@article{franzen_brown_gaff_delley_2012, title={A resonance Raman enhancement mechanism for axial vibrational modes in the pyridine adduct of myoglobin proximal cavity mutant (H93G)}, volume={116}, number={35}, journal={Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical}, author={Franzen, S. and Brown, D. and Gaff, J. and Delley, B.}, year={2012}, pages={10514–10521} }
 @article{gaff_franzen_2012, title={Resonance Raman enhancement of pyridine on Ag clusters}, volume={397}, number={1}, journal={Chemical Physics}, author={Gaff, J. and Franzen, S.}, year={2012}, pages={34–41} }
 @article{gaff_franzen_delley_2010, title={Ab Initio Calculation of Resonance Raman Cross Sections Based on Excited State Geometry Optimization}, volume={114}, ISSN={["1089-5639"]}, DOI={10.1021/jp103321x}, abstractNote={A method for the calculation of resonance Raman cross sections is presented on the basis of calculation of structural differences between optimized ground and excited state geometries using density functional theory. A vibrational frequency calculation of the molecule is employed to obtain normal coordinate displacements for the modes of vibration. The excited state displacement relative to the ground state can be calculated in the normal coordinate basis by means of a linear transformation from a Cartesian basis to a normal coordinate one. The displacements in normal coordinates are then scaled by root-mean-square displacement of zero point motion to calculate dimensionless displacements for use in the two-time-correlator formalism for the calculation of resonance Raman spectra at an arbitrary temperature. The method is valid for Franck-Condon active modes within the harmonic approximation. The method was validated by calculation of resonance Raman cross sections and absorption spectra for chlorine dioxide, nitrate ion, trans-stilbene, 1,3,5-cycloheptatriene, and the aromatic amino acids. This method permits significant gains in the efficiency of calculating resonance Raman cross sections from first principles and, consequently, permits extension to large systems (>50 atoms).}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Gaff, J. F. and Franzen, S. and Delley, B.}, year={2010}, month={Nov}, pages={11681–11690} }
 @article{ma_thompson_gaff_franzen_2010, title={Kinetic Analysis of a Naturally Occurring Bioremediation Enzyme: Dehaloperoxidase-Hemoglobin from Amphitrite ornata}, volume={114}, ISSN={["1520-6106"]}, DOI={10.1021/jp1014516}, abstractNote={The temperature dependence of the rate constant for substrate oxidation by the dehaloperoxidase-hemoglobin (DHP) of Amphitrite ornata has been measured from 278 to 308 K. The rate constant is observed to increase over this range by approximately a factor of 2 for each 10 °C temperature increment. An analysis of the initial rates using a phenomenological approach that expresses the peroxidase ping-pong mechanism in the form of the Michaelis-Menten equation leads to an interpretation of the effects in terms of the fundamental rate constants. The analysis of kinetic data considers a combination of diffusion rate constants for substrate and H(2)O(2), elementary steps involving activation and heterolysis of the O-O bond of H(2)O(2), and two electron transfers from the substrate to the iron. To complete the analysis from the perspective of turnover of substrate into product, density function theory (DFT) calculations were used to address the fate of phenoxy radical intermediates. The analysis suggests a dominant role for diffusion in the kinetics of DHP.}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Ma, Huan and Thompson, Matthew K. and Gaff, John and Franzen, Stefan}, year={2010}, month={Nov}, pages={13823–13829} }
 @article{serrano_davis_gaff_zhang_chen_d'antonio_bowden_rose_franzen_2010, title={X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: Evidence for photoreductive dissociation of the iron-cyanide bond}, volume={66}, journal={Acta Crystallographica. Section D, Biological Crystallography}, author={Serrano, V. S. and Davis, M. F. and Gaff, J. F. and Zhang, Q. and Chen, Z. and D'Antonio, E. L. and Bowden, E. F. and Rose, R. and Franzen, S.}, year={2010}, pages={770–782} }
 @article{gaff_franzen_2009, title={Excited-State Geometry Method for Calculation of the Absolute Resonance Raman Cross Sections of the Aromatic Amino Acids}, volume={113}, ISSN={["1089-5639"]}, DOI={10.1021/jp809431k}, abstractNote={The time correlator formalism was used to calculate the absolute resonance Raman cross sections for the aromatic amino acids based on density functional theory calculations of the ground-state potential energy surfaces combined with projection along normal mode eigenvectors in the excited state. The geometric difference between the minima of the ground and excited states along each normal mode was calculated to provide inputs for the time correlator in the linear approximation. The calculated dimensionless nuclear displacements, Delta(i), provide the electron-phonon coupling constants, S(i) = Delta(i)(2)/2, for the corresponding Raman active mode of frequency omega(t). The method is generally applicable to molecules that are Franck-Condon active. As an example we have chosen to calculate the absolute resonance Raman cross sections of models of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. We discuss the role played by substituents on the aromatic ring that decrease vibronic activity to a level that permits application of the time correlator. While the method may have limitations for molecules of high symmetry, the current study of excited-state displacements and electronic structure indicates that the L(a),(b) states are Franck-Condon active in the aromatic molecules studied.}, number={18}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Gaff, John F. and Franzen, Stefan}, year={2009}, month={May}, pages={5414–5422} }
 @article{kramer_xie_gaff_williamson_tkachenko_nouri_feldheim_feldheim_2004, title={Preparation of protein gradients through the controlled deposition of protein-nanoparticle conjugates onto functionalized surfaces}, volume={126}, ISSN={["0002-7863"]}, DOI={10.1021/ja031674n}, abstractNote={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.}, number={17}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Kramer, S and Xie, H and Gaff, J and Williamson, JR and Tkachenko, AG and Nouri, N and Feldheim, DA and Feldheim, DL}, year={2004}, month={May}, pages={5388–5395} }