated measles-mumps-rubella II (MMR-II) subjects (HLA discordant) were studied for peptide recognition by T cells. Significant gamma interferon (IFN-γ) responses to MV-P and MV-N peptides were observed in 55.9 and 15.3% of subjects, respectively. MV-P- and MV-N-specific interleukin-4 (IL-4) responses were detected in 19.2 and 23.1%, respectively, of PBMC samples. Peptide-specific cytokine responses and HLA-DRB1 allele associations revealed that, for the MV-P peptide, the allele with the strongest association with both IFN-γ ( P = 0.02) and IL-4 ( P = 0.03) secretion was DRB1*0301. For MV-N, the allele with the strongest association with IFN-γ secretion was DRB1*1501 ( P = 0.04), and the alleles with the strongest associations with IL-4 secretion were DRB1*1103 and DRB1*1303 ( P = 0.01). These results indicate that HLA class II MV proteins can be processed, presented, and identified, and the ability to generate cell-mediated immune responses can be demonstrated. This information is promising for new vaccine design strategies with peptide-based vaccines. DA - 2004/1/1/ PY - 2004/1/1/ DO - 10.1128/jvi.78.1.42-51.2004 VL - 78 IS - 1 SP - 42-51 J2 - JVI LA - en OP - SN - 0022-538X 1098-5514 UR - http://dx.doi.org/10.1128/jvi.78.1.42-51.2004 DB - Crossref ER - TY - JOUR TI - The Effects of Vesicular Volume on Secretion through the Fusion Pore in Exocytotic Release from PC12 Cells AU - Sombers, L. A. T2 - Journal of Neuroscience AB - Many spikes in amperometric records of exocytosis events initially exhibit a prespike feature, or foot, which represents a steady-state flux of neurotransmitter through a stable fusion pore spanning both the vesicle and plasma membranes and connecting the vesicle lumen to the extracellular fluid. Here, we present the first evidence indicating that vesicular volume before secretion is strongly correlated with the characteristics of amperometric foot events. L-3,4-dihydroxyphenylalanine and reserpine have been used to increase and decrease, respectively, the volume of single pheochromocytoma cell vesicles. Amperometry and transmission electron microscopy have been used to determine that as vesicle size is decreased the frequency with which foot events are observed increases, the amount and duration of neurotransmitter released in the foot portion of the event decreases, and vesicles release a greater percentage of their total contents in the foot portion of the event. This previously unidentified correlation provides new insight into how vesicle volume can modulate the activity of the exocytotic fusion pore. DA - 2004/1/14/ PY - 2004/1/14/ DO - 10.1523/jneurosci.1119-03.2004 VL - 24 IS - 2 SP - 303-309 J2 - Journal of Neuroscience LA - en OP - SN - 0270-6474 1529-2401 UR - http://dx.doi.org/10.1523/jneurosci.1119-03.2004 DB - Crossref KW - fusion pore KW - exocytosis KW - amperometry KW - transmission electron microscopy KW - PC12 cells KW - vesicle volume KW - foot ER - TY - JOUR TI - “In Silico” Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands:  QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests AU - Varnek, A. AU - Fourches, D. AU - Solov'e, V. P. AU - Baulin, V. E. AU - Turanov, A. N. AU - Karandashev, V. K. AU - Fara, D. AU - Katritzky, A. R. T2 - Journal of Chemical Information and Computer Sciences AB - This paper is devoted to computer-aided design of new extractants of the uranyl cation involving three main steps: (i) a QSPR study, (ii) generation and screening of a virtual combinatorial library, and (iii) synthesis of several predicted compounds and their experimental extraction studies. First, we performed a QSPR modeling of the distribution coefficient (logD) of uranyl extracted by phosphoryl-containing podands from water to 1,2-dichloroethane. Two different approaches were used: one based on classical structural and physicochemical descriptors (implemented in the CODESSA PRO program) and another one based on fragment descriptors (implemented in the TRAIL program). Three statistically significant models obtained with TRAIL involve as descriptors either sequences of atoms and bonds or atoms with their close environment (augmented atoms). The best models of CODESSA PRO include its own molecular descriptors as well as fragment descriptors obtained with TRAIL. At the second step, a virtual combinatorial library of 2024 podands has been generated with the CombiLib program, followed by the assessment of logD values using developed QSPR models. At the third step, eight of these hypothetical compounds were synthesized and tested experimentally. Comparison with experiment shows that developed QSPR models successfully predict logD values for 7 of 8 compounds from that “blind test” set. DA - 2004/7// PY - 2004/7// DO - 10.1021/ci049976b VL - 44 IS - 4 SP - 1365-1382 J2 - J. Chem. Inf. Comput. Sci. LA - en OP - SN - 0095-2338 UR - http://dx.doi.org/10.1021/ci049976b DB - Crossref ER - TY - JOUR TI - Heme-copper/dioxygen adduct formation relevant to cytochrome c oxidase: spectroscopic characterization of [(6L)FeIII-(O22?)-CuII]+ AU - Ghiladi, Reza A. AU - Huang, Hong-wei AU - Mo�nne-Loccoz, Pierre AU - Stasser, Jay AU - Blackburn, Ninian J. AU - Woods, Amina S. AU - Cotter, Robert J. AU - Incarvito, Christopher D. AU - Rheingold, Arnold L. AU - Karlin, Kenneth D. T2 - JBIC Journal of Biological Inorganic Chemistry DA - 2004/12/4/ PY - 2004/12/4/ DO - 10.1007/s00775-004-0609-1 VL - 10 IS - 1 SP - 63-77 J2 - J Biol Inorg Chem LA - en OP - SN - 0949-8257 1432-1327 UR - http://dx.doi.org/10.1007/s00775-004-0609-1 DB - Crossref KW - heme-copper KW - iron(II)-copper(I) complex KW - peroxo complex KW - mass spectrometry KW - resonance Raman spectroscopy KW - dioxygen adduct KW - model compound ER - TY - JOUR TI - Analytical Performance of a Venturi Device Integrated into an Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Analysis of Nucleic Acids AU - Hawkridge, Adam M. AU - Zhou, Li AU - Lee, Milton L. AU - Muddiman, David C. T2 - Analytical Chemistry AB - A voltage-assisted venturi device modeled after an industrial air amplifier was used to improve the ion transmission efficiency of a 16.2 kDa oligonucleotide and a 53-mer PCR product in the high-pressure region between an electrospray ionization (ESI) emitter and the sampling orifices of two Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR-MS). The venturi device increased the total ion abundance of the oligonucleotide and the PCR product by more than 6-fold relative to the best achievable signal without the device. Furthermore, the average charge states of the oligonucleotide and PCR product shifted from 12.5- to 14.5- and 10.9- to 12.6-, respectively, with the addition of the venturi device. Specific to FT-ICR mass spectrometry, this increase in the charge state directly translates to an increase in theoretical mass resolving power (>10000 full width half-maximum for the results presented here at 7 T). Adduction was still observed while using the device, suggesting that it is "soft" relative to other high-pressure ion focusing methods. DA - 2004/7// PY - 2004/7// DO - 10.1021/ac049677l VL - 76 IS - 14 SP - 4118-4122 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac049677l DB - Crossref ER - TY - JOUR TI - Utility of accurate monoisotopic mass measurements to confidently identify lambda exonuclease generated single-stranded amplicons containing 7-deaza analogs by electrospray ionization FT-ICR mass spectrometry AU - Frahm, Jennifer L AU - Mason, Christopher J AU - Muddiman, David C T2 - International Journal of Mass Spectrometry AB - A 53-base pair region on the long arm of chromosome 22 was amplified using PCR with 7-deaza-modified deoxynucleotides. Increased amplification efficiency was achieved by doubling the concentration of the modified deoxynucleotide triphosphates. Incorporation of 7-deaza purines has been previously shown to selectively eliminate fragmentation pathways during gas-phase sequencing of nucleic acids by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) and infrared multiphoton dissociation. However, 7-deaza analogs result in significant duplex stability precluding interrogation of the single-stranded species by tandem mass spectrometry. Herein, we demonstrate the use of lambda exonuclease to successfully overcome this problem and are able to obtain single-stranded PCR products containing 7-deaza adenine and guanine nucleobases. Mass accuracy was used as our metric to determine complete incorporation of 7-deaza residues in PCR products>15 kDa; ≤ 3 ppm neutral monoisotopic mass measurement accuracies were routinely achieved. High mass measurement accuracy was obtained using a dual electrospray source and subsequently, using an isotopic fitting algorithm, the best fit between the theoretical and experimental isotopic distributions was determined using a chi-square value. Theoretical isotopic distributions were generated using an average nucleotide (averatide) chemical formula developed herein which was based on the relative frequencies of AT and GC base pairs in the human genome. Single-stranded PCR products were fragmented using SORI-CID and as expected, cleavage at the 7-deaza modified sites was not observed. Collectively, this integrated approach can facilitate top–down sequencing of PCR products by a variety of tandem mass spectrometry methods. DA - 2004/5// PY - 2004/5// DO - 10.1016/j.ijms.2004.02.004 VL - 234 IS - 1-3 SP - 79-87 J2 - International Journal of Mass Spectrometry LA - en OP - SN - 1387-3806 UR - http://dx.doi.org/10.1016/j.ijms.2004.02.004 DB - Crossref ER - TY - BOOK TI - Phenanthroline Ligands AU - Luman, C.R. AU - Castellano, F.N. DA - 2004/// PY - 2004/// DO - 10.1016/B0-08-043748-6/01202-0 VL - 1 SE - 25-39 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84902415875&partnerID=MN8TOARS ER - TY - JOUR TI - Room temperature phosphorescence from Ruthenium(II) complexes bearing conjugated pyrenylethynylene subunits AU - Kozlov, D.V. AU - Tyson, D.S. AU - Goze, C. AU - Ziessel, R. AU - Castellano, F.N. T2 - Inorganic Chemistry AB - We describe the synthesis, electrochemistry, and photophysical properties of several Ru(II) complexes bearing different numbers of pyrenylethynylene substituents in either the 5- or 5,5'-positions of 2,2'-bipyridine, along with the appropriate Ru(II) model complexes bearing either bromo- or ethynyltoluene functionalities. In addition, we prepared and studied the photophysical behavior of the diimine ligands 5-pyrenylethynylene-2,2'-bipyridine and 5,5'-dipyrenylethynylene-2,2'-bipyridine. Static and dynamic absorption and luminescence measurements reveal the nature of the lowest excited states in each molecule. All model Ru(II) complexes are photoluminescent at room temperature and exhibit excited-state behavior consistent with metal-to-ligand charge transfer (MLCT) characteristics. In the three Ru(II) molecules bearing multiple pyrenylethynylene substituents, there is clear evidence that the lowest excited state is triplet intraligand (3IL)-based, yielding long-lived room temperature phosphorescence in the red and near IR. This phosphorescence emanates from either 5-pyrenylethynylene-2,2'-bipyridine or 5,5'-dipyrenylethynylene-2,2'-bipyridine, depending upon the composition of the coordination compound. In the former case, the excited-state absorption difference spectra that were measured for the free ligand are easily superimposed with those obtained for the metal complexes coordinated to either one or two of these species. The latter instance is slightly complicated since coordination of the 5,5'-ligand to the Ru(II) center planarizes the diimine structure, leading to an extended conjugation on the long axis with a concomitant red shift of the singlet pi-pi absorption transitions and the observed room temperature phosphorescence. As a result, transient absorption measurements obtained using free 5,5'-dipyrenylethynylene-2,2'-bipyridine show a marked blue shift relative to its Ru(II) complex, and this extended pi-conjugation effect was confirmed by coordinating this ligand to Zn(II) at room temperature. In essence, all three pyrenylethynylene-containing Ru(II) complexes are unique in this genre of chromophores since the lowest excited state is 3IL-based at room temperature and at 77 K, and there is no compelling evidence of interacting or equilibrated excited states. DA - 2004/// PY - 2004/// DO - 10.1021/ic049288+ VL - 43 IS - 19 SP - 6083-6092 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-4644352861&partnerID=MN8TOARS ER - TY - JOUR TI - Two-Dimensional Metallic Chain Compounds Y5M2Te2(M = Fe, Co, Ni) That Are Related to Gd3MnI3. The Hydride Derivative Y5Ni2Te2D0.4 AU - Maggard, Paul A. AU - Corbett, John D. T2 - Inorganic Chemistry AB - Y(5)M(2)Te(2) (M = Fe, Co, Ni) have been prepared by high-temperature solid-state techniques and shown to be isostructural and orthorhombic Cmcm (No. 63), Z = 4. The structure was established by single crystal X-ray methods at 23 degrees C for M = Fe, with a = 3.9594(3) A, b = 15.057(1) A, and c = 15.216(1) A. The new structure contains zigzag chains of the late transition metal sheathed by a column of yttrium atoms that are in turn condensed through trans vertices on the latter to yield 2D bimetallic layers separated by single layers of tellurium atoms. Reaction of hydrogen with Y(5)Ni(2)Te(2) causes a rumpling of the Y-Ni layers as determined by both single X-ray crystal means at 23 degrees C and neutron powder diffraction at -259 degrees C for Y(5)Ni(2)Te(2)D(0.41(1)), Pnma (No. 62), Z = 4. Lattice constants from the former study are a = 14.3678(7) A, b = 4.0173(2) A, and c = 15.8787(7) A. The hydrogen is accommodated in tetrahedral yttrium cavities generated by bending the formerly flat sheets at the trans Y vertices. A higher hydride version also exists. Band structure calculations confirm the 2D metal-bonded character of the compounds and also help illustrate the bonding/matrix changes that accompany the bonding of hydrogen. The ternary structures for both Y(5)M(2)Te(2) and Sc(5)Ni(2)Te(2) can be derived from that of Gd(3)MnI(3), the group illustrating three different kinds of metal chain condensation. DA - 2004/4// PY - 2004/4// DO - 10.1021/ic0303136 VL - 43 IS - 8 SP - 2556-2563 J2 - Inorg. Chem. LA - en OP - SN - 0020-1669 1520-510X UR - http://dx.doi.org/10.1021/ic0303136 DB - Crossref ER - TY - JOUR TI - Interaction of triplet excitations with spin chain ends in the Haldane magnet PbNi2V2O8 AU - Smirnov, A.I. AU - Krug Von Nidda, H.-A. AU - Loidl, A. AU - Demianets, L.N. AU - Shapiro, A.Ya. T2 - Journal of Magnetism and Magnetic Materials AB - ESR signals of two kinds were detected in the doped Haldane magnet Pb(Ni1−xMgx)2V2O8. The low-temperature ESR with the value of g-factor 2.2 corresponds to effective spins S=12 at the ends of the spin chains. The signal of the second type is thermally activated, has a spectrum with the zero-field frequency 86GHz and is described by an effective spin S=1 in an axial crystal field. The last signal is due to the splitting of the spin sublevels of the triplet excitations in a magnetic and crystal fields. An exchange coupled ESR mode of triplets and spin-chain ends is found at intermediate temperatures. DA - 2004/// PY - 2004/// DO - 10.1016/j.jmmm.2003.12.1144 VL - 272-276 SP - 880-881 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-2642515798&partnerID=MN8TOARS KW - low dimensional magnets KW - Haldane gap KW - spin chains ER - TY - JOUR TI - Convolution-Based Algorithm: from Analysis of Rotational Dynamics to EPR Oximetry and Protein Distance Measurements AU - Smirnov, Alex I. AU - Smirnova, Tatyana I. T2 - EPR: Instrumental Methods AB - Spectral simulations and optimization of simulation parameters to fit experimental data are very powerful tools for data analysis in EPR spectroscopy. Data modeling serves two purposes, namely, (i) an aid to the interpretation of raw spectra, and (ii) reducuction of the data file, which usually contains from a few hundred to thousands of data points, to a much smaller set of meaningful physical parameters. It has been shown (e.g., Halpern et al., 1993) that the use of the whole EPR spectrum instead of a few characteristic data points can significantly, sometimes by an order of magnitude, increase the accuracy of the extracted spectral parameters. If the theoretical model is suitable for the experiment, and the experimental noise has a Gaussian or similar distribution, then the least square’s criterion (χ2) can be chosen for parameter optimization. Since the EPR spectrum usually depends on several (≥3) parameters, a multi-dimensional minimization algorithm is required to optimize parameters based on the value of χ2. DA - 2004/// PY - 2004/// DO - 10.1007/978-1-4419-8951-2_6 SP - 277-348 ER - TY - JOUR TI - High Field ESR: Applications to Protein Structure and Dynamics AU - Earle, Keith A. AU - Smirnov, Alex I. T2 - Very High Frequency (VHF) ESR/EPR AB - Electron Spin Resonance at high magnetic fields (HF ESR) is rapidly developing into a powerful biophysical tool which is uniquely positioned to address complex aspects of structure and dynamics of proteins, membranes, and macromolecular assemblies at molecular level. The source of the contemporary resurgence of interest in ESR as a biophysical tool is that there are, broadly speaking, three large groups of problems, which can be approached with ESR methods but cannot easily be studied by traditional structural techniques: (1) structure and dynamics of large molecular weight proteins in solution; (2) membrane and membrane-associated proteins: structure, location with respect to the membrane, side-chain dynamics, and interactions with other membrane components or DNA’s and RNA’s; (3) fast conformational transitions of proteins and RNA’s in solution, protein folding and re-folding. The focus of this review is mainly on HF ESR spin-labeling techniques, primarily via nitroxide spin labels, as this method is the most flexible and is even applicable to proteins which are otherwise ESR-silent. We start with physical aspects of ESR of nitroxide spin labels at high magnetic fields in order to categorize the characteristic information that can be gained from such experiments. Then we describe practical applications of spin-labeling HF ESR to study structure and dynamics of complex biophysical systems. We also discuss several details of the ESR motional theory based on the stochastic Liouville equation (SLE) that are relevant to nitroxide line shape analysis in order to appreciate both the information available from and the limitations of the method. Particular emphasis is given to multifrequency HF ESR methods in studies of spin-labeled membranes and biopolymers. Finally, we review the use of HF ESR in applications to molecular structure including distance measurements, determination of molecular orientations from ESR of ordered samples, and structural studies based on g-factor measurements. DA - 2004/// PY - 2004/// DO - 10.1007/978-1-4757-4379-1_4 SP - 95-143 ER - TY - JOUR TI - Erratum to: “Recurrence plot analysis of nonlinear vibrational dynamics in H3+ molecule” [Chaos, Solitons and Fractals 17 (5) (2003) 981–984] AU - Babinec, Peter AU - Jakubı́ková, Elena AU - Leszczynski, Jerzy T2 - Chaos, Solitons & Fractals DA - 2004/7// PY - 2004/7// DO - 10.1016/j.chaos.2003.12.002 VL - 21 IS - 2 SP - 513-514 J2 - Chaos, Solitons & Fractals LA - en OP - SN - 0960-0779 UR - http://dx.doi.org/10.1016/j.chaos.2003.12.002 DB - Crossref ER - TY - JOUR TI - A Molecular Dynamics Study of Aggregation Phenomena in Aqueousn-Propanol AU - Roney, Alfred B. AU - Space, Brian AU - Castner, Edward W. AU - Napoleon, Raeanne L. AU - Moore, Preston B. T2 - The Journal of Physical Chemistry B AB - Low-frequency Raman studies of various concentrations of aqueous n-propanol at room temperature indicate that both water and n-propanol form single-component aggregates in solution. Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) studies also provide evidence of this tendency toward aggregation. Molecular dynamics simulations of 16% aqueous n-propanol, a concentration for which maximum segregation of n-propanol and water is observed, have been carried out in an attempt to elucidate the structure of these aggregates. Kirkwood−Buff integrals calculated from the radial distribution functions of the components show excellent agreement with experimentally derived values. Analysis of the atomic coordinates from the simulations reveal that approximately 50% of the n-propanol molecules are members of homogeneous hydrogen-bonded chains of up to 16 members in length, the majority of which are dimers. The g(r) data also indicate that a strong hydrophobic association exists between the hydrocarbon tails. This hydrophobic association is independent of hydrogen-bonding state, and results in the formation of an approximately 10-member micelle structure centered around the n-propanol chains. Water is excluded from the regions occupied by the n-propanol micelles. The water structure is largely unaffected except for a small amount of disruption at the interface between the bulk solvent and the n-propanol clusters, and the formation of small water clusters at the interface with the bulklike solvent that interact with hydroxyl groups at the ends of the propanol chains. DA - 2004/6// PY - 2004/6// DO - 10.1021/jp037922j VL - 108 IS - 22 SP - 7389-7401 J2 - J. Phys. Chem. B LA - en OP - SN - 1520-6106 1520-5207 UR - http://dx.doi.org/10.1021/jp037922j DB - Crossref ER - TY - JOUR TI - A time correlation function theory of two-dimensional infrared spectroscopy with applications to liquid water AU - DeVane, Russell AU - Space, Brian AU - Perry, Angela AU - Neipert, Christine AU - Ridley, Christina AU - Keyes, T. T2 - The Journal of Chemical Physics AB - A theory describing the third-order response function R(3)(t1,t2,t3), which is associated with two-dimensional infrared (2DIR) spectroscopy, has been developed. R(3) can be written as sums and differences of four distinct quantum mechanical dipole (multi)time correlation functions (TCF’s), each with the same classical limit; the combination of TCF’s has a leading contribution of order ℏ3 and thus there is no obvious classical limit that can be written in terms of a TCF. In order to calculate the response function in a form amenable to classical mechanical simulation techniques, it is rewritten approximately in terms of a single classical TCF, BR(t1,t2,t3)=〈μj(t2+t1)μi(t3+t2+t1)μk(t1)μl(0)〉, where the subscripts denote the Cartesian dipole directions. The response function is then given, in the frequency domain, as the Fourier transform of a classical TCF multiplied by frequency factors. This classical expression can then further be quantum corrected to approximate the true response function, although for low frequency spectroscopy no correction is needed. In the classical limit, R(3) becomes the sum of multidimensional time derivatives of BR(t1,t2,t3). To construct the theory, the response function’s four TCF’s are rewritten in terms of a single TCF: first, two TCF’s are eliminated from R(3) using frequency domain detailed balance relationships, and next, two more are removed by relating the remaining TCF’s to each other within a harmonic oscillator approximation; the theory invokes a harmonic approximation only in relating the TCF’s and applications of theory involve fully anharmonic, atomistically detailed molecular dynamics (MD). Writing the response function as a single TCF thus yields a form amenable to calculation using classical MD methods along with a suitable spectroscopic model. To demonstrate the theory, the response function is obtained for liquid water with emphasis on the OH stretching portion of the spectrum. This approach to evaluating R(3) can easily be applied to chemically interesting systems currently being explored experimentally by 2DIR and to help understand the information content of the emerging multidimensional spectroscopy. DA - 2004/8/22/ PY - 2004/8/22/ DO - 10.1063/1.1776119 VL - 121 IS - 8 SP - 3688-3701 J2 - The Journal of Chemical Physics LA - en OP - SN - 0021-9606 1089-7690 UR - http://dx.doi.org/10.1063/1.1776119 DB - Crossref ER - TY - JOUR TI - Tractable theory of nonlinear response and multidimensional nonlinear spectroscopy AU - DeVane, Russell AU - Ridley, Christina AU - Space, Brian AU - Keyes, T. T2 - Physical Review E AB - Nonlinear spectroscopy provides insights into dynamics, but the response functions required for its interpretation pose a challenge to theorists. We proposed an approach in which the fifth-order response function $[{R}^{(5)}({t}_{1},{t}_{2})]$ was expressed as a two-time classical time correlation function (TCF). Here, we present TCF theory results for ${R}^{(5)}({t}_{1},{t}_{2})$ in liquid xenon. Using a first-order dipole-induced dipole polarizability model, the result is compared to an exact numerical calculation showing remarkable agreement. In addition, ${R}^{(5)}({t}_{1},{t}_{2})$ is calculated using the exactly solved polarizability model, yielding different results and predicting an echo signal. DA - 2004/11/16/ PY - 2004/11/16/ DO - 10.1103/physreve.70.050101 VL - 70 IS - 5 J2 - Phys. Rev. E LA - en OP - SN - 1539-3755 1550-2376 UR - http://dx.doi.org/10.1103/physreve.70.050101 DB - Crossref ER - TY - JOUR TI - Scanned probe lithography patterns to probe intermolecular interactions. AU - GORMAN, CB T2 - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY DA - 2004/// PY - 2004/// VL - 227 SP - U514 ER - TY - JOUR TI - The Role of Dendrimer Structure on the Rate and Driving Force for Electron Transfer to its Core AU - Gorman, C.B. T2 - Polymer Preprints DA - 2004/// PY - 2004/// VL - 45 SP - 365–366 ER - TY - JOUR TI - Installation of benzylic cyano groups as a methodology for novel monomer synthesis AU - CARSON, BE AU - MONCEAUX, CJ AU - GORMAN, CB T2 - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY DA - 2004/// PY - 2004/// VL - 227 SP - U639-U640 ER - TY - JOUR TI - Attenuating negative differential resistance in an electroactive self-assembled monolayer-based junction. AU - WASSEL, RA AU - CREDO, GM AU - FUIERER, R AU - al., T2 - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY DA - 2004/// PY - 2004/// VL - 228 SP - U480 ER - TY - JOUR TI - Performance of search algorithms in the examination of chemical reaction spaces with an automated chemistry workstation AU - Dixon, James M. AU - Lindsey, Jonathan S. T2 - Journal of the Association for Laboratory Automation AB - One of the challenges in applying automated chemistry workstations to problems of reaction optimization entails choosing an appropriate optimization algorithm. In the study described herein, 10 different algorithms have been examined for efficacy in searching reaction spaces using scenarios that explore effects of workstation parallelism and search space size. The algorithms differ in scheduling (serial vs. parallel), adaptive features (open loop vs. closed loop), and methods for stepping through the search space. Several two-tiered algorithms enable a breadth-first survey followed by an indepth optimization. For a workstation with modest parallel capacity, a parallel but nonadaptive algorithm is most effective in small or coarse-grained search spaces, whereas parallel adaptive algorithms are superior for examining large or fine-grained search spaces. The parallel adaptive algorithms become increasingly effective as the size of the search space increases. A serial algorithm is most attractive with a serial workstation, or when chemical resources are limited regardless of workstation or search space. The breadth-first survey of the twotiered algorithms significantly improves the efficiency of the subsequent in-depth optimization. The results obtained provide guidance in choosing optimization algorithms, designing more sophisticated algorithms, and developing workstations with parallel and/or adaptive features that use such algorithms. DA - 2004/12// PY - 2004/12// DO - 10.1016/j.jala.2004.08.004 VL - 9 IS - 6 SP - 364-374 J2 - Journal of the Association for Laboratory Automation LA - en OP - SN - 1535-5535 UR - http://dx.doi.org/10.1016/j.jala.2004.08.004 DB - Crossref KW - automated chemistry KW - reaction KW - optimization KW - simplex KW - parallel KW - adaptive KW - high throughput ER - TY - JOUR TI - An experiment planner for parallel multidirectional searches using an automated chemistry workstation AU - Dixon, James M. AU - Lindsey, Jonathan S. T2 - Journal of the Association for Laboratory Automation AB - Automated chemical workstations capable of parallel, adaptive experimentation are well suited for performing reaction optimization. A new method for simplex-based optimization has been developed that enables multiple multidirectional search (MDS) procedures to be implemented in parallel. The MDS method employs a simplex with n + 1 points, where n is the number of dimensions or variables of the optimization. After the initial simplex is evaluated, a new simplex is generated by reflection about the one best point, where n new points are projected and all but the one best point are discarded. The MDS movements continue in the same fashion until a termination criterion is satisfied. The parallel version (PMDS') enables multiple, distinct optimizations in parallel in a single search space to find the global optimum, or individual optimizations in parallel of multiple independent search spaces. The PMDS' method is complementary to the parallel Simplex search method, in which only one new point is projected to generate a new simplex in each cycle of experimentation. DA - 2004/12// PY - 2004/12// DO - 10.1016/j.jala.2004.08.001 VL - 9 IS - 6 SP - 355-363 J2 - Journal of the Association for Laboratory Automation LA - en OP - SN - 1535-5535 UR - http://dx.doi.org/10.1016/j.jala.2004.08.001 DB - Crossref KW - automated chemistry KW - reaction KW - optimization KW - simplex KW - parallel KW - adaptive KW - high throughput ER - TY - JOUR TI - Anti-Stokes delayed fluorescence from metal–organic bichromophores AU - Kozlov, Denis V. AU - Castellano, Felix N. T2 - Chem. Commun. AB - Long wavelength excitation of [Ru(dmb)2(bpy-An)]2+ (dmb is 4,4′-dimethyl-2,2′-bipyridine and bpy-An is 4-methyl-4′-(9-anthrylethyl)-2,2′-bipyridine) in CH3CN solution produces upconverted delayed singlet anthracene fluorescence via bimolecular triplet–triplet annihilation. DA - 2004/// PY - 2004/// DO - 10.1039/b412681e IS - 24 SP - 2860-2861 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/b412681e DB - Crossref ER - TY - JOUR TI - Near-Field Optical Addressing of Luminescent Photoswitchable Supramolecular Systems Embedded in Inert Polymer Matrices AU - Ferri, Violetta AU - Scoponi, Marco AU - Bignozzi, Carlo A. AU - Tyson, Daniel S. AU - Castellano, Felix N. AU - Doyle, Hugh AU - Redmond, Gareth T2 - Nano Letters AB - Optical recording and luminescence readout of novel covalently linked photochrome/luminophore supramolecular complexes has been demonstrated by near-field scanning optical microscopy (NSOM). Localized UV irradiation of these complexes dispersed in polymeric matrices resulted in photoinduced state switching and a concomitant increase in emission intensity. Subsequent luminescence imaging showed well-resolved luminescent data bit arrays with good signal-to-noise ratios. Spatially resolved emission spectra of the luminescent data bits confirmed the switching mechanism. DA - 2004/5// PY - 2004/5// DO - 10.1021/nl049770p VL - 4 IS - 5 SP - 835-839 J2 - Nano Lett. LA - en OP - SN - 1530-6984 1530-6992 UR - http://dx.doi.org/10.1021/nl049770p DB - Crossref ER - TY - JOUR TI - Solvent Switching between Charge Transfer and Intraligand Excited States in a Multichromophoric Platinum(II) Complex AU - Pomestchenko, Irina E. AU - Castellano, Felix N. T2 - The Journal of Physical Chemistry A AB - The photophysical properties of a new multichromophoric platinum(II) complex, Pt(dbbpy)(C≡C−nap)2 (1) (dbbpy = 4,4‘-(di-tert-butyl)-2,2‘-bipyridine; C≡C−nap = 1-ethynylnaphthalene), is reported in four different solvent systems of varying polarity: toluene, 2-methyltetrahydrofuran, dichloromethane, and acetonitrile. Since the low-energy dπ Pt → π* dbbpy metal-to-ligand charge transfer (MLCT) transitions in this chromophore are negative solvatochromic in nature, increasing solvent polarity raises the energy of the MLCT state. At the same time, the low-lying, metal-perturbed π,π* triplet intraligand (3IL) state present within the molecule on the −C≡C−nap fragments are largely invariant to solvent polarity as evidenced by the absorption and emission properties of the model chromophore lacking the low-energy charge transfer state, Pt(dppe)(C≡C−nap)2 (2) (dppe = 1,2-bis(diphenylphosphino)ethane). In solvents of low polarity, the static and dynamic absorption and luminescence spectroscopy of 1 are largely consistent with a dπ Pt → π* dbbpy MLCT assignment. As the solvent polarity is increased, the excited-state absorption and emission properties of 1 are significantly altered, eventually resembling the spectral features seen in 2. However, the excited-state decay kinetics for the structured emission measured in 2 is well beyond that observed for 1. The discrepancy in lifetime indicates that the excited state of 1 in high polarity solvents is not composed of pure 3IL character. In fact it is very likely that a significant electronic interaction exists between the 3MLCT and 3IL states in this molecule at ambient temperature. To further probe this possibility, static and dynamic luminescence experiments were performed on 1 and Pt(dbbpy)(C≡C−Ph)2 (3), C≡C−Ph is phenylacetylene, at 77 K as a function of matrix polarity. In all glass matrixes at low temperature, the lowest-lying state in 1 is 3IL, whose energy is nearly independent of the matrix. The reference molecule 3 possesses a low-lying 3MLCT state, and we believe it reasonably models the 3MLCT energy in 1 at low temperature. In essence, variation in the solvent glass changes the 3MLCT−3IL energy gap which modifies the observed excited-state lifetimes at 77 K, decreasing as the apparent energy gap decreases. The experimental results suggest stronger mixing of the two triplet states at room temperature relative to 77 K, but we cannot definitively rule out contributions from thermal equilibrium. Unfortunately, the relative energy separation of the two states in 1 does not permit a quantitative evaluation of potential configuration mixing of the two states. However, the close energetic proximity of the two triplets along with the solvent-dependent nature of the charge transfer state permits a wide variety of photophysical properties to be displayed by a single molecular system. DA - 2004/4// PY - 2004/4// DO - 10.1021/jp049641x VL - 108 IS - 16 SP - 3485-3492 J2 - J. Phys. Chem. A LA - en OP - SN - 1089-5639 1520-5215 UR - http://dx.doi.org/10.1021/jp049641x DB - Crossref ER - TY - JOUR TI - Photochemically Reversible Luminescence Lifetime Switching in Metal−Organic Systems AU - Kozlov, Denis V. AU - Castellano, Felix N. T2 - The Journal of Physical Chemistry A AB - We use a diarylethene with solution-stable open and closed forms (1,2-bis(2-methylbenzo[b]thiophen-3-yl) hexafluorocyclopentene), BTF6, as a photochromic energy transfer quencher of the metal-to-ligand charge-transfer (MLCT) based luminescence in [Ru(dpp)3]2+, dpp = 4,7-diphenyl-1,10-phenanthroline. As only the closed form of BTF6 serves as a quencher for the MLCT luminescence, and the read (390 nm), write (λ < 360 nm), and erase (λ > 500 nm) wavelengths are well-separated, this system potentially represents an economic alternative to covalent systems. For the first time, we demonstrate the concept of using luminescence lifetimes to transduce the photochromic binary state of the quencher as opposed to the intensity-based readout schemes that are traditionally employed. The luminescence quenching process is described in terms of Förster-type resonance energy transfer (RET) enhanced by diffusion. DA - 2004/12// PY - 2004/12// DO - 10.1021/jp045818b VL - 108 IS - 48 SP - 10619-10622 J2 - J. Phys. Chem. A LA - en OP - SN - 1089-5639 1520-5215 UR - http://dx.doi.org/10.1021/jp045818b DB - Crossref ER - TY - JOUR TI - Superoxide Reactivity of KatG:  Insights into Isoniazid Resistance Pathways in TB AU - Ghiladi, Reza A. AU - Cabelli, Diane E. AU - Ortiz de Montellano, Paul R. T2 - Journal of the American Chemical Society AB - To gain insight into the mechanism of INH activation by KatG and to understand how resistance is conferred by the single active-site point mutation of KatG(S315T), we have employed pulse radiolysis as the means to initiate a catalytic pathway capable of mimicking the in vivo oxidation of isoniazid (INH). Radiolysis of a solution containing WT KatG revealed two intermediates: compound III (oxyferrous KatG) [415 (Soret), 545, 580 nm] formed [k1 = (4.47 +/- 0.91) x 105 M-1 s-1] in the absence of INH and compound II (410 (Soret), 540, 575 nm) formed [k1 = (4.43 +/- 0.69) x 105 M-1 s-1] in the presence of INH, with a comparison of the rates suggesting that compound III (rate-limiting) precedes compound II formation. By contrast, radiolysis of KatG(S315T) only led to compound III formation, whether INH was present [k1 = (4.72 +/- 0.99) x 105 M-1 s-1] or not [k1 = (4.51 +/- 1.38) x 105 M-1 s-1]. HPLC studies to determine the rates of INH-NADH adduct formation (an inhibitor of InhA) as catalyzed by KatG were also performed employing various oxidants: air [WT: (7.18 +/- 1.25) x 10-4, S315T: (0.74 +/- 0.39) x 10-4], superoxide (SOTS-1) [WT: (9.22 +/- 1.10) x 10-4, S315T: not detected], and tert-butylhydroperoxide [WT: (20.5 +/- 1.13) x 10-4, S315T: (10.15 +/- 0.19) x 10-4]. Taken together, the results from the pulse radiolysis work as well as the InhA inhibitor studies allow us to propose a mechanism capable of correlating the inability for the oxyferrous intermediate of KatG(S315T) to oxidize ("activate") INH to the suppressed formation of the INH-NADH adduct, thereby leading to INH resistance in Mycobacterium tuberculosis. DA - 2004/4// PY - 2004/4// DO - 10.1021/ja031728t VL - 126 IS - 15 SP - 4772-4773 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja031728t DB - Crossref ER - TY - JOUR TI - Absolute Quantification of the Model Biomarker Prostate-Specific Antigen in Serum by LC−MS/MS Using Protein Cleavage and Isotope Dilution Mass Spectrometry AU - Barnidge, David R. AU - Goodmanson, Marcia K. AU - Klee, George G. AU - Muddiman, David C. T2 - Journal of Proteome Research AB - Protein cleavage-isotope dilution mass spectrometry (PC-IDMS) can be used to quantify proteins, with an isotope-labeled analogue of the peptide fragment used as an internal standard. Here, we investigate use of a standard LC−MS/MS platform for quantifying a model biomarker directly from serum by this technique. We synthesized a peptide (IVGGWECEK) identical to the N-terminal tryptic fragment of PSA but with each glycine containing two 13C atoms and one 15N atom. PSA-free human serum was denatured with urea followed by the introduction of PSA standard and the stable isotope labeled internal standard peptide. The sample was then proteolyzed with trypsin and subjected to quantification using LC−MS/MS on a triple quadrupole mass spectrometer. A linear least squares calibration curve made from five different concentrations of PSA added to serum and digested (each made in triplicate and randomly injected three times) had a mean slope of 0.973 (SE = 0.023), intercept of −0.003 (SE = 0.022), and R2 of 0.971. Recovery of calibrators ranged from 70 to 85% with a mean run-to-run CV of 13% and a mean within-run CV of 5.7%. PC-IDMS is a promising technique for quantifying proteins covering a broad range of applications from standardizing immunoassays to monitoring post-translational modifications to quantifying newly discovered biomarkers prior to the development and implementation of an immunoassay, just to name a few. Issues surrounding the application of PC-IDMS for the absolute quantification of proteins include selection of a proteolytic fragment for quantification that can be cleaved and isolated reproducibly over a broad dynamic range, stable isotope labeled synthetic peptide standards that give consistent results, and LC−MS/MS methods that provide adequate sensitivity and reproducibility without creating impractical analysis times. The results presented here show that absolute quantification can be performed on the model biomarker PSA introduced into denatured serum when analyzed by LC−MS/MS. However, concerns still exist regarding sensitivity compared to existing immunoassays as well as the reproducibility of PC-IDMS performed in different matrixes. Keywords: LC−MS/MS • absolute quantification • serum • biomarker • prostate-specific antigen • protein DA - 2004/6// PY - 2004/6// DO - 10.1021/pr049963d VL - 3 IS - 3 SP - 644-652 J2 - J. Proteome Res. LA - en OP - SN - 1535-3893 1535-3907 UR - http://dx.doi.org/10.1021/pr049963d DB - Crossref KW - LC-MS/MS KW - absolute quantification KW - serum KW - biomarker KW - prostate-specific antigen KW - protein ER - TY - JOUR TI - Evaluation of a Cleavable Stable Isotope Labeled Synthetic Peptide for Absolute Protein Quantification Using LC−MS/MS AU - Barnidge, David R. AU - Hall, Gregory D. AU - Stocker, Jeanne L. AU - Muddiman, David C. T2 - Journal of Proteome Research AB - Protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS) has the potential to provide the absolute concentration of a specific protein, or multiple proteins, in complex mixtures. However, PC-IDMS differs from standard IDMS since the internal standard is a different molecule than the analyte at the start of the experiment, more specifically, the internal standard is a peptide and the analyte is a protein prior to cleavage. It is not until after the cleavage process that the stable isotope labeled synthetic peptide has the same physicochemical behavior as the peptide cleaved from the protein. The work presented here evaluates the use of tryptic cleavage sites incorporated into the internal standard synthetic peptide in an attempt to create an internal standard that has cleavage characteristics more similar to the protein being quantified. Results presented here suggest that an internal standard synthetic peptide incorporating internal cleavage sites does not improve the accuracy and precision of the values obtained when performing PC-IDMS. DA - 2004/6// PY - 2004/6// DO - 10.1021/pr034124x VL - 3 IS - 3 SP - 658-661 J2 - J. Proteome Res. LA - en OP - SN - 1535-3893 1535-3907 UR - http://dx.doi.org/10.1021/pr034124x DB - Crossref KW - LC-MS/MS KW - absolute quantification KW - biomarker KW - cleavable internal standard ER - TY - JOUR TI - Analysis of the Low Molecular Weight Fraction of Serum by LC-Dual ESI-FT-ICR Mass Spectrometry:  Precision of Retention Time, Mass, and Ion Abundance AU - Johnson, Kenneth L. AU - Mason, Christopher J. AU - Muddiman, David C. AU - Eckel, Jeanette E. T2 - Analytical Chemistry AB - This study quantifies the experimental uncertainty for LC retention time, mass measurement precision, and ion abundance obtained from replicate nLC-dual ESI−FT-ICR analyses of the low molecular weight fraction of serum. We used ultrafiltration to enrich the <10-kDa fraction of components from the high-abundance proteins in a pooled serum sample derived from ovarian cancer patients. The THRASH algorithm for isotope cluster detection was applied to five replicate nLC-dual ESI-FT-ICR chromatograms. A simple two-level grouping algorithm was applied to the more than 7000 isotope clusters found in each replicate and identified 497 molecular species that appeared in at least four of the replicates. In addition, a representative set of 231 isotope clusters, corresponding to 188 unique molecular species, were manually interpreted to verify the automated algorithm and to set its tolerances. For nLC retention time reproducibility, 95% of the 497 species had a 95% confidence interval of the mean of ±0.9 min or less without the use of chromatographic alignment procedures. Furthermore, 95% of the 497 species had a mass measurement precision of ≤3.2 and ≤6.3 ppm for internally and externally calibrated spectra, respectively. Moreover, 95% of replicate ion abundance measurements, covering an ion abundance range of ∼3 orders of magnitude, had a coefficient of variation of less than 62% without using any normalization functions. The variability of ion abundance was independent of LC retention time, mass, and ion abundance quartile. These measures of analytical reproducibility establish a statistical rationale for differentiating healthy and disease patient populations for the elucidation of biomarkers in the low molecular fraction of serum. DA - 2004/9// PY - 2004/9// DO - 10.1021/ac0497003 VL - 76 IS - 17 SP - 5097-5103 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac0497003 DB - Crossref ER - TY - JOUR TI - Synthesis, Structure, and Dynamics of Molybdenum Imido Alkyne Complexes AU - Ison, Elon A. AU - Cameron, Thomas M. AU - Abboud, Khalil A. AU - Boncella, James M. T2 - Organometallics AB - The monomeric alkyne complexes (η2-alkyne)Mo(NPh)(o-(Me3SiN)2C6H4) (3) have been synthesized by the displacement of isobutylene from (η2-isobutylene)Mo(NPh)(o-(Me3SiN)2C6H4) (2). The alkyne fragment in these complexes is oriented perpendicular to the MoN bond of the cis imido ligand, as confirmed by an X-ray structural analysis of 3e. The deshielded nature of the chemical shifts of the α-carbons and terminal protons of the alkyne fragments in these complexes strongly suggests the participation of the alkyne π⊥ electrons in the Mo−alkyne interaction. The alkyne fragment in 3 rotates freely about the Mo−alkyne bond, resulting in the fluxional behavior of these complexes at room temperature. An activation barrier of 13.2 kcal/mol for the alkyne rotation was measured using VT NMR spectroscopy. Computational studies using a two-layer ONIOM model, and the B3LYP hybrid functional, provided insight into the Mo−alkyne bonding. The transition state for alkyne rotation has been calculated and is characterized by a parallel orientation of the alkyne fragment to the cis imido ligand. A natural bond orbital (NBO) population analysis reveals that alkyne π⊥ donation to Mo is more extensive in the transition state than in the ground state. Weaker Mo−N(imido) bonds are also observed in the transition state, because π donation from the alkyne ligand competes with imido π donation. DA - 2004/8// PY - 2004/8// DO - 10.1021/om049942t VL - 23 IS - 17 SP - 4070-4076 J2 - Organometallics LA - en OP - SN - 0276-7333 1520-6041 UR - http://dx.doi.org/10.1021/om049942t DB - Crossref ER - TY - JOUR TI - Alkyl aluminum-Induced Diamide Transfer from Group 6 Imido Diamido Complexes AU - Ison, Elon A. AU - Abboud, Khalil A. AU - Ghiviriga, Ion AU - Boncella, James M. T2 - Organometallics AB - Reaction of AlMe3 with the imido compounds Mo(NPh)(o-(SiMe3N)2C6H4)(CH2)4 (1) and Mo(NPh)(o-(SiMe3N)2C6H4)L (2; L = diphenylacetylene) results in the transfer of the diamide ligand to the Al, giving the unusual arene complexes 3 and 4. DA - 2004/3// PY - 2004/3// DO - 10.1021/om034322y VL - 23 IS - 5 SP - 929–931 SN - 0276-7333 1520-6041 UR - http://dx.doi.org/10.1021/om034322y ER - TY - JOUR TI - Androgens Negatively Regulate Forkhead Transcription Factor FKHR (FOXO1) through a Proteolytic Mechanism in Prostate Cancer Cells AU - Huang, Haojie AU - Muddiman, David C. AU - Tindall, Donald J. T2 - Journal of Biological Chemistry AB - The ability of androgens to inhibit apoptosis in both normal and malignant prostatic cells has been well documented. However, the underlying mechanisms are understood poorly. Here we demonstrated that forkhead transcription factor FKHR (FOXO1)-induced death of LNCaP cells was blocked by a synthetic androgen R1881. Androgen treatment also resulted in a reduction in transcriptional activity of FKHR in these cells. Moreover, treatment of LNCaP cells with R1881 led to a decrease in the intact FKHR protein (70 kDa) and an increase in a faster migrating protein band (60 kDa). Androgen-enhanced appearance of the 60-kDa protein was diminished specifically by lysosomal acidic cysteine protease inhibitors. Mass spectrometry analyses of the purified FLAG-tagged 70- and 60-kDa proteins demonstrated that the 60-kDa species is a FKHR protein product that lacks about 120 amino acid residues of the C-terminal end. Mutagenesis of the basic amino acid Arg537 in the protease cleavage region, as suggested by mass spectrometry, abrogated both the androgen-induced accumulation of the 60-kDa product and decrease in cell death induced by FKHR, suggesting that the residue Arg537 is a potential protease cleavage site. Finally, ectopic expression of the first 537 amino acids of FKHR produced an inhibitory effect on transcriptional activity of the intact protein. Together, these results suggest that androgens induce increased activity of an acidic cysteine protease, which in turn cleaves FKHR. This provides a mechanism by which androgens protect prostate cancer cells from the killing effect of FKHR. The ability of androgens to inhibit apoptosis in both normal and malignant prostatic cells has been well documented. However, the underlying mechanisms are understood poorly. Here we demonstrated that forkhead transcription factor FKHR (FOXO1)-induced death of LNCaP cells was blocked by a synthetic androgen R1881. Androgen treatment also resulted in a reduction in transcriptional activity of FKHR in these cells. Moreover, treatment of LNCaP cells with R1881 led to a decrease in the intact FKHR protein (70 kDa) and an increase in a faster migrating protein band (60 kDa). Androgen-enhanced appearance of the 60-kDa protein was diminished specifically by lysosomal acidic cysteine protease inhibitors. Mass spectrometry analyses of the purified FLAG-tagged 70- and 60-kDa proteins demonstrated that the 60-kDa species is a FKHR protein product that lacks about 120 amino acid residues of the C-terminal end. Mutagenesis of the basic amino acid Arg537 in the protease cleavage region, as suggested by mass spectrometry, abrogated both the androgen-induced accumulation of the 60-kDa product and decrease in cell death induced by FKHR, suggesting that the residue Arg537 is a potential protease cleavage site. Finally, ectopic expression of the first 537 amino acids of FKHR produced an inhibitory effect on transcriptional activity of the intact protein. Together, these results suggest that androgens induce increased activity of an acidic cysteine protease, which in turn cleaves FKHR. This provides a mechanism by which androgens protect prostate cancer cells from the killing effect of FKHR. Androgens are critical for proliferation and apoptosis in both normal and malignant prostatic epithelial cell (1Isaacs J.T. Vitam. Horm. 1994; 49: 433-502Google Scholar). Orchitectomy results in extensive apoptosis and involution of the rat ventral prostate and human prostate cancer xenografts (2Kerr J.F. Searle J. Virchows Arch. B Cell Pathol. 1973; 13: 87-102Google Scholar, 3Kyprianou N. English H.F. Isaacs J.T. Cancer Res. 1990; 50: 3748-3753Google Scholar, 4Brandstrom A. Westin P. Bergh A. Cajander S. Damber J.E. Cancer Res. 1994; 54: 3594-3601Google Scholar). Regression of prostatic tumors in patients following androgen ablation therapy is associated with apoptotic death in malignant prostatic epithelium (5Westin P. Stattin P. Damber J.E. Bergh A. Am. J. Pathol. 1995; 146: 1368-1375Google Scholar, 6Cardillo M. Berchem G. Tarkington M.A. Krajewski S. Krajewski M. Reed J.C. Tehan T. Ortega L. Lage J. Gelmann E.P. J. Urol. 1997; 158: 212-216Google Scholar). These findings suggest that androgens function as antiapoptotic factors in both normal and malignant prostatic cells. The tumor suppressor gene PTEN (phosphatase and tensin homolog deleted on chromosome ten; also known as MMAC1/TEP1) is mutated frequently in a variety of tumors including prostate, brain, and endometrium (7Li J. Yen C. Liaw D. Podsypanina K. Bose S. Wang S.I. Puc J. Miliaresis C. Rodgers L. McCombie R. Bigner S.H. Giovanella B.C. Ittmann M. Tycko B. Hibshoosh H. Wigler M.H. Parsons R. Science. 1997; 275: 1943-1947Google Scholar, 8Steck P.A. Pershouse M.A. Jasser S.A. Yung W.K. Lin H. Ligon A.H. Langford L.A. Baumgard M.L. Hattier T. Davis T. Frye C. Hu R. Swedlund B. Teng D.H. Tavtigian S.V. Nat. Genet. 1997; 15: 356-362Google Scholar, 9Li D.M. Sun H. Cancer Res. 1997; 57: 2124-2129Google Scholar). Although the overall prevalence of PTEN mutations in primary prostate cancer is low relative to other tumors (10Ali I.U. Schriml L.M. Dean M. J. Natl. Cancer Inst. 1999; 91: 1922-1932Google Scholar), the gene product is lost frequently in advanced prostate tumors (11McMenamin M.E. Soung P. Perera S. Kaplan I. Loda M. Sellers W.R. Cancer Res. 1999; 59: 4291-4296Google Scholar, 12Huang H. Cheville J.C. Pan Y. Roche P.C. Schmidt L.J. Tindall D.J. J. Biol. Chem. 2001; 276: 38830-38836Google Scholar). Inactivation of PTEN through different mechanisms such as deletion, methylation, or protein degradation has been implicated in progression of a number of tumors (7Li J. Yen C. Liaw D. Podsypanina K. Bose S. Wang S.I. Puc J. Miliaresis C. Rodgers L. McCombie R. Bigner S.H. Giovanella B.C. Ittmann M. Tycko B. Hibshoosh H. Wigler M.H. Parsons R. Science. 1997; 275: 1943-1947Google Scholar, 8Steck P.A. Pershouse M.A. Jasser S.A. Yung W.K. Lin H. Ligon A.H. Langford L.A. Baumgard M.L. Hattier T. Davis T. Frye C. Hu R. Swedlund B. Teng D.H. Tavtigian S.V. Nat. Genet. 1997; 15: 356-362Google Scholar, 13Whang Y.E. Wu X. Suzuki H. Reiter R.E. Tran C. Vessella R.L. Said J.W. Isaacs W.B. Sawyers C.L. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 5246-5250Google Scholar, 14Lee J.O. Yang H. Georgescu M.M. Di Cristofano A. Maehama T. Shi Y. Dixon J.E. Pandolfi P. Pavletich N.P. Cell. 1999; 99: 323-334Google Scholar, 15Vazquez F. Ramaswamy S. Nakamura N. Sellers W.R. Mol. Cell. Biol. 2000; 20: 5010-5018Google Scholar, 16Georgescu M.M. Kirsch K.H. Kaloudis P. Yang H. Pavletich N.P. Hanafusa H. Cancer Res. 2000; 60: 7033-7038Google Scholar, 17Torres J. Pulido R. J. Biol. Chem. 2001; 276: 993-998Google Scholar). Heterozygous disruption results in hyperplasia of the prostate, skin, and colon. Prostate-specific homozygous deletion of PTEN alleles in mice results in metastatic prostate cancer (18Wang S. Gao J. Lei Q. Rozengurt N. Pritchard C. Jiao J. Thomas G.V. Li G. Roy-Burman P. Nelson P.S. Liu X. Wu H. Cancer Cell. 2003; 4: 209-221Google Scholar). PTEN acts as a tumor suppressor protein primarily via its phosphatidylinositol phosphatase activity, which antagonizes the phosphatidylinositol 3-kinase/Akt pathway (19Maehama T. Dixon J.E. J. Biol. Chem. 1998; 273: 13375-13378Google Scholar, 20Cantley L.C. Neel B.G. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 4240-4245Google Scholar). Loss of PTEN in prostate cancer cells results in the constitutive activation of the oncoprotein Akt. Moreover, restoration of PTEN expression in PTEN-mutated prostate cancer cell lines abolishes the activation of Akt and subsequently induces cell death (12Huang H. Cheville J.C. Pan Y. Roche P.C. Schmidt L.J. Tindall D.J. J. Biol. Chem. 2001; 276: 38830-38836Google Scholar, 21Davies M.A. Koul D. Dhesi H. Berman R. McDonnell T.J. McConkey D. Yung W.K. Steck P.A. Cancer Res. 1999; 59: 2551-2556Google Scholar, 22Persad S. Attwell S. Gray V. Delcommenne M. Troussard A. Sanghera J. Dedhar S. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 3207-3212Google Scholar, 23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar). Active Akt phosphorylates many downstream proapoptotic proteins, which include Bad, caspase-9, and members of the FOXO subfamily of forkhead transcription factors FKHR (forkhead transcription factors in rhabdomyosarcoma) (FOXO1), FKHRL1 (FOXO3a), and AFX (FOXO4) (24Datta S.R. Dudek H. Tao X. Masters S. Fu H. Gotoh Y. Greenberg M.E. Cell. 1997; 91: 231-241Google Scholar, 25Cardone M.H. Roy N. Stennicke H.R. Salvesen G.S. Franke T.F. Stanbridge E. Frisch S. Reed J.C. Science. 1998; 282: 1318-1321Google Scholar, 26Biggs III, W.H. Meisenhelder J. Hunter T. Cavenee W.K. Arden K.C. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 7421-7426Google Scholar). Phosphorylated forkhead proteins remain inactive in the cytoplasm. The forkhead proteins undergo dephosphorylation due to the inhibition of Akt activity by factors such as PTEN or phosphatidylinositol 3-kinase inhibitors. Activated forkhead proteins translocate from the cytoplasm to the nucleus and subsequently bind to promoters of their target genes (27Nakae J. Barr V. Accili D. EMBO J. 2000; 19: 989-996Google Scholar). Recent studies have suggested that FOXO forkhead transcription factors may play important roles in regulating many cellular functions including proliferation, cell survival, and DNA damage. The members of this family regulate G1 cell cycle progression by modulating expression of the cyclin-dependent kinase inhibitor p27Kip1 and D type cyclins (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar, 28Medema R.H. Kops G.J. Bos J.L. Burgering B.M. Nature. 2000; 404: 782-787Google Scholar, 29Ramaswamy S. Nakamura N. Sansal I. Bergeron L. Sellers W.R. Cancer Cell. 2002; 2: 81-91Google Scholar). They also mediate transition from M to G1 of the cell cycle by directly regulating expression of mitotic genes such as cyclin B and polo-like kinase (plk) (30Alvarez B. Martinez A.C. Burgering B.M. Carrera A.C. Nature. 2001; 413: 744-747Google Scholar). Forkhead transcription factors affect the expression of several other genes that are involved in the cell cycle including Wip1, EXT1, and cyclin G2 (31Tran H. Brunet A. Grenier J.M. Datta S.R. Fornace Jr., A.J. DiStefano P.S. Chiang L.W. Greenberg M.E. Science. 2002; 296: 530-534Google Scholar). Expression of scavenger proteins such as cytosolic catalase and superoxide dismutase and the DNA damage response gene gadd45 are regulated by FOXO forkhead transcription factors, suggesting that these proteins play a role in surveillance of DNA damage (31Tran H. Brunet A. Grenier J.M. Datta S.R. Fornace Jr., A.J. DiStefano P.S. Chiang L.W. Greenberg M.E. Science. 2002; 296: 530-534Google Scholar, 32Furukawa-Hibi Y. Yoshida-Araki K. Ohta T. Ikeda K. Motoyama N. J. Biol. Chem. 2002; 277: 26729-26732Google Scholar, 33Nemoto S. Finkel T. Science. 2002; 295: 2450-2452Google Scholar). A number of proapoptotic proteins such as FasL (Fas ligand), the insulin-like growth factor-binding protein-1, Bim, NIP3, and legumain are transcriptionally regulated by members of this subfamily (31Tran H. Brunet A. Grenier J.M. Datta S.R. Fornace Jr., A.J. DiStefano P.S. Chiang L.W. Greenberg M.E. Science. 2002; 296: 530-534Google Scholar, 34Brunet A. Bonni A. Zigmond M.J. Lin M.Z. Juo P. Hu L.S. Anderson M.J. Arden K.C. Blenis J. Greenberg M.E. Cell. 1999; 96: 857-868Google Scholar, 35Tang E.D. Nunez G. Barr F.G. Guan K.L. J. Biol. Chem. 1999; 274: 16741-16746Google Scholar, 36Dijkers P.F. Medema R.H. Lammers J.W. Koenderman L. Coffer P.J. Curr. Biol. 2000; 10: 1201-1204Google Scholar, 37Gilley J. Coffer P.J. Ham J. J. Cell Biol. 2003; 162: 613-622Google Scholar). FOXO1 (FKHR) regulates cell survival in hepatic cells through modulation of gluconeo-genesis by interacting with PGC-1 (38Puigserver P. Rhee J. Donovan J. Walkey C.J. Yoon J.C. Oriente F. Kitamura Y. Altomonte J. Dong H. Accili D. Spiegelman B.M. Nature. 2003; 423: 550-555Google Scholar). Foxo3a (FKHRL1) knockout female mice exhibit a distinctive ovarian phenotype of global follicular activation leading to oocyte death (39Castrillon D.H. Miao L. Kollipara R. Horner J.W. DePinho R.A. Science. 2003; 301: 215-218Google Scholar). Expression of active FKHR induces death in different types of mammalian cell lines including LNCaP prostate cancer cells (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar, 35Tang E.D. Nunez G. Barr F.G. Guan K.L. J. Biol. Chem. 1999; 274: 16741-16746Google Scholar). Thus, regulation of FKHR function may be a critical factor for survival of prostate cancer cells. Our laboratory and others have shown previously that androgens act as survival factors by antagonizing PTEN activity in LNCaP cells (40Murillo H. Huang H. Schmidt L.J. Smith D.I. Tindall D.J. Endocrinology. 2001; 142: 4795-4805Google Scholar, 41Li P. Nicosia S.V. Bai W. J. Biol. Chem. 2001; 276: 20444-20450Google Scholar). In the present study, we demonstrate that the FKHR-induced decrease in cell viability and increase in cell death is blocked by androgen treatment, which is concomitant with inhibition of transactivation of FKHR in androgen-treated cells. We further provide evidence that the inhibitory effect of androgens on FKHR is mediated primarily through a proteolytic mechanism. Materials—N-terminal FLAG-tagged pcDNA3 expression plasmids for wild-type FKHR, FKHR(WT), a constitutively active form, FKHR(AAA), and the luciferase reporter construct 3×IRS-Luc were kindly provided by Drs. K. L. Guan and E. D. Tang (35Tang E.D. Nunez G. Barr F.G. Guan K.L. J. Biol. Chem. 1999; 274: 16741-16746Google Scholar). The substitution mutants R537G, R554G, K559G, and P538G were constructed by PCR mutagenesis (Stratagene). Two truncation mutants WT(Δ) and AAA(Δ) were constructed from FKHR(WT) and FKHR(AAA), respectively, by deleting a C-terminal fragment after the residue Arg537. These mutations were verified by sequencing. Construction of the mammalian expression vector for PTEN has been described previously (12Huang H. Cheville J.C. Pan Y. Roche P.C. Schmidt L.J. Tindall D.J. J. Biol. Chem. 2001; 276: 38830-38836Google Scholar). A 2.5-kb fragment of the human FasL promoter was kindly provided by Dr. C. V. Paya (42Holtz-Heppelmann C.J. Algeciras A. Badley A.D. Paya C.V. J. Biol. Chem. 1998; 273: 4416-4423Google Scholar). The fragment of the FasL promoter containing the FKHR response element located between nucleotides -930 and -821 (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar) was amplified by PCR and subcloned between the MluI and BglII sites of the pGL3-promoter vector (Promega). A polyclonal antibody against FKHR was purchased from Cell Signaling Technology (Beverly, MA). A monoclonal antibody against PTEN (6H2.1) was purchased from Cascade BioScience (Winchester, MA). Erk2 (D-2) monoclonal antibodies were purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA). Mouse monoclonal antibodies against α-FLAG were purchased from Sigma. R1881 (DuPont), bicalutamide (Zeneca Pharmaceuticals), and cycloheximide (Sigma) were dissolved in ethanol. LY294002 (Calbiochem), MG132 (Calbiochem), lactacystin (Calbiochem), and ALLnL (Sigma) were prepared in Me2SO (Sigma). Chloroquine (Sigma), ammonium chloride (Sigma), leupeptin (Sigma), and EGTA (Sigma) were prepared in water. Phenylmethylsulfonyl fluoride (Sigma) was dissolved in isopropyl alcohol (Sigma). Cell Lines and Cell Culture—The prostate cancer cell line LNCaP (purchased from the American Type Culture Collection, Manassas, VA) was cultured in RPMI 1640 medium containing 10% fetal bovine serum. In the experiments where LNCaP cells were treated with the synthetic androgen R1881 and/or the anti-androgen bicalutamide, these chemicals were refreshed every 48 h. The immortalized prostatic epithelial cell line BPH-1 was kindly provided by Dr. S. W. Hayward (43Hayward S.W. Dahiya R. Cunha G.R. Bartek J. Deshpande N. Narayan P. In Vitro Cell Dev. Biol. Anim. 1995; 31: 14-24Google Scholar) and cultured in RPMI 1640 medium (Invitrogen) containing 5% fetal bovine serum. Cell Transfections—Transient transfection of LNCaP cells was performed by electroporation as described previously (12Huang H. Cheville J.C. Pan Y. Roche P.C. Schmidt L.J. Tindall D.J. J. Biol. Chem. 2001; 276: 38830-38836Google Scholar). Cells were mixed with DNA in 400 μl of RPMI 1640 medium. The DNA/cell mixture was transferred into a 4-mm cuvette (BTX Inc., San Diego, CA) and electroporated with a 305-V/10-ms pulse using a BTX T820 square wave electroporator (BTX Inc., San Diego, CA). Transfection efficiency was monitored 12 h after transfection with green fluorescent protein (GFP) 1The abbreviations used are: GFP, green fluorescent protein; RT, reverse transcriptase; PSA, prostate-specific antigen; PBS, phosphate-buffered saline; AR, androgen receptor; MS, mass spectrometry. by examining aliquots of cells under a Zeiss fluorescence microscope with a wavelength of 488 nm. Transfection efficiency was determined by the percentage of the green cells in the whole cell population. Routinely, transfection efficiency met 60–90% was used for experiments. Western Blot Analysis—Protein samples were prepared by lysing cells in radioimmune precipitation assay buffer (50 mm Tris-HCl, pH 7.4, 1% Nonidet P-40, 0.25% sodium deoxycholate, 150 mm NaCl, 1 mm EGTA, 1 mm phenylmethylsulfonyl fluoride, 1 μg/ml leupeptin, 1 μg/ml aprotinin, 1 μg/ml pepstatin, 1 mm Na3VO4, and 1 mm NaF). Equal amounts of protein (30–80 μg) from cell lysates were denatured in sample buffer, subjected to 4–12% SDS-PAGE gels (Invitrogen), and transferred to nitrocellulose membranes (Bio-Rad). The filters were immunoblotted with specific primary antibodies, horseradish peroxidase-conjugated secondary antibodies, and visualized by enhanced chemilluminescence (Amersham Biosciences). Reverse Transcriptase (RT)-PCR and Northern Blot Analysis—Total RNA was isolated from cells treated with R1881, bicalutamide, or vehicle by TRIzol (Invitrogen). The first-strand cDNAs were synthesized by SuperScript II reverse transcriptase (RT) (Invitrogen). The forward 5′-AAGAGCGTGCCCTACTTCAA-3′ and reverse primer 5′-CAGTTCCTGCTGTCAGACAATC-3′ were used for PCR. Samples of 15 μg of total RNA from each treatment were separated on 1.2% denatured formaldehyde-agarose gels and transferred to nylon membranes (Bio-Rad). Filters were analyzed for expression of FKHR, prostate-specific antigen (PSA), or glyceraldehyde-3-phosphate dehydrogenase by using an isotope-labeled cDNA fragment of the FKHR coding region or probes as described previously (40Murillo H. Huang H. Schmidt L.J. Smith D.I. Tindall D.J. Endocrinology. 2001; 142: 4795-4805Google Scholar, 44Huang H. Reed C.P. Zhang J.S. Shridhar V. Wang L. Smith D.I. Cancer Res. 1999; 59: 2981-2988Google Scholar). Luciferase Reporter Assay—LNCaP cells were harvested after transfections, and cell lysates were prepared by adding lysis buffer directly to the cells on ice. Firefly luciferase and Renilla luciferase activities in cell lysates were determined using a dual luciferase kit (Promega, Madison, WI). Renilla luciferase activities of cells were used as internal controls. Immunofluorescence Chemistry and Confocal Microscopy—For cell viability assays, cells were replated into 6-well plates after transfection. After 12 h, cells were treated with 1 nm R1881 or ethanol for an additional 36 h. Cells were examined under a Zeiss LSM-510 confocal laser microscope. Cells were photographed with a wavelength of 488 nm for GFP. For immunofluorescence chemistry, cells on coverslips (Eppendorf Scientific, Inc., Hamburg, Germany) were washed briefly in 1× PBS and fixed for 20 min in 2% paraformaldehyde (Toussins) in 1× PBS. Cells were permeabilized by incubating with 0.3% Triton X-100 for 15 min. Cells were washed three times in 1× PBS and incubated in blocking buffer (5% goat serum in 1× PBS) for 1 h at room temperature. Cells were incubated with a rabbit anti-AR polyclonal antibody (1:500) and a mouse anti-FLAG monoclonal antibody (1:1000) for 2 h at room temperature. After washing with 1× PBS three times for 5 min each, cells were incubated for 1 h at room temperature with the following secondary antibodies: Alexa Fluor 594 goat anti-rabbit IgG conjugate (Molecular Probes, Inc., Eugene, OR) (1:1000) and Alexa Fluor 488 goat anti-mouse IgG conjugate (Molecular Probes) (1:1000) prepared in blocking buffer for 1 h at room temperature. Coverslips were washed with three changes of 1× PBS for 5 min each and mounted in ProLong (Molecular Probes). Cells were analyzed with a laser-scanning microscope LSM510. Argon ion and HeNe lasers were used to excite fluorescein isothiocyante and Texas Red fluorescence, respectively, and UV laser was used to excite 4′,6-diamidino-2-phenylindole. Cell Death Assay—Nuclear fragment and chromatin condensation were measured as described previously (40Murillo H. Huang H. Schmidt L.J. Smith D.I. Tindall D.J. Endocrinology. 2001; 142: 4795-4805Google Scholar). Briefly, cells treated for 48 h after transfections were collected at 4 °C. Supernatant medium was aspirated, and cells were treated with fixative solution (4% formaldehyde in 1× PBS). Bis-benzimide was added at a final concentration of 1 μg/ml and incubated for 10 min at room temperature. Cell aliquots were placed on slides and viewed under UV and a wavelength of 488 nm (Carl Zeiss Axiophot). Green cells with signs of chromatin condensation and/or nuclear fragmentation (apoptotic) were scored as dead. Purification of FLAG-tagged FKHR Proteins—LNCaP cells grown in 50 150-mm dishes were transfected with FLAG-tagged FKHR by electroporation. All subsequent steps were performed at 4 °C. Cells were washed once with ice-cold 1× PBS and lysed in Triton lysis buffer (50 mm Tris-HCl, pH 7.4, 150 mm NaCl, 1 mm EDTA, 1% Triton X-100) plus 1% of protease inhibitor mixture (Sigma). Cells were lysated at 4 °C for 30 min. Whole cell lysates were cleared at 12,000 × g for 20 min. Protein samples were incubated with anti-FLAG M2 affinity resins (Sigma) in protein binding buffer (190 mm NaCl, 50 mm Tris-HCl, pH 7.4, 6 mm EDTA, 2.5% Triton X-100) for 2 h. The beads were washed three times with washing buffer (150 mm NaCl, 10 mm Tris-HCl, pH 9.0, 5 mm EDTA, 0.1% Triton X-100) and once with Tris-buffered saline (10 mm Tris-HCl, pH 7.4, 150 mm NaCl). Proteins were eluted with SDS-PAGE sample buffer (Invitrogen), analyzed by SDS-PAGE, and stained with GelCode blue (Pierce) and Western blotting using anti-FKHR antibody (Cell Signaling). In-gel Trypsin Digestion of FLAG-tagged FKHR—The GelCode blue-stained gel bands were destained with 50% acetonitrile, 50 mm Tris, pH 8.1, for 30 min at room temperature and then reduced with 20 mm dithiothreitol, 50 mm Tris, pH 8.1, for 20 min at 55 °C, followed by alkylation with 40 mm iodoacetamide, 50 mm Tris, pH 8.1, for 20 min at room temperature. Overnight digestion was performed with trypsin (Promega Corp., Madison WI) in 25 mm Tris, pH 8.1, at 37 °C. Peptides were extracted from the gel bands, first with 2% formic acid followed by 70% acetonitrile, 30% water, 0.1% formic acid. Mass Spectrometry—Liquid chromatography-MS/MS analysis of the peptides was performed on a ThermoFinnigan LCQ Deca ion trap mass spectrometer (ThermoFinnigan, San Jose, CA). The LCQ Deca ion trap was coupled with an Applied Biosystems 140D pump, with a 1:100 split into a New Objective ProteoPep C18 PicoFrit column (75 μm × 5.0 cm) mounted on the New Objective PicoView source (New Objective, Woburn, MA). Peptides were loaded onto a 100-μm × 2.0-cm C18 trap and then eluted and chromatographed with a gradient of 4% acetonitrile, 0.1% formic acid to 40% acetonitrile, 0.1% formic acid in 50 min. The LCQ was set to run in data-dependant triple play mode consisting of full scan (400–1900 atomic mass units), zoom scan on most abundant ion, followed by MS/MS mode on that ion. Once a precursor ion was fragmented, it was placed on an exclusion list for 5 min, to avoid repeating tandem MS analysis of the same precursor ion. The MS/MS raw data were converted to DTA files using Bioworks 3.0 and correlated to theoretical fragmentation patterns using the SEQUEST search algorithm with tryptic peptide sequences from the NCBI data base downloaded in February of 2003. Statistics—Statistical analyses were performed by Student's t test. Values of p < 0.05 were considered significant and are presented under “Results.” Androgens Protect LNCaP Cells from Apoptosis Induced by FKHR—Ectopic expression of PTEN in LNCaP cells induces apoptosis, which can be inhibited by androgen treatment (40Murillo H. Huang H. Schmidt L.J. Smith D.I. Tindall D.J. Endocrinology. 2001; 142: 4795-4805Google Scholar, 41Li P. Nicosia S.V. Bai W. J. Biol. Chem. 2001; 276: 20444-20450Google Scholar). Downstream of PTEN, members of the FOXO subfamily of forkhead transcription factors are critical effectors of cell death, since overexpression of active FKHR mediates death in LNCaP cells (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar). To examine whether androgens affect FKHR-induced death in these cells, we conducted cell viability analyses. In cells without androgen treatment, fewer cells remained viable after being transfected with a constitutively active form of FKHR, FKHR(AAA), in comparison with cells transfected with the empty vector (Fig. 1, A and B, left panel). However, the killing effect of FKHR(AAA) was inhibited by the treatment of cells with 1 nm of the synthetic androgen R1881 (Fig. 1B, right panel). There was only a slight decease in cell viability when cells were transfected with wild-type FKHR, FKHR(WT) (Fig. 1C, left panel). This confirms a previous report that wild-type FKHR is only partially active because of its phosphorylation state (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar). This slight difference was attenuated following androgen treatment (Fig. 1C, right panel). Co-transfection of FKHR(WT) along with PTEN resulted in a marked decrease in cell viability (Fig. 1D, left panel), which is consistent with the decreased phosphorylation of FKHR and thereby activation of FKHR in cells in the presence of PTEN (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar). This effect of PTEN was inhibited by androgen treatment (Fig. 1D, right panel). As shown in Fig. 1E, PTEN-induced loss of cell viability was also inhibited markedly by androgens. Next we measured apoptosis by a nuclear condensation and fragmentation assay (40Murillo H. Huang H. Schmidt L.J. Smith D.I. Tindall D.J. Endocrinology. 2001; 142: 4795-4805Google Scholar). The constitutively active FKHR induced more than 15% apoptosis in LNCaP cells, and this was largely inhibited by androgens (Fig. 2). The death of LNCaP cells induced by FKHR(WT) alone or plus PTEN was markedly abrogated by androgen treatment. Androgens also inhibited PTEN-induced cell death (Fig. 2). Importantly, the androgen-mediated effects were reversed completely by co-treatment of cells with an androgen antagonist, bicalutamide, indicating that this is an androgen receptor-dependent event. Therefore, androgens inhibit cell death that is either induced by activated FKHR or potentiated by PTEN. Moreover, the androgen receptor appears to mediate these effects. Transactivation of FKHR Is Diminished by Androgen Action—Akt remains constitutively activated in PTEN-mutated LNCaP cells (7Li J. Yen C. Liaw D. Podsypanina K. Bose S. Wang S.I. Puc J. Miliaresis C. Rodgers L. McCombie R. Bigner S.H. Giovanella B.C. Ittmann M. Tycko B. Hibshoosh H. Wigler M.H. Parsons R. Science. 1997; 275: 1943-1947Google Scholar, 21Davies M.A. Koul D. Dhesi H. Berman R. McDonnell T.J. McConkey D. Yung W.K. Steck P.A. Cancer Res. 1999; 59: 2551-2556Google Scholar, 22Persad S. Attwell S. Gray V. Delcommenne M. Troussard A. Sanghera J. Dedhar S. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 3207-3212Google Scholar, 45Wu X. Senechal K. Neshat M.S. Whang Y.E. Sawyers C.L. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 15587-15591Google Scholar). This results in FKHR phosphorylation and disruption of its transactivation ability. However, the entire process can be reversed in LNCaP cells by forced expression of PTEN (23Nakamura N. Ramaswamy S. Vazquez F. Signoretti S. Loda M. Sellers W.R. Mol. Cell. Biol. 2000; 20: 8969-8982Google Scholar). Therefore, we were interested to determine whether PTEN-stimulated transactivation of FKHR is regulated by androgens. LNCaP cells were co-transfected transiently with PTEN and a luciferase reporter 3× IRS, which contains three copies of an FKHR response element from the promoter of the insulin-like growth factor-binding protein-1 gene. Ectopic expression of PTEN resulted in an ∼8-fold increase in the transcriptional activity of endogenous FKHR protein in cells without R1881 treatment (Fig. 3A, white column 2 versus 1). However, this effect of PTEN was diminished by androgen treatment (Fig. 3A, black column 2 versus white column 2). Co-expression of PTEN and FKHR in LNCaP cells resulted in a robust increase in activity of the reporter gene (Fig. 3A, white columns 3 and 4) in comparison with the level activated by endogenous FKHR. However, this increase was also inhibited by the treatment of cells with 1 nm R1881 (Fig. 3A, black columns 3 and 4). These results suggest that androgens inhibit transcriptional activities of both the endogenous and transfected FKHR protein. A similar inhibitory effect of androgens on transactivation of FKHR was observed i DA - 2004/1/15/ PY - 2004/1/15/ DO - 10.1074/jbc.M314143200 VL - 279 IS - 14 SP - 13866-13877 J2 - J. Biol. Chem. LA - en OP - SN - 0021-9258 1083-351X UR - http://dx.doi.org/10.1074/jbc.M314143200 DB - Crossref ER - TY - JOUR TI - A method for calculating 16o/18o peptide ion ratios for the relative quantification of proteomes AU - Johnson, Kenneth L. AU - Muddiman, David C. T2 - Journal of the American Society for Mass Spectrometry AB - A method is described for the identification and relative quantification of proteomes using accurate mass tags (AMT) generated by nLC-dual ESI-FT-ICR-MS on a 7T instrument in conjunction with stable isotope labeling using 16O/18O ratios. AMTs were used for putative peptide identification, followed by confirmation of peptide identity by tandem mass spectrometry. For a combined set of 58 tryptic peptides from bovine serum albumin (BSA) and human transferrin, a mean mass measurement accuracy of 1.9 ppm +/-0.94 ppm (CIM99%) was obtained. This subset of tryptic peptides was used to measure 16O/18O ratios of 0.36 +/- 0.09 (CIM99%) for BSA (micro = 0.33) and 1.48 +/- 0.47 (CIM99%) for transferrin (micro = 1.0) using a method for calculating 16O/18O ratios from overlapping isotopic multiplets arising from mixtures of 16O, 18O1, and 18O2 labeled C-termini. The model amino acid averagine was used to calculate a representative molecular formula for estimating and subtracting the contributions of naturally occurring isotopes solely as a function of peptide molecular weight. The method was tested against simulated composite 16O/18O spectra where peptide molecular weight, 16O/18O ratio, 18O1/18O2 ratios, and number of sulfur atoms were varied. Relative errors of 20% or less were incurred when the 16O/18O ratios were less than three, even for peptides where the number of sulfur atoms was over- or under-estimated. These data demonstrate that for biomarker discovery, it is advantageous to label the proteome representing the disease state with 18O; and the method is not sensitive to variations in 18O1/18O2 ratio. This approach allows a comprehensive differentiation of expression levels and tentative identification via AMTs, followed by targeted analysis of over- and under-expressed peptides using tandem mass spectrometry, for applications such as the discovery of disease biomarkers. DA - 2004/4// PY - 2004/4// DO - 10.1016/j.jasms.2003.11.016 VL - 15 IS - 4 SP - 437-445 J2 - J Am Soc Mass Spectrom LA - en OP - SN - 1044-0305 1879-1123 UR - http://dx.doi.org/10.1016/j.jasms.2003.11.016 DB - Crossref ER - TY - JOUR TI - Determination of the relative energies of activation for the dissociation of aromatic versus aliphatic phosphopeptides by ESI-FTICR-MS and IRMPD AU - Flora, Jason W. AU - Muddiman, David C. T2 - Journal of the American Society for Mass Spectrometry AB - Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (ESI-FTICR-MS) coupled with infrared multiphoton dissociation (IRMPD) is potentially a powerful method for rapid phosphopeptide mapping of complex proteolytic digests. The dissociation of deprotonated phosphopeptides by IRMPD is energetically favorable over unmodified deprotonated peptides because of a lower energy of activation and a higher internal energy under identical irradiation conditions. The energies of activation for dissociation are determined for model peptides phosphorylated on an aliphatic side chain (serine) and an aromatic side chain (tyrosine). The determination of phosphorylation location provides important biochemical information identifying the kinase involved in specific phosphorylation mechanisms. The data presented in this manuscript also support the theory that for phosphopeptides, the phosphate moiety's P-O stretch is in direct resonance with the infrared laser (10.6 microm), thus increasing the relative absorptivity of the modified species. A greater extinction coefficient affords more extensive photon absorption and subsequently a greater internal energy at the rapid exchange limit. DA - 2004/1// PY - 2004/1// DO - 10.1016/j.jasms.2003.10.004 VL - 15 IS - 1 SP - 121-127 J2 - J Am Soc Mass Spectrom LA - en OP - SN - 1044-0305 1879-1123 UR - http://dx.doi.org/10.1016/j.jasms.2003.10.004 DB - Crossref ER - TY - JOUR TI - Informed use of proteolytic inhibitors in biomarker discovery AU - Bergen, H. Robert AU - Klug, Michael G. AU - Bolander, Mark E. AU - Muddiman, David C. T2 - Rapid Communications in Mass Spectrometry AB - Rapid Communications in Mass SpectrometryVolume 18, Issue 9 p. 1001-1002 Letter to the Editor Informed use of proteolytic inhibitors in biomarker discovery H. Robert Bergen III, H. Robert Bergen III W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMichael G. Klug, Michael G. Klug W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMark E. Bolander, Mark E. Bolander Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorDavid C. Muddiman, Corresponding Author David C. Muddiman [email protected] W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USAMedical Science Building 3-115, Mayo Clinic College of Medicine, 200 First Street, SW, Rochester, MN 55905, USA.Search for more papers by this author H. Robert Bergen III, H. Robert Bergen III W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMichael G. Klug, Michael G. Klug W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMark E. Bolander, Mark E. Bolander Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorDavid C. Muddiman, Corresponding Author David C. Muddiman [email protected] W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USAMedical Science Building 3-115, Mayo Clinic College of Medicine, 200 First Street, SW, Rochester, MN 55905, USA.Search for more papers by this author First published: 01 April 2004 https://doi.org/10.1002/rcm.1439Citations: 5Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. REFERENCES 1 Bergen HR III, Zeldenrust SR, Naylor S. Amyloid 2003; 10: 190. 2 Riordan JF, Vallee BL. Methods Enzymol. 1972; 25: 449. 3 Brewer C, Riehm J. Anal. Biochem. 1967; 18: 248. 4 Bergen HR III, Vasmatzis G, Cliby WA, Johnson KL, Oberg AL, Muddiman DC. Dis. Markers 2004; in press. Citing Literature Volume18, Issue915 May 2004Pages 1001-1002 ReferencesRelatedInformation DA - 2004/4/23/ PY - 2004/4/23/ DO - 10.1002/rcm.1439 VL - 18 IS - 9 SP - 1001-1002 J2 - Rapid Commun. Mass Spectrom. LA - en OP - SN - 0951-4198 1097-0231 UR - http://dx.doi.org/10.1002/rcm.1439 DB - Crossref ER - TY - JOUR TI - Attenuating Negative Differential Resistance in an Electroactive Self-Assembled Monolayer-Based Junction AU - Wassel, Ronald A. AU - Credo, Grace M. AU - Fuierer, Ryan R. AU - Feldheim, Daniel L. AU - Gorman, Christopher B. T2 - Journal of the American Chemical Society AB - The negative differential resistance (NDR) peak current observed in redox active self-assembled monolayer-based molecular junctions has been attenuated by controlling the composition of the molecular junction. Two approaches studied here include capping the electroactive ferrocenyl groups with beta-cyclodextrin and functionalizing the scanning tunneling microscope tip used to probe the self-assembled monolayer (SAM) with n-alkanethiols of different lengths. These are the first examples of systematic modification of the magnitude of the NDR response in a molecule-based system. DA - 2004/1// PY - 2004/1// DO - 10.1021/ja037651q VL - 126 IS - 1 SP - 295-300 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja037651q DB - Crossref ER - TY - JOUR TI - Molecular Lithography for Wafer-Scale Fabrication of Molecular Junctions AU - McCarty, Gregory S. T2 - Nano Letters AB - High-resolution patterning is critical for the development of functional devices and sensors with nanometer dimensions. To date, no patterning methodology exists with the capability to produce molecular-scale features reliably over an entire wafer. In this paper, a lithographic process is presented to fabricate pairs of electrodes reproducibly with nanometer-scale resolution quickly, efficiently, and economically. Additionally, this work demonstrates that molecules of interest can be added to, or removed from, patterned molecular junctions. This novel technology provides a relatively simple and economical means to produce devices capable of monitoring the addition of molecules to a structure. DA - 2004/8// PY - 2004/8// DO - 10.1021/nl049375z VL - 4 IS - 8 SP - 1391-1394 J2 - Nano Lett. LA - en OP - SN - 1530-6984 1530-6992 UR - http://dx.doi.org/10.1021/nl049375z DB - Crossref ER - TY - JOUR TI - Formation and Manipulation of Protopolymer Chains AU - McCarty, Gregory S. AU - Weiss, Paul S. T2 - Journal of the American Chemical Society AB - We define “protopolymer” to mean that the monomer units of a polymer are together and aligned, but are not yet reacted to their final form, the polymer. We have created, observed, and manipulated this new chemical state in linear chains of phenylene on Cu{111} at low temperature. We demonstrate that protopolyphenylene forms by manipulating individual monomer units out of the chains using a scanning tunneling microscope. Both the bare and the phenylene-covered Cu{111} surface can serve as an extended catalytic active site to bring together and to align the monomer phenylene units formed from the dissociative chemisorption of p-diiodobenzene. When short segments of protopolymer chains are moved on the phenylene-covered surface, the intermolecular interactions are sufficiently strong to realign the chains in new locations. The alignment due to these interactions may be used in the controlled growth and assembly, as well as for the simplified manipulation of complex, hierarchical structures. DA - 2004/12// PY - 2004/12// DO - 10.1021/ja038930g VL - 126 IS - 51 SP - 16772-16776 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja038930g DB - Crossref ER - TY - CHAP TI - The ion mobility mass spectrometry method and its application to duplex formation of oligonucleotides and aggregation of proteins AU - Wyttenbach, T AU - Baker, ES AU - Bernstein, SL AU - Ferzoco, A AU - Gidden, J AU - Liu, DF AU - Bowers, MT T2 - Advances in Mass Spectrometry, Vol 16 PY - 2004/// VL - 16 SP - 189-200 PB - SE - UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000226631200011&KeyUID=WOS:000226631200011 ER - TY - JOUR TI - Sodium stabilization of dinucleotide multiplexes in the gas phase AU - Baker, E.S. AU - Gidden, J. AU - Ferzoco, A. AU - Bowers, M.T. T2 - Physical Chemistry Chemical Physics AB - The aggregation and conformations of sodiated dinucleotides were studied in the gas phase. MALDI was used to generate [M − (n − 1)H + nNa]+ ions, yielding single-strand ions having n = 1–3, duplex ions with n = 1–7 and triplex ions with n = 3–10. Collision cross-sections of each sodiated complex were measured in helium using ion mobility based methods and compared to calculated cross-sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct single-strand conformers were observed: one with the nucleobases stacked, one with the planes oriented perpendicular to each other and one with the bases coplanar to each other. One conformer is observed for all of the duplexes except dTG·dTG, dGT·dGT and dTT·dTT (in which two conformers are observed depending on whether the guanine or thymine bases stack). For low values of n, the Na+ ions cluster around the two deprotonated phosphates. However, as n increases, the Na+ ions become more dispersed along the duplex. One conformer is also observed for all of the triplexes. For n = 3–6, three Na+ ions and the three phosphates form a quasi-planar ring with the additional Na+ ions resting above, below and in the middle of the ring. Cytosine and thymine also coordinate to the Na+ ions but adenine and guanine prefer to stack and do not coordinate to the Na+ ions in the ring. The addition of the seventh to tenth Na+ ions breaks the sodium-phosphate ring and the Na+ ions become scattered around the triplex. Differences between experimental and theoretical cross-sections (averaged over the lowest 5 kcal mol−1 structures) of each sodiated complex fell between 1–2%. DA - 2004/// PY - 2004/// DO - 10.1039/b315727j VL - 6 IS - 10 SP - 2786-2795 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-3042559886&partnerID=MN8TOARS ER - TY - JOUR TI - Sequence Dependent Conformations of Glycidyl Methacrylate/Butyl Methacrylate Copolymers in the Gas Phase AU - Baker, E.S. AU - Gidden, J. AU - Simonsick, W.J. AU - Grady, M.C. AU - Bowers, M.T. T2 - The International Journal of Mass Spectrometry AB - Sequence dependent conformations of a series of glycidyl methacrylate/butyl methacrylate (GMA/BMA) copolymers cationized by sodium were analyzed in the gas phase using ion mobility methods. GMA and BMA have the same nominal mass but vary in exact mass by 0.036 Da (CH4 versus O). Matrix assisted laser desorption/ionization (MALDI) was used to form Na + (GMA/BMA) copolymer ions and their collision cross-sections were measured in helium using ion mobility methods. The copolymer sequences from Na + (GMA/BMA)3 to Na + (GMA/BMA)5 (i.e. for the trimer to the pentamer) were studied. Analysis by molecular mechanics/dynamics indicates that each copolymer (regardless of sequence) forms a ring around the sodium ions due to Na + /oxygen electrostatic interactions. However, the structures vary in size, since the epoxy oxygen atoms in the glycidyl groups are attracted to the sodium ions while the carbon-composed butyl groups are not. This allows copolymers with more GMA segments to fold tighter (more spherically) around the sodium ion and have smaller cross-sections than copolymers with a larger amount of BMA segments in the sequence. Due to this cross-sectional difference, the GMA/BMA sequence compositions of the trimer and tetramer could be quantified. © 2004 Elsevier B.V. All rights reserved. DA - 2004/11/15/ PY - 2004/11/15/ DO - 10.1016/j.ijms.2004.04.020 VL - 238 IS - 3 SP - 279-286 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000225740000009&KeyUID=WOS:000225740000009 KW - glycidyl methacrylate/butyl methacrylate KW - gas phase KW - MALDI KW - ion mobility ER - TY - JOUR TI - Microstructural and Conformational Studies of Polyether Copolymers AU - Jackson, A.T. AU - Scrivens, J.H. AU - Williams, J.P. AU - Baker, E.S. AU - Gidden, J. AU - Bowers, M.T. T2 - The International Journal of Mass Spectrometry AB - A combined structural/conformational study of ethylene oxide/propylene oxide (EO/PO) copolymers has been undertaken. Electrospray ionisation (ESI) and matrix-assisted laser desorption/ionisation (MALDI) methods have been utilised and ESI-tandem mass spectrometry (MS/MS) product ion spectra, including accurate mass measurements, utilised to establish fragmentation pathways. This has enabled end group and sequence information to be obtained. Ion mobility mass spectrometry experimental, along with theoretical, approaches has been used in tandem to probe the gas-phase conformation of selected cationised species from the block and random copolymers. The cross-sections established from these measurements and calculations have been shown to be dependent on molecular weight of the oligomer and radii of the cation but largely independent of the sequence of the ion in the gas-phase. The ion mobility results have been used to aid the understanding of the fragmentation of these copolymers by means of ESI-MS/MS. DA - 2004/11/15/ PY - 2004/11/15/ DO - 10.1016/j.ijms.2004.09.025 VL - 238 IS - 3 SP - 287-297 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000225740000010&KeyUID=WOS:000225740000010 KW - oligomer KW - ion mobility KW - ESI-MS/MS ER - TY - JOUR TI - Isomeric structural characterization of polyhedral oligomeric silsesquioxanes (POSS) with styryl and epoxy phenyl capping agents AU - Baker, ES AU - Gidden, J AU - Anderson, SE AU - Haddad, TS AU - Bowers, MT T2 - Nano Letters AB - Ion mobility and molecular modeling methods were used to examine the gas-phase structures of sodiated POSS capped with styryl and epoxy phenyl substituents (Na+StyxEp8-xT8). Results were obtained for x = 5−7 and indicated that three distinct isomers with different collision cross-sections were present for each value of x. Theoretical modeling also yielded three different families of structures for each POSS system, and their calculated cross-sections agreed very well with experimental values (<1% difference). For Na+Sty7EpT8, the three families differ in the number of “paired” Sty groups. For Na+Sty6Ep2T8 and Na+Sty5Ep3T8, the three isomers correspond to the three different ways the Ep groups can be positioned on the POSS cage. DA - 2004/// PY - 2004/// DO - 10.1021/nl049957g VL - 4 IS - 5 SP - 779-785 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000221410000004&KeyUID=WOS:000221410000004 ER - TY - JOUR TI - Duplex formation and the onset of helicity in poly d(CG)(n) oligonucleotides in a solvent-free environment AU - Gidden, J AU - Ferzoco, A AU - Baker, ES AU - Bowers, MT T2 - Journal of the American Chemical Society AB - The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale. DA - 2004/// PY - 2004/// DO - 10.1021/ja046433+ VL - 126 IS - 46 SP - 15132-15140 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000225233600035&KeyUID=WOS:000225233600035 ER - TY - JOUR TI - Duplex formation and the onset of helicity in oligonucleotides. AU - Gidden, J AU - Baker, ES AU - Ferzoco, A AU - Bowers, MT T2 - Abstracts of Papers of the American Chemical Society DA - 2004/// PY - 2004/// VL - 227 SP - U258 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000223655701333&KeyUID=WOS:000223655701333 ER - TY - JOUR TI - Diastereomer assignment of an olefin-linked bis-paracyclophane by ion mobility mass spectrometry AU - Baker, ES AU - Hong, JW AU - Gidden, J AU - Bartholomew, GP AU - Bazan, GC AU - Bowers, MT T2 - Journal of the American Chemical Society AB - trans-1,2-Bis([2.2]paracyclophanyl)ethene (1) exists as a pair of diastereomers whose conformations, and thus effective collision cross sections, are quite different. The two forms can be obtained by different transition metal-catalyzed reactions. To assign meso and racemic structures, a novel method is reported in which experimental gas-phase ion mobility data are compared with theoretical structures obtained from molecular mechanics calculations. DA - 2004/// PY - 2004/// DO - 10.1021/ja039486k VL - 126 IS - 20 SP - 6255-6257 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000221526800027&KeyUID=WOS:000221526800027 ER - TY - PAT TI - Multistate triple-decker dyads in three distinct architectures for information storage applications AU - Lindsey, J. S. AU - Bocian, D. F. AU - Schweikart, K. H. AU - Kuhr, W. G. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - PAT TI - Methods for fabricating nanopores for single-electron devices AU - Brousseau, L. C. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - PAT TI - Method and system for molecular charge storage field effect transistor AU - Misra, V. AU - Bocian, D. AU - Kuhr, W. AU - Lindsey, J. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - PAT TI - Amino acid derivatives AU - Alla, S. AU - Choi, S. Y. AU - Dhanoa, D. AU - DiFranco, E AU - Krokhina, G. AU - Li, K. AU - Balasubramanian, T. AU - Zhang, W. C. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - PAT TI - Preparation of a camptothecin derivative by intramolecular cyclisation AU - Fang, F. G. AU - Huie, E. M. AU - Xie, S. AU - Comins, D. L. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - CHAP TI - SCALE-UP: Bringing inquiry-guided learning to large enrollment courses AU - Oliver-Hoyo, M. AU - Beichner, R. T2 - Teaching and learning through inquiry : a guidebook for institutions and instructors A2 - Lee, V. S. PY - 2004/// PB - Sterling, Va.: Stylus Pub. SN - 1579220800 ER - TY - JOUR TI - One-pot, one-catalyst synthesis of graft copolymers by controlled ROMP and ATRP polymerizations AU - Charvet, R AU - Novak, BM T2 - MACROMOLECULES AB - ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTOne-Pot, One-Catalyst Synthesis of Graft Copolymers by Controlled ROMP and ATRP PolymerizationsRichard Charvet and Bruce M. NovakView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695 Cite this: Macromolecules 2004, 37, 23, 8808–8811Publication Date (Web):October 16, 2004Publication History Received19 April 2004Revised13 August 2004Published online16 October 2004Published inissue 1 November 2004https://doi.org/10.1021/ma049244kCopyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1132Altmetric-Citations57LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. 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Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (86 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Copolymerization,Copolymers,Monomers,Organic compounds,Radical polymerization Get e-Alerts DA - 2004/11/16/ PY - 2004/11/16/ DO - 10.1021/ma049244k VL - 37 IS - 23 SP - 8808-8811 SN - 1520-5835 ER - TY - JOUR TI - The atomic computer simulation of triple junctions of special tilt boundaries in nickel AU - Nazarov, A. A. AU - Shenderova, O. A. AU - Brenner, D. W. T2 - Physics of Metals and Metallography DA - 2004/// PY - 2004/// VL - 98 IS - 4 SP - 339-343 ER - TY - JOUR TI - Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap AU - Nicely, NI AU - Kosak, J AU - Serrano, V AU - Mattos, C T2 - STRUCTURE AB - RalA is a GTPase with effectors such as Sec5 and Exo84 in the exocyst complex and RalBP1, a GAP for Rho proteins. We report the crystal structures of Ral-GppNHp and Ral-GDP. Disordered switch I and switch II, located away from crystal contacts, are observed in one of the molecules in the asymmetric unit of the Ral-GppNHp structure. In the other molecule in the asymmetric unit, a second Mg(2+) ion is bound to the GppNHp gamma-phosphate in an environment in which switch I is pulled away from the nucleotide and switch II is found in a tight beta turn. Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction. One site is adjacent to switch I. The other is modulated by switch II and is obstructed in Ral-GDP. The Ral structures are discussed in the context of the published structures of the Ral/Sec5 complex, Ras, and Rap. DA - 2004/11// PY - 2004/11// DO - 10.1016/j.str.2004.08.011 VL - 12 IS - 11 SP - 2025-2036 SN - 1878-4186 ER - TY - BOOK TI - Teaching and learning through inquiry: A guidebook for institutions and instructors AU - Lee, V. S. AU - Greene, D. B. AU - Wellman, D. J. AU - al., CN - LB1027.44 .T43 2004 DA - 2004/// PY - 2004/// PB - Sterling, Va.: Stylus Pub. ER - TY - JOUR TI - T7 RNA polymerase transcription with 5-position modified UTP derivatives AU - Vaught, JD AU - Dewey, T AU - Eaton, BE T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Seven UTP derivatives modified at the 5-position through an amide linkage were tested as substrates for T7 RNA polymerase (T7 RNAP) transcription. All UTP derivatives gave good yields of full-length transcript even from DNA templates that showed a significant number of abortive transcripts using unmodified UTP. A kinetic assay to determine the relative K(m) and V(max) for T7 RNAP transcription gave surprisingly similar values for UTP and the 5-position hydrophobic modifications phenyl, 4-pyridyl, 2-pyridyl, indolyl, and isobutyl. The 5-position modifications imidazole and amino, which could both be positively charged, gave K(m) values significantly higher than UTP. All seven UTP derivatives gave relative V(max) values similar to UTP, indicating that insertion of these modified bases into the transcript did not impede its elongation. DA - 2004/9/15/ PY - 2004/9/15/ DO - 10.1021/ja049009h VL - 126 IS - 36 SP - 11231-11237 SN - 0002-7863 ER - TY - JOUR TI - Structural and electron-transfer characteristics of O-, S-, and Se-tethered porphyrin monolayers on Si(100) AU - Yasseri, AA AU - Syomin, D AU - Loewe, RS AU - Lindsey, JS AU - Zaera, F AU - Bocian, DF T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Monolayers of two classes of Zn porphyrins have been prepared and examined on Si(100). These molecules, designated as ZnPBzX− and ZnPCH2X−, contain either a benzyl (−Bz−) or a methylene (−CH2−) unit terminated with a Group VI atom (X = O, S, Se) appended to a meso-position of the porphyrin, with the nonlinking meso-substituents consisting of either mesityl (−Bz− class) or p-tolyl and phenyl (−CH2− class) units. The two series of ZnPBzX− and ZnPCH2X− monolayers on Si(100) were examined using a variety of techniques, including X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and various electrochemical methods. The studies reveal the following characteristics of the ZnPBzX− and ZnPCH2X− monolayers. (1) Surface binding can be readily achieved to Si(100) with both relatively short (−Bz−) and very short (−CH2−) tethers regardless of the nature of the Group VI anchoring atom (O, S, Se). (2) The longer −Bz− tether affords monolayers with the porphyrin ring in a somewhat more upright orientation with respect to the surface than the shorter −CH2− tether. The more upright adsorption geometry of the porphyrins bearing the former type of linker leads to a higher packing density and more homogeneous redox thermodynamics. (3) The kinetics of electron transfer does not depend on the type of Group VI atom used for anchoring to the Si(100) surface. On the other hand, the type of linker does affect the electron-transfer rates, with the monolayers bearing the −CH2− linker exhibiting systematically faster rates than those bearing the −Bz− linker. Collectively, the studies reported herein provide a detailed picture of how the anchor atom and the linker type influence the structural and electron-transfer characteristics of these general classes of monolayers. DA - 2004/12/1/ PY - 2004/12/1/ DO - 10.1021/ja045243w VL - 126 IS - 47 SP - 15603-15612 SN - 0002-7863 ER - TY - JOUR TI - Regulating the fluorescence intensity of an anthracene boronic acid system: a B-N bond or a hydrolysis mechanism? AU - Ni, WJ AU - Kaur, G AU - Springsteen, G AU - Wang, BH AU - Franzen, S T2 - BIOORGANIC CHEMISTRY AB - An anthracene-based fluorescent boronic acid system developed by the Shinkai group has been widely used for the preparation of fluorescent sensors for carbohydrates. Such application is based on the significant fluorescence intensity increase of this system upon binding with a carbohydrate. The mechanism through which this fluorescence intensity change happens was originally proposed to go through a B–N bond formation mechanism, which masks the nitrogen lone pair electrons. However, our own fluorescence studies suggest a possible alternative mechanism for the fluorescence change upon the formation of a boronic acid (1a) complex with diols. In this new proposed mechanism, complex formation induces solvolysis, which results in the protonation of the amine nitrogen if the reactions are carried out in a protic solvent such as water. This protonation prevents the photoinduced electron transfer, resulting in reduced quenching of the anthracene fluorescence. Such a solvolysis mechanism is supported by evidence from various types of experiments and theoretical calculations. DA - 2004/12// PY - 2004/12// DO - 10.1016/j.bioorg.2004.06.004 VL - 32 IS - 6 SP - 571-581 SN - 1090-2120 KW - anthracene-based fluorescent boronic acid KW - B-N bond KW - PET ER - TY - JOUR TI - Novel heterocyclic systems. Synthesis of 2,7-dimethyl-10-oxa-1,8-diaza-anthracen-9-one and derivatives AU - Gotchev, DB AU - Comins, DL T2 - TETRAHEDRON AB - Synthesis of novel heterocycles, which contain the unique 10-oxa-1,8-diazaanthracen-9-one tricyclic core, is reported. The core structure was assembled via a dehydrative-cyclization strategy. DA - 2004/12/13/ PY - 2004/12/13/ DO - 10.1016/j.tet.2004.09.111 VL - 60 IS - 51 SP - 11751-11758 SN - 0040-4020 KW - heterocycle KW - 10-oxa-1,8-diaza-anthracen-9-one KW - dehydrative cyclization ER - TY - JOUR TI - Identification of an adsorption complex between an alkane and zeolite active sites AU - Truitt, MJ AU - Toporek, SS AU - Rovira-Hernandez, R AU - Hatcher, K AU - White, JL T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Direct observation of the Bronsted acid site signal in an active zeolite catalyst following adsorption of stoichiometric quantities of isobutane reveals the presence of a specific adsorption complex. Independent polarization transfer experiments in which magnetization originates with either the catalyst or the adsorbed isobutane confirm this assignment. The initial steps in alkane reactivity are poorly defined, and this experimentally verified complex is proposed as a route to C-H bond activation in solid acids. DA - 2004/9/15/ PY - 2004/9/15/ DO - 10.1021/ja046729f VL - 126 IS - 36 SP - 11144-11145 SN - 0002-7863 ER - TY - JOUR TI - Controlling the polymorphic behaviors of semicrystalline polymers with cyclodextrins AU - Rusa, CC AU - Wei, M AU - Bullions, TA AU - Rusa, M AU - Gomez, MA AU - Porbeni, FE AU - Wang, XG AU - Shin, ID AU - Balik, CM AU - White, JL AU - Tonelli, AE T2 - CRYSTAL GROWTH & DESIGN AB - We present a review of our initial studies concerning the control of polymorphism in semicrystalline polymers with cyclodextrins (CDs). CDs are cyclic starch oligomers with six (α-CD), seven (β-CD), and eight (γ-CD) α-1,4-linked glucose units possessing bracelet structures with hydrophobic and hydrophilic interiors and exteriors, respectively. They are able to act as hosts to form noncovalent inclusion compounds (ICs) with a large variety of guest molecules, including a wide range of high molecular weight guest polymers. In polymer-CD-ICs, the CD host crystalline lattice consists of hexagonally packed CD stacks with guest polymers occupying the narrow channels (∼0.5−1.0 nm) extending down the interiors of the stacked CDs. As a consequence, the included guest polymers must adopt highly extended conformations and are segregated from neighboring guest polymer chains. When the host CDs are appropriately removed from polymer-CD-ICs, the included guest polymers are forced to coalesce into a pure polymer solid, which has been observed to affect their conformations, morphologies, and, for crystallizable polymers, even their polymorphism. Here we present a comparison of the polymorphism observed in nylon-6, PET, polycarbonate, and the polyolefins, isotactic-polypropylene and -poly-1-butene, coalesced from their CD-ICs with that observed when they are crystallized from their melts and/or solutions. Generally, a higher level of crystallinity and higher melting and melt recrystallization temperatures are observed for the CD-IC coalesced samples, and they also often crystallize into different polymorphs. DA - 2004/// PY - 2004/// DO - 10.1021/cg049821w VL - 4 IS - 6 SP - 1431-1441 SN - 1528-7505 ER - TY - JOUR TI - A new route to meso-formyl porphyrins AU - Balakumar, A AU - Muthukumaran, K AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Prior syntheses of porphyrins bearing meso-formyl groups have generally employed the Vilsmeier formylation of an acid-resistant copper or nickel porphyrin. A new approach for the synthesis of free base porphyrins bearing one or two (cis or trans) meso-formyl substituents entails the use of a dipyrromethane bearing an acetal group at the 5-position, a dipyrromethane-1-carbinol bearing an acetal group at the 5-position or carbinol position, or a dipyrromethane-1,9-dicarbinol bearing an acetal group at a carbinol position. Treatment of the resulting meso-acetal-substituted free base porphyrin to gentle acidic hydrolysis yields the corresponding meso-formyl porphyrin. DA - 2004/7/23/ PY - 2004/7/23/ DO - 10.1021/jo049819b VL - 69 IS - 15 SP - 5112-5115 SN - 0022-3263 ER - TY - JOUR TI - 9-Acylation of 1-acyldipyrromethanes containing a dialkylboron mask for the alpha-acylpyrrole motif AU - Zaidi, SHH AU - Muthukumaran, K AU - Tamaru, S AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - 1,9-Diacyldipyrromethanes are important precursors to porphyrins, yet synthetic access remains limited owing to (1) poor conversion in the 9-acylation of 1-acyldipyrromethanes and (2) handling difficulties because acyldipyrromethanes typically streak upon chromatography and give amorphous powders upon attempted crystallization. A reliable means for converting a dipyrromethane to a 1-acyldipyrromethane−dialkylboron complex was recently developed, where the dialkylboron (BR2) unit renders the complex hydrophobic and thereby facilitates isolation. Herein a refined preparation of 1,9-diacyldipyrromethanes is presented that employs the 1-acyldipyrromethane−BR2 complex as a substrate for 9-acylation. The dialkylboron unit provides protection for the α-acylpyrrole unit. 9-Acylation requires formation of the pyrrolyl−MgBr reagent and the presence of 1 equiv of a nonnucleophilic base to quench the proton liberated upon α-acylation. Reaction of the 1-acyldipyrromethane−BR2 complex (1 equiv) with mesitylmagnesium bromide (2 equiv) followed by the addition of an acylating agent (S-2-pyridyl thioate or acid chloride, 1.1 equiv) gives the corresponding 1,9-diacyldipyrromethane−BR2 complex. The acylation method afforded 1,9-diacyldipyrromethane−BR2 complexes with limited or no chromatography in yields of 64−92%. The 1,9-diacyldipyrromethane−BR2 complexes are stable to routine handling, are readily soluble in common organic solvents, crystallize readily, and can now be prepared in multigram quantities through use of stoichiometric quantities of reagents. DA - 2004/11/26/ PY - 2004/11/26/ DO - 10.1021/jo048587d VL - 69 IS - 24 SP - 8356-8365 SN - 0022-3263 ER - TY - JOUR TI - The mechanism of beta-hairpin formation AU - Dyer, RB AU - Maness, SJ AU - Peterson, ES AU - Franzen, S AU - Fesinmeyer, RM AU - Andersen, NH T2 - BIOCHEMISTRY AB - Beta-hairpins constitute an important class of connecting protein secondary structures. Several groups have postulated that such structures form early in the folding process and serve to nucleate the formation of extended beta-sheet structures. Despite the importance of beta-hairpins in protein folding, little is known about the mechanism of formation of these structures. While it is well established that there is a complex interplay between the stability of a beta-hairpin and loop conformational propensity, loop length, and the formation of stabilizing cross-strand interactions (H-bonds and hydrophobic interactions), the influence of these factors on the folding rate is poorly understood. Peptide models provide a simple framework for exploring the molecular details of the formation of beta-hairpin structures. We have explored the fundamental processes of folding in two linear peptides that form beta-hairpin structures, having a stabilizing hydrophobic cluster connected by loops of differing lengths. This approach allows us to evaluate existing models of the mechanism of beta-hairpin formation. We find a substantial acceleration of the folding rate when the connecting loop is made shorter (i.e., the hydrophobic cluster is moved closer to the turn). Analysis of the folding kinetics of these two peptides reveals that this acceleration is a direct consequence of the reduced entropic cost of the smaller loop search. DA - 2004/9/14/ PY - 2004/9/14/ DO - 10.1021/bi049177m VL - 43 IS - 36 SP - 11560-11566 SN - 0006-2960 ER - TY - JOUR TI - Synthesis and characterization of ReO4-containing microporous and open framework structures AU - Luo, JH AU - Alexander, B AU - Wagner, TR AU - Maggard, PA T2 - INORGANIC CHEMISTRY AB - A microporous and an open framework structure, [Cu2(pzc)2(H2O)2ReO4] (I) and [Cu(pzc)(H2O)ReO4]·2H2O (II) (pzc = 2-pyrazinecarboxylate), respectively, have been prepared using hydrothermal methods and characterized using IR, TGA, and X-ray diffraction (I Pnma, No. 62, Z = 4, a = 7.4949(9) Å, b = 24.975(3) Å, c = 9.141(1) Å; II P21/c, No. 14, Z = 4, a = 8.5878(9) Å, b = 12.920(1) Å, c = 9.741(1) Å, β = 92.830(2)°). I and II crystallize as red and blue solids, respectively, and each contains chains constructed from alternating Cu(pzc)2/ReO4 oxide-bridged metal sites. The bidentate pzc ligand further bridges each −Cu−O−Re−O− chain to adjacent chains, via the Cu sites, to form a 3D net in I, with ellipsoidal channels that are ∼3.3−4.7 Å × 12.5 Å, and in II, stacked layers of square nets with H2O-filled cavities that are ∼4.4 × 5.1 Å. Local ReO4- groups, a component of common oxidation catalysts, are directed at the channels and cavities of each structure, respectively. Thermogravimetric analysis indicates that I loses up to 64% of its H2O content before decomposition at 225 °C, while II loses ∼100% of its H2O content by 265 °C. DA - 2004/9/6/ PY - 2004/9/6/ DO - 10.1021/ic049609h VL - 43 IS - 18 SP - 5537-5542 SN - 1520-510X ER - TY - JOUR TI - Multiple-bit storage properties of porphyrin monolayers on SiO2 AU - Li, QL AU - Surthi, S AU - Mathur, G AU - Gowda, S AU - Zhao, Q AU - Sorenson, TA AU - Tenent, RC AU - Muthukumaran, K AU - Lindsey, JS AU - Misra, V T2 - APPLIED PHYSICS LETTERS AB - Hybrid molecule-silicon capacitors have been fabricated by the self-assembly of a monolayer of porphyrin molecules on a silicon oxide surface. The porphyrin employed [5-(4-dihydroxyphosphorylphenyl)-10,15,20-trimesitylporphinatozinc(II)] attaches to silicon oxide via a phosphonate linkage. Cyclic voltammetry current and capacitance/conductance measurements have been used to characterize the capacitors. The presence of multiple distinct peaks in current density and capacitance/conductance measurements are associated with oxidation and reduction of the molecular monolayer. The charge-storage states of the capacitor indicate applicability for use in multiple-bit memory devices. DA - 2004/9/6/ PY - 2004/9/6/ DO - 10.1063/1.1782254 VL - 85 IS - 10 SP - 1829-1831 SN - 1077-3118 ER - TY - JOUR TI - Magneto-optical properties of Li0.9Mo6O17: Color change in applied magnetic field AU - Choi, J AU - Woodward, JD AU - Musfeldt, JL AU - Wei, X AU - Whangbo, MH AU - He, J AU - Jin, R AU - Mandrus, D T2 - PHYSICAL REVIEW B AB - The polarized magneto-optical response of ${\mathrm{Li}}_{0.9}{\mathrm{Mo}}_{6}{\mathrm{O}}_{17}$ was measured in order to investigate the effect of a high magnetic field on the optical properties of a quasi-one-dimensional conductor. The observed magnetochromic effect is attributed to field-induced changes in the density of states near the Fermi level and is manifest in both $\mathrm{Mo}\phantom{\rule{0.3em}{0ex}}d\ensuremath{\rightarrow}d$ on-site and $\mathrm{O}\phantom{\rule{0.3em}{0ex}}p\ensuremath{\rightarrow}\mathrm{Mo}\phantom{\rule{0.3em}{0ex}}d$ charge transfer excitations. The observed polarization dependence of the field-induced color change is consistent with the low energy scale of this effect. DA - 2004/8// PY - 2004/8// DO - 10.1103/physrevb.70.085107 VL - 70 IS - 8 SP - SN - 1098-0121 ER - TY - JOUR TI - Fabrication of inclusion compounds with solid host gamma-cyclodextrins and water-soluble guest polymers: Inclusion of poly(N-acylethylenimine)s in gamma-cyclodextrin channels as monitored by solution H-1 NMR AU - Rusa, M AU - Wang, XW AU - Tonelli, AE T2 - MACROMOLECULES AB - We successfully report the formation of poly(N-acylethylenimine)−γ-cyclodextrin inclusion compounds (PNAI-γ-CD ICs). The PNAI-γ-CD ICs were obtained by three techniques:  (a) the precipitation of γ... DA - 2004/9/7/ PY - 2004/9/7/ DO - 10.1021/ma040081+ VL - 37 IS - 18 SP - 6898-6903 SN - 1520-5835 ER - TY - JOUR TI - Electronic properties of diamond clusters: self-consistent tight binding simulation AU - Areshkin, DA AU - Shenderova, OA AU - Adiga, SP AU - Brenner, DW T2 - DIAMOND AND RELATED MATERIALS AB - A self-consistent environment-dependent tight binding method is used to examine electron emission-related properties of hydrogen passivated nano-diamond (ND) particles. For sizes larger than 2.5 nm particle bandgap was found to be equal to the bandgap of bulk diamond. Coulomb potential distributions and electron affinities of clusters were found to be insensitive to the particle size if it exceeds 1.0 nm. Tunneling probabilities for homogeneous and inhomogeneous emission models were estimated. The simulation results indicate that the low emission threshold for hydrogen passivated diamond nano-clusters is due to hydrogen-assisted emission from the edges of small unpassivated islands. Essentially the same mechanism is claimed to be responsible for good emission properties of hydrogen passivated diamond films by Ristein [Diam. Relat. Mater. 9, 1129 (2000)]. DA - 2004/10// PY - 2004/10// DO - 10.1016/j.diamond.2004.04.012 VL - 13 IS - 10 SP - 1826-1833 SN - 1879-0062 KW - diamond clusters KW - field emission KW - electron affinity ER - TY - JOUR TI - Effect of structure on the reduction potentials of films of constitutional isomers of iron-sulfur cluster core dendrimers AU - Chasse, TL AU - Gorman, CB T2 - LANGMUIR AB - The thermodynamic redox potentials of films of constitutional isomers of iron−sulfur cluster core dendrimers were measured and compared. It was determined that the primary structure of the dendrimer influences its reduction potential. Dendrimers containing so-called backfolded linkages were more difficult to reduce than their extended analogues. This behavior is rationalized by suggesting that the backfolded isomers pack more tightly around the iron−sulfur cluster, creating a more hydrophobic local microenvironment. Also, all of these molecules are easier to reduce in the film than in dimethyl formamide solution. The variation in redox potential between film and solution environment was compared to that of dendrimers of differing generations and correlated with the amount of hydrophobic dendron surrounding the cluster. DA - 2004/9/28/ PY - 2004/9/28/ DO - 10.1021/la048733a VL - 20 IS - 20 SP - 8792-8795 SN - 0743-7463 ER - TY - PAT TI - Templated compositions of inorganic liquids and glasses AU - Martin, J. D. AU - Thornton, T. A. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Site-Directed Electrostatic Measurements with a Thiol-Specific pH-Sensitive Nitroxide:  Differentiating Local pK and Polarity Effects by High-Field EPR AU - Smirnov, Alex I. AU - Ruuge, Andres AU - Reznikov, Vladimir A. AU - Voinov, Maxim A. AU - Grigor'ev, Igor A. T2 - Journal of the American Chemical Society AB - This communication describes the use of a methanethiosulfonate derivative of an imidazolidine nitroxide, methanethiosulfonic acid S-(1-oxyl-2,2,3,5,5-pentamethyl-imidazolidin-4-ylmethyl) ester, IMTSL, for site-directed pKa determination of peptides by electron paramagnetic resonance. This spin label is covalently attached to the thiol group of unique cysteines incorporated into peptide structures. The tertiary amine nitrogen N3 of the label readily participates in proton exchange reactions, which are monitored through changes in EPR spectra of nitroxide moiety. Using EPR at 95 GHz (W-band) isotropic magnetic parameters of this nitroxide, both Aiso and giso, were calibrated in solvents of different polarity and pH. Two different linear correlations between Aiso and giso for acidic and basic forms of IMTSL were observed, making it possible to differentiate effects of local polarity from N3 protonation on nitroxide EPR spectra. Titration of a synthetic P11 peptide fragment of the laminin B1 chain illustrates the utility of this method. DA - 2004/7// PY - 2004/7// DO - 10.1021/ja048801f VL - 126 IS - 29 SP - 8872–8873 SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja048801f ER - TY - PAT TI - Regioisomerically pure oxochlorins and methods of synthesis AU - Lindsey, J. S. AU - Taniguchi, M. AU - Prathapan, S. AU - Kim, M. N. AU - Kim, H.-J. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Optimal regulation of private production contracts with environmental externalities AU - Bontems, P AU - Dubois, P AU - Vukina, T T2 - JOURNAL OF REGULATORY ECONOMICS DA - 2004/11// PY - 2004/11// DO - 10.1007/s11149-004-7552-5 VL - 26 IS - 3 SP - 287-301 SN - 0922-680X KW - regulation KW - pollution KW - principal-agent relationship KW - moral hazard ER - TY - JOUR TI - Model for the influence of boron impurities on the morphology of AIN grown by physical vapor transport AU - Brenner, DW AU - Schlesser, R AU - Sitar, Z AU - Dalmau, R AU - Collazo, R AU - Li, Y T2 - SURFACE SCIENCE AB - We propose that the reduction of the Schwoebel barrier by trace B impurities is responsible for the relatively flat c-plane morphology observed in AlN crystals that are deposited via physical vapor transport in BN crucibles relative to crystals grown in boron-free conditions. The model is supported by molecular statics calculations that predict that B substitutional impurities are energetically preferred at steps on the (0 0 0 1) surface, and that these impurities enhance binding and incorporation of growth species onto steps. DA - 2004/7/1/ PY - 2004/7/1/ DO - 10.1016/j.susc.2004.05.003 VL - 560 IS - 1-3 SP - L202-L206 SN - 1879-2758 KW - nitrides KW - boron KW - growth KW - surface structure KW - morphology KW - roughness KW - and topography ER - TY - JOUR TI - Interaction of basic drugs with lipid bilayers using liposome electrokinetic chromatography AU - Carrozzino, JM AU - Khaledi, MG T2 - PHARMACEUTICAL RESEARCH DA - 2004/12// PY - 2004/12// DO - 10.1007/s11095-004-7685-3 VL - 21 IS - 12 SP - 2327-2335 SN - 1573-904X KW - basic drugs KW - liposomes KW - octanol KW - partitioning ER - TY - JOUR TI - Eigenvector mapping: a method for discerning solvent effects on vibrational spectra AU - Lappi, S. E. AU - Franzen, Stefan T2 - Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy. AB - This paper reports a density functional theory (DFT) analysis of the adenine spectra in a hydrogen-bonding environment. We compare the theoretical vibrational spectra of 26 model systems in which water has been hydrogen bonded to adenine with the experimental frequencies of the solid state infrared spectra (150-1700 cm(-1)) of polycrystalline adenine and the experimental frequencies observed in matrix isolation spectra of adenine [J. Phys. Chem. 100 (1996) 3527]. The vibrational eigenvectors of adenine are compared by taking the dot product to determine how the normal modes of the 15-adenine atoms are affected by different hydrogen bonding geometries. Using the isolated adenine molecule as a reference permits a comparison of different calculated spectra in terms of the projections of various normal modes and the determination of the potential energy redistribution among normal modes. This method creates a map of the normal modes using the isolated adenine molecule as a reference. Improvement in agreement between the polycrystalline data and a model of adenine with four waters is most striking. The improvement in the fit between matrix isolation data and a model of adenine with a single water was not as dramatic as the fit seen for the polycrystalline data, but the fact that a single hydrogen-bonded water shifted the spectra of the model to a closer fit than that of isolated adenine is important. We call this method eigenvector mapping. The eigenvector mapping method can be used to extract the normal modes of a parent molecule from a solvent model system. The application of this method is important because it aids in the interpretation of complex molecular interactions in terms of the spectrum of an isolated molecule. The eigenvector mapping procedure will be shown to greatly improve the correspondence between the model and the experimental data. DA - 2004/// PY - 2004/// DO - 10.1016/S1386-1425(03)00248-8 VL - 60 IS - 02-Jan SP - 357–370 ER - TY - JOUR TI - Determination of the kinetic parameters of atom transfer radical polymerizations AU - Kwark, YJ AU - Novak, BM T2 - MACROMOLECULES AB - In an attempt to find a novel catalyst system for atom transfer radical polymerization (ATRP), a parameter estimation method based on nonlinear regression was developed to evaluate various catalyst systems by determining kinetic parameters of polymerization. From our model system considering small molecular atom transfer addition reaction, we found that equilibrium constant of atom transfer reaction could be successfully determined using our parameter estimation method. However, the each value of activation rate constant and deactivation reaction constant is hard to be determined ubiquitously because of the poor sensitivities of them and the local minima trapping. By applying second minimization algorithm, the parameter estimation algorithm achieves higher propensity to reach global minimum, yet not all the time. The simulation results using kinetic rate constants determined by our method shows better agreement with the experimental data than that using literature values. This is because the current method uses fewer assumptions than other literature methods in determining rate constants. We also demonstrated the determination of kinetic constants in the polymerization of styrene and MMA using various metal catalysts, and the simulations using these kinetic constants agree well with the experimental data. DA - 2004/12/14/ PY - 2004/12/14/ DO - 10.1021/ma049627i VL - 37 IS - 25 SP - 9395-9401 SN - 1520-5835 ER - TY - JOUR TI - Characterization of single- and double-stranded DNA on gold surfaces AU - Moses, S AU - Brewer, SH AU - Lowe, LB AU - Lappi, SE AU - Gilvey, LBG AU - Sauthier, M AU - Tenent, RC AU - Feldheim, DL AU - Franzen, S T2 - LANGMUIR AB - Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5‘-C6H12SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation−infrared reflection absorption spectroscopy (PM−IRRAS). The formation of dsDNA on the surface was identified by PM−IRRAS by a dsDNA IR signature at ∼1678 cm-1 that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 °C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au−S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces. DA - 2004/12/7/ PY - 2004/12/7/ DO - 10.1021/la0492815 VL - 20 IS - 25 SP - 11134-11140 SN - 0743-7463 ER - TY - JOUR TI - Bifunctional, conjugated oligomers for orthogonal self-assembly: Selectivity varies from planar substrates to nanoparticles AU - Walker, BR AU - Wassel, RA AU - Stefanescu, DM AU - Gorman, CB T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - A diphenylacetylene containing two different end groups (isonitrile and thioacetate) was synthesized, showing that the chemistry used to install each end group is compatible with that of the others. The isonitrile group binds preferentially to platinum, and the thiol group binds preferentially to gold. However, the selectivity was different when nanoparticles were compared to planar substrates. DA - 2004/12/22/ PY - 2004/12/22/ DO - 10.1021/ja046491v VL - 126 IS - 50 SP - 16330-16331 SN - 0002-7863 ER - TY - JOUR TI - Atomistic simulation of the influence of pre-existing stress on the interpretation of nanoindentation data AU - Schall, JD AU - Brenner, DW T2 - JOURNAL OF MATERIALS RESEARCH DA - 2004/11// PY - 2004/11// DO - 10.1557/JMR.2004.0410 VL - 19 IS - 11 SP - 3172-3180 SN - 0884-2914 ER - TY - JOUR TI - A new type of water-soluble fluorescent boronic acid suitable for construction of polyboronic acids for carbohydrate recognition AU - Yang, W. Q. AU - Li, L. AU - Wang, B. H. T2 - Heterocyclic Communications DA - 2004/// PY - 2004/// VL - 10 IS - 6 SP - 383-388 ER - TY - JOUR TI - The design of boronic acid spectroscopic reporter compounds by taking advantage of the pK(a)-lowering effect of diol binding: Nitrophenol-based color reporters for diols AU - Ni, WJ AU - Fang, H AU - Springsteen, G AU - Wang, BH T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The complex that forms between a boronic acid and a diol is often much more acidic than the starting boronic acid. In conditions where the solution pH is between the two pKa values, the boron atom will convert from a neutral trigonal form to an anionic tetrahedral form upon complexation. Such a change is likely to dramatically alter the electron density of neighboring groups. Utilizing this effect, we have designed and synthesized two nitrophenol-based boronic acid reporter compounds that change ionization states and therefore spectroscopic properties upon diol binding. Both compounds show significant UV changes upon addition of saccharides. For example, a blue shift of the absorption max from 373 to 332 nm was observed with the addition of d-fructose to 2-hydroxy-5-nitrophenylboronic acid at neutral pH. Such a reporter compound can be used as a recognition and signaling unit for the construction of polyboronic acid sensors for the selective and specific recognitions of saccharides of biological significance. DA - 2004/3/19/ PY - 2004/3/19/ DO - 10.1021/jo0350357 VL - 69 IS - 6 SP - 1999-2007 SN - 1520-6904 ER - TY - JOUR TI - Synthesis of oxygen- and nitrogen-containing heterocycles by ring-closing metathesis AU - Deiters, A AU - Martin, SF T2 - CHEMICAL REVIEWS AB - ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Oxygen- and Nitrogen-Containing Heterocycles by Ring-Closing MetathesisAlexander Deiters and Stephen F. MartinView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Chemistry and Biochemistry, The University of Texas, Austin, Texas 78712 Cite this: Chem. Rev. 2004, 104, 5, 2199–2238Publication Date (Web):April 27, 2004Publication History Received16 October 2003Published online27 April 2004Published inissue 1 May 2004https://doi.org/10.1021/cr0200872Copyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views12619Altmetric-Citations1164LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. 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Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (1 MB) Get e-AlertsSUBJECTS:Catalysts,Cyclization,Ethers,Lactones,Metathesis Get e-Alerts DA - 2004/5// PY - 2004/5// DO - 10.1021/cr0200872 VL - 104 IS - 5 SP - 2199-2238 SN - 1520-6890 ER - TY - JOUR TI - Synthesis and reactivity of a coordinatively unsaturated ruthenium(II) parent amido complex: Studies of X-H activation (X = H or C) AU - Conner, D AU - Jayaprakash, KN AU - Cundari, TR AU - Gunnoe, TB T2 - ORGANOMETALLICS AB - The five-coordinate parent amido complex (PCP)Ru(CO)(NH2) (2) (PCP = 2,6-(CH2PtBu2)2C6H3) has been prepared by two independent routes that involve deprotonation of Ru(II) ammine complexes. Complex 2 reacts with phenylacetylene to yield the Ru(II) acetylide complex (PCP)Ru(CO)(C⋮CPh) (5) and ammonia. In addition, complex 2 rapidly activates dihydrogen at room temperature to yield ammonia and the previously reported hydride complex (PCP)Ru(CO)(H). The ability of the amido complex 2 to cleave the H−H bond is attributed to the combination of a vacant coordination site for binding/activation of dihydrogen and a basic amido ligand. Complex 2 also undergoes an intramolecular C−H activation of a methyl group on the PCP ligand to yield ammonia and a cyclometalated complex. The reaction of (PCP)Ru(CO)(Cl) with MeLi allows the isolation of (PCP)Ru(CO)(Me) (8), and complex 8 undergoes an intramolecular C−H activation analogous to the amido complex 2 to produce methane and the cyclometalated complex. Determination of activation parameters for the intramolecular C−H activation transformations of 2 and 8 reveal identical ΔH⧧ {18(1) kcal/mol} with ΔS⧧ = −23(4) eu and −18(4) eu, respectively. Density functional theory has been applied to the study of intermolecular activation of methane and dihydrogen by (PCP‘)Ru(CO)(NH2) to yield (PCP‘)Ru(CO)(NH3)(X) (X = Me or H; PCP‘ = 2,6-(CH2PH2)2C6H3). The results indicate that the activation of dihydrogen is both exoergic and exothermic. In contrast, the addition of a C−H bond of methane across the Ru−NH2 bond has been calculated to be endoergic and endothermic. The surprising endoergic nature of the methane C−H activation has been attributed to a large and unfavorable change in Ru−N bond dissociation energy upon conversion from Ru-amido to Ru-ammine. DA - 2004/5/24/ PY - 2004/5/24/ DO - 10.1021/om049836r VL - 23 IS - 11 SP - 2724-2733 SN - 1520-6041 ER - TY - JOUR TI - Spin dimer and classical spin analyses of the ordered magnetic structures of alkali iron pyrophosphates NaFeP2O7 and LiFeP2O7 AU - Whangbo, M. H. AU - Dai, D. AU - Koo, H. J. T2 - Dalton Transactions (Cambridge, England : 2003) DA - 2004/// PY - 2004/// IS - 19 SP - 3019-3025 ER - TY - JOUR TI - Separate and independent control of interfacial band alignments and dielectric constants in transition metal rare earth complex oxides AU - Lucovsky, G AU - Zhang, Y AU - Whitten, JL AU - Schlom, DG AU - Freeouf, JL T2 - MICROELECTRONIC ENGINEERING AB - Spectroscopic studies of transition metal (Tm) and rare earth (Re) oxides, combined with ab initio theory, identify the band edge electronic structure of alternative high-k dielectrics. The lowest conduction band states are derived from anti-bonding transition metal d*-states with a π symmetry and show strong final state effects. Applied to the complex Tm/Re mixed oxides of the general form ReTmO3, this approach identifies a novel way for obtaining separate and independent control of band gap energies and dielectric constants through local bonding arrangements in which Tm and Re atoms are nearest neighbors to the same oxygen atom. DA - 2004/4// PY - 2004/4// DO - 10.1016/j.mee.2004.01.006 VL - 72 IS - 1-4 SP - 288-293 SN - 0167-9317 KW - high-k dielectrics KW - transition metal oxides KW - rare earth oxides KW - complex mixed oxides ER - TY - JOUR TI - Probing Helix Formation in Chains of Vertex-Linked Octahedra AU - Maggard, P.A. AU - Kopf, A.L. AU - Stern, C.L. AU - Poeppelmeier, K.R. T2 - CrystEngComm AB - The rational design of crystal structures based on the chemical nature of molecular components, a longstanding and exciting research topic in organic solid state chemistry, is an emerging theme of crystal engineering in inorganic solid state chemistry. In particular, noncentrosymmetric structures, or those lacking inversion symmetry, are important for future technologies that are based on piezoelectricity, pyroelectricity, ferroelectricity and second harmonic generation (SHG). Materials that exhibit these properties provide a large and new class of solids for studies in basic science associated with the noncentrosymmetric (chiral, polar, or chiral–polar) space groups. Structures comprised of vertex-linked octahedra are common in inorganic solids. The subject of our Highlight is the rational synthesis of linear, zigzag or helical chains when two vertices of an octahedron, which are either adjacent (cis) or opposite (trans), are linked. DA - 2004/// PY - 2004/// DO - 10.1039/b406621a VL - 6 IS - Sep 17 2004 SP - 452-457 SN - 1466-8033 ER - TY - JOUR TI - Preparation of protein gradients through the controlled deposition of protein-nanoparticle conjugates onto functionalized surfaces AU - Kramer, S AU - Xie, H AU - Gaff, J AU - Williamson, , JR AU - Tkachenko, AG AU - Nouri, N AU - Feldheim, DA AU - Feldheim, DL T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - This paper describes a simple method for the preparation and characterization of protein density gradients on solid supports. The method employs colloidal metal nanoparticles as protein carriers and optical tags and is capable of forming linear, exponential, 1D, 2D, and multiprotein gradients of varying slope without expensive or sophisticated surface patterning techniques. Surfaces patterned with proteins using the procedures described within are shown to support cell growth and are thus suitable for studies of protein−cell interactions. DA - 2004/5/5/ PY - 2004/5/5/ DO - 10.1021/ja031674n VL - 126 IS - 17 SP - 5388-5395 SN - 0002-7863 ER - TY - JOUR TI - Porphyrin architectures tailored for studies of molecular information storage AU - Carcel, CM AU - Laha, JK AU - Loewe, RS AU - Thamyongkit, P AU - Schweikart, KH AU - Misra, V AU - Bocian, DF AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Zinc porphyrins tethered to Au(111) or Si(100) provide a benchmark for studies of information storage. Three sets of porphyrins have been synthesized for studies of the interplay of molecular design and charge-storage properties: (1) A set of porphyrins is described for probing the effect of surface attachment atom on electron-transfer kinetics. Each porphyrin bears a meso-CH2X group for surface attachment where X = OH, SAc, or SeAc. (2) A set of porphyrins is described for studying the effect of surface-charge density in monolayers. Each porphyrin bears a benzyl alcohol for surface attachment and three nonlinking meso substituents of a controlled degree of bulkiness. (3) A set of porphyrins is described that enables investigation of on-chip patterning of the electrolyte. Each porphyrin bears a formyl group distal to the surface attachment group for subsequent derivatization with a molecular entity that comprises the electrolyte. Taken together, this collection of molecules enables a variety of studies to elucidate design issues in molecular-based information storage. DA - 2004/10/1/ PY - 2004/10/1/ DO - 10.1021/jo0498260 VL - 69 IS - 20 SP - 6739-6750 SN - 0022-3263 ER - TY - JOUR TI - Infrared spectra of (H2O)-O-16, (H2O)-O-18 and D2O in the liquid phase by single-pass attenuated total internal reflection spectroscopy AU - Lappi, SE AU - Smith, B AU - Franzen, S T2 - SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY AB - Mid-infrared attenuated total internal reflection (ATR) spectra of H216O, H218O and D216O in the liquid state were obtained and normal coordinate analysis was performed based on the potential energy surface obtained from density functional theory (DFT) calculations. Fits of the spectra to multiple Gaussians showed a consistent fit of three bands for the bending region and five bands for the stretching region for three isotopomers, H216O, H218O and D216O. The results are consistent with previous work and build on earlier studies by the inclusion of three isotopomers and mixtures using the advantage of single-pass ATR to obtain high quality spectra of the water stretching bands. DFT calculation of the vibrational spectrum of liquid water was conducted on seven model systems, two systems with periodic boundary conditions (PBC) consisting of four and nine H216O molecules, and five water clusters consisting of 4, 9, 19, 27 and 32 H216O molecules. The PBC and cluster models were used to obtain a representation of bulk water for comparison with experiment. The nine-water PBC model was found to give a good fit to the experimental line shapes. A difference is observed in the broadening of the water bending and stretching vibrations indicative of a difference in the rate of pure dephasing. The nine-water PBC calculation was also used to calculate the wavenumber shifts observed in the water isotopomers. DA - 2004/9// PY - 2004/9// DO - 10.1016/j.saa.2003.12.042 VL - 60 IS - 11 SP - 2611-2619 SN - 1386-1425 KW - IR KW - attenuated total reflection KW - (H2O)-O-16 KW - (H2O)-O-18 KW - (D2O)-O-16 KW - density functional theory calculations ER - TY - JOUR TI - Grower risk aversion and the cost of moral hazard in livestock production contracts AU - Dubois, P AU - Vukina, T T2 - AMERICAN JOURNAL OF AGRICULTURAL ECONOMICS AB - American Journal of Agricultural EconomicsVolume 86, Issue 3 p. 835-841 Proceeding Grower Risk Aversion and the Cost of Moral Hazard in Livestock Production Contracts Pierre Dubois, Pierre Dubois Research fellow INRA and IDEI, University of ToulouseSearch for more papers by this authorTomislav Vukina, Tomislav Vukina Professor Department of Agricultural and Resource Economics, North Carolina State UniversitySearch for more papers by this author Pierre Dubois, Pierre Dubois Research fellow INRA and IDEI, University of ToulouseSearch for more papers by this authorTomislav Vukina, Tomislav Vukina Professor Department of Agricultural and Resource Economics, North Carolina State UniversitySearch for more papers by this author First published: 01 August 2004 https://doi.org/10.1111/j.0002-9092.2004.00634.xCitations: 17 We are thankful to Laura Martin for the permission to use her contract settlements data set. This article was presented at the ASSA winter meetings (San Diego, CA, January 2004). Articles in these sessions are not subjected to the journal's standard refereeing process. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume86, Issue3August 2004Pages 835-841 RelatedInformation DA - 2004/8// PY - 2004/8// DO - 10.1111/j.0002-9092.2004.00634.x VL - 86 IS - 3 SP - 835-841 SN - 0002-9092 ER - TY - JOUR TI - Experimental and theoretical investigation on the relative stability of the PdS2- and pyrite-type structures of PdSe2 AU - Soulard, C. AU - Rocquefelte, X. AU - Petit, P. E. AU - Evain, M. AU - Jobic, S. AU - Itie, J. P. AU - Munsch, P. AU - Koo, H. J. AU - Whangbo, M. H. T2 - Inorganic Chemistry DA - 2004/// PY - 2004/// DO - 10.1021/ic035396 VL - 43 IS - 6 SP - 1943-1949 ER - TY - JOUR TI - Experimental and computational studies of ruthenium(II)-catalyzed addition of arene C-H bonds to olefins AU - Lail, M AU - Bell, CM AU - Conner, D AU - Cundari, TR AU - Gunnoe, TB AU - Petersen, JL T2 - ORGANOMETALLICS AB - Hydroarylation reactions of olefins are catalyzed by the octahedral Ru(II) complex TpRu-(CO)(NCMe)(Ph) (1) (Tp ) hydridotris(pyrazolyl)borate).Experimental studies and density functional theory calculations support a reaction pathway that involves initial acetonitrile/ olefin ligand exchange and subsequent olefin insertion into the ruthenium-phenyl bond.Metal-mediated C-H activation of arene to form a Ru-aryl bond with release of alkyl arene completes the proposed catalytic cycle.The cyclopentadienyl complex CpRu(PPh 3 ) 2 (Ph) produces ethylbenzene and styrene from a benzene/ethylene solution at 90 °C; however, the transformation is not catalytic.A benzene solution of (PCP)Ru(CO)(Ph) (PCP ) 2,6-(CH 2 P t -Bu 2 ) 2 C 6 H 3 ) and ethylene at 90 °C produces styrene in 12% yield without observation of ethylbenzene.Computational studies (DFT) suggest that the C-H activation step does not proceed through the formation of a Ru(IV) oxidative addition intermediate but rather occurs by a concerted pathway. DA - 2004/10/11/ PY - 2004/10/11/ DO - 10.1021/om049404g VL - 23 IS - 21 SP - 5007-5020 SN - 1520-6041 ER - TY - JOUR TI - Establishing the molecular basis for molecular electronics AU - Wassel, RA AU - Gorman, CB T2 - ANGEWANDTE CHEMIE-INTERNATIONAL EDITION AB - Molecular structure–property relationships for molecular electronics are beginning to emerge. Recent experiments lend credibility to the single-molecule nature of transport measurements and illustrate the molecular features that give rise to various interesting conductance behaviors (see picture). DA - 2004/// PY - 2004/// DO - 10.1002/anie.200301735 VL - 43 IS - 39 SP - 5120-5123 SN - 1521-3773 KW - electron transport KW - molecular devices KW - molecular electronics KW - single-molecule studies KW - structure-activity relationships ER - TY - JOUR TI - Characterization of small unilamellar vesicles using solvatochromic pi* indicators and particle sizing AU - Carrozzino, JM AU - Fuguet, E AU - Helburn, R AU - Khaledi, MG T2 - JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS AB - A suite of small unilamellar vesicles (SUVs) composed of mixtures of phospholipids and cholesterol (CH) or the synthetic surfactant dihexadecyl phosphate (DHP) and cholesterol was investigated using a homologous series of solvatochromic pi* indicators coupled with size exclusion methods and photon correlation spectroscopy (PCS). The solvatochromic method, which is based on the measurement of solvent-dependent shifts in lambda(max) from UV-Vis spectra of solubilized indicators, was used to quantify the dipolarity and polarizability (pi*) of probe solvation environments. The partitioning of the series of individual di-n-alkyl-p-nitroaniline (DNAP) pi* indicators in PG(24)PC(46)Chol(30) and DHP(70)Chol(30) SUVs was examined as a function of the head group structure as well as the method of dye-vesicle preparation. Solubilization of the larger more hydrophobic probes in the bilayer portion of PG(24)PC(46)Chol(30) SUVs was aided through physical entrapment. Such physical methods were not needed for the smaller indicators or for the range of indicators in the DHP(70)Chol(30) dispersions. Extrusion and size-exclusion chromatographic methodologies for the preparation of physically entrapped dopants in SUVs of fixed size range demonstrated that the larger (longer alkyl chain) dopants in the series resided in PG(24)PC(46)Chol(30) liposomes with a wider range of sizes, while the smaller more polar solutes tended to be entrapped in smaller vesicles with a narrower size range. DA - 2004/8/31/ PY - 2004/8/31/ DO - 10.1016/j.jbbm.2004.04.014 VL - 60 IS - 2 SP - 97-115 SN - 0165-022X KW - vesicles KW - liposomes KW - microenvironment polarity KW - electrokinetic chromatography KW - drug delivery ER - TY - JOUR TI - Characterization of self-assembled monolayers of porphyrins bearing multiple thiol-derivatized rigid-rod tethers AU - Yasseri, AA AU - Syomin, D AU - Malinovskii, VL AU - Loewe, RS AU - Lindsey, JS AU - Zaera, F AU - Bocian, DF T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - A series of multithiol-functionalized zinc porphyrins has been prepared and characterized as self-assembled monolayers (SAMs) on Au. The molecules, designated ZnPS(n) (n = 1-4), contain from one to four [(S-acetylthio)methyl]phenylethynylphenyl groups appended to the meso-position of the porphyrin; the other meso-substituents are phenyl groups. For the dithiol-functionalized molecules, both the cis- and the trans-appended structures were examined. The ZnPS(n) SAMs were investigated using X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and various electrochemical methods. The studies reveal the following characteristics of the ZnPS(n) SAMs. (1) The ZnPS(n) molecules bind to the Au surface via a single thiol regardless of the number of thiol appendages that are available per molecular unit. (2) The porphyrins in the ZnPS(3) and ZnPS(4) SAMs bind to the surface in a more upright orientation than the porphyrins in the ZnPS(1), cis-ZnPS(2), and trans-ZnPS(2) SAMs. The porphyrins in the ZnPS(3) and ZnPS(4) SAMs are also more densely packed than those in the cis-ZnPS(2) and trans-ZnPS(2) SAMs. The packing density of the ZnPS(3) and ZnPS(4) SAMs is similar to that of the ZnPS(1) SAMs, despite the larger size of the molecules in the former SAMs. (3) The thermodynamics and kinetics of electron transfer are generally similar for all of the ZnPS(n) SAMs. The general similarities in the electron-transfer characteristics for all of the SAMs are attributed to the similar binding motif. DA - 2004/9/29/ PY - 2004/9/29/ DO - 10.1021/ja047723t VL - 126 IS - 38 SP - 11944-11953 SN - 0002-7863 ER - TY - JOUR TI - CO vibration as a probe of ligand dissociation and transfer in myoglobin AU - Polack, T AU - Ogilvie, JP AU - Franzen, S AU - Vos, MH AU - Joffre, M AU - Martin, JL AU - Alexandrou, A T2 - PHYSICAL REVIEW LETTERS AB - We report femtosecond visible pump, midinfrared probe, spectrally integrated experiments resolving the dynamics of CO in myoglobin upon photodissociation. Our results show a progressive change in absorption strength of the CO vibrational transition during its transfer from the heme to the docking site, whereas the vibrational frequency change is faster than our time resolution. A phenomenological model gives good qualitative agreement with our data for a time constant of 400 fs for the change in oscillator strength. Density-functional calculations demonstrate that indeed vibrational frequency and absorption strength are not linearly coupled and that the absorption strength varies in a slower manner due to charge transfer from the heme iron to CO. DA - 2004/7/2/ PY - 2004/7/2/ DO - 10.1103/physrevlett.93.018102 VL - 93 IS - 1 SP - SN - 0031-9007 ER - TY - JOUR TI - An intimate polycarbonate/poly(methyl methacrylate)/poly(vinyl acetate) ternary blend via coalescence from their common inclusion compound with gamma-cyclodextrin AU - Rusa, CC AU - Uyar, T AU - Rusa, M AU - Hunt, MA AU - Wang, XW AU - Tonelli, AE T2 - JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS AB - Abstract In this study, we successfully report an intimate ternary blend system of polycarbonate (PC)/poly(methyl methacrylate) (PMMA)/poly(vinyl acetate) (PVAc) obtained by the simultaneous coalescence of the three guest polymers from their common γ‐cyclodextrin (γ‐CD) inclusion compound (IC). The thermal transitions and the homogeneity of the coalesced ternary blend were studied by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The observation of a single, common glass transition strongly suggests the presence of a homogeneous amorphous phase in the coalesced ternary polymer blend. This was further substantiated by solid‐state 13 C NMR observation of the T 1ρ ( 1 H)s for each of the blend components. For comparison, ternary blends of PC/PMMA/PVAc were also prepared by traditional coprecipitation and solution casting methods. TGA data showed a thermal stability for the coalesced ternary blend that was improved over the coprecipitated blend, which was phase‐segregated. The presence of possible interactions between the three polymer components was investigated by infrared spectroscopy (FTIR). The analysis indicates that the ternary blend of these polymers achieved by coalescence from their common γ‐CD–IC results in a homogeneous polymer blend, possibly with improved properties, whereas coprecipitation and solution cast methods produced phase separated polymer blends. It was also found that control of the component polymer molar ratios plays a key role in the miscibility of their coalesced ternary blends. Coalescence of two or more normally immiscible polymers from their common CD–ICs appears to be a general method for obtaining well‐mixed, intimate blends. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4182–4194, 2004 DA - 2004/11/15/ PY - 2004/11/15/ DO - 10.1002/polb.20273 VL - 42 IS - 22 SP - 4182-4194 SN - 1099-0488 KW - cyclodextrin KW - inclusion compound KW - miscibility KW - ternary blend KW - polycarbonate KW - poly(methyl methacrylate) KW - poly(vinyl acetate) KW - compatibilization ER - TY - JOUR TI - A self-consistent tight binding model for hydrocarbon systems: application to quantum transport simulation AU - Areshkin, DA AU - Shenderova, OA AU - Schall, JD AU - Adiga, SP AU - Brenner, DW T2 - JOURNAL OF PHYSICS-CONDENSED MATTER AB - A self-consistent environment-dependent (SC-ED) tight binding (TB) method for hydrocarbons that was developed for quantum transport simulations is presented. The method builds on a non-self-consistent environment-dependent TB model for carbon (Tang et al 1996 Phys. Rev. B 53 979) with parameters added to describe hydrocarbon bonds and to account for self-consistent charge transfer. The SC-EDTB model assumes an orthogonal basis set. Orthogonality is a key element for adapting the SC-EDTB scheme to transport problems because it substantially increases the efficiency of the Newton–Raphson algorithm used to accelerate self-consistency convergence under non-equilibrium conditions. Compared to most existing TB schemes the SC-EDTB scheme is distinctive in two respects. First, self-consistency is added through the exact evaluation of Hartree and linear expansion of exchange integrals. All Hamiltonian elements belonging to the same atom are affected by charge transfer, not just the diagonal elements. The second distinction is the choice of SC-EDTB parameters; they were fitted to Mulliken populations and eigenvalue spectra rather than energies or elastic properties. The former are directly related to the conductivity and potential profile, which are essential for transport simulation. No two-centre repulsive term parametrization was performed. The functionality of the method is exemplified by computing I–V curves, non-equilibrium potential profiles and current density for a resonant tunnelling device. DA - 2004/10/6/ PY - 2004/10/6/ DO - 10.1088/0953-8984/16/39/018 VL - 16 IS - 39 SP - 6851-6866 SN - 1361-648X ER - TY - JOUR TI - Synthesis of [NH4]MnCl2(OAc) and [NH4](2)MnCl4(H2O)(2) by solvothermal dehydration and structure/property correlations in a one-dimensional antiferromagnet AU - Martin, JD AU - Hess, RF AU - Boyle, PD T2 - INORGANIC CHEMISTRY AB - The utility of the solvothermal dehydration strategy whereby superheated acetonitrile reacts with water of hydration to form ammonium acetate is demonstrated in the synthesis of [NH4]MnCl2(OAc), I, and [NH4]2MnCl4(H2O)2, II, from MnCl2·4H2O. The structure of I is shown to crystallize in the monoclinic space group C2/c (No. 15) with a = 15.191(6) Å, b = 7.044(2) Å, c = 13.603(6) Å, β = 107.31°, V = 1389.7(9) cm-1, and Z = 8. The structure of II crystallizes in the space group I4/mmm (No. 139) with a = 7.5250(5) Å, b = 8.276(2) Å, V = 468.6(1) cm-1, and Z = 2. Both structures exhibit extensive hydrogen bonding that controls both local Mn−Cl bonding and the interchain organization. I is shown to be a one-dimensional Heisenberg antiferromagnet with an intrachain exchange constant J/k = −2.39 K. This structure exhibits exchange coupling intermediate between the well-studied triply and doubly chloride-bridged one-dimensional manganese Heisenberg antiferromagnets. The structure/property correlation demonstrates a linear dependence of the exchange constant on the Mn−Cl−Mn bond angle, α, for α < 94°. DA - 2004/5/17/ PY - 2004/5/17/ DO - 10.1021/ic049881r VL - 43 IS - 10 SP - 3242-3247 SN - 0020-1669 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-2442565694&partnerID=MN8TOARS ER - TY - JOUR TI - Stable helical polyguanidines: Poly{N-(1-anthryl)-N '-[(R)- and/or (S)-3,7-dimethyloctyl]guanidines} AU - Tang, HZ AU - Lu, YJ AU - Tian, GL AU - Capracotta, MD AU - Novak, BM T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Using chiral catalysts of (R)- and/or (S)-BINOL-Ti, the asymmetrical polymerization of achiral monomer, N-(1-anthryl)-N'-n-octadecylcarbodiimide, yielded soluble nonregioregular polyguanidines of Poly-R1 and Poly-S1. A racemization process occurred when the toluene solution of Poly-R1 was annealed at elevated temperatures (70-80 degrees C). Kinetic studies reveal this to be a slow process with an activation energy of ca. 36 kcal/mol. On the other hand, using titanium(IV) trifluoroethoxide catalyst, the polymerization of N-(1-anthryl)-N'-[(R)- and/or (S)-3,7-dimethyloctyl]carbodiimides afforded highly regioregular polyguanidines of Poly-R2 and Poly-S2. These polymers adopt stable helices in various solvents and elevated temperatures, whose kinetically controlled conformations and thermodynamically controlled conformations are essentially the same. DA - 2004/3/31/ PY - 2004/3/31/ DO - 10.1021/ja049937g VL - 126 IS - 12 SP - 3722-3723 SN - 1520-5126 ER - TY - PAT TI - Pesticidal activity of functionalized cyclopropanes AU - Linderman, R. J. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Excited-state energy flow in covalently linked multiporphyrin arrays: The essential contribution of energy transfer between nonadjacent chromophores AU - Hindin, E AU - Forties, RA AU - Loewe, RS AU - Ambroise, A AU - Kirmaier, C AU - Bocian, DF AU - Lindsey, JS AU - Holten, D AU - Knox, RS T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - A series of multiporphyrin arrays has been studied to probe the contribution of energy transfer between second-neighbor (“nonadjacent”) porphyrins and to determine the rate of energy transfer between identical porphyrins at adjacent sites. The arrays, organized in linear or branched architectures, contain up to 21 constituents, domains of 2−5 zinc porphyrins, and a single energy trap. The study has involved iterative cycles of molecular design, synthesis, determination of rates via transient absorption spectroscopy, and kinetic analysis. A rate constant of (30 ± 10 ps)-1 is deduced for bidirectional energy transfer between adjacent zinc porphyrins joined by a diphenylethyne linker. The value is (50 ± 10 ps)-1 when the porphyrin-linker internal rotation is hindered by o,o‘-methyl groups on one aryl ring of the linker. Rates of nonadjacent energy transfers are typically only 5−10-fold less than the rates of adjacent transfers. Thus, the nonadjacent pathway has a significant impact on the overall rate of energy flow to the trap, even in architectures as small as triads. These findings provide information that will be essential for the rational design of multichromophore arrays whose function is to transfer excitation energy efficiently over large distances to a trap site. DA - 2004/8/26/ PY - 2004/8/26/ DO - 10.1021/jp047803j VL - 108 IS - 34 SP - 12821-12832 SN - 1520-6106 ER - TY - JOUR TI - Classical spin and quantum-mechanical descriptions of geometric spin frustration AU - Dai, DD AU - Whangbo, MH T2 - JOURNAL OF CHEMICAL PHYSICS AB - Geometric spin frustration (GSF) in isolated plaquettes with local spin s, i.e., an equilateral-triangle spin trimer and a regular-tetrahedron spin tetramer, was examined on the basis of classical spin and quantum-mechanical descriptions to clarify their differences and similarities. An analytical proof was given for how the state degeneracy and the total spin S of their ground states depend on the local spin s. The quantum-mechanical conditions for the occurrence of GSF in isolated plaquettes were clarified, and their implications were explored. Corner sharing between plaquettes and how it affects GSF in the resulting spin systems was examined. DA - 2004/7/8/ PY - 2004/7/8/ DO - 10.1063/1.1760749 VL - 121 IS - 2 SP - 672-680 SN - 0021-9606 ER - TY - JOUR TI - Ab initio theory calculations of the electronic structure of nc-AS(2)S(3) and GeS2: an intrinsic mechanism for reversible photo-darkening AU - Mowrer, T. AU - Lucovsky, G. AU - Sremaniak, L. S. AU - Whitten, Jerry T2 - Journal of Non-crystalline Solids DA - 2004/// PY - 2004/// DO - 10.1016/j.jnocrysol.2004.03.038 VL - 338-40 IS - Jun 15 2004 SP - 543–547 ER - TY - JOUR TI - A neural network model with bounded-weights for pattern classification AU - Liao, Y AU - Fang, SC AU - Nuttle, HLW T2 - COMPUTERS & OPERATIONS RESEARCH AB - A new neural network model is proposed based on the concepts of multi-layer perceptrons, radial basis functions, and support vector machines (SVM). This neural network model is trained using the least squared error as the optimization criterion, with the magnitudes of the weights on the links being limited to a certain range. Like the SVM model, the weight specification problem is formulated as a convex quadratic programming problem. However, unlike the SVM model, it does not require that kernel functions satisfy Mercer's condition, and it can be readily extended to multi-class classification. Some experimental results are reported. Scopeandpurpose For the past decade, there has been increasing interest in solving nonlinear pattern classification problems. Among the various approaches, Multi-layer perceptrons, radial basis function networks and support vector machines have received most attention due to their tremendous success in real-world applications. Compared with the other two, The support vector machines approach is relatively new and often performs better in many applications. However, it also has some limitations, for example, kernel functions are required to satisfy Mercer's condition and it is not easily applicable for multi-class classification. In this paper, we propose a new neural network model which overcomes these limitations. DA - 2004/8// PY - 2004/8// DO - 10.1016/S0305-0548(03)00097-2 VL - 31 IS - 9 SP - 1411-1426 SN - 1873-765X KW - pattern classification KW - neural networks KW - multi-layer perceptrons KW - radial basis function networks KW - support vector machines ER - TY - JOUR TI - Synthesis, optical properties and electronic structures of polyoxometalates K3P(Mo1-xWx)(12)O-40 (0 <= x <= 1) AU - Goubin, F AU - Guenee, L AU - Deniard, P AU - Koo, HJ AU - Whangbo, MH AU - Montardi, Y AU - Jobic, S T2 - JOURNAL OF SOLID STATE CHEMISTRY AB - Various compositions of solid solutions K3P(Mo1−xWx)12O40 (0⩽x⩽1) were prepared using two solid state synthetic routes. The crystallite size was determined by linewidth refinements of X-ray diffraction patterns using the Warren–Averbach method, and the grain size distribution by laser scattering experiments. Optical properties were determined by diffuse reflectance measurements in the UV-visible range. The optical gap Eg was found to increase exponentially from ∼2.5 to ∼3.30 eV with increasing x, and is systematically shifted to a higher energy when the grain size decreases. The relation between Eg and x was analyzed by calculating the HOMO-LUMO gaps of the [P(Mo1−xWx)12O40]3− anions on the basis of tight-binding electronic structure calculations. DA - 2004/12// PY - 2004/12// DO - 10.1016/j.jssc.2004.08.046 VL - 177 IS - 12 SP - 4528-4534 SN - 1095-726X KW - polyoxometalates KW - K3P(Mo1-xWx)(12)O-40 (0 <= X <= 1) KW - grain size KW - optical properties KW - HOMO-LUMO gaps ER - TY - JOUR TI - Synthesis and characterization of a magnetic semiconductor Na2RuO4 containing one-dimensional chains of RU6+ AU - Shikano, M. AU - Kremer, R. K. AU - Ahrens, M. AU - Koo, H. J. AU - Whangbo, M. H. AU - Darriet, J. T2 - Inorganic Chemistry DA - 2004/// PY - 2004/// VL - 43 IS - 1 SP - 07- ER - TY - JOUR TI - Switching potentials and conductivity of polypyrrole films prepared in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate AU - Boxall, DL AU - Osteryoung, RA T2 - JOURNAL OF THE ELECTROCHEMICAL SOCIETY AB - Polypyrrole (ppy) and poly(N-methylpyrrole) (pmpy) films were prepared galvanostatically at the ring of a rotating ring-disk electrode from the corresponding monomers dissolved in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate Rotating ring-disk voltammetry was used to determine switching potentials and conductivity of the films while immersed in Switching potentials of and V vs. the cobaltocenium/cobaltocene couple, were determined for the ppy and pmpy films, respectively, from negative potential scan voltammograms. Positive potential scan voltammetry was used to obtain the potential-dependent conductivity of the films as the films switched from their insulating (at potentials more negative than switching potential) to a quasi-metallic state. Two different computational models (nonlinear vs. linear conductance gradients) and two different redox probes and decamethylferrocenium/decamethylferrocene) were used in the calculation of the film conductivity. The conductivity of the ppy films increased by an order of magnitude for every mV change in the applied potential. At potentials less than the switching potential, the conductivity of the pmpy films increased tenfold for every mV change in the applied potential. At potentials greater than the switching potential, the pmpy films required a 200 mV change to induce the same degree of change in film conductivity. © 2004 The Electrochemical Society. All rights reserved. DA - 2004/2// PY - 2004/2// DO - 10.1149/1.1634275 VL - 151 IS - 2 SP - E41-E45 SN - 1945-7111 ER - TY - JOUR TI - Structural characterization of modular supramolecular architectures in solution AU - Tiede, DM AU - Zhang, RT AU - Chen, LX AU - Yu, LH AU - Lindsey, JS T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Structures of modular supramolecular architectures consisting of a hexameric, diphenylethyne-linked porphyrin macrocyclic array and the corresponding host−guest complex formed by inclusion of a tripyridyl guest molecule were characterized in solution using high-angle X-ray scattering. Scattering measurements made to 6 Å resolution coupled with pair distance function (PDF) analyses demonstrated that (1) the porphyrin architectures are not rigid but are distributed across a conformational ensemble with a mean diameter that is 1.5 Å shorter than the diameter of a symmetric, energy-minimized model structure, (2) the conformational envelope has limits of 3 Å positional dispersion and full rotational freedom for all six porphyrin groups, and (3) insertion of the tripyridyl guest molecule expands the diameter of the host conformer by 0.6 Å and decreases the configurational dispersion by approximately 2-fold. These results validate the molecular design, provide a new measure of conformational ensembles in solution that cannot be obtained by other techniques, and establish a structural basis for understanding the photophysical and guest−hosting functions of the hexameric porphyrin architectures in liquids. DA - 2004/11/3/ PY - 2004/11/3/ DO - 10.1021/ja048209q VL - 126 IS - 43 SP - 14054-14062 SN - 1520-5126 ER - TY - JOUR TI - Reactions of TpRu(CO)(NCMe)(Me) (Tp = hydridotris(pyrazolyl)borate) with heteroaromatic substrates: Stoichiometric and catalytic C-H activation AU - Pittard, KA AU - Lee, JP AU - Cundari, TR AU - Gunnoe, TB AU - Petersen, JL T2 - ORGANOMETALLICS AB - The Ru(II) complex TpRu(CO)(NCMe)(Me) (Tp = hydridotris(pyrazolyl)borate) initiates carbon−hydrogen bond activation at the 2-position of furan and thiophene to produce methane and TpRu(CO)(NCMe)(aryl) (aryl = 2-furyl or 2-thienyl). Solid-state structures have been determined for TpRu(CO)(NCMe)(2-thienyl) and [TpRu(CO)(μ-C,S-thienyl)]2. The complex TpRu(CO)(NCMe)(2-furyl) serves as a catalyst for the formation of 2-ethylfuran from ethylene and furan. DFT calculations of the C−H activation of furan by {(Tab)Ru(CO)(Me)} (Tab = tris(azo)borate) indicate that the C−H activation sequence does not proceed through a Ru(IV) oxidative addition intermediate. DA - 2004/11/8/ PY - 2004/11/8/ DO - 10.1021/om049508r VL - 23 IS - 23 SP - 5514-5523 SN - 1520-6041 ER - TY - JOUR TI - Porphyrins bearing mono or tripodal benzylphosphonic acid tethers for attachment to oxide surfaces AU - Loewe, RS AU - Ambroise, A AU - Muthukumaran, K AU - Padmaja, K AU - Lysenko, AB AU - Mathur, G AU - Li, QL AU - Bocian, DF AU - Misra, V AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The ability to attach redox-active molecules to oxide surfaces in controlled architectures (distance, orientation, packing density) is essential for the design of a variety of molecular-based information storage devices. We describe the synthesis of a series of redox-active molecules wherein each molecule bears a benzylphosphonic acid tether. The redox-active molecules include zinc porphyrins, a cobalt porphyrin, and a ferrocene-zinc porphyrin. An analogous tripodal tether has been prepared that is based on a tris[4-(dihydroxyphosphorylmethyl)phenyl]-derivatized methane. A zinc porphyrin is linked to the methane vertex by a 1,4-phenylene unit. The tripodal systems are designed to improve monolayer stability and ensure vertical orientation of the redox-active porphyrin on the electroactive surface. For comparison purposes, a zinc porphyrin bearing a hexylphosphonic acid tether also has been prepared. The synthetic approaches for introduction of the phosphonic acid group include derivatization of a bromoalkyl porphyrin or use of a dimethyl or diethyl phosphonate substituted precursor in a porphyrin-forming reaction. The latter approach makes use of dipyrromethane building blocks bearing mono or tripodal dialkyl phosphonate groups. The zinc porphyrin-tripodal compound bearing benzylphosphonic acid legs tethered to a SiO(2) surface (grown on doped Si) was electrically well-behaved and exhibited characteristic porphyrin oxidation/reduction waves. Collectively, a variety of porphyrinic molecules can now be prepared with tethers of different length, composition, and structure (mono or tripodal) for studies of molecular-based information storage on oxide surfaces. DA - 2004/3/5/ PY - 2004/3/5/ DO - 10.1021/jo034946d VL - 69 IS - 5 SP - 1453-1460 SN - 1520-6904 ER - TY - JOUR TI - Porphyrins bearing arylphosphonic acid tethers for attachment to oxide surfaces AU - Muthukumaran, K AU - Loewe, RS AU - Ambroise, A AU - Tamaru, SI AU - Li, QL AU - Mathur, G AU - Bocian, DF AU - Misra, V AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Synthetic molecules bearing phosphonic acid groups can be readily attached to oxide surfaces. As part of a program in molecular-based information storage, we have developed routes for the synthesis of diverse porphyrinic compounds bearing phenylphosphonic acid tethers. The routes enable (1) incorporation of masked phosphonic acid groups in precursors for use in the rational synthesis of porphyrinic compounds and (2) derivatization of porphyrins with masked phosphonic acid groups. The precursors include dipyrromethanes, monoacyldipyrromethanes, and diacyldipyrromethanes. The tert-butyl group has been used to mask the dihydroxyphosphoryl substituent. The di-tert-butyloxyphosphoryl unit is stable to the range of conditions employed in syntheses of porphyrins and multiporphyrin arrays yet can be deprotected under mild conditions (TMS-Cl/TEA or TMS-Br/TEA in refluxing CHCl3) that do not cause demetalation of zinc or magnesium porphyrins. The porphyrinic compounds that have been prepared include (1) A3B-, trans-AB2C-, and ABCD-porphyrins that bear a single phenylphosphonic acid group, (2) a trans-A2B2-porphyrin bearing two phenylphosphonic acid groups, (3) a chlorin that bears a single phenylphosphonic acid group, and (4) a porphyrin dyad bearing a single phenylphosphonic acid group. For selected porphyrin-phosphonic acids, the electrochemical characteristics have been investigated for molecules tethered to SiO2 surfaces grown on doped Si. The voltammetric behavior indicates that the porphyrin-phosphonic acids form robust, electrically well-behaved monolayers on the oxide surface. DA - 2004/3/5/ PY - 2004/3/5/ DO - 10.1021/jo034945l VL - 69 IS - 5 SP - 1444-1452 SN - 0022-3263 ER - TY - JOUR TI - Morphological, mechanical and gas-transport characteristics of crosslinked poly(propylene glycol): homopolymers, nanocomposites and blends AU - Patel, NP AU - Aberg, CM AU - Sanchez, AM AU - Capracotta, MD AU - Martin, JD AU - Spontak, RJ T2 - POLYMER AB - Linear polyethers possess unusually high CO2 solubility and, hence, selectivity due to the presence of accessible ether linkages that can interact with the quadrupolar moment of CO2 molecules. In this work, membranes derived from crosslinked poly(propylene glycol) diacrylate (PPGda) oligomers differing in molecular weight (M), as well as PPGda nanocomposites containing either an organically-modified montmorillonite clay or a methacrylate-terminated fumed silica are investigated and compared with highly CO2-selective poly(ethylene glycol) diacrylate (PEGda) homopolymer and nanocomposite membranes previously reported. The rheological and permeation properties of PPGda depend sensitively on M, with the elastic modulus decreasing, but CO2 permeability and CO2/H2 selectivity increasing, with increasing M. Incorporation of either nanofiller into PPGda enhances the elastic modulus and reduces the gas permeability in the resultant nanocomposites without strongly affecting CO2/H2 selectivity. Blending PPGda and PEGda prior to chemical crosslinking yields binary membranes that exhibit intermediate gas-transport properties accurately described by a linear rule of mixtures. DA - 2004/8/5/ PY - 2004/8/5/ DO - 10.1016/j.polymer.2004.06.024 VL - 45 IS - 17 SP - 5941-5950 SN - 1873-2291 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-3342879397&partnerID=MN8TOARS KW - reverse-selective KW - polymer membrane KW - nanocomposite ER - TY - JOUR TI - Mechanism of p-type-to-n-type conductivity conversion in boron-doped diamond AU - Dai, Y AU - Dai, D AU - Liu, DH AU - Han, SH AU - Huang, BB T2 - APPLIED PHYSICS LETTERS AB - We report on the role of two boron–hydrogen complexes in the conductivity conversion from p-type to n-type in boron-doped diamond samples. The calculated electronic structures of the simulated clusters show that the boron–hydrogen complex of hydrogen–boron pairs (BH1) is characteristic of p-type conductivity, and that of two hydrogen–boron centers (BH2) or three-hydrogen-boron centers (BH3) have a character of n-type conductivity. The phenomenon of conversion from p-type-to-n-type conductivity through deuteration may be explained by the transformation from the BH1 into BH2 and/or BH3 complexes. DA - 2004/3/15/ PY - 2004/3/15/ DO - 10.1063/1.1650909 VL - 84 IS - 11 SP - 1895-1897 SN - 0003-6951 ER - TY - JOUR TI - Investigation of the relative stabilities of various allotropic phases of elemental tellurium under pressure and their interconversion paths by electronic structure calculations and crystal structure analyses AU - Soulard, C AU - Rocquefelte, X AU - Evain, M AU - Jobic, S AU - Koo, H AU - Whangbo, MH T2 - JOURNAL OF SOLID STATE CHEMISTRY AB - Elemental tellurium adopts a number of different structures under pressure. The relative stabilities of these allotropes and the interconversion between them were examined on the basis of first principles electronic band structure calculations with and without external pressure. The relative stabilities of the allotropes were also analyzed by estimating the overall strength of covalent bonding on the basis of the Te-Te overlap populations determined from tight-binding electronic structure calculations. The crystal structures of the allotropes were analyzed to determine how one form can transform into another form under pressure. Our study leads to the energy profile of tellurium as a function of pressure consistent with experiment, shows that the relative stabilities of the allotropic phases of Te are mainly governed by the overall strength of covalent bonding, and that all the allotropes are intimately related in structure, and one form can be readily converted to another form under pressure via a simple interconversion path. DA - 2004/12// PY - 2004/12// DO - 10.1016/j.jssc.2004.08.040 VL - 177 IS - 12 SP - 4724-4731 SN - 1095-726X KW - tellurium KW - phase transition KW - high pressure KW - electronic structure ER - TY - JOUR TI - Investigation of the origin of the empirical relationship between refractive index and density on the basis of first principles calculations for the refractive indices of various TiO2 phases AU - Rocquefelte, X AU - Goubin, F AU - Koo, HJ AU - Whangbo, MH AU - Jobic, S T2 - INORGANIC CHEMISTRY AB - On the basis of first principles electronic structure calculations, we determined the dielectric functions, the refractive indices, and the extinction coefficients of the seven different phases of TiO2 and then examined why the refractive index is related to the density by the empirical Glastone−Dale equation. The zero frequency limit of the refractive index, n0, is found to be a good approximation for the refractive index n determined around 2 eV. Our study indicates that the major factor influencing n in a series of closely related systems is the structure compactness. This finding suggests a way of preparing new UV absorbers with low refractive index. DA - 2004/4/5/ PY - 2004/4/5/ DO - 10.1021/ic035383r VL - 43 IS - 7 SP - 2246-2251 SN - 1520-510X ER - TY - JOUR TI - Fast directed motion of "Fakir" droplets AU - Petrie, RJ AU - Bailey, T AU - Gorman, CB AU - Genzer, J T2 - LANGMUIR AB - In this Letter, we report on the motion of water droplets on surfaces decorated with molecular gradients comprising semifluorinated (SF) organosilanes. SF molecular gradients deposited on flat silica substrates facilitate faster motion of water droplets relative to the specimens covered with an analogous hydrocarbon gradient. Further increase in the drop speed is achieved by advancing it along porous substrates coated with the SF wettability gradients. The results of our experiments are in quantitative agreement with a simple scaling theory that describes the faster liquid motion in terms of reduced friction at the liquid/substrate interface. DA - 2004/11/9/ PY - 2004/11/9/ DO - 10.1021/la048612a VL - 20 IS - 23 SP - 9893-9896 SN - 0743-7463 ER - TY - JOUR TI - Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome AU - Shapkina, T AU - Lappi, S AU - Franzen, S AU - Wollenzien, P T2 - NUCLEIC ACIDS RESEARCH AB - Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10–40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 × 109 W m–2, to determine strand breakage yields and the frequency and pattern of RNA–RNA cross‐ linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 × 10–3 over the incident intensity range studied. The yield for RNA–RNA cross‐linking was 3 × 10–4 cross‐links/photon at the intensity of 4.5 × 109 W m–2, an ∼4‐fold higher yield per photon than obtained with a transilluminator. The cross‐link yield/photon decreased at higher light intensities, probably due to intensity‐dependent photoreversal. The pattern of cross‐linking was similar to that observed with low intensity irradiation but with four additional long‐range cross‐links not previously seen in E.coli ribosomes. Cross‐ linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation. DA - 2004/2// PY - 2004/2// DO - 10.1093/nar/gkh320 VL - 32 IS - 4 SP - 1518-1526 SN - 1362-4962 ER - TY - JOUR TI - Diverse redox-active molecules bearing O-, S-, or Se-terminated tethers for attachment to silicon in studies of molecular information storage AU - Balakumar, A AU - Lysenko, AB AU - Carcel, C AU - Malinovskii, VL AU - Gryko, DT AU - Schweikart, KH AU - Loewe, RS AU - Yasseri, AA AU - Liu, ZM AU - Bocian, DF AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Attachment of the molecules to electroactive surfaces requires control over the nature of the tether (linker and surface attachment group). We have synthesized a collection of redox-active molecules bearing different linkers and surface anchor groups in free or protected form (hydroxy, mercapto, S-acetylthio, and Se-acetylseleno) for attachment to surfaces such as silicon, germanium, and gold. The molecules exhibit a number of cationic oxidation states, including one (ferrocene), two [zinc(II)porphyrin], three [cobalt(II)porphyrin], or four (lanthanide triple-decker sandwich compound). Electrochemical studies of monolayers of a variety of the redox-active molecules attached to Si(100) electrodes indicate that molecules exhibit a regular mode of attachment (via a Si-X bond, X = O, S, or Se), relatively homogeneous surface organization, and robust reversible electrochemical behavior. The acetyl protecting group undergoes cleavage during the surface deposition process, enabling attachment to silicon via thio or seleno groups without handling free thiols or selenols. DA - 2004/3/5/ PY - 2004/3/5/ DO - 10.1021/jo034944t VL - 69 IS - 5 SP - 1435-1443 SN - 1520-6904 ER - TY - JOUR TI - Design and synthesis of a 4-(2 '-pyridyl)-1,2,3,5-dithiadiazolyl cobalt complex AU - Hearns, NGR AU - Preuss, KE AU - Richardson, JF AU - Bin-Salamon, S T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - The 4-(2'-pyridyl)-1,2,3,5-dithiadiazolyl neutral radical 1 has been prepared for use as a spin-bearing bidentate ligand. The coordination of this ligand to bis(hexafluoroacetylacetonato)cobalt affords a thermally stable complex 2. Magnetic susceptibility measurements of the crystalline complex indicate ferromagnetic coupling between the ligand-centered spin and the unpaired electrons of the high-spin Co(II). DA - 2004/8/18/ PY - 2004/8/18/ DO - 10.1021/ja046304t VL - 126 IS - 32 SP - 9942-9943 SN - 1520-5126 ER - TY - JOUR TI - Boron-complexation strategy for use with 1-acyldipyrromethanes AU - Muthukumaran, K AU - Ptaszek, M AU - Noll, B AU - Scheidt, WR AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - 1-Acyldipyrromethanes are important precursors in rational syntheses of diverse porphyrinic compounds. 1-Acyldipyrromethanes are difficult to purify, typically streaking upon chromatography and giving amorphous powders upon attempted crystallization. A solution to this problem has been achieved by reacting the 1-acyldipyrromethane with a dialkylboron triflate (e.g., Bu2B-OTf or 9-BBN-OTf) to give the corresponding B,B-dialkyl-B-(1-acyldipyrromethane)boron(III) complex. The reaction is selective for a 1-acyldipyrromethane in the presence of a dipyrromethane. The 1-acyldipyrromethane−boron complexes are stable to routine handling, are soluble in common organic solvents, are hydrophobic, crystallize readily, and chromatograph without streaking. The 1-acyldipyrromethane can be liberated in high yield from the boron complex upon treatment with 1-pentanol. Alternatively, the 1-acyldipyrromethane−boron complex can be used in the formation of a trans-A2B2-porphyrin. In summary, the boron-complexation strategy has broad scope and greatly facilitates the isolation of 1-acyldipyrromethanes. DA - 2004/8/6/ PY - 2004/8/6/ DO - 10.1021/jo0492620 VL - 69 IS - 16 SP - 5354-5364 SN - 1520-6904 ER - TY - JOUR TI - Attenuating negative differential resistance in an electroactive self-assembled monolayer-based junction AU - Wassel, R. A. AU - Credo, G. M. AU - Fuierer, R. R. AU - Feldheim, D. L. AU - Gorman, Christopher T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY DA - 2004/// PY - 2004/// DO - 10.1021/ja037851q VL - 126 IS - 1 SP - 295-300 ER - TY - JOUR TI - Asymmetric total synthesis of (+)-cannabisativine AU - Kuethe, JT AU - Comins, DL T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The asymmetric total synthesis of natural (+)-cannabisativine 1 was completed in 19 steps and 7% overall yield. The key synthetic intermediate 29 was prepared with a high degree of stereocontrol in 12 steps starting from chiral 1-acylpyridinium salt 10. Addition of zinc enolate 11 to pyridinium salt 10 furnished dihydropyridone 12 containing two contiguous stereocenters of the correct absolute configuration. Luche reduction of ketone 16 afforded diol 17 in high yield (96%) and excellent diastereoselectivity. The Mukaiyama-Michael reaction of pyridones 27a/b with O-silyl ketene acetal 32 gave phenyl selenyl ketones 33a/b with complete stereoselectivity. Elimination of cis-beta-hydroxyselenides 34 and 35 effected the regiocontrolled preparation of tetrahydropyridine derivative 29. Several approaches to the macrocyclic ring closure of the 13-membered ring were investigated, ultimately leading to the completion of an asymmetric synthesis of the target compound with a high degree of stereocontrol. DA - 2004/8/6/ PY - 2004/8/6/ DO - 10.1021/jo049724+ VL - 69 IS - 16 SP - 5219-5231 SN - 0022-3263 ER - TY - JOUR TI - The league composition effect in tournaments with heterogeneous players: An empirical analysis of broiler contracts AU - Levy, A AU - Vukina, T T2 - JOURNAL OF LABOR ECONOMICS AB - We compare welfare effects of tournaments and piece rates in contracts with heterogeneous ability agents and demonstrate that tournaments that mix players of unequal abilities create a league composition effect. When leagues are fixed and the time horizon sufficiently long, piece rates improve welfare over tournaments. Using contract production data for broiler chickens, we estimate the variances of growers’ abilities, common production shock, and grower’s idiosyncratic shock. Growers' abilities are heterogeneous, and common production shocks are significant. Leagues in broiler tournaments disintegrate rapidly over time, suggesting that tournament contracts offer more welfare than piece rates. DA - 2004/4// PY - 2004/4// DO - 10.1086/381253 VL - 22 IS - 2 SP - 353-377 SN - 1537-5307 ER - TY - JOUR TI - The effect of substitution patterns on the release rates of opioid peptides DADLE and [Leu(5)]-enkephalin from coumarin prodrug moieties AU - Zych, LA AU - Yang, WQ AU - Liao, Y AU - Griffin, KR AU - Wang, BH T2 - BIOORGANIC CHEMISTRY AB - A coumarin-based prodrug system has been developed in our laboratory for the preparation of esterase-sensitive prodrugs of amines, peptides, and peptidomimetics. The drug release rates from this prodrug system were found to be dependent on the structural features of the drug moiety. The effect of the phenyl ring substitutions on the release kinetics of such prodrugs of model amines was examined recently and it was found that appropriately positioned alkyl substituents on the phenyl ring could help to facilitate the release. Aimed at further understanding the structure-release rate relationship of the coumarin-based cyclic prodrugs, we synthesized and examined a series of substituted coumarinic acid derivatives of opioid peptides, DADLE, and [Leu(5)]-enkephalin. DA - 2004/4// PY - 2004/4// DO - 10.1016/j.bioorg.2003.12.002 VL - 32 IS - 2 SP - 109-123 SN - 1090-2120 KW - coumarin KW - cyclic prodrug KW - opioid peptide KW - esterase KW - structural effect ER - TY - JOUR TI - Synthesis of porphyrins bearing hydrocarbon tethers and facile covalent attachment to Si(100) AU - Liu, ZM AU - Yasseri, AA AU - Loewe, RS AU - Lysenko, AB AU - Malinovskii, VL AU - Zhao, Q AU - Surthi, S AU - Li, QL AU - Misra, V AU - Lindsey, JS AU - Bocian, DF T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The use of redox-active molecules as the active storage elements in memory chips requires the ability to attach the molecules to an electroactive surface in a reliable and robust manner. To explore the use of porphyrins tethered to silicon via carbosilane linkages, 17 porphyrins have been synthesized. Fourteen porphyrins bear a tether at a single meso site, and three porphyrins bear functional groups at two β sites for possible two-point attachment. Two high-temperature processing methods (400 °C under inert atmosphere) have been developed for rapid (minutes), facile covalent attachment to Si platforms. The high-temperature processing conditions afford attachment either by direct deposition of a dilute solution (1 μM−1 mM) of the porphyrin sample onto the Si substrate or sublimation of a neat sample onto the Si substrate. The availability of this diverse collection of porphyrins enables an in-depth examination of the effects of the tether (length, composition, terminal functional group, number of tethers) and steric bulk of nonlinking substituents on the information-storage properties of the porphyrin monolayers obtained upon attachment to silicon. Attachment proceeds readily with a wide variety of hydrocarbon tethers, including 2-(trimethylsilyl)ethynyl, vinyl, allyl, or 3-butenyl directly appended to the porphyrin and iodo, bromomethyl, 2-(trimethylsilyl)ethynyl, ethynyl, vinyl, or allyl appended to the 4-position of a meso-phenyl ring. No attachment occurs with substituents such as phenyl, p-tolyl, mesityl, or ethyl. Collectively, the studies show that the high-temperature attachment procedure (1) has broad scope encompassing diverse functional groups, (2) tolerates a variety of arene substituents, and (3) does not afford indiscriminate attachment. The high-temperature processing conditions are ideally suited for use in fabrication of hybrid molecular/semiconductor circuitry. DA - 2004/8/20/ PY - 2004/8/20/ DO - 10.1021/jo049439q VL - 69 IS - 17 SP - 5568-5577 SN - 0022-3263 ER - TY - JOUR TI - Swallowtail porphyrins: Synthesis, characterization and incorporation into porphyrin dyads AU - Thamyongkit, P AU - Speckbacher, M AU - Diers, , JR AU - Kee, HL AU - Kirmaier, C AU - Holten, D AU - Bocian, DF AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid. DA - 2004/5/28/ PY - 2004/5/28/ DO - 10.1021/jo049860e VL - 69 IS - 11 SP - 3700-3710 SN - 1520-6904 ER - TY - JOUR TI - Non-mutagenic organic pigment intermediates. II. Isomorphous 2,2 '-dichloro-5,5 '-dipropoxybenzidine and 2,2 '-dimethyl-5,5 '-dipropoxybenzidine AU - El-Shafei, A AU - Hinks, D AU - Boyle, PD AU - Freeman, HS T2 - ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY AB - The title compounds, C18H22Cl2N2O2 and C20H28N2O2, respectively, are isomorphous. The mol­ecules lie at general positions in the unit cell. In each structure, chemically equivalent but crystallographically inequivalent amine N atoms exhibit different degrees of pyramidalization. The structures exhibit weak N—H⋯N hydrogen bonding, which is influenced by the differences in hybridization around the amine N atoms. The torsion angles across the bi­phenyl linkage for the two compounds are 67.2 (2) and 68.3 (3)°. DA - 2004/8// PY - 2004/8// DO - 10.1107/S0108270104014763 VL - 60 SP - O569-O571 SN - 2053-2296 ER - TY - JOUR TI - Investigation of the electronic and structural properties of potassium hexaboride, KB6, by transport, magnetic susceptibility, EPR, and NMR measurements, temperature-dependent crystal structure determination, and electronic band structure calculations AU - Ammar, A AU - Menetrier, M AU - Villesuzanne, A AU - Matar, S AU - Chevalier, B AU - Etourneau, J AU - Villeneuve, G AU - Rodriguez-Carvajal, J AU - Koo, HJ AU - Smirnov, AI AU - Whangbo, MH T2 - INORGANIC CHEMISTRY AB - The electronic and structural properties of potassium hexaboride, KB(6), were examined by transport, magnetic susceptibility, EPR, and NMR measurements, temperature-dependent crystal structure determination, and electronic band structure calculations. The valence bands of KB(6) are partially empty, but the electrical resistivity of KB(6) reveals that it is not a normal metal. The magnetic susceptibility as well as EPR and NMR measurements show the presence of localized electrons in KB(6). The EPR spectra of KB(6) have two peaks, a broad ( approximately 320 G) and a narrow (less than approximately 27 G) line width, and the temperature-dependence of the magnetic susceptibility of KB(6) exhibits a strong hysteresis below 70 K. The temperature-dependent crystal structure determination of KB(6) shows the occurrence of an unusual variation in the unit cell parameter hence supporting that the hysteresis of the magnetic susceptibility is a bulk phenomenon. The line width DeltaH(pp) of the broad EPR signal is independent of temperature and EPR frequency. This finding indicates that the line broadening results from the dipole-dipole interaction, and the spins responsible for the broad EPR peak has the average distance of approximately 1.0 nm. To explain these apparently puzzling properties, we examined a probable mechanism of electron localization in KB(6) and its implications. DA - 2004/8/9/ PY - 2004/8/9/ DO - 10.1021/ic049444c VL - 43 IS - 16 SP - 4974-4987 SN - 1520-510X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-3843112209&partnerID=MN8TOARS ER - TY - JOUR TI - Helix-sense selective polymerization of carbodiimides: Building permanently optically active polymers from achiral monomers AU - Tian, GL AU - Lu, YJ AU - Novak, BM T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - The helix-sense selective polymerization of achiral monomers by homochiral catalysts was investigated. Polymerization of chiral carbodiimides (N-(R)-2,6-(dimethylheptyl)-N'-phenylcarbodiimide) by achiral catalysts yields polymers that undergo mutorotation at elevated temperatures, thus illustrating that these chains are formed under kinetic rather than thermodynamic control. Building on this observation, the polymerization of achiral carbodiimides by (S-BINOL)Ti(OiPr)2, I, was studied. Monomers (N-hexyl-N'-(X)carbodiimide, where X = isopropyl (3), hexyl (4) or phenyl (5)), N-methyl-N'-(2-methyl-6-isopropylphenyl)carbodiimide, 6, and N-dodecyl-N'-(1-naphthyl)carbodiimide, 7, were all polymerized with I in good yields (86-95%), and all showed varying degrees of asymmetric induction. Poly-3, -4, and -5 racemized upon heating at elevated temperatures, but poly-6 and poly-7, bearing nonsymmetric phenyl groups, yielded optically active polymers that could not be racemized even at elevated temperatures. Thin films of poly-7 were found to be highly opalescent. DA - 2004/4/7/ PY - 2004/4/7/ DO - 10.1021/ja049548m VL - 126 IS - 13 SP - 4082-4083 SN - 1520-5126 ER - TY - JOUR TI - Ethylene polymerization catalyzed by neutral nickel(II) complex with ON-chelating ligand AU - Nodono, M AU - Novak, BM AU - Boyle, PT T2 - POLYMER JOURNAL AB - We have achieved the synthesis of neutral nickel catalyst with the modified O^N-chelating ligand for the ethylene polymerization. The activity of the catalyst, and the molecular weight and the branching structure of the polymer obtained strongly depend on the ligand structure as well as the presence of Ni(COD)2 which is used as an activator. The crystal structure of the catalyst was determined and the long nickel–phosphine bond length seems to play an important role for increasing the polymerization activity. DA - 2004/// PY - 2004/// DO - 10.1295/polymj.36.140 VL - 36 IS - 2 SP - 140-145 SN - 0032-3896 KW - neutral nickel complex KW - ethylene polymerization KW - oligomerization KW - polyethylene ER - TY - JOUR TI - Electrochemical charging of a fullerene-functionalized self-assembled monolayer on Au(111) AU - Gu, T AU - Whitesell, JK AU - Fox, MA T2 - JOURNAL OF ORGANIC CHEMISTRY AB - A fullerene derivative 10 with a terminal thiol group dissolves easily in common organic solvents and forms a densely packed self-assembled monolayer on gold surfaces. The functionalization of C(60) is based on the 1,3-dipolar cycloaddition of the azomethine ylide generated in situ from the corresponding aldehyde and N-methylglycine. The monolayers were characterized by grazing angle reflectance FTIR spectroscopy, scan tunneling microscopy, and cyclic voltammetry. The cyclic voltammogram of a SAM of 10 showed two well-resolved reversible cathodic waves corresponding to the first two one-electron reductions of the fullerene fragment. DA - 2004/6/11/ PY - 2004/6/11/ DO - 10.1021/jo049939j VL - 69 IS - 12 SP - 4075-4080 SN - 0022-3263 ER - TY - JOUR TI - Cellular trajectories of peptide-modified gold particle complexes: Comparison of nuclear localization signals and peptide transduction domains AU - Tkachenko, AG AU - Xie, H AU - Liu, YL AU - Coleman, D AU - Ryan, J AU - Glomm, WR AU - Shipton, MK AU - Franzen, S AU - Feldheim, DL T2 - BIOCONJUGATE CHEMISTRY AB - Gold nanoparticles modified with nuclear localization peptides were synthesized and evaluated for their subcellular distribution in HeLa human cervical epithelium cells, 3T3/NIH murine fibroblastoma cells, and HepG2 human hepatocarcinoma cells. Video-enhanced color differential interference contrast microscopy and transmission electron microscopy indicated that transport of nanoparticles into the cytoplasm and nucleus depends on peptide sequence and cell line. Recently, the ability of certain peptides, called protein transduction domains (PTDs), to transclocate cell and nuclear membranes in a receptor- and temperature-independent manner has been questioned (see for example, Lundberg, M.; Wikstrom, S.; Johansson, M. (2003) Mol. Ther. 8, 143−150). We have evaluated the cellular trajectory of gold nanoparticles carrying the PTD from HIV Tat protein. Our observations were that (1) the conjugates did not enter the nucleus of 3T3/NIH or HepG2 cells, and (2) cellular uptake of Tat PTD peptide−gold nanoparticle conjugates was temperature dependent, suggesting an endosomal pathway of uptake. Gold nanoparticles modified with the adenovirus nuclear localization signal and the integrin binding domain also entered cells via an energy-dependent mechanism, but in contrast to the Tat PTD, these signals triggered nuclear uptake of nanoparticles in HeLa and HepG2 cell lines. DA - 2004/// PY - 2004/// DO - 10.1021/bc034189q VL - 15 IS - 3 SP - 482-490 SN - 1520-4812 ER - TY - JOUR TI - Ruthenium(II) anilido complex containing a bisphosphine pincer ligand: Reversible formation of amidinate ligands via intramolecular C-N bond formation AU - Zhang, J AU - Gunnoe, TB AU - Boyle, PD T2 - ORGANOMETALLICS AB - The reaction of the octahedral anilido complex (PCP)Ru(CO)(NHPh)(PMe3) with acetonitrile produces the amidinate complex (PCP)Ru(CO){N(H)C(Me)N(Ph)}. Mechanistic studies indicate that the reaction proceeds through coordination of the nitrile to the Ru(II) metal center, followed by intramolecular nucleophilic addition of the amido ligand. DA - 2004/6/21/ PY - 2004/6/21/ DO - 10.1021/om0497543 VL - 23 IS - 13 SP - 3094-3097 SN - 1520-6041 ER - TY - JOUR TI - RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles AU - Gugliotti, LA AU - Feldheim, DL AU - Eaton, BE T2 - SCIENCE AB - RNA sequences have been discovered that mediate the growth of hexagonal palladium nanoparticles. In vitro selection techniques were used to evolve an initial library of ∼10 14 unique RNA sequences through eight cycles of selection to yield several active sequence families. Of the five families, all representative members could form crystalline hexagonal palladium platelets. The palladium particle growth occurred in aqueous solution at ambient temperature, without any endogenous reducing agent, and at low concentrations of metal precursor (100 micromolar). Relative to metal precursor, the RNA concentration was significantly lower (1 micromolar), yet micrometer-size crystalline hexagonal palladium particles were formed rapidly (7.5 to 1 minutes). DA - 2004/5/7/ PY - 2004/5/7/ DO - 10.1126/science.1095678 VL - 304 IS - 5672 SP - 850-852 SN - 1095-9203 ER - TY - PAT TI - Process for treating textile substrates AU - Smith, C. B. AU - Hendrix, W. A. AU - Butcher, D. L. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Photophysical properties of phenylethyne-linked porphyrin and oxochlorin dyads AU - Hindin, E AU - Kirmaier, C AU - Diers, , JR AU - Tomizaki, KY AU - Taniguchi, M AU - Lindsey, JS AU - Bocian, DF AU - Holten, D T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - A set of porphyrin−porphyrin and oxochlorin−oxochlorin dyads has been prepared in which the constituent pigments are joined at the meso-positions by a phenylethyne linker. Attachment of an ethynyl substituent to the meso-position of a tetrapyrrolic macrocycle strongly perturbs the electronic properties of the ring. The inherent asymmetry of the phenylethyne linker affords the possibility of perturbing either end of the dyad. The porphyrin dyads include bis-Zn, Zn-free base (Fb), and bis-Zn species wherein 0, 1, or 2 of the three nonlinking aryl rings of one of the Zn porphyrins are perfluorinated. The two oxochlorin dyads are both ZnFb species in which the meso-ethyne substituent is located on either the Zn complex or the Fb. The dyads have been studied using static and time-resolved absorption and emission spectroscopy and electrochemical techniques. The optical and electrochemical properties of a series of monomeric reference compounds were also examined. The time-resolved optical studies reveal that energy transfer in the phenylethyne-linked dyads is faster by ∼10-fold or more than in analogous dyads joined by a diphenylethyne linker. In particular, energy transfer occurs with a rate constant of >(20 ps)-1 between the phenylethyne-linked oxochlorins and an efficiency of >98%, to be compared with a rate of (140 ps)-1 and an efficiency of 83% found previously for diphenylethyne-linked oxochlorins. Taken together, these results should be useful in the design of multipigment architectures that absorb in the red and undergo fast and efficient energy transfer, as required for light-harvesting applications. DA - 2004/6/17/ PY - 2004/6/17/ DO - 10.1021/jp037614l VL - 108 IS - 24 SP - 8190-8200 SN - 1520-6106 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-3042636305&partnerID=MN8TOARS ER - TY - JOUR TI - Length scales which perturb chain packing in amorphous polymers AU - Wachowicz, M AU - Wolak, J AU - Gracz, H AU - Stejskal, EO AU - Jurga, S AU - McCord, EF AU - White, JL T2 - MACROMOLECULES AB - Direct spectroscopic probes of individual chain conformation and free volume are used to measure the increasing perturbation in the local glass-transition temperature of one polymer chain with decreasing length scale of mixing in binary polyolefin blends. Solid-state 2H and 129Xe NMR experiments reveal a compositional miscibility window in side-chain concentration for polyisobutylene (PIB)/poly(ethylene-co-butene) (PEB) blends. A combination of pulsed-field gradient and chemical shift data for xenon gas absorbed in these polymer blends indicates that the presence of polymer chains within a radius of ∼35 nm of a different chain structure will perturb the intermolecular packing contribution to the total conformational energy of that chain, thereby changing its Tg. DA - 2004/6/15/ PY - 2004/6/15/ DO - 10.1021/ma049263u VL - 37 IS - 12 SP - 4573-4579 SN - 1520-5835 ER - TY - JOUR TI - Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces AU - Brewer, SH AU - Allen, AM AU - Lappi, SE AU - Chasse, TL AU - Briggman, KA AU - Gorman, CB AU - Franzen, S T2 - LANGMUIR AB - Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C−O stretching mode of glucose and the observed O−H stretching mode of glucose that is shifted in position relative to the O−H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm-1 upon the binding of glucose. Additionally, changes in the peak profile of the B−O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at ∼1736 to 1742 cm-1 depending on the identity of the bound sugar. DA - 2004/6/22/ PY - 2004/6/22/ DO - 10.1021/la035037m VL - 20 IS - 13 SP - 5512-5520 SN - 0743-7463 ER - TY - JOUR TI - Influence of chemisorption on the thermal conductivity of single-wall carbon nanotubes AU - Padgett, CW AU - Brenner, DW T2 - NANO LETTERS AB - The thermal conductivity at 300 K of (10,10) carbon nanotubes that have been functionalized by chemical attachment of phenyl rings through covalent bonding (chemisorption) at random positions has been calculated as a function of adsorption density using classical trajectories. The system exhibits a rapid drop in thermal conductivity with chemisorption, where chemisorption to as little as 1.0% of the nanotube carbon atoms reduces the thermal conductivity by over a factor of 3. The simulation results indicate that the effect is due to a reduction in phonon scattering length rather than changes in the vibrational frequencies of the carbon atoms in the nanotube. DA - 2004/6// PY - 2004/6// DO - 10.1021/nl049645d VL - 4 IS - 6 SP - 1051-1053 SN - 1530-6992 ER - TY - JOUR TI - Electron emission properties of detonation nanodiamonds AU - Zhirnov, , VV AU - Shenderova, OA AU - Jaeger, DL AU - Tyler, T AU - Areshkin, DA AU - Brenner, DW AU - Hren, JJ T2 - PHYSICS OF THE SOLID STATE DA - 2004/// PY - 2004/// DO - 10.1134/1.1711444 VL - 46 IS - 4 SP - 657-661 SN - 1063-7834 ER - TY - JOUR TI - Calculation of the electronic and optical properties of indium tin oxide by density functional theory AU - Brewer, SH AU - Franzen, S T2 - CHEMICAL PHYSICS AB - Density functional theory (DFT) was used to calculate the bulk electronic and optical properties of indium tin oxide (ITO). The ITO model was constructed replacing indium atoms with tin atoms in the cubic unit cell of indium oxide. To allow more possibilities for tin atom substitution than afforded by the forty-atom primitive cell of indium oxide all eighty atoms of the unit cell were included in the stoichiometry (In32−xSnxO48) using periodic boundary conditions. A number of properties of ITO were calculated including the optical band gap, charge carrier density and plasma frequency. The dependence of the electronic and optical properties of ITO on a variety of parameters such as the tin content, cubic lattice parameter and the distance between adjacent tin atoms was investigated. The electronic and optical properties agreed well with experimental data and allowed insight into the origin of the electronic and optical properties of ITO. DA - 2004/5/10/ PY - 2004/5/10/ DO - 10.1016/j.chemphys.2003.11.039 VL - 300 IS - 1-3 SP - 285-293 SN - 1873-4421 KW - transparent conducting oxide KW - plasma frequency KW - charge carrier density ER - TY - JOUR TI - Addition of indolyl and pyrrolyl grignard reagents to 1-acylpyridinium salts AU - Kuethe, JT AU - Comins, DL T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Certain indolyl and pyrrolyl Grignard reagents add to 1-acyl salts of 4-methoxy-3-(triisopropylsilyl)pyridine to give the corresponding 1-acyl-2-heteroaryl-2,3-dihydro-4-pyridones in good to high yield. When the 1-acyl group contained a chiral auxiliary, (+/-)-trans-2-(alpha-cumyl)cyclohexyloxy, addition of the indolyl Grignards resulted in a separable mixture of diastereomeric 2,3-dihydro-4-pyridones. DA - 2004/4/16/ PY - 2004/4/16/ DO - 10.1021/jo049943v VL - 69 IS - 8 SP - 2863-2866 SN - 0022-3263 ER - TY - JOUR TI - Synthesis of phenylethyne-linked porphyrin dyads AU - Tomizaki, K AU - Lysenko, AB AU - Taniguchi, M AU - Lindsey, JS T2 - TETRAHEDRON AB - Four new porphyrin dyads have been prepared for studies in artificial photosynthesis. The two porphyrins are joined at the meso positions via a phenylethyne linker and are present in zinc/zinc or zinc/free base metalation states. The porphyrin bearing the ethynyl unit incorporates zero, one, or two pentafluorophenyl groups at non-linking meso positions for tuning the porphyrin redox potentials. The synthetic approach entailed Pd-mediated coupling of porphyrin building blocks that bear a single ethynylphenyl or bromo/iodo substituent. DA - 2004/2/23/ PY - 2004/2/23/ DO - 10.1016/j.tet.2004.01.003 VL - 60 IS - 9 SP - 2011-2023 SN - 0040-4020 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-1042275557&partnerID=MN8TOARS KW - porphyrin KW - dipyrromethane KW - ethyne KW - phenylethyne KW - energy transfer ER - TY - PAT TI - Substrates carrying polymers of linked sandwich coordination compounds and methods of use thereof AU - Li, J.-Z AU - Gryko, D. AU - Lindsey, J. S. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Spectroscopic studies of the electrical structure of transition metal and rare earth complex oxides AU - Lucovsky, G AU - Zhang, Y AU - Whitten, JL AU - Schlom, DG AU - Freeouf, JL T2 - PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES AB - Spectroscopic studies of transition metal (Tm) and rare earth (Re) oxides, combined with ab initio theory identify the band edge electronic structure of high-K dielectrics. The lowest conduction band states are derived from anti-bonding Tm (Re) d∗-states. A novel method for obtaining independent control of band gap energies and dielectric constants in complex oxides, ReTmO3, results from coupling of Tm and Re atom d-states bonded to the same oxygen atom. DA - 2004/3// PY - 2004/3// DO - 10.1016/j.physe.2003.11.111 VL - 21 IS - 2-4 SP - 712-716 SN - 1386-9477 KW - high-K dielectrics KW - transition metal oxides KW - rare earth oxides KW - complex oxides ER - TY - PAT TI - Short synthesis of pyridine-based pharmaceutical intermediates AU - Comins, D. L. AU - Huang, S.-L. C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Reexamination of the magnetic properties of Cu-2(dca)(4)(2,5-me(2)pyz) {dca = dicyanamide; me(2)pyz = dimethylpyrazine}: isolated spin-1/2 dimers versus long-range magnetic ordering AU - Manson, JL AU - Schlueter, JA AU - Koo, HJ AU - Whangbo, MH T2 - INORGANIC CHEMISTRY AB - The magnetic properties of Cu2(dca)4(2,5-me2pyz) have been reexamined. The extended structure of Cu2(dca)4(2,5-me2pyz) can be viewed in terms of Cu2(2,5-me2pyz)4+ dimer units interconnected via μ1,5-dca ligands. The bulk magnetic susceptibility χ(T) and the isothermal M(H) of Cu2(dca)4(2,5-me2pyz) are shown to be well described by an isolated dimer model. This finding was confirmed by carrying out a spin dimer analysis based on tight-binding calculations, which shows that the 2,5-me2pyz ligand provides a substantial spin exchange interaction between the Cu2+ ions while the dca ligands do not. DA - 2004/6/28/ PY - 2004/6/28/ DO - 10.1021/ic0354769 VL - 43 IS - 13 SP - 4007-4011 SN - 0020-1669 ER - TY - JOUR TI - Multibit memory using self-assembly of mixed ferrocene/porphyrin monolayers on silicon AU - Li, QL AU - Mathur, G AU - Gowda, S AU - Surthi, S AU - Zhao, Q AU - Yu, LH AU - Lindsey, JS AU - Bocian, DF AU - Misra, V T2 - ADVANCED MATERIALS AB - An alternative strategy for achieving multi‐bit functionality , which uses mixed self‐assembled monolayers of a benzyl alcohol‐tethered ferrocene (Fc‐BzOH) and a benzyl alcohol‐tethered porphyrin (Por‐BzOH) on silicon surfaces to achieve a four‐state (2‐bit) memory element, is presented. The four states include the neutral state and three distinct cationic states obtained upon oxidation of Fc‐BzOH (monopositive) and Por‐BzOH (monopositive, dipositive) molecules. Conventional cyclic voltammetry, capacitance, and conductance methods have been used to characterize the mixed monolayer. DA - 2004/1/16/ PY - 2004/1/16/ DO - 10.1002/adma.200305680 VL - 16 IS - 2 SP - 133-+ SN - 1521-4095 ER - TY - PAT TI - Methods of fabricating single electron transistors in which the thickness of an insulating layer defines spacing between electrodes AU - Brousseau, L. C., III C2 - 2004/// DA - 2004/// PY - 2004/// ER - TY - JOUR TI - Lyotropic liquid crystalline properties of poly(N,N '-di-n-hexylguanidine) AU - Kim, J AU - Novak, BM AU - Waddon, AJ T2 - MACROMOLECULES AB - ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTLyotropic Liquid Crystalline Properties of Poly(N,N‘-di-n-hexylguanidine)Jeonghan Kim, Bruce M. Novak, and Alan John WaddonView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695 Department of Polymer Science & Engineering, University of Massachusetts, Amherst, Massachusetts 01003 Cite this: Macromolecules 2004, 37, 4, 1660–1662Publication Date (Web):January 30, 2004Publication History Received5 August 2003Revised29 December 2003Published online30 January 2004Published inissue 1 February 2004https://doi.org/10.1021/ma035135eCopyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views289Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. 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Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (104 KB) Get e-AlertsSUBJECTS:Liquid crystals,Mesostructures,Physical and chemical processes,Polymer solutions,Polymers Get e-Alerts DA - 2004/2/24/ PY - 2004/2/24/ DO - 10.1021/ma035135e VL - 37 IS - 4 SP - 1660-1662 SN - 1520-5835 ER - TY - JOUR TI - Investigation of the incommensurate and commensurate magnetic superstructures of LiCuVO4 and CuO on the basis of the isotropic spin exchange and classical spin approximations AU - Dai, D AU - Koo, HJ AU - Whangbo, MH T2 - INORGANIC CHEMISTRY AB - The spin lattices of magnetic oxides LiCuVO4 and CuO are made up of CuO2 ribbon chains. The incommensurate and commensurate magnetic superstructures of these oxides were examined by calculating the total spin exchange interaction energies of their long-range order spin arrangements on the basis of the isotropic spin exchange and classical spin approximations. The incommensurate superstructure (0, 0.532, 0) of LiCuVO4 was analyzed to find that the next-nearest-neighbor spin exchange interaction Jnnn is more strongly antiferromagnetic than the nearest-neighbor spin exchange interaction Jnn in the CuO2 chains. With this finding, we reassessed the relative strengths of the spin exchange interactions of LiCuVO4 and CuO and then analyzed the relative energies of their long-range order spin arrangements. The incommensurate superstructure (0, 0.532, 0) of LiCuVO4 is explained when the Jnn/Jnnn ratio is −0.40. Both the incommensurate superstructure (0.506, 0, −0.483) and the commensurate superstructure (0.5, 0, −0.5) of CuO, which occur at 231 and 212.5 K, respectively, are well explained in terms of the calculated total spin exchange interaction energies. The incommensurate superstructure of CuO becomes commensurate by a slight change in one interchain spin exchange interaction, which is due probably to a slight structure change brought about by the temperature lowering. DA - 2004/6/28/ PY - 2004/6/28/ DO - 10.1021/ic035314c VL - 43 IS - 13 SP - 4026-4035 SN - 1520-510X ER - TY - JOUR TI - Factors influencing the course of the macrocyclization of alpha,omega-diamines with esters of alpha,omega-dicarboxylic acids AU - Gryko, D AU - Gryko, DT AU - Sierzputowska-Gracz, H AU - Piatek, P AU - Jurczak, J T2 - HELVETICA CHIMICA ACTA AB - Abstract The efficient synthesis of eight new macrocyclic amides (lactams) via reaction of diesters with diamines under normal dilution conditions is described. The role of intermolecular H‐bond formation and steric hindrance is discussed based on 1 H‐ and 15 N‐NMR studies of appropriate model compounds. Principles for the optimal choice of esters that can be efficiently transformed into diamides have been developed. DA - 2004/// PY - 2004/// DO - 10.1002/hlca.200490004 VL - 87 IS - 1 SP - 156-166 SN - 1522-2675 ER - TY - JOUR TI - Experimental and theoretical characterization of the optical properties of CeO2, SrCeO3, and Sr2CeO4 containina Ce4+ (f(0)) ions AU - Goubin, F AU - Rocquefelte, X AU - Whangbo, MH AU - Montardi, Y AU - Brec, R AU - Jobic, S T2 - CHEMISTRY OF MATERIALS AB - In an effort to find new UV absorbers, the optical properties of CeO2, SrCeO3, and Sr2CeO4 were examined by UV−visible diffuse reflectance measurements and electron energy-loss spectroscopy (EELS), and their electronic structures were investigated on the basis of first-principles density functional theory (DFT) calculations. The extinction coefficient k and the refractive index n determined from the loss function Im(−1/ε) by EELS were compared with the corresponding quantities calculated from DFT calculations. The UV absorption thresholds of these materials were determined by the electron excitation from the O 2p anionic band to the empty Ce 4f orbitals. The calculated and measured refractive indices were in satisfactory agreement. The applicability of CeO2, SrCeO3, and Sr2CeO4 as potential UV absorbers was assessed. DA - 2004/2/24/ PY - 2004/2/24/ DO - 10.1021/cm034618u VL - 16 IS - 4 SP - 662-669 SN - 1520-5002 ER - TY - JOUR TI - Effects of an active learning environment: Teaching innovations at a research I institution AU - Oliver-Hoyo, MT AU - Allen, D AU - Hunt, WF AU - Hutson, J AU - Pitts, A T2 - JOURNAL OF CHEMICAL EDUCATION AB - This paper describes a new approach for teaching general chemistry that combines lecture and laboratory into one seamless session and incorporates instructional methods supported by research-based findings. The results of a study that compared two instructional formats, conventional passive lecture and the student-centered, highly collaborative format known as cAcL2 (concept Advancement through chemistry Lab–Lecture), are also presented. Factors carefully controlled in this study include content material, time of day, time on task, and test format, scheduling, and grading. The results of the analysis of variance and the evaluation of the means conclude that the cAcL2 instructional method had a positive effect on student performance in an introductory chemistry class. DA - 2004/3// PY - 2004/3// DO - 10.1021/ed081p441 VL - 81 IS - 3 SP - 441-U2 SN - 1938-1328 ER - TY - JOUR TI - Effect of temperature and pressure in the photocatalytic oxidation of n-octanol on partially desilanized hydrophobic TiO2 suspended in aerated supercritical CO2 AU - Hirakawa, T AU - Whitesell, JK AU - Fox, MA T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Reaction temperature and CO2 pressure affect the rate of reaction in photocatalytic oxidations in supercritical (sc) CO2 on partially silanized TiO2. In supercritical CO2, the photocatalytic oxidation of octanol appeared to follow pseudo-first-order kinetics, with octanal being produced as the initial product. At 309 K, the pseudo-first-order rate constant kdis decreased upon increasing CO2 pressure from 8 to 20 MPa, giving rise to an increased yield of octanal. When the temperature was raised within the range from 299 to 319 K at constant CO2 pressure (10 MPa), kdis increased while the net yield of octanal decreased. These changes are rationalized as being caused by changes in near-surface CO2 density and, hence, in efficiency of mass transport of octanal to and from the catalytically active site. The observed dependence of the photoactivity of hydrophobic T805 TiO2 in scCO2 on temperature and pressure likely varies with surface conditions promoted by irradiation, which effects partial desilanization photocatalytically active sites. When scCO2 density was very low, T805 TiO2 did not suspend well into the scCO2 fluid; that is, almost all of the T805 TiO2 precipitated on a window or inner wall of the cell. At scCO2 densities between 8 and 20 MPa, T805 TiO2 was efficiently dispersed under stirring. At very low pressures near the critical point, the kinetic analysis was complicated by incident light scattering caused by suspended particles which act as inhibitory inner filters. DA - 2004/7/22/ PY - 2004/7/22/ DO - 10.1021/jp0364957 VL - 108 IS - 29 SP - 10213-10218 SN - 1520-6106 ER - TY - JOUR TI - Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element AU - Smith, BM AU - Lappi, SE AU - Brewer, SH AU - Dembowy, S AU - Belyea, J AU - Franzen, S T2 - LANGMUIR AB - The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1'-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable. DA - 2004/2/17/ PY - 2004/2/17/ DO - 10.1021/la034194i VL - 20 IS - 4 SP - 1184-1188 SN - 0743-7463 ER - TY - JOUR TI - Controlled fabrication of gold/polymer nanocomposites with a highly structured poly(N-acylethylenimine) shell AU - Rusa, M AU - Whitesell, JK AU - Fox, MA T2 - MACROMOLECULES AB - Two families of well-defined organic−inorganic nanocomposites have been synthesized either by attachment of an initiator as a capping self-assembled monolayer on a gold cluster onto which a macromolecule is grown in situ or by preformation of a defined polymer, followed by covalent or adsorptive attachment to a surface-capped metal cluster. The characteristics of these composites are compared in size and local organization. Possessing nanometer-sized gold clusters at the core and poly(N-acylethylenimine) chains radially or tangentially connected to the core, the resulting materials were characterized by TEM, GPC, UV, IR, NMR, and XPS spectroscopies. Larger particles with narrower polydispersity were obtained by in situ growth of the polymer on a preformed metal cluster, with best results being attained with a mixture of brominated and nonbrominated thiols in which steric accessibility to the initiator sites is varied. DA - 2004/4/20/ PY - 2004/4/20/ DO - 10.1021/ma035008i VL - 37 IS - 8 SP - 2766-2774 SN - 1520-5835 ER - TY - JOUR TI - A tin-complexation strategy for use with diverse acylation methods in the preparation of 1,9-diacyldipyrromethanes AU - Tamaru, S AU - Yu, LH AU - Youngblood, WJ AU - Muthukumaran, K AU - Taniguchi, M AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The acylation of dipyrromethanes to form 1,9-diacyldipyrromethanes is an essential step in the rational synthesis of porphyrins. Although several methods for acylation are available, purification is difficult because 1,9-diacyldipyrromethanes typically streak extensively upon chromatography and give amorphous powders upon attempted crystallization. A solution to this problem has been achieved by reacting the 1,9-diacyldipyrromethane with Bu(2)SnCl(2) to give the corresponding dibutyl(5,10-dihydrodipyrrinato)tin(IV) complex. The reaction is selective for dipyrromethanes that bear acyl groups at both the 1- and 9-positions but otherwise is quite tolerant of diverse substituents. The diacyldipyrromethane-tin complexes are stable to air and water, are highly soluble in common organic solvents, crystallize readily, and chromatograph without streaking. Four methods (Friedel-Crafts, Grignard, Vilsmeier, benzoxathiolium salt) were examined for the direct 1,9-diacylation of a dipyrromethane or the 9-acylation of a 1-acyldipyrromethane. In each case, treatment of the crude reaction mixture with Bu(2)SnCl(2) and TEA at room temperature enabled facile isolation of multigram quantities of the 1,9-diacyldipyrromethane-tin complex. The diacyldipyrromethane-tin complexes could be decomplexed with TFA in nearly quantitative yield. Alternatively, use of a diacyldipyrromethane-tin complex in a porphyrin-forming reaction (reduction with NaBH(4), acid-catalyzed condensation with a dipyrromethane, DDQ oxidation) afforded the desired free base porphyrin in yield comparable to that obtained from the uncomplexed diacyldipyrromethane. The acylation/tin-complexation strategy has been applied to a bis(dipyrromethane) and a porphyrin-dipyrromethane. In summary, the tin-complexation strategy has broad scope, is compatible with diverse acylation methods, and greatly facilitates access to 1,9-diacyldipyrromethanes. DA - 2004/2/6/ PY - 2004/2/6/ DO - 10.1021/jo035622s VL - 69 IS - 3 SP - 765-777 SN - 0022-3263 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0842285782&partnerID=MN8TOARS ER - TY - JOUR TI - Time-resolved fluorescence investigation of energy transfer in compact phenylacetylene dendrimers AU - Ranasinghe, MI AU - Hager, MW AU - Gorman, CB AU - Goodson, T T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Excitation energy transfer dynamics in light-harvesting dendritic macromolecules has generated a great deal of interest due to the fact that such systems can be used in photovoltaic and light-emitting devices. Studies on phenylacetylene-based dendrimers played a key role in stimulating this interest and extensive theoretical as well as experimental investigations have been carried out to get a better insight into the phenomena behind the excitation energy transfer dynamics of these dendrimers. In this manuscript, time-resolved femtosecond fluorescence and fluorescence anisotropy dynamics as well as temperature dependent steady state spectral studies of a second generation homogeneous (compact) phenylacetylene dendrimer are reported. The low-temperature fluorescence spectrum of the dendrimer showed two distinctive emission peaks that can be related to the existence of two closely spaced electronic states of the chromophore. Time-resolved fluorescence results suggest delocalization of the excitation energy in the excited state. The ultrafast fluorescence anisotropy decay dynamics further supports the existence of a delocalized state. DA - 2004/6/24/ PY - 2004/6/24/ DO - 10.1021/jp036877c VL - 108 IS - 25 SP - 8543-8549 SN - 1520-5207 ER - TY - JOUR TI - Structural control of the excited-state dynamics of bis(dipyrrinato)zinc complexes: Self-assembling chromophores for light-harvesting architectures AU - Sazanovich, , IV AU - Kirmaier, C AU - Hindin, E AU - Yu, LH AU - Bocian, DF AU - Lindsey, JS AU - Holten, D T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - The replacement of the phenyl rings at the 5,5‘-positions of a bis(dipyrrinato)zinc complex with mesityl groups transforms the molecule from a very weak emitter that deactivates rapidly after photoexcitation (Φf = 0.006; τ ≈ 90 ps) to a highly fluorescent chromophore with a long-lived singlet excited state (Φf = 0.36; τ ≈ 3 ns). The results demonstrate that steric constraints on aryl-ring internal rotation dramatically alter the excited-state properties of 5,5‘-substituted bis(dipyrrinato)metal complexes. The insights establish the foundation for tuning the photophysical properties of these chromophores for use in diverse photochemical applications. DA - 2004/3/10/ PY - 2004/3/10/ DO - 10.1021/ja038763k VL - 126 IS - 9 SP - 2664-2665 SN - 1520-5126 ER - TY - JOUR TI - Scanning tunneling microscope-based replacement lithography on self-assembled monolayers. Investigation of the relationship between monolayer structure and replacement bias AU - Lewis, MS AU - Gorman, CB T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Organothiolate self-assembled monolayers (SAMs) can be patterned using a scanning tunneling microscopy (STM) tip. Upon elevating the bias, the SAM is locally desorbed. By conducting this process in the presence of a second thiol component in a nonpolar solution (dodecane) above it, a different SAM component is locally introduced. Here, the influence of the chain length and headgroup of the initial SAM on this process is elucidated. SAMs composed of longer molecules require higher biases to effect this process, similar to the electrochemical desorption behavior of these molecules. When initial SAMs composed of headgroups other than methyl were studied, poor results were obtained: features were broad and replacement occurred more inconsistently. Several possible explanations for this behavior are discussed. DA - 2004/6/24/ PY - 2004/6/24/ DO - 10.1021/jp0379244 VL - 108 IS - 25 SP - 8581-8583 SN - 1520-6106 ER - TY - JOUR TI - Diverse redox-active molecules bearing identical thiol-terminated tripodal tethers for studies of molecular information storage AU - Wei, LY AU - Padmaja, K AU - Youngblood, WJ AU - Lysenko, AB AU - Lindsey, JS AU - Bocian, DF T2 - JOURNAL OF ORGANIC CHEMISTRY AB - To examine the effects of molecular structure on charge storage in self-assembled monolayers (SAMs), a family of redox-active molecules has been prepared wherein each molecule bears a tether composed of a tripodal linker with three protected thiol groups for surface attachment. The redox-active molecules include ferrocene, zinc porphyrin, ferrocene-zinc porphyrin, magnesium phthalocyanine, and triple-decker lanthanide sandwich coordination compounds. The tripodal tether is based on a tris[4-(S-acetylthiomethyl)phenyl]-derivatized methane. Each redox-active unit is linked to the methane vertex by a 4,4‘-diphenylethyne unit. The electrochemical characteristics of each compound were examined in solution and in SAMs on Au. Redox-kinetic measurements were also performed on the SAMs (with the exception of the magnesium phthalocyanine) to probe (1) the rate of electron transfer in the presence of an applied potential and (2) the rate of charge dissipation after the applied potential is disconnected. The electrochemical studies of the SAMs indicate that the tripodal tether provides a more robust anchor to the Au surface than does a tether with a single site of attachment. However, the electron-transfer and charge-dissipation characteristics of the two tethers are generally similar. These results suggest that the tripodal tether offers superior stability characteristics without sacrificing electrochemical performance. DA - 2004/3/5/ PY - 2004/3/5/ DO - 10.1021/jo0349476 VL - 69 IS - 5 SP - 1461-1469 SN - 0022-3263 ER - TY - JOUR TI - Synthesis of swallowtail-substituted multiporphyrin rods AU - Thamyongkit, P AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The availability of multiporphyrin arrays with defined architectures and good solubility in organic solvents is essential for a wide variety of physical studies. Herein the synthesis of linear multiporphyrin arrays (triads, tetrad, pentad) bearing solubilizing 7-tridecyl (swallowtail) groups is presented. The rodlike arrays are composed of zinc porphyrins at the termini and 1, 2, or 3 free base porphyrins at the core. The free base porphyrins in the tetrad and pentad are joined to each other via p-phenylene linkers whereas the zinc porphyrins in each array are attached to the core free base porphyrins via 1,4-diphenylethyne linkers. The arrays are designed for studies of interporphyrin electronic communication. DA - 2004/8/20/ PY - 2004/8/20/ DO - 10.1021/jo049348t VL - 69 IS - 17 SP - 5796-5799 SN - 0022-3263 ER - TY - JOUR TI - Liquid crystalline properties of polyguanidines AU - Kim, J AU - Novak, BM AU - Waddon, AJ T2 - MACROMOLECULES AB - Modified polyguanidines were prepared, and their liquid crystalline properties were studied using optical polarizing microscopy and X-ray diffraction. Parameters examined include chirality, the uniformity of the lengths of side chains, and attached side-chain mesogens. If the side chains on the repeat units are identical, then polymer has a more ordered structure in both solution and the solid state. Uniform lengths of the side chains are also important. Poly(N,N‘-di-n-hexylguanidine), poly-I, exhibited a lyotropic smectic texture in contrast to a nematic texture of poly(N-(rac)-2-phenylethyl)-N‘-methylguanidine) (poly-(rac-II)). Optically pure poly(N-((R)-2-phenylethyl)-N‘-methylguanidine) (poly-(R-II)) formed a cholesteric texture, whereas the corresponding racemic polyguanidine, poly-(rac-II), formed a nematic texture. Additionally, poly-(R-II) displayed a mesophase at a lower critical concentration than either poly-I or poly-(rac-II), implying that poly-(R-II) is stiffer than these two other derivatives. Poly(N-6-((4‘-methoxyphenylazo)phenyl-4-oxy)hexyl-N‘-n-hexylguanidine) (poly-IV), one of combined liquid crystalline structures (liquid crystalline backbone plus liquid crystalline side chains), displayed a lyotropic nematic texture presumably due to the strong dipolar−dipolar interaction between the main chain and side chains that folds the appendages parallel to the molecular axis. Poly(N-12-((4‘-methoxybiphenyl-4-oxy)dodecyl-N‘-n-dodecylguanidine) (poly-V) and poly(N,N‘-di-n-dodecylguanidine) (poly-VI) exhibited thermotropic liquid crystalline behavior. DA - 2004/11/2/ PY - 2004/11/2/ DO - 10.1021/ma0493527 VL - 37 IS - 22 SP - 8286-8292 SN - 1520-5835 ER - TY - JOUR TI - Transport properties of hectorite based nanocomposite single ion conductors AU - Singhal, RG AU - Capracotta, MD AU - Martin, JD AU - Khan, SA AU - Fedkiw, PS T2 - JOURNAL OF POWER SOURCES AB - The ionic conductivity and rheological properties of clay filled nanocomposite electrolytes are reported. These electrolytes, which have potential use in lithium-ion batteries, consist of lithium-exchanged hectorite, a 2:1 layered smectite clay, dispersed in ethylene carbonate (EC) or a mixture of EC+polyethylene glycol di-methyl ether (PEG-dm, 250 MW). All samples exhibit elastic, gel-like characteristics and room temperature conductivities of order 0.1 mS/cm. A maximum in conductivity is observed at about 25 wt.% clay concentration. A maximum in hectorite basal layer spacing is also observed in the same concentration range, suggesting a direct correlation between conductivity and layer spacing. The elastic modulus and yield stress increase by two orders of magnitude and the conductivity increases by one order of magnitude with increase in hectorite concentration from 5 to 25%, which indicates the significant influence of hectorite content in determining the characteristics of these single-ion conductors. The solvent composition plays a secondary role in this regard, with addition of PEG-dm to the base EC+hectorite electrolyte producing moderate improvement in conductivity. Similarly, the addition of PEG-dm to EC+hectorite affects an increase by only a factor of three in the elastic modulus and yield stress of the electrolyte. DA - 2004/4/5/ PY - 2004/4/5/ DO - 10.1016/j.jpowsour.2003.09.064 VL - 128 IS - 2 SP - 247-255 SN - 0378-7753 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-1542333424&partnerID=MN8TOARS KW - lithium-ion cell KW - composite gel electrolyte KW - clay nanocomposite KW - hectorite KW - polyethylene glycol KW - small angle X-ray diffraction ER - TY - JOUR TI - The effect of mutation on RNA Diels-Alderases AU - Tarasow, TM AU - Kellogg, E AU - Holley, BL AU - Nieuwlandt, D AU - Tarasow, SL AU - Eaton, BE T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Chemical mutagenesis of a previously reported RNA Diels-Alderase (DA22) was followed by in vitro selection based on [4 + 2] catalysis. New mutated families of RNA Diels-Alderases closely related in sequence space were obtained. The mutated Diels-Alderases selected showed significant improvements in catalytic efficiency (k(cat)/K(m)) as compared to the original DA22. The improvement in catalytic activity was primarily due to a decrease in K(m), but modest increases in k(cat) were also observed. The increase in catalytic activity of these new Diels-Alderases was found not to negatively affect their dienophile specificity. Surprisingly, one of the most active Diels-Alderases (DAM 40), a subtle sequence mutant of DA22, was found to show a new metal dependence and could function with Ni(2+) as the only transition-metal ion. Truncation experiments of DA22 showed that the region shown to be hypervariable at the 3'-end of the structure could be deleted without a significant decrease in the relative rate of Diels-Alder catalysis. DA - 2004/9/29/ PY - 2004/9/29/ DO - 10.1021/ja0494149 VL - 126 IS - 38 SP - 11843-11851 SN - 0002-7863 ER - TY - JOUR TI - The distance-dependence of colloidal Au-amplified surface plasmon resonance AU - He, L AU - Smith, EA AU - Natan, MJ AU - Keating, CD T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Au nanoparticle-amplified surface plasmon resonance (PA-SPR), like traditional SPR, is typically used to detect binding events at a thin noble metal film. Here we describe the use of SiO2-overcoated Au films as a substrate for PA-SPR. Changes in SPR angle shift upon Au nanosphere binding were investigated as a function of the SiO2 thickness. In these experiments, a submonolayer of Au nanoparticles was immobilized atop a thin Au film separated by an intervening SiO2 layer. Although SPR is an evanescent wave technique, the observed SPR angle shift does not decrease monotonically with increasing Au nanoparticle−Au surface separation, but rather increases to a maximum at ∼32 nm separation before decreasing. In contrast to the previously proposed electromagnetic coupling between the metal particles and the surface as the main cause for the observed distance-dependent SPR response, we propose and have demonstrated qualitatively that the energy modulating capability of the SiO2 spacing layer is the main contributor. The impact of the particle size, composition, and surface densities on this maximum in SPR angle shifts was also examined. The results indicate that the optimal SiO2 thickness was independent of Au nanoparticle surface coverage for coverage less than 10%. This work extends the use of PA-SPR to monitoring binding events at glass interfaces and points to a route for increased sensitivity, as evidenced in an PA-SPR assay for human immunoglobin G in a sandwich immunoassay format. DA - 2004/7/29/ PY - 2004/7/29/ DO - 10.1021/jp048536k VL - 108 IS - 30 SP - 10973-10980 SN - 1520-5207 ER - TY - JOUR TI - Predictions of micelle-water partition coefficients and retention in micellar electrokinetic chromatography from solute structure. 2. Fragmental constant approach AU - Burns, ST AU - Khaledi, MG T2 - ANALYTICAL CHEMISTRY AB - The fragmental constant approach (FCA) was used to calculate water-sodium dodecyl sulfate (SDS) micelle partition coefficients, K(mw), for uncharged solutes from their structure. Subsequently, the availability of K(mw) values allows prediction of retention factor, k, in micellar electrokinetic chromatography (MEKC) using the simple relationship k = K(mw)phi, where phi is the phase ratio. The FCA model describes a micelle-water partition coefficient as the sum of the partition coefficients of the constituent atomic/molecular fragments, measured by fragmental constant values, f (i), as well as correction factors to account for various "intramolecular effects" that cause deviations from the predicted partition coefficients as, log K(mw) = sum(n)(i=1)aif i+sum(m)(i=1)kiCm. The fragmental constants for a set of 41 fragments were determined using a training set of 229 aromatic solutes and 198 aliphatic compounds. The K(mw) of the aromatic compounds in the training set were determined by MEKC, while the K(mw) of the aliphatic solutes were estimated using the linear solvation energy relationship (LSER) for the SDS micelles. The fragments consisted of both aromatic fragments (i.e., directly attached to an aromatic ring) and aliphatic fragments. The FCA predictions agree nicely with the observed and LSER partition coefficient values, even for complex molecular structures such as beta-blocker drugs. The results show the great potential of the FCA for a priori prediction of retention behavior in MEKC from solute structure. DA - 2004/9/15/ PY - 2004/9/15/ DO - 10.1021/ac0498718 VL - 76 IS - 18 SP - 5451-5458 SN - 1520-6882 ER - TY - BOOK TI - Organic chemistry (3rd ed.) AU - Fox, M. A. AU - Whitesell, J. K. CN - QD251.3 .F69 2004 DA - 2004/// PY - 2004/// PB - Sudbury, MA: Jones and Bartlett Publishers SN - 0763721972 ER - TY - JOUR TI - Growth of diamond film on single crystal lithium niobate for surface acoustic wave devices AU - Jagannadham, K. AU - Lance, M. J. AU - Watkins, T. R. T2 - Journal of Vacuum Science & Technology. A, Vacuum, Surfaces, and Films DA - 2004/// PY - 2004/// VL - 22 IS - 4 SP - 1105-1109 ER - TY - JOUR TI - First principles prediction of the gas-phase precursors for AlN sublimation growth AU - Li, YX AU - Brenner, DW T2 - PHYSICAL REVIEW LETTERS AB - Using a new, parameter-free first principles strategy for modeling sublimation growth, we show that while Al and ${\mathrm{N}}_{2}$ dominate gas concentrations in AlN sublimation growth chambers under typical growth conditions, ${\mathrm{N}}_{2}$ is undersaturated with respect to the crystal and therefore cannot be a growth precursor. Instead, our calculations predict that the nitrogen-containing precursors are ${\mathrm{A}\mathrm{l}}_{n}\mathrm{N}$ ($n=2,3,4$), in stark contrast to assumptions used in all previous modeling studies of this system. DA - 2004/2/20/ PY - 2004/2/20/ DO - 10.1103/physrevlett.92.075503 VL - 92 IS - 7 SP - SN - 1079-7114 ER - TY - JOUR TI - Electrical characterization of B-10 doped diamond irradiated with low thermal neutron fluence AU - Reed, ML AU - Reed, MJ AU - Jagannadham, K AU - Verghese, K AU - Bedair, SM AU - El-Masry, N AU - Butler, JE T2 - JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A AB - A sample of B10 isotope doped diamond was neutron irradiated to a thermal fluence of 1.3×1019 neutron cm−2. The diamond sample was cooled continuously during irradiation in a nuclear reactor. Li7 is formed by nuclear transmutation reaction from B10. Characterization for electrical conductance in the temperature range of 160 K&lt;T&lt;600 K was performed on an unirradiated B10 doped sample and the B10 doped and irradiated sample. The unirradiated diamond sample showed p-type conductance at higher temperature (T&gt;200 K) and p-type surface conductance at lower temperature (T&lt;200 K). The irradiated sample showed decreasing conductance below 230 K and increasing conductance above 230 K with increasing temperature. Furthermore, the conductance showed a decrease above 400 K followed by an increase above 500 K. The observed behavior below 400 K with increase in temperature is interpreted in terms of compensation of surface p-type carriers by n-type bulk carriers generated from Li7 that is formed by nuclear transmutation reaction from B10 atoms. Also, compensation of n-type carriers from Li7 by p-type carriers from B10 is used to interpret the conductance above 400 K. A low concentration of radiation induced defects, absence of defect complexes, and the low activation energy of n-type Li7 are thought responsible for the observed variation of conductance in the irradiated diamond. The present results illustrate that neutron transmutation from B10 doped diamond is a useful method to achieve n-type conductivity in diamond. DA - 2004/// PY - 2004/// DO - 10.1116/1.1763910 VL - 22 IS - 4 SP - 1191-1194 SN - 1520-8559 ER - TY - JOUR TI - Effects of aldehyde or dipyrromethane substituents on the reaction course leading to meso-substituted porphyrins AU - Geier, GR AU - Lindsey, JS T2 - TETRAHEDRON AB - To better understand the effects of diverse substituents on reactions leading to porphyrins, pyrrole+aldehyde condensations and related reactions of dipyrromethanes were examined. The course of pyrrole+aldehyde condensations was investigated by monitoring the yield of porphyrin (by UV–Vis spectroscopy), reaction of aldehyde (by TLC), and changes in the composition of oligomers (by laser desorption mass spectrometry). Reaction reversibility was examined via exchange experiments. Reversibility of reactions leading to porphyrin was further probed with studies of dipyrromethanes. The reaction course was found to depend on the nature of the substituent and the acid catalyst. Alkyl or electron-donating substituents displayed levels of reversibility (exchange/scrambling) on par or greater than that of the phenyl substituent, whereas electron-withdrawing or sterically bulky substituents exhibited little to no reversibility. The results obtained provide insight into the electronic and steric effects of different substituents and should facilitate the design of synthetic plans for preparing porphyrinic macrocycles. DA - 2004/12/6/ PY - 2004/12/6/ DO - 10.1016/j.tet.2004.09.081 VL - 60 IS - 50 SP - 11435-11444 SN - 0040-4020 KW - porphyrin KW - porphyrinogen KW - dipyrromethane KW - polypyrromethane KW - pyrrole KW - laser desorption mass spectrometry ER - TY - JOUR TI - Barcoding the microworld AU - Finkel, N. H. AU - Lou, X. H. AU - Wang, C. Y. AU - He, L. T2 - Analytical Chemistry DA - 2004/// PY - 2004/// VL - 76 IS - 19 SP - 353A-359 ER - TY - JOUR TI - Local atomic structure and infrared effective charges in tetrahedrally-bonded glasses from ab initio theory electronic structure calculations AU - Lucovsky, G AU - Mowrer, T AU - Sremaniak, LS AU - Whitten, JL T2 - JOURNAL OF NON-CRYSTALLINE SOLIDS AB - Ab initio calculations are applied to small clusters containing the elements of short range order determined from X-ray and electron diffraction radial distributions for tetrahedrally-bonded, continuous random networks glasses including SiO2, GeO2, BeF2, and GeS2. The calculations have been used to determine the dependence of the total energy on the bond-angle at the two-fold coordinated O-, F-, and S-atom sites, and the infrared effective charges for normal mode infrared active network vibrations. The results of these calculations are in excellent agreement with experiment. Of particular significance are the calculated bond angle distributions for SiO2 and GeO2, which are significantly narrower than previously assumed, but in good agreement with recent modeling and experimental studies. DA - 2004/6/15/ PY - 2004/6/15/ DO - 10.1016/j.jnoncrysol.2004.02.043 VL - 338 IS - Jun 15 2004 SP - 155-158 SN - 0022-3093 ER - TY - JOUR TI - Effect of the counterion on the rate of electron transfer in dendrimer films AU - Chasse, TL AU - Smith, JC AU - Carroll, RL AU - Gorman, CB T2 - LANGMUIR AB - The electrochemical behavior of a film composed of a redox-active dendrimer was studied as a function of the type of counterion available during its reduction and reoxidation. The rate of permeation/migration of counterions into the film appeared to be the bottleneck to electron transfer through the film. Because the dendrimer is rather hydrophobic, increasing the hydrophobicity of the counterion increased the rate and extent of electron hopping within the films. DA - 2004/4/27/ PY - 2004/4/27/ DO - 10.1021/la049818e VL - 20 IS - 9 SP - 3501-3503 SN - 0743-7463 ER -