@article{pauly_white_deegbey_fosu_keller_mcguigan_dianat_gabilondo_wong_murphey_et al._2024, title={Coordination of copper within a crystalline carbon nitride and its catalytic reduction of CO<sub>2</sub>}, volume={3}, ISSN={["1477-9234"]}, DOI={10.1039/d4dt00359d}, abstractNote={Inherently disordered structures of carbon nitrides have hindered an atomic level tunability and understanding of their catalytic reactivity. Starting from a crystalline carbon nitride, poly(triazine imide) or PTI/LiCl, the coordination of copper cations to its intralayer N-triazine groups was investigated using molten salt reactions. The reaction of PTI/LiCl within CuCl or eutectic KCl/CuCl2 molten salt mixtures at 280 to 450 °C could be used to yield three partially disordered and ordered structures, wherein the Cu cations are found to coordinate within the intralayer cavities. Local structural differences and the copper content, i.e., whether full or partial occupancy of the intralayer cavity occurs, were found to be dependent on the reaction temperature and Cu-containing salt. Crystallites of Cu-coordinated PTI were also found to electrophoretically deposit from aqueous particle suspensions onto either graphite or FTO electrodes. As a result, electrocatalytic current densities for the reduction of CO2 and H2O reached as high as ∼10 to 50 mA cm-2, and remained stable for >2 days. Selectivity for the reduction of CO2 to CO vs. H2 increases for thinner crystals as well as for when two Cu cations coordinate within the intralayer cavities of PTI. Mechanistic calculations have also revealed the electrocatalytic activity for CO2 reduction requires a smaller thermodynamic driving force with two neighboring Cu atoms per cavity as compared to a single Cu atom. These results thus establish a useful synthetic pathway to metal-coordination in a crystalline carbon nitride and show great potential for mediating stable CO2 reduction at sizable current densities.}, journal={DALTON TRANSACTIONS}, author={Pauly, Magnus and White, Ethan and Deegbey, Mawuli and Fosu, Emmanuel Adu and Keller, Landon and Mcguigan, Scott and Dianat, Golnaz and Gabilondo, Eric and Wong, Jian Cheng and Murphey, Corban G. E. and et al.}, year={2024}, month={Mar} }
 @article{may_deegbey_edme_lee_perutz_jakubikova_dempsey_2024, title={Electronic Structure and Photophysics of Low Spin d<SUP>5</SUP> Metallocenes}, volume={63}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.3c03451}, abstractNote={The electronic structure and photophysics of two low spin metallocenes, decamethylmanganocene (MnCp*2) and decamethylrhenocene (ReCp*2), were investigated to probe their promise as photoredox reagents. Computational studies support the assignment of 2E2 ground state configurations and low energy ligand-to-metal charge transfer transitions for both complexes. Weak emission is observed at room temperature for ReCp*2 with τ = 1.8 ns in pentane, whereas MnCp*2 is not emissive. Calculation of the excited state reduction potentials for both metallocenes reveal their potential potency as excited state reductants (E°'([MnCp*2]+/0*) = -3.38 V and E°'([ReCp*2]+/0*) = -2.61 V vs Fc+/0). Comparatively, both complexes exhibit mild potentials for photo-oxidative processes (E°'([MnCp*2]0*/-) = -0.18 V and E°'([ReCp*2]0*/-) = -0.20 V vs Fc+/0). These results showcase the rich electronic structure of low spin d5 metallocenes and their promise as excited state reductants.}, number={4}, journal={INORGANIC CHEMISTRY}, author={May, Ann Marie and Deegbey, Mawuli and Edme, Kedy and Lee, Katherine J. and Perutz, Robin N. and Jakubikova, Elena and Dempsey, Jillian L.}, year={2024}, month={Jan}, pages={1858–1866} }
 @article{kwon_curtin_morrow_kelley_jakubikova_2023, title={Adaptive basis sets for practical quantum computing}, volume={4}, ISSN={["1097-461X"]}, url={https://doi.org/10.1002/qua.27123}, DOI={10.1002/qua.27123}, abstractNote={Electronic structure calculations on small systems such as H$_2$, H$_2$O, LiH, and BeH$_2$ with chemical accuracy are still a challenge for the current generation of the noisy intermediate-scale quantum (NISQ) devices. One of the reasons is that due to the device limitations, only minimal basis sets are commonly applied in quantum chemical calculations, which allow one to keep the number of qubits employed in the calculations at minimum. However, the use of minimal basis sets leads to very large errors in the computed molecular energies as well as potential energy surface shapes. One way to increase the accuracy of electronic structure calculations is through the development of small basis sets better suited for quantum computing. In this work, we show that the use of adaptive basis sets, in which exponents and contraction coefficients depend on molecular structure, provide an easy way to dramatically improve the accuracy of quantum chemical calculations without the need to increase the basis set size and thus the number of qubits utilized in quantum circuits. As a proof of principle, we optimize an adaptive minimal basis set for quantum computing calculations on an H$_2$ molecule, in which exponents and contraction coefficients depend on the H-H distance, and apply it to the generation of H$_2$ potential energy surface on IBM-Q quantum devices. The adaptive minimal basis set reaches the accuracy of the double-zeta basis sets, thus allowing one to perform double-zeta quality calculations on quantum devices without the need to utilize twice as many qubits in simulations. This approach can be extended to other molecular systems and larger basis sets in a straightforward manner.}, journal={INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY}, author={Kwon, Hyuk-Yong and Curtin, Gregory M. M. and Morrow, Zachary and Kelley, C. T. and Jakubikova, Elena}, year={2023}, month={Apr} }
 @article{johnson_schwarz_deegbey_prakash_sharma_huang_ericsson_haggstrom_bendix_gupta_et al._2023, title={Ferrous and ferric complexes with cyclometalating N-heterocyclic carbene ligands: a case of dual emission revisited}, volume={8}, ISSN={["2041-6539"]}, DOI={10.1039/d3sc02806}, journal={CHEMICAL SCIENCE}, author={Johnson, Catherine Ellen and Schwarz, Jesper and Deegbey, Mawuli and Prakash, Om and Sharma, Kumkum and Huang, Ping and Ericsson, Tore and Haggstrom, Lennart and Bendix, Jesper and Gupta, Arvind Kumar and et al.}, year={2023}, month={Aug} }
 @article{johnson_schwarz_deegbey_prakash_sharma_huang_ericsson_haggstrom_bendix_gupta_et al._2023, title={Ferrous and ferric complexes with cyclometalating N-heterocyclic carbene ligands: a case of dual emission revisited}, volume={14}, ISSN={["2041-6539"]}, DOI={10.1039/d3sc02806b}, abstractNote={Iron N-heterocyclic carbene (FeNHC) complexes with long-lived charge transfer states are emerging as a promising class of photoactive materials. We have synthesized [FeII(ImP)2] (ImP = bis(2,6-bis(3-methylimidazol-2-ylidene-1-yl)phenylene)) that combines carbene ligands with cyclometalation for additionally improved ligand field strength. The 9 ps lifetime of its 3MLCT (metal-to-ligand charge transfer) state however reveals no benefit from cyclometalation compared to Fe(ii) complexes with NHC/pyridine or pure NHC ligand sets. In acetonitrile solution, the Fe(ii) complex forms a photoproduct that features emission characteristics (450 nm, 5.1 ns) that were previously attributed to a higher (2MLCT) state of its Fe(iii) analogue [FeIII(ImP)2]+, which led to a claim of dual (MLCT and LMCT) emission. Revisiting the photophysics of [FeIII(ImP)2]+, we confirmed however that higher (2MLCT) states of [FeIII(ImP)2]+ are short-lived (<10 ps) and therefore, in contrast to the previous interpretation, cannot give rise to emission on the nanosecond timescale. Accordingly, pristine [FeIII(ImP)2]+ prepared by us only shows red emission from its lower 2LMCT state (740 nm, 240 ps). The long-lived, higher energy emission previously reported for [FeIII(ImP)2]+ is instead attributed to an impurity, most probably a photoproduct of the Fe(ii) precursor. The previously reported emission quenching on the nanosecond time scale hence does not support any excited state reactivity of [FeIII(ImP)2]+ itself.}, number={37}, journal={CHEMICAL SCIENCE}, author={Johnson, Catherine Ellen and Schwarz, Jesper and Deegbey, Mawuli and Prakash, Om and Sharma, Kumkum and Huang, Ping and Ericsson, Tore and Haggstrom, Lennart and Bendix, Jesper and Gupta, Arvind Kumar and et al.}, year={2023}, month={Sep}, pages={10129–10139} }
 @article{rodriguez_deegbey_chen_jakubikova_dempsey_2023, title={Isocyanide Ligands Promote Ligand-to-Metal Charge Transfer Excited States in a Rhenium(II) Complex}, volume={1}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.2c03193}, abstractNote={A metal-to-ligand charge transfer with mixed intraligand character is observed for the rhenium hexakisarylisocyanide complex [Re(CNAr)6]PF6 (CNAr = 2,6-dimethylphenylisocyanide, λmax = 300 nm). Upon oxidation to [Re(CNAr)6](PF6)2, the dominant low energy optical transition is a ligand-to-metal charge transfer (LMCT) mixed with intraligand transitions (λmax = 650 nm). TD-DFT was used to identify the participating ligand-based orbitals in the LMCT transition, revealing that the majority of the donor orbital is based on the aryl ring (85%) as opposed to the CN bond (14%). For both [Re(CNAr)6]+ and [Re(CNAr)6]2+, structural characterization by X-ray diffraction reveals deviations from Oh geometry at the central Re ion, with larger reduction in symmetry observed for Re(II). For [Re(CNAr)6]+, these structural changes lead to a broadening of the strong ν(C≡N) stretch (2065 cm-1), as the degeneracy of the T1u IR-active mode is broken. Furthermore, a shoulder is observed for this ν(C≡N) stretch, resulting from deviation of the C-N-Ar bond from linearity. By contrast, [Re(CNAr)6]2+ has two weak bands in the ν(C≡N) region (2065 and 2121 cm-1). DFT calculations indicate that reduction of symmetry at the central rhenium ion manifests in the decrease in intensity and the observed split of the ν(C≡N) band. Stability of both complexes are limited by light-induced decomposition where Re(I) dissociates a isocyanide ligand upon irradiation and Re(II) absorbance decays under ambient light. These data provide new insights to the electronic structure of [Re(CNAr)6]2+, enhancing our understanding of LMCT excited states and the versatility of isocyanide ligands.}, journal={INORGANIC CHEMISTRY}, author={Rodriguez, Tayliz M. and Deegbey, Mawuli and Chen, Chun-Hsing and Jakubikova, Elena and Dempsey, Jillian L.}, year={2023}, month={Jan} }
 @article{johnsen_deegbey_grills_polyansky_goldberg_jakubikova_mallouk_2023, title={Lewis Acids and Electron-Withdrawing Ligands Accelerate CO Coordination to Dinuclear Cu-I Compounds}, volume={62}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.3c01003}, abstractNote={A series of dinuclear molecular copper complexes were prepared and used to model the binding and Lewis acid stabilization of CO in heterogeneous copper CO2 reduction electrocatalysts. Experimental studies (including measurement of rate and equilibrium constants) and electronic structure calculations suggest that the key kinetic barrier for CO binding may be a σ-interaction between CuI and the incoming CO ligand. The rate of CO coordination can be increased upon the addition of Lewis acids or electron-withdrawing substituents on the ligand backbone. Conversely, Keq for CO coordination can be increased by adding electron density to the metal centers of the compound, consistent with stronger π-backbonding. Finally, the electrochemically measured kinetic results were mapped onto an electrochemical zone diagram to illustrate how these system changes enabled access to each zone.}, number={23}, journal={INORGANIC CHEMISTRY}, author={Johnsen, Walter D. and Deegbey, Mawuli and Grills, David C. and Polyansky, Dmitry E. and Goldberg, Karen I. and Jakubikova, Elena and Mallouk, Thomas E.}, year={2023}, month={May}, pages={9146–9157} }
 @article{lee_son_deegbey_woodhouse_hart_beissel_cesana_jakubikova_mccusker_schlau-cohen_2023, title={Observation of parallel intersystem crossing and charge transfer-state dynamics in [Fe(bpy)<sub>3</sub>]<SUP>2+</SUP> from ultrafast 2D electronic spectroscopy}, volume={14}, ISSN={["2041-6539"]}, DOI={10.1039/d3sc02613b}, abstractNote={Transition metal-based charge-transfer complexes represent a broad class of inorganic compounds with diverse photochemical applications. Charge-transfer complexes based on earth-abundant elements have been of increasing interest, particularly the canonical [Fe(bpy)3]2+. Photoexcitation into the singlet metal–ligand charge transfer (1MLCT) state is followed by relaxation first to the ligand-field manifold and then to the ground state. While these dynamics have been well-studied, processes within the MLCT manifold that facilitate and/or compete with relaxation have been more elusive. We applied ultrafast two-dimensional electronic spectroscopy (2DES) to disentangle the dynamics immediately following MLCT excitation of this compound. First, dynamics ascribed to relaxation out of the initially formed 1MLCT state was found to correlate with the inertial response time of the solvent. Second, the additional dimension of the 2D spectra revealed a peak consistent with a ∼20 fs 1MLCT → 3MLCT intersystem crossing process. These two observations indicate that the complex simultaneously undergoes intersystem crossing and direct conversion to ligand-field state(s). Resolution of these parallel pathways in this prototypical earth-abundant complex highlights the ability of 2DES to deconvolve the otherwise obscured excited-state dynamics of charge-transfer complexes.}, number={45}, journal={CHEMICAL SCIENCE}, author={Lee, Angela and Son, Minjung and Deegbey, Mawuli and Woodhouse, Matthew D. and Hart, Stephanie M. and Beissel, Hayden F. and Cesana, Paul T. and Jakubikova, Elena and McCusker, James K. and Schlau-Cohen, Gabriela S.}, year={2023}, month={Nov}, pages={13140–13150} }
 @article{amunugama_asempa_jakubikova_verani_2023, title={Probing the effect of nitro-substituents in the modulation of LUMO energies for directional electron transport through 4d(6) ruthenium(ii)-based metallosurfactants}, volume={8}, ISSN={["1477-9234"]}, DOI={10.1039/d3dt01797d}, abstractNote={Electron-withdrawing nitro-substituents were installed onto terpyridine- and phenanthroline-based metallosurfactants with 4d6 ruthenium(II), which were deposited as Langmuir-Blodgett monolayers aiming to study the feasibility of charge transport in Au|LB|Au junctions. The nitro groups are intended to modulate the energy of the frontier molecular orbitals to near to, or match that of Fermi levels in the gold electrodes. A series of heteroleptic metallosurfactants [RuII(C18OPh-terpy)(X-terpy)](PF6)2 and [RuII(C18OPh-terpy)(X-phen)Cl]PF6 were synthesized, where C18OPh-terpy is the 4'-[4-(octadecyloxy)phenyl]-2,2':6',2''-terpyridine amphiphile common to all species, X-terpy is a terpyridine with-H (1) or-phenyl-NO2 (2) and X-phen is a phenanthroline with-H (3) or-NO2 (4) groups. These metallosurfactants were characterized by experimental and computational methods, and the presence of nitro groups affect more affordable reductions at less negative potentials, as well as slightly more positive oxidations, these changes are less pronounced in species 2 than in 4. Species 1 and 2 showed limited Pockels-Langmuir and Langmuir-Blodgett film formation with lower collapse pressure of 27 mN m-1. In contrast, metallosurfactants 3 and 4 showed enhanced hydrophilicity indicated by higher collapse pressures of ca. 36 mN m-1. The LB monolayers of 3 and 4 were deposited on gold electrodes to form Au|LB|Au junctions and electron transport was measured as I/V curves. The NO2-bearing species 4 showed asymmetric curves associated with directional electron transport with amplitudes up to -2.0 nA and rectification ratios from 5 to 26 between -1 to +1 V and from 3 to 14 between -3 to +3 V.}, journal={DALTON TRANSACTIONS}, author={Amunugama, Samudra and Asempa, Eyram and Jakubikova, Elena and Verani, Claudio N.}, year={2023}, month={Aug} }
 @article{ghosh_braley_ezhov_worster_valdez-moreira_losovyj_jakubikova_pushkar_smith_2022, title={A Spectroscopically Observed Iron Nitrosyl Intermediate in the Reduction of Nitrate by a Surface-Conjugated Electrocatalyst}, volume={9}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.2c03487}, abstractNote={We report an iron-based graphite-conjugated electrocatalyst (GCC-FeDIM) that combines the well-defined nature of homogeneous molecular electrocatalysts with the robustness of a heterogeneous electrode. A suite of spectroscopic methods, supported by the results of DFT calculations, reveals that the electrode surface is functionalized by high spin (S = 5/2) Fe(III) ions in an FeN4Cl2 coordination environment. The chloride ions are hydrolyzed in aqueous solution, with the resulting cyclic voltammogram revealing a Gaussian-shaped wave assigned to 1H+/1e- reduction of surface Fe(III)-OH surface. A catalytic wave is observed in the presence of NO3-, with an onset potential of -1.1 V vs SCE. At pH 6.0, GCC-FeDIM rapidly reduces NO3- to ammonium and nitrite with 88 and 6% Faradaic efficiency, respectively. Mechanistic studies, including in situ X-ray absorption spectroscopy, suggest that electrocatalytic NO3- reduction involves an iron nitrosyl intermediate. The Fe-N bond length (1.65 Å) is similar to that observed in {Fe(NO)}6 complexes, which is supported by the results of DFT calculations.}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Ghosh, Moumita and Braley, Sarah E. and Ezhov, Roman and Worster, Harrison and Valdez-Moreira, Juan A. and Losovyj, Yaroslav and Jakubikova, Elena and Pushkar, Yulia N. and Smith, Jeremy M.}, year={2022}, month={Sep} }
 @article{braley_kwon_xu_dalton_jakubikova_smith_2022, title={Buffer Assists Electrocatalytic Nitrite Reduction by a Cobalt Macrocycle Complex}, volume={8}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.2c00909}, abstractNote={This work reports a combined experimental and computational study of the activation of an otherwise catalytically inactive cobalt complex, [Co(TIM)Br2]+, for aqueous nitrite reduction. The presence of phosphate buffer leads to efficient electrocatalysis, with rapid reduction to ammonium occurring close to the thermodynamic potential and with high Faradaic efficiency. At neutral pH, increasing buffer concentrations increase catalytic current while simultaneously decreasing overpotential, although high concentrations have an inhibitory effect. Controlled potential electrolysis and rotating ring-disk electrode experiments indicate that ammonium is directly produced from nitrite by [Co(TIM)Br2]+, along with hydroxylamine. Mechanistic investigations implicate a vital role for the phosphate buffer, specifically as a proton shuttle, although high buffer concentrations inhibit catalysis. These results indicate a role for buffer in the design of electrocatalysts for nitrogen oxide conversion.}, journal={INORGANIC CHEMISTRY}, author={Braley, Sarah E. and Kwon, Hyuk-Yong and Xu, Song and Dalton, Evan Z. and Jakubikova, Elena and Smith, Jeremy M.}, year={2022}, month={Aug} }
 @article{amunugama_asempa_tripathi_wanniarachchi_baydoun_hoffmann_jakubikova_verani_2022, title={Electron transport through a (terpyridine) ruthenium metallo-surfactant containing a redox-active aminocatechol derivative}, volume={5}, ISSN={["1477-9234"]}, DOI={10.1039/d2dt00938b}, abstractNote={Aiming to develop a new class of metallosurfactants with unidirectional electron transfer properties, a (terpyridine) ruthenium complex containing a semiquinone derivative L2, namely [RuIII(Lterpy)(L2)Cl]PF6 (1), was synthesized and structurally characterized as a solid and in solution. The electronic and redox behaviour of 1 was studied experimentally as well as by means of DFT methods, and is indicative of significant orbital mixing and overlap between metal and ligands. The complex forms stable Pockels-Langmuir films at the air-water interface and allows for the formation of thin films onto gold electrodes to prepare nanoscale Au|LB 1|Au junctions for current-voltage (I/V) analysis. Complex 1 shows asymmetric electron transfer with a maximum rectification ratio of 32 based on tunnelling through MOs of the aminocatechol derivative.}, journal={DALTON TRANSACTIONS}, author={Amunugama, Samudra and Asempa, Eyram and Tripathi, Ramesh Chandra and Wanniarachchi, Dakshika and Baydoun, Habib and Hoffmann, Peter and Jakubikova, Elena and Verani, Claudio N.}, year={2022}, month={May} }
 @article{curtin_jakubikova_2022, title={Extended pi-Conjugated Ligands Tune Excited-State Energies of Iron(II) Polypyridine Dyes}, volume={11}, ISSN={["1520-510X"]}, url={https://doi.org/10.1021/acs.inorgchem.2c02362}, DOI={10.1021/acs.inorgchem.2c02362}, abstractNote={Over the past decade, iron(II) polypyridines have gained a lot of attention as potential chromophores and sensitizers due to the low cost and high abundance of iron. Unfortunately, most iron(II) polypyridines are poor chromophores since their initially excited, photoactive metal-to-ligand charge transfer (MLCT) states quickly decay into non-photoactive metal-centered (MC) states. Many strategies to increase their lifetime have been pursued, built mainly around increasing the ligand field strength of these complexes and thus destabilizing the MC states. In this work, we aim to design a new class of Fe(II) complexes by stabilizing the energies of their MLCT states. To this end, we employ density functional theory (DFT) and time-dependent DFT to investigate a series of Fe(II) complexes, [Fe(L/X)2,4(N^N)]2+/2- where L/X represents either cyanide, isocyanide, or bipyridine ligands and N̂N stands for bidentate-extended π-conjugated ligands derived from the bipyridine. The L/X ligands tune the energetics of the Fe-based t2g molecular orbitals, while the amount of π-conjugation on the N^N ligand impacts the energies of its π and π* orbitals, thus tuning the energetics of the MLCT and the ligand-centered (LC) states. Overall, our results suggest that the use of N^N ligands with the extended π-conjugation is a viable strategy to tune the relative energies of MLCT, LC, and MC states.}, journal={INORGANIC CHEMISTRY}, author={Curtin, Gregory M. and Jakubikova, Elena}, year={2022}, month={Nov} }
 @article{turner_breen_kosgei_crandall_curtin_jakubikova_ryan m. o'donnell_ziegler_rack_2022, title={Manipulating Excited State Properties of Iridium Phenylpyridine Complexes with ?Push-Pull? Substituents}, volume={11}, ISSN={["1520-510X"]}, url={https://doi.org/10.1021/acs.inorgchem.2c02269}, DOI={10.1021/acs.inorgchem.2c02269}, abstractNote={We have prepared a series of complexes of the type [IrIII(ppy)2(L]n+ complexes (1-4), where ppy is a substituted 2-phenylpyridine and L is a chelating phosphine thioether ligand. The parent complex (1) comprises an unsubstituted phenylpyridine ligand, whereas complex 2 contains a nitro substituent on the pyridine ring, complex 3 features a diphenylamine group on the phenyl ring, and 4 has both nitro and diphenylamine groups. Crystallographic, 1H NMR, and elemental analysis data are consistent with each of the chemical formulae. DFT (density functional theory) computational results show a complicated electronic structure with contributions from Ir, ppy, and the PS ligand. Ultrafast pump-probe data show strong contributions from the phenylpyridine moieties as well as strong panchromatic excited state absorption transitions. The data show that nitro and/or diphenylamine substituents dominate the spectroscopy of this series of compounds.}, journal={INORGANIC CHEMISTRY}, author={Turner, Emigdio E. and Breen, Douglas J. and Kosgei, Gilbert and Crandall, Laura A. and Curtin, Gregory M. and Jakubikova, Elena and Ryan M. O'Donnell and Ziegler, Christopher J. and Rack, Jeffrey J.}, year={2022}, month={Nov} }
 @article{marshburn_ashley_curtin_sultana_liu_vinueza_ison_jakubikova_2021, title={Are all charge-transfer parameters created equally? A study of functional dependence and excited-state charge-transfer quantification across two dye families}, volume={8}, ISSN={["1463-9084"]}, url={https://doi.org/10.1039/D1CP03383B}, DOI={10.1039/d1cp03383b}, abstractNote={Small molecule organic dyes have many potential uses in medicine, textiles, forensics, and light-harvesting technology. Being able to computationally predict the spectroscopic properties of these dyes could greatly expedite screening efforts, saving time and materials. Time-dependent density functional theory (TD-DFT) has been shown to be a good tool for this in many instances, but characterizing electronic excitations with charge-transfer (CT) character has historically been challenging and can be highly sensitive to the chosen exchange-correlation functional. Here we present a combined experimental and computational study of the excited-state electronic structure of twenty organic dyes obtained from the Max Weaver Dye Library at NCSU. Results of UV-vis spectra calculations on these dyes with six different exchange-correlation functionals, BP86, B3LYP, PBE0, M06, BH and HLYP, and CAM-B3LYP, were compared against their measured UV-vis spectra. It was found that hybrid functionals with modest amounts (20-30%) of included Hartree-Fock exchange are the most effective at matching the experimentally determined λmax. The interplay between the observed error, the functional chosen, and the degree of CT was analyzed by quantifying the CT character of λmax using four orbital and density-based metrics, Λ, Δr, SC and DCT, as well as the change in the dipole moment, Δμ. The results showed that the relationship between CT character and the functional dependence of error is not straightforward, with the observed behavior being dependent both on how CT was quantified and the functional groups present in the molecules themselves. It is concluded that this may be a result of the examined excitations having intermediate CT character. Ultimately it was found that the nature of the molecular "family" influenced how a given functional behaved as a function of CT character, with only two of the examined CT quantification methods, Δr and DCT, showing consistent behavior between the different molecular families. This suggests that further work needs to be done to ensure that currently used CT quantification methods show the same general trends across large sets of multiple dye families.}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, publisher={Royal Society of Chemistry (RSC)}, author={Marshburn, Richard Drew and Ashley, Daniel C. and Curtin, Gregory M. and Sultana, Nadia and Liu, Chang and Vinueza, Nelson R. and Ison, Elon A. and Jakubikova, Elena}, year={2021}, month={Aug} }
 @article{morrow_kwon_kelley_jakubikova_2021, title={Efficient Approximation of Potential Energy Surfaces with Mixed-Basis Interpolation}, volume={17}, ISSN={["1549-9626"]}, url={https://doi.org/10.1021/acs.jctc.1c00569}, DOI={10.1021/acs.jctc.1c00569}, abstractNote={The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in modern chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as stable conformers (local minima) and transition states (first-order saddle points) connected by a minimum-energy path. Our group has previously produced surrogate reduced-dimensional PESs using sparse interpolation along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. These surrogates used a single interpolation basis, either polynomials or trigonometric functions, in every dimension. However, relevant molecular dynamics (MD) simulations often involve some combination of both periodic and nonperiodic coordinates. Using a trigonometric basis on nonperiodic coordinates, such as bond lengths, leads to inaccuracies near the domain boundary. Conversely, polynomial interpolation on the periodic coordinates does not enforce the periodicity of the surrogate PES gradient, leading to nonconservation of total energy even in a microcanonical ensemble. In this work, we present an interpolation method that uses trigonometric interpolation on the periodic reaction coordinates and polynomial interpolation on the nonperiodic coordinates. We apply this method to MD simulations of possible isomerization pathways of azomethane between cis and trans conformers. This method is the only known interpolative method that appropriately conserves total energy in systems with both periodic and nonperiodic reaction coordinates. In addition, compared to all-polynomial interpolation, the mixed basis requires fewer electronic structure calculations to obtain a given level of accuracy, is an order of magnitude faster, and is freely available on GitHub.}, number={9}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, publisher={American Chemical Society (ACS)}, author={Morrow, Zachary and Kwon, Hyuk-Yong and Kelley, C. T. and Jakubikova, Elena}, year={2021}, month={Sep}, pages={5673–5683} }
 @article{kwon_braley_madriaga_smith_jakubikova_2021, title={Electrocatalytic nitrate reduction with Co-based catalysts: comparison of DIM, TIM and cyclam ligands}, volume={8}, ISSN={["1477-9234"]}, DOI={10.1039/d1dt02175c}, abstractNote={Over the past century, the global concentration of environmental nitrate has increased significantly from human activity, which has resulted in the contamination of drinking water and aquatic hypoxia around the world, so the development of effective nitrate-reducing agents is urgent. This work compares three potential macrocycle-based nitrate reduction electrocatalysts: [Co(DIM)]3+, [Co(cyclam)]3+ and [Co(TIM)]3+. Although all three complexes have similar structures, only [Co(DIM)]3+ has been experimentally determined to be an active electrocatalyst for selective nitrate reduction to produce ammonia in water. While [Co(cyclam)]3+ can reduce aqueous nitrate to ammonia and hydroxylamine at heavy metal electrodes, [Co(TIM)]3+ is inactive for the reduction of nitrate. As an initial step to understanding what structural and electronic properties are important for efficient electrocatalysts for nitrate reduction, density functional theory (DFT) was employed to investigate the electronic structure of the three Co complexes, with the reduction potentials calibrated to experimental results. Moreover, DFT was employed to explore four different reaction mechanisms for the first steps of nitrate reduction. The calculated reaction barriers reveal how a combination of electron transfer in a redox non-innocent complex, substrate binding, and intramolecular hydrogen bonding dictates the activity of Co-based catalysts toward nitrate reduction.}, journal={DALTON TRANSACTIONS}, author={Kwon, Hyuk-Yong and Braley, Sarah E. and Madriaga, Jose P. and Smith, Jeremy M. and Jakubikova, Elena}, year={2021}, month={Aug} }
 @article{braley_ashley_kulesa_jakubikova_smith_2021, title={Electrode-adsorption activates trans-[Cr(cyclam)Cl-2](+) for electrocatalytic nitrate reduction (vol 56, pg 603, 2020)}, volume={57}, ISSN={["1364-548X"]}, DOI={10.1039/d1cc90148f}, abstractNote={Correction for 'Electrode-adsorption activates trans-[Cr(cyclam)Cl2]+ for electrocatalytic nitrate reduction' by Sarah E. Braley et al., Chem. Commun., 2020, 56, 603-606, DOI: 10.1039/C9CC08550E.}, number={35}, journal={CHEMICAL COMMUNICATIONS}, author={Braley, Sarah E. and Ashley, Daniel C. and Kulesa, Krista M. and Jakubikova, Elena and Smith, Jeremy M.}, year={2021}, month={May}, pages={4332–4332} }
 @article{vittardi_magar_schrage_ziegler_jakubikova_rack_2021, title={Evidence for a lowest energy 3MLCT excited state in [Fe(tpy)(CN)3]−}, volume={57}, ISSN={1359-7345 1364-548X}, url={http://dx.doi.org/10.1039/d1cc01090e}, DOI={10.1039/d1cc01090e}, abstractNote={Transient absorption data of [FeII(tpy)(CN)3]- reveals spectroscopic signatures indicative of 3MLCT with a ∼10 ps kinetic component. These data are supported by DFT and TD-DFT calculations, which show that excited state ordering is responsive to the number of cyanide ligands on the complex.}, number={38}, journal={Chemical Communications}, publisher={Royal Society of Chemistry (RSC)}, author={Vittardi, Sebastian B. and Magar, Rajani Thapa and Schrage, Briana R. and Ziegler, Christopher J. and Jakubikova, Elena and Rack, Jeffrey J.}, year={2021}, pages={4658–4661} }
 @article{kwon_ashley_jakubikova_2021, title={Halogenation affects driving forces, reorganization energies and "rocking" motions in strained [Fe(tpy)(2)](2+) complexes}, volume={9}, ISSN={["1477-9234"]}, DOI={10.1039/d1dt02314d}, abstractNote={Controlling the energetics of spin crossover (SCO) in Fe(II)-polypyridine complexes is critical for designing new multifunctional materials or tuning the excited-state lifetimes of iron-based photosensitizers. It is well established that the Fe-N "breathing" mode is important for intersystem crossing from the singlet to the quintet state, but this does not preclude other, less obvious, structural distortions from affecting SCO. Previous work has shown that halogenation at the 6 and 6'' positions of tpy (tpy = 2,2';6',2''-terpyridine) in [Fe(tpy)2]2+ dramatically increased the lifetime of the excited MLCT state and also had a large impact on the ground state spin-state energetics. To gain insight into the origins of these effects, we used density functional theory calculations to explore how halogenation impacts spin-state energetics and molecular structure in this system. Based on previous work we focused on the ligand "rocking" motion associated with SCO in [Fe(tpy)2]2+ by constructing one-dimensional potential energy surfaces (PESs) along the tpy rocking angle for various spin states. It was found that halogenation has a clear and predictable impact on ligand rocking and spin-state energetics. The rocking is correlated to numerous other geometrical distortions, all of which likely affect the reorganization energies for spin-state changes. We have quantified trends in reorganization energy and also driving force for various spin-state changes and used them to interpret the experimentally measured excited-state lifetimes.}, journal={DALTON TRANSACTIONS}, author={Kwon, Hyuk-Yong and Ashley, Daniel C. and Jakubikova, Elena}, year={2021}, month={Sep} }
 @article{kwon_morrow_kelley_jakubikova_2021, title={Interpolation Methods for Molecular Potential Energy Surface Construction}, volume={125}, ISSN={["1520-5215"]}, url={https://doi.org/10.1021/acs.jpca.1c06812}, DOI={10.1021/acs.jpca.1c06812}, abstractNote={The concept of a potential energy surface (PES) is one of the most important concepts in modern chemistry. A PES represents the relationship between the chemical system's energy and its geometry (i.e., atom positions) and can provide useful information about the system's chemical properties and reactivity. Construction of accurate PESs with high-level theoretical methodologies, such as density functional theory, is still challenging due to a steep increase in the computational cost with the increase of the system size. Thus, over the past few decades, many different mathematical approaches have been applied to the problem of the cost-efficient PES construction. This article serves as a short overview of interpolative methods for the PES construction, including global polynomial interpolation, trigonometric interpolation, modified Shepard interpolation, interpolative moving least-squares, and the automated PES construction derived from these.}, number={45}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, publisher={American Chemical Society (ACS)}, author={Kwon, Hyuk-Yong and Morrow, Zachary and Kelley, C. T. and Jakubikova, Elena}, year={2021}, month={Nov}, pages={9725–9735} }
 @article{morrow_kwon_kelley_jakubikova_2021, title={Reduced-dimensional surface hopping with offline-online computations}, volume={8}, ISSN={["1463-9084"]}, url={https://doi.org/10.1039/D1CP03446D}, DOI={10.1039/d1cp03446d}, abstractNote={Molecular dynamics simulations often classically evolve the nuclear geometry on adiabatic potential energy surfaces (PESs), punctuated by random hops between energy levels in regions of strong coupling, in an algorithm known as surface hopping. However, the computational expense of integrating the geometry on a full-dimensional PES and computing the required couplings can quickly become prohibitive as the number of atoms increases. In this work, we describe a method for surface hopping that uses only important reaction coordinates, performs all expensive evaluations of the true PESs and couplings only once before simulating dynamics (offline), and then queries the stored values during the surface hopping simulation (online). Our Python codes are freely available on GitHub. Using photodissociation of azomethane as a test case, this method is able to reproduce experimental results that have thus far eluded ab initio surface hopping studies.}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, publisher={Royal Society of Chemistry (RSC)}, author={Morrow, Zachary and Kwon, Hyuk-Yong and Kelley, C. T. and Jakubikova, Elena}, year={2021}, month={Aug} }
 @article{shaikh_ilic_gibbons_yang_jakubikova_morris_2021, title={Role of a 3D Structure in Energy Transfer in Mixed-Ligand Metal-Organic Frameworks}, volume={125}, ISSN={["1932-7455"]}, DOI={10.1021/acs.jpcc.1c06427}, abstractNote={We present a detailed investigation of the photophysical properties of mixed-ligand pyrene- and porphyrin-based metal–organic frameworks (MOFs) as a function of their 3D structure. Solvothermal reactions between metal salts (InCl3, Zr(acac)4, and ZrCl4) and suitable ratios of 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy) and meso-tetrakis(4-carboxyphenyl)porphyrin (TCPP) were performed to prepare a series of mixed-ligand ROD-7, NU-901, and NU-1000 MOFs. Time-resolved and steady-state fluorescence measurements were conducted on the mixed-ligand MOFs to study their photophysics. Based on the results, we concluded that upon excitation of TBAPy linkers in the MOFs, singlet excitation energy migrates across TBAPy linkers until it finds a TCPP unit. TCPP acts as an energy trap and quenches the excitation. The efficiency of TBAPy-to-TBAPy energy transfer was found to be sensitive to the structural parameters of MOFs. Analysis of steady-state and time-resolved fluorescence data revealed that excitation energy transfer (EET) is most efficient in ROD-7, followed by NU-901 and NU-1000. We propose that topology that invokes the shorter interchromophoric distances between TBAPy linkers in ROD-7 is responsible for its higher EET efficiency. The distance dependence of the EET rate constant (kEET) was investigated to gain insight into the mechanistic aspects of energy transfer in MOFs. This study revealed that (a) energy transfer in MOFs deviates from the classical Förster model and (b) the geometrical arrangement of linkers influences the mechanism of EET in MOFs. A theoretical investigation was also performed to determine energy-transfer rate constants along different directions and assess the directionality of energy transfer in these MOFs. The magnitude of rate constants indicated that energy transfer in ROD-7 should be highly anisotropic along the stacking direction. These findings suggest that ROD-7 is a promising candidate to play the role of the light-harvesting and energy-transfer component in solar energy conversion devices, where directional energy transfer is required.}, number={42}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Shaikh, Shaunak M. and Ilic, Stefan and Gibbons, Bradley J. and Yang, Xiaozhou and Jakubikova, Elena and Morris, Amanda J.}, year={2021}, month={Oct}, pages={22998–23010} }
 @article{rodriguez_deegbey_jakubikova_dempsey_2021, title={The ligand-to-metal charge transfer excited state of [Re(dmpe)(3)](2+)}, volume={7}, ISSN={["1573-5079"]}, DOI={10.1007/s11120-021-00859-7}, journal={PHOTOSYNTHESIS RESEARCH}, author={Rodriguez, Tayliz M. and Deegbey, Mawuli and Jakubikova, Elena and Dempsey, Jillian L.}, year={2021}, month={Jul} }
 @article{braley_ashley_jakubikova_smith_2020, title={Electrode-adsorption activates trans-[Cr(cyclam)Cl-2](+) for electrocatalytic nitrate reduction}, volume={56}, ISSN={["1364-548X"]}, DOI={10.1039/c9cc08550e}, abstractNote={Cyclic voltammetry reveals that aqueous trans-[Cr(cyclam)Cl2]+ is reversibly reduced at a mercury electrode, with a small prewave suggesting an adsorptive interaction between the complex and electrode surface. A catalytic current is observed in the presence of excess nitrate, with the onset potential for catalysis at the prewave. Nitrate is electrocatalytically reduced to nitrite, with preliminary mechanistic investigations implicating a chromium oxo intermediate.}, number={4}, journal={CHEMICAL COMMUNICATIONS}, author={Braley, Sarah E. and Ashley, Daniel C. and Jakubikova, Elena and Smith, Jeremy M.}, year={2020}, month={Jan}, pages={603–606} }
 @article{tichnell_miller_liu_mukherjee_jakubikova_mccusker_2020, title={Influence of Electrolyte Composition on Ultrafast Interfacial Electron Transfer in Fe-Sensitized TiO2-Based Solar Cells}, volume={124}, ISSN={["1932-7455"]}, DOI={10.1021/acs.jpcc.9b09404}, abstractNote={TiO2-based dye-sensitized solar cells employing Fe(2,2′-bipyridine-4,4′-dicarboxylic acid)2(CN)2 (F2CA) have been studied by spectroscopic, electrochemical, photoelectrochemical, time-resolved spec...}, number={3}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Tichnell, Christopher R. and Miller, Jennifer N. and Liu, Chang and Mukherjee, Sriparna and Jakubikova, Elena and McCusker, James K.}, year={2020}, month={Jan}, pages={1794–1811} }
 @article{liu_batista_aguirre_yang_cawkwell_jakubikova_2020, title={SCC-DFTB Parameters for Fe-C Interactions}, volume={124}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.0c08202}, abstractNote={We present an optimized density-functional tight-binding (DFTB) parameterization for iron-based complexes based on the popular trans3d set of parameters. The transferability of the original and optimized parameterizations is assessed using a set of 50 iron complexes, which include carbonyl, cyanide, polypyridine, and cyclometalated ligands. DFTB-optimized structures predicted using the trans3d parameters show a good agreement with both experimental crystal geometries and density functional theory (DFT)-optimized structures for Fe-N bond lengths. Conversely, Fe-C bond lengths are systematically overestimated. We improve the accuracy of Fe-C interactions by truncating the Fe-O repulsive potential and reparameterizing the Fe-C repulsive potential using a training set of six isolated iron complexes. The new trans3d*-LANLFeC parameter set can produce accurate Fe-C bond lengths in both geometry optimizations and molecular dynamics (MD) simulations, without significantly affecting the accuracy of Fe-N bond lengths. Moreover, the potential energy curves of Fe-C interactions are considerably improved. This improved parameterization may open the door to accurate MD simulations at the DFTB level of theory for large systems containing iron complexes, such as sensitizer-semiconductor assemblies in dye-sensitized solar cells, that are not easily accessible with DFT approaches because of the large number of atoms.}, number={46}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Liu, Chang and Batista, Enrique R. and Aguirre, Nestor F. and Yang, Ping and Cawkwell, M. J. and Jakubikova, Elena}, year={2020}, month={Nov}, pages={9674–9682} }
 @article{labrum_curtin_jakubikova_caulton_2020, title={The Influence of Nucleophilic and Redox Pincer Character as well as Alkali Metals on the Capture of Oxygen Substrates: The Case of Chromium(II)}, volume={26}, ISSN={["1521-3765"]}, url={https://doi.org/10.1002/chem.202000457}, DOI={10.1002/chem.202000457}, abstractNote={Dimeric [CrL] 2 , where L is the conjugate base of bis -pyrazolyl pyridine, is evaluated for its ability to undergo inner sphere and outer sphere redox chemistry. It reacts with Cp 2 Fe + to give the surprising [Cr 4 (HL) 4 (μ 4 -O)] 2+ , still containing divalent Cr. Reduction (KC 8 ) of [CrL] 2 by 2 electrons gives [K 2 (THF) 3 Cr 3 L 3 (μ 3 -O)], and by 4 electrons gives [K 4 (THF) 10 Cr 2 L 2 (μ-O)], each of which has scavenged (hydr)oxide from glass surface because of the electrophilicity of the underligated Cr. The remarkable [K 4 (THF) 10 Cr 2 L 2 (μ-O)], is shown by comprehensive DFT calculations and analysis of intra-ligand bond lengths to contain a pyridyl radical L 3- and Cr II , illustrating that this pincer is proton-responsive, redox active, and a versatile donor to associated K + ions here. The K + electrophiles interact with electron rich oxo, but do not significantly (> 5 kcal/mol) alter spin state energies. Inner sphere oxidation of [CrL] 2 with a quinone gives [Cr 2 L 2 (semiquinone) 2 ], while pre-reduced [CrL] 2 2- reacts with quinone to give [K 3 (THF) 3 Cr 2 L 2 (catecholate) 2 (μ-OH)], a product of capture of two undercoordinated LCr(catecholate) 1- by hydroxide.}, number={43}, journal={CHEMISTRY-A EUROPEAN JOURNAL}, publisher={Wiley}, author={Labrum, Nicholas S. and Curtin, Gregory M. and Jakubikova, Elena and Caulton, Kenneth G.}, year={2020}, month={Aug}, pages={9547–9555} }
 @article{morrow_liu_kelley_jakubikova_2019, title={Approximating Periodic Potential Energy Surfaces with Sparse Trigonometric Interpolation}, volume={123}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/acs.jpcb.9b08210}, DOI={10.1021/acs.jpcb.9b08210}, abstractNote={The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in computational chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as local minima, maxima, and transition states. Construction of full-dimensional PESs for molecules with more than ten atoms is computationally expensive and often not feasible. Previous work in our group used sparse interpolation with polynomial basis functions to construct a surrogate reduced-dimensional PESs along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. However, polynomial interpolation does not preserve the periodicity of the PES gradient with respect to angular components of geometry, such as torsion angles, which can lead to nonphysical phenomena. In this work, we construct a surrogate PES using trigonometric basis functions, for a system where the selected reaction coordinates all correspond to the torsion angles, resulting in a periodically repeating PES. We find that a trigonometric interpolation basis not only guarantees periodicity of the gradient, but also results in slightly lower approximation error than polynomial interpolation.}, number={45}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Morrow, Zack and Liu, Chang and Kelley, C. T. and Jakubikova, Elena}, year={2019}, month={Oct}, pages={9677–9684} }
 @article{ashley_mukherjee_jakubikova_2019, title={Designing air-stable cyclometalated Fe(II) complexes: stabilization via electrostatic effects}, volume={48}, ISSN={["1477-9234"]}, DOI={10.1039/c8dt04402c}, abstractNote={Designing efficient Fe(ii) chromophores requires optimization of numerous, at times conflicting, properties. It has been suggested that replacement of polypyridine ligands with cyclometalated analogs will be effective at destabilizing the quintet state and therefore extending the lifetime of photoactive metal-to-ligand charge transfer states. However, cyclometalated Fe(ii) complexes are not oxidatively stable due to the strong electron-donating nature of this ligand, which limits their applicability. Here we use density functional theory calculations to show how simple addition of nitro and carboxylic acid groups to these cyclometalated complexes can engender a less oxidizable Fe(ii) center while maintaining, or even improving, the favorable ligand field strength.}, number={2}, journal={Dalton Transactions}, author={Ashley, D.C. and Mukherjee, S. and Jakubikova, E.}, year={2019}, pages={374–378} }
 @article{xu_kwon_ashley_chen_jakubikova_smith_2019, title={Intramolecular Hydrogen Bonding Facilitates Electrocatalytic Reduction of Nitrite in Aqueous Solutions}, volume={58}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.9b01274}, abstractNote={This work reports a combined experimental and computational mechanistic investigation into the electrocatalytic reduction of nitrite to ammonia by a cobalt macrocycle in an aqueous solution. In the presence of a nitrite substrate, the Co(III) precatalyst, [Co(DIM)(NO2)2]+ (DIM = 2,3-dimethyl-1,4,8,11-tetraazacyclotetradeca-1,3-diene), is formed in situ. Cyclic voltammetry and density functional theory (DFT) calculations show that this complex is reduced by two electrons, the first of which is coupled with nitrite ligand loss, to provide the active catalyst. Experimental observations suggest that the key N-O bond cleavage step is facilitated by intramolecular proton transfer from an amine group of the macrocycle to a nitro ligand, as supported by modeling several potential reaction pathways with DFT. These results provide insights into how the combination of a redox active ligand and first-row transition metal can facilitate the multiproton/electron process of nitrite reduction.}, number={14}, journal={INORGANIC CHEMISTRY}, author={Xu, Song and Kwon, Hyuk-Yong and Ashley, Daniel C. and Chen, Chun-Hsing and Jakubikova, Elena and Smith, Jeremy M.}, year={2019}, month={Jul}, pages={9443–9451} }
 @article{datko_livshits_zhang_qin_jakubikova_rack_grey_2019, title={Large Excited-State Conformational Displacements Expedite Triplet Formation in a Small Conjugated Oligomer}, volume={10}, ISSN={["1948-7185"]}, DOI={10.1021/acs.jpclett.9b00495}, abstractNote={Intersystem crossing in conjugated organic molecules is most conveniently viewed from pure electronic perspectives; yet, vibrational displacements may often drive these transitions. We investigate an alkyl-substituted thienylene-vinylene dimer (dTV) displaying efficient triplet formation. Steady-state electronic and Raman spectra display large Stokes shifts (∼4000 cm-1) involving high-frequency skeletal symmetric stretching modes (∼900-1600 cm-1) in addition to large displacements of low-frequency torsional motions (∼300-340 cm-1). Transient absorption spectroscopy reveals the emergence of distorted singlet (S1) and triplet signatures following initial vibrational relaxation dynamics that dominate spectral dynamics on time scales > 100 ps, with the latter persisting on time scales up to ca. 7 μs. Potential energy surfaces calculated along the dominant displaced out-of-plane torsional mode reveal shallow energy barriers for entering the triplet manifold from S1. We propose that dTV is a good model system for understanding vibrational contributions to intersystem crossing events in related polymer systems.}, number={6}, journal={JOURNAL OF PHYSICAL CHEMISTRY LETTERS}, author={Datko, Benjamin D. and Livshits, Maksim and Zhang, Zhen and Qin, Yang and Jakubikova, Elena and Rack, Jeffrey J. and Grey, John K.}, year={2019}, month={Mar}, pages={1259–1263} }
 @article{liu_kelley_jakubikova_2019, title={Molecular Dynamics Simulations on Relaxed Reduced-Dimensional Potential Energy Surfaces}, volume={123}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/acs.jpca.9b02298}, DOI={10.1021/acs.jpca.9b02298}, abstractNote={Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensional PESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard microcanonical (NVE) and canonical (NVT) MD simulations. The method is applied to the pyramidal inversion of a NH3 molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.}, number={21}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={Liu, Chang and Kelley, C. T. and Jakubikova, Elena}, year={2019}, month={Apr}, pages={4543–4554} }
 @article{ashley_jakubikova_2019, title={Predicting the electrochemical behavior of Fe(II) complexes from ligand orbital energies}, volume={376}, ISSN={["1010-6030"]}, DOI={10.1016/j.jphotochem.2019.01.026}, abstractNote={Abstract An attractive strategy for harvesting solar energy is to use dye-sensitized solar cells employing earth-abundant Fe(II) chromophores. These dyes need to meet several criteria to be effective for this purpose, including air stability, and an ability to be regenerated by common electrolytes. Both of these properties are related to the Fe(III/II) reduction potentials. Here we show how the Fe(III/II) reduction potentials of Fe(II) complexes can be estimated from a single experimental Fe(III/II) reduction potential and computationally cheap calculations on single isolated ligands. This method requires refinement, but could prove highly useful for large-scale computational screening and design of Fe(II) dyes.}, journal={JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY}, author={Ashley, Daniel C. and Jakubikova, Elena}, year={2019}, month={May}, pages={7–11} }
 @article{britz_gawelda_assefa_jamula_yarranton_galler_khakhulin_diez_hardee_doumy_et al._2019, title={Using Ultrafast X-ray Spectroscopy To Address Questions in Ligand-Field Theory: The Excited State Spin and Structure of [Fe(dcpp)(2)](2+)}, volume={58}, ISBN={1520-510X}, DOI={10.1021/acs.inorgchem.9b01063}, abstractNote={We have employed a range of ultrafast X-ray spectroscopies in an effort to characterize the lowest energy excited state of [Fe(dcpp)2]2+ (where dcpp is 2,6-(dicarboxypyridyl)pyridine). This compound exhibits an unusually short excited-state lifetime for a low-spin Fe(II) polypyridyl complex of 270 ps in a room-temperature fluid solution, raising questions as to whether the ligand-field strength of dcpp had pushed this system beyond the 5T2/3T1 crossing point and stabilizing the latter as the lowest energy excited state. Kα and Kβ X-ray emission spectroscopies have been used to unambiguously determine the quintet spin multiplicity of the long-lived excited state, thereby establishing the 5T2 state as the lowest energy excited state of this compound. Geometric changes associated with the photoinduced ligand-field state conversion have also been monitored with extended X-ray absorption fine structure. The data show the typical average Fe-ligand bond length elongation of ∼0.18 Å for a 5T2 state and suggest a high anisotropy of the primary coordination sphere around the metal center in the excited 5T2 state, in stark contrast to the nearly perfect octahedral symmetry that characterizes the low-spin 1A1 ground state structure. This study illustrates how the application of time-resolved X-ray techniques can provide insights into the electronic structures of molecules-in particular, transition metal complexes-that are difficult if not impossible to obtain by other means.}, number={14}, journal={INORGANIC CHEMISTRY}, author={Britz, Alexander and Gawelda, Wojciech and Assefa, Tadesse A. and Jamula, Lindsey L. and Yarranton, Jonathan T. and Galler, Andreas and Khakhulin, Dmitry and Diez, Michael and Hardee, Manuel and Doumy, Gilles and et al.}, year={2019}, pages={9341–9350} }
 @article{xu_ashley_kwon_ware_chen_losovyj_gao_jakubikova_smith_2018, title={A flexible, redox-active macrocycle enables the electrocatalytic reduction of nitrate to ammonia by a cobalt complex}, volume={9}, ISSN={["2041-6539"]}, DOI={10.1039/c8sc00721g}, abstractNote={Mechanistic investigations into electrocatalytic nitrate reduction by a cobalt complex reveal the critical role played by the flexible, redox-active ligand.}, number={22}, journal={CHEMICAL SCIENCE}, author={Xu, Song and Ashley, Daniel C. and Kwon, Hyuk-Yong and Ware, Gabrielle R. and Chen, Chun-Hsing and Losovyj, Yaroslav and Gao, Xinfeng and Jakubikova, Elena and Smith, Jeremy M.}, year={2018}, month={Jun}, pages={4950–4958} }
 @article{mukherjee_liu_jakubikova_2018, title={Comparison of Interfacial Electron Transfer Efficiency in [Fe(ctpy)(2)](2+)-TiO2 and [Fe(cCNC)(2)](2+)-TiO2 Assemblies: Importance of Conformational Sampling}, volume={122}, ISSN={["1089-5639"]}, DOI={10.1021/acs.jpca.7b10932}, abstractNote={Fe(II)-polypyridines have limited applications as chromophores in dye-sensitized solar cells due to the short lifetimes (∼100 fs) of their photoactive metal-to-ligand charge transfer (MLCT) states formed upon photoexcitation. Recently, a 100-fold increase in the MLCT lifetime was observed in a [Fe(CNC)2]2+ complex (CNC = 2,6-bis(3-methylimidazole-1-ylidine)pyridine) which has strong σ-donating N-heterocyclic carbene ligand in comparison to the weaker field parent [Fe(tpy)2]2+ complex (tpy = 2,2':6',2″-terpyridine). This study utilizes density functional theory (DFT), time-dependent DFT, and quantum dynamics simulations to investigate the interfacial electron transfer (IET) in [Fe(cCNC)2]2+ (cCNC = 4'-carboxy-2,6-bis(3-methylimidazole-1-ylidine)pyridine) and [Fe(ctpy)2]2+ (ctpy = 4'-carboxy-2,2':6',2″-terpyridine) sensitized TiO2. Our results suggest that the replacement of tpy by CNC ligand does not significantly speed up the IET kinetics in the [Fe(cCNC)2]2+-TiO2 assembly in comparison to the [Fe(ctpy)2]2+-TiO2 analogue. The high IET efficiency in the [Fe(cCNC)2]2+-TiO2 assemblies is therefore due to longer lifetime of [Fe(cCNC)2]2+ photoactive 3MLCT states rather than faster electron injection kinetics. It was also found that the inclusion of conformational sampling in the computational model is important for proper description of the IET processes in these systems, as the models relying on the use of only fully optimized structures may yield misleading results. The simulations presented in this work also illustrate various pitfalls of utilizing properties such as electronic coupling, number of available acceptor states, and driving force, as well as calculations based on Fermi's golden rule framework, to reach conclusions on the IET efficiency in dye-semiconductor systems.}, number={7}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Mukherjee, Sriparna and Liu, Chang and Jakubikova, Elena}, year={2018}, month={Feb}, pages={1821–1830} }
 @article{deaton_taliaferro_pitman_czerwieniec_jakubikova_miller_castellano_2018, title={Excited-State Switching between Ligand-Centered and Charge Transfer Modulated by Metal–Carbon Bonds in Cyclopentadienyl Iridium Complexes}, volume={57}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/acs.inorgchem.8b02753}, DOI={10.1021/acs.inorgchem.8b02753}, abstractNote={Three series of pentamethylcyclopentadienyl (Cp*) Ir(III) complexes with different bidentate ligands were synthesized and structurally characterized, [Cp*Ir(tpy)L] n+ (tpy = 2-tolylpyridinato; n = 0 or 1), [Cp*Ir(piq)L] n+ (piq = 1-phenylisoquinolinato; n = 0 or 1), and [Cp*Ir(bpy)L] m+ (bpy = 2,2'-bipyridine; m = 1 or 2), featuring a range of monodentate carbon-donor ligands within each series [L = 2,6-dimethylphenylisocyanide; 3,5-dimethylimidazol-2-ylidene (NHC); methyl)]. The spectroscopic and photophysical properties of these molecules and those of the photocatalyst [Cp*Ir(bpy)H]+ were examined to establish electronic structure-photophysical property relationships that engender productive photochemical reactivity of this hydride and its methyl analogue. The Ir(III) chromophores containing ancillary CNAr ligands exhibited features anticipated for predominantly ligand-centered (LC) excited states, and analogues bearing the NHC ancillary exhibited properties consistent with LC excited states containing a small admixture of metal-to-ligand charge-transfer (MLCT) character. However, the molecules featuring anionic and strongly σ-donating methyl or hydride ligands exhibited photophysical properties consistent with a high degree of CT character. Density functional theory calculations suggest that the lowest energy triplet states in these complexes are composed of a mixture of MLCT and ligand-to-ligand CT originating from both the Cp* and methyl or hydride ancillary ligands. The high degree of CT character in the triplet excited states of methyliridium complexes bearing C^N-cyclometalated ligands offer a striking contrast to the photophysical properties of pseudo-octahedral structures fac-Ir(C^N)3 or Ir(C^N)2(acac) that have lowest-energy triplet excited states characterized as primarily LC character with a more moderate MLCT admixture.}, number={24}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Deaton, Joseph C. and Taliaferro, Chelsea M. and Pitman, Catherine L. and Czerwieniec, Rafał and Jakubikova, Elena and Miller, Alexander J. M. and Castellano, Felix N.}, year={2018}, month={Dec}, pages={15445–15461} }
 @article{ashley_jakubikova_2018, title={Ray-Dutt and Bailar Twists in Fe(II)-Tris(2,2'-bipyridine): Spin States, Sterics, and Fe-N Bond Strengths}, volume={57}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.8b00560}, abstractNote={Twisting motions in six-coordinate trischelate transition-metal complexes have long been recognized as a potential reaction coordinate for nondissociative racemization by changing the coordination geometry from octahedral to trigonal prismatic in the transition state. These pathways have been previously established as the Bailar twist (conversion to D3 h symmetry) and the Ray-Dutt twist (conversion to C2 v symmetry). Twisting motions have been shown to be associated with changes in spin state and are therefore of relevance not only to thermal isomerization pathways but also to spin-crossover (SCO) and intersystem crossing mechanisms. In this work, density functional theory and complete active space self-consistent field calculations are used to probe the structural and energetic features of idealized Bailar and Ray-Dutt twisting mechanisms for a model Fe(II) polypyridine complex, [Fe(bpy)3]2+ (bpy = 2,2'-bipyridine). We find that the energies of the D3 h and C2 v trigonal prismatic structures are strongly dependent on spin state, with thermally accessible species only being possible on the quintet surface, enforcing the necessary relationship between SCO and torsional motion. The Ray-Dutt twist on the quintet surface is calculated to proceed with a low barrier, and is likely the preferable twisting mechanism for this complex. We additionally identify a new distorted Bailar twist of C3 h geometry, which is considerably lower in energy than the idealized D3 h structure due to a combination of both steric and electronic factors. The computational analysis presented herein offers insight into how Fe-N bond strength, interligand steric repulsion, and ligand flexibility can be exploited to influence the rates of different twisting mechanisms and the critical motions involved.}, number={9}, journal={INORGANIC CHEMISTRY}, author={Ashley, Daniel C. and Jakubikova, Elena}, year={2018}, month={May}, pages={5585–5596} }
 @article{ashley_jakubikova_2018, title={Tuning the Redox Potentials and Ligand Field Strength of Fe(II) Polypyridines: The Dual pi-Donor and pi-Acceptor Character of Bipyridine}, volume={57}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.8b01002}, abstractNote={The quintet-singlet energy difference (Δ EQ/S) in Fe(II) polypyridine complexes is often interpreted in terms of metal-ligand π interactions. DFT calculations on a series of substituted [Fe(bpy)3]2+ (bpy = 2,2'-bipyridine) complexes show the disparate magnitudes of substituent effects on tuning Δ EQ/S and reduction potentials ( E°). In this series, E° spans a much larger range than Δ EQ/S (2.07 vs 0.29 eV). While small changes in Δ EQ/S are controlled by metal-ligand π interactions, large changes in E° arise from modification of the electrostatic environment around the Fe center. Molecular orbital analysis reveals that, contrary to the typical description of bpy as a π-acceptor, bpy is better described as acting as both a π-donor and π-acceptor in [Fe(bpy)3]2+ complexes, even when it is substituted with highly electron withdrawing substituents. Overall, substituent modification is a useful strategy for fine-tuning the ligand field strength but not for significant reordering of the spin-state manifold, despite the large effect on metal-ligand electrostatic interactions.}, number={16}, journal={INORGANIC CHEMISTRY}, author={Ashley, Daniel C. and Jakubikova, Elena}, year={2018}, month={Aug}, pages={9907–9917} }
 @article{mukherjee_torres_jakubikova_2017, title={HOMO inversion as a strategy for improving the light-absorption properties of Fe(II) chromophores}, volume={8}, ISSN={["2041-6539"]}, DOI={10.1039/c7sc02926h}, abstractNote={Substitution of π-conjugated donor groups onto the polypyridine ligands in Fe(ii) complexes inverts the HOMO character and improves the light-absorption.}, number={12}, journal={CHEMICAL SCIENCE}, author={Mukherjee, Sriparna and Torres, David E. and Jakubikova, Elena}, year={2017}, month={Dec}, pages={8115–8126} }
 @misc{ashley_jakubikova_2017, title={Ironing out the photochemical and spin-crossover behavior of Fe(II) coordination compounds with computational chemistry}, volume={337}, ISSN={["1873-3840"]}, DOI={10.1016/j.ccr.2017.02.005}, abstractNote={Effective strategies for designing Fe(II) coordination complexes with specifically tailored spin-state energetics can lead to advances in many areas of inorganic and materials chemistry. These include, but are not limited to, rational development of novel spin crossover complexes, efficient chromophores for photosensitization of dye-sensitized solar cells, and multifunctional materials. As the spin-state ordering of transition metal complexes is strongly rooted in their electronic structures, computational chemistry has naturally played an important role in assisting experimental work in this area. Unfortunately, despite many advances, accurate determination of the spin-state energetics of Fe(II) complexes still poses a remarkable challenge for virtually all applicable forms of electronic structure theory due to being controlled by a delicate balancing between correlation and exchange effects. This review focuses on some of the more notable successes and failures of modern electronic structure theory in properly describing these systems in the absence of solid-state effects. The strengths and weaknesses of using traditional wavefunction based methods and density functional theory are considered, and illustrative examples are provided to demonstrate that the modern computational chemist should make use of experimental data whenever possible and expect to utilize a combination of methods to obtain the best results. The review closes by briefly surveying some of the many interesting combined computational and experimental studies of Fe(II) chemistry that have lead to greater fundamental insight and practical understanding of this challenging class of systems.}, journal={COORDINATION CHEMISTRY REVIEWS}, author={Ashley, Daniel C. and Jakubikova, Elena}, year={2017}, month={Apr}, pages={97–111} }
 @article{liu_jakubikova_2017, title={Two-step model for ultrafast interfacial electron transfer: limitations of Fermi's golden rule revealed by quantum dynamics simulations}, volume={8}, ISSN={["2041-6539"]}, DOI={10.1039/c7sc01169e}, abstractNote={A two-step model of interfacial electron transfer is proposed along with a practical approach to screening dye-sensitizers based on a calculation of the percentage of electron density on the linker group and the number of available semiconductor acceptor states.}, number={9}, journal={CHEMICAL SCIENCE}, author={Liu, Chang and Jakubikova, Elena}, year={2017}, month={Sep}, pages={5979–5991} }
 @article{shrestha_virgil_jakubikova_2016, title={Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study}, volume={120}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.6b04797}, abstractNote={Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.}, number={29}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Shrestha, Kushal and Virgil, Kyle A. and Jakubikova, Elena}, year={2016}, month={Jul}, pages={5816–5825} }
 @article{frasco_mukherjee_sommer_perry_lambic_abboud_jakubikoya_ison_2016, title={Nondirected C-H Activation of Arenes with Cp*Ir(III) Acetate Complexes: An Experimental and Computational Study}, volume={35}, ISSN={["1520-6041"]}, DOI={10.1021/acs.organomet.6b00308}, abstractNote={Combined experimental and computational studies have revealed factors that influence the nondirected C–H activation in Cp*Ir complexes that contain carboxylate ligands. A two-step acetate-assisted pathway was shown to be operational where the first step involves substrate binding and the second step involves cleavage of the C–H bond of the substrate. A nonlinear Hammett plot was obtained to examine substituted arenes where a strong electronic dependence (ρ = 1.67) was observed for electron-donating groups, whereas no electronic dependence was observed for electron-withdrawing groups. Electron-donating substituents in the para position were shown to have a bigger impact on the C–H bond cleavage step, whereas electron-withdrawing substituents influenced the substrate-binding step. Although cleavage of the C–H bond was predicted to be more facile with arenes that contain substituents in the para position by DFT calculations, the cyclometalations of anisole and benzonitrile were observed experimentally. This ...}, number={15}, journal={ORGANOMETALLICS}, publisher={American Chemical Society (ACS)}, author={Frasco, Daniel A. and Mukherjee, Sriparna and Sommer, Roger D. and Perry, Cody M. and Lambic, Nikola S. and Abboud, Khalil A. and Jakubikoya, Elena and Ison, Elon A.}, year={2016}, month={Aug}, pages={2435–2445} }
 @article{high_rego_jakubikova_2016, title={Quantum Dynamics Simulations of Excited State Energy Transfer in a Zinc-Free-Base Porphyrin Dyad}, volume={120}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.6b05739}, abstractNote={Rational design of artificial light-harvesting molecular architectures entails building systems that absorb strongly in the visible and near-IR region of the electromagnetic spectrum and also funnel excited state energy to a single site. The ability to model nonadiabatic processes, such as excited-state energy transfer (EET), that occur on a picosecond time scale can aid in the development of novel artificial light-harvesting arrays. A combination of density functional theory (DFT), time-dependent DFT, tight-binding molecular dynamics, and quantum dynamics is employed here to simulate EET in the ZnFbΦ dyad, a model artificial light-harvesting array that undergoes EET with an experimentally measured rate constant of (3.5 ps)-1 upon excitation at 550 nm in toluene [ Yang et al. J. Phys. Chem. B 1998 , 102 , 9426 - 9436 ]. We find that to successfully simulate the EET process, it is important to (1) include coupling between nuclear and electronic degrees of freedom in the QD simulation, (2) account for Coulomb coupling between the electron and hole wavepackets, and (3) parametrize the extended Hückel model Hamiltonian employed in the QD simulations with respect to the DFT.}, number={41}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={High, Judah S. and Rego, Luis G. C. and Jakubikova, Elena}, year={2016}, month={Oct}, pages={8075–8084} }
 @article{mukherjee_bowman_jakubikova_2015, title={Cyclometalated Fe(II) Complexes as Sensitizers in Dye-Sensitized Solar Cells}, volume={54}, ISSN={["1520-510X"]}, DOI={10.1021/ic502438g}, abstractNote={Dye-sensitized solar cells (DSSCs) often utilize transition metal-based chromophores for light absorption and semiconductor sensitization. Ru(II)-based dyes are among the most commonly used sensitizers in DSSCs. As ruthenium is both expensive and rare, complexes based on cheaper and more abundant iron could serve as a good alternative. In this study, we investigate Fe(II)-bis(terpyridine) and its cyclometalated analogues, in which pyridine ligands are systematically replaced by aryl groups, as potential photosensitizers in DSSCs. We employ density functional theory at the B3LYP/6-31G*,SDD level to obtain the ground state electronic structure of these complexes. Quantum dynamics simulations are utilized to study interfacial electron transfer between the Fe(II) photosensitizers and a titanium dioxide semiconductor. We find that cyclometalation stabilizes the singlet ground state of these complexes by 8-19 kcal/mol but reduces the electron density on the carboxylic acid attached to the aryl ring. The results suggest that cyclometalation provides a feasible route to increasing the efficiency of Fe(II) photosensitizers but that care should be taken in choosing the substitution position for the semiconductor anchoring group.}, number={2}, journal={INORGANIC CHEMISTRY}, author={Mukherjee, Sriparna and Bowman, David N. and Jakubikova, Elena}, year={2015}, month={Jan}, pages={560–569} }
 @article{mara_bowman_buyukcakir_shelby_haldrup_huang_harpham_stickrath_zhang_stoddart_et al._2015, title={Electron Injection from Copper Diimine Sensitizers into TiO2: Structural Effects and Their Implications for Solar Energy Conversion Devices}, volume={137}, ISSN={["0002-7863"]}, DOI={10.1021/jacs.5b04612}, abstractNote={Copper(I) diimine complexes have emerged as low cost replacements for ruthenium complexes as light sensitizers and electron donors, but their shorter metal-to-ligand-charge-transfer (MLCT) states lifetimes and lability of transient Cu(II) species impede their intended functions. Two carboxylated Cu(I) bis-2,9-diphenylphenanthroline (dpp) complexes [Cu(I)(dpp-O(CH2CH2O)5)(dpp-(COOH)2)](+) and [Cu(I)(dpp-O(CH2CH2O)5)(dpp-(Φ-COOH)2)](+) (Φ = tolyl) with different linker lengths were synthesized in which the MLCT-state solvent quenching pathways are effectively blocked, the lifetime of the singlet MLCT state is prolonged, and the transient Cu(II) ligands are stabilized. Aiming at understanding the mechanisms of structural influence to the interfacial charge transfer in the dye-sensitized solar cell mimics, electronic and geometric structures as well as dynamics for the MLCT state of these complexes and their hybrid with TiO2 nanoparticles were investigated using optical transient spectroscopy, X-ray transient absorption spectroscopy, time-dependent density functional theory, and quantum dynamics simulations. The combined results show that these complexes exhibit strong absorption throughout the visible spectrum due to the severely flattened ground state, and a long-lived charge-separated Cu(II) has been achieved via ultrafast electron injection (<300 fs) from the (1)MLCT state into TiO2 nanoparticles. The results also indicate that the TiO2-phen distance in these systems does not have significant effect on the efficiency of the interfacial electron-transfer process. The mechanisms for electron transfer in these systems are discussed and used to develop new strategies in optimizing copper(I) diimine complexes in solar energy conversion devices.}, number={30}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Mara, Michael W. and Bowman, David N. and Buyukcakir, Onur and Shelby, Megan L. and Haldrup, Kristoffer and Huang, Jier and Harpham, Michael R. and Stickrath, Andrew B. and Zhang, Xiaoyi and Stoddart, J. Fraser and et al.}, year={2015}, month={Aug}, pages={9670–9684} }
 @article{high_virgil_jakubikova_2015, title={Electronic Structure and Absorption Properties of Strongly Coupled Porphyrin-Perylene Arrays}, volume={119}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.5b05600}, abstractNote={Porphyrin-perylene arrays are ideal candidates for light-harvesting systems capable of panchromatic absorption. In this work, we employ density functional theory (DFT) and time-dependent DFT to investigate the unique UV-vis absorption properties exhibited by a series of ethynyl-linked porphyrin-perylene arrays that were previously synthesized and characterized spectroscopically [Chem. Commun. 2014, 50, 14512-5]. We find that the ethynyl linker is responsible for strong electronic coupling of porphyrin and perylene subunits in these systems. Additionally, these arrays exhibit a low barrier to rotation around the ethynyl linker (<1.4 kcal/mol per one perylene substituent), which results in a wide range of molecular conformations characterized by different porphyrin-perylene dihedral angles being accessible at room temperature. The best match between the calculated and experimental UV-vis spectra is obtained by averaging the calculated UV-vis spectra over the range of conformations defined by the porphyrin-perylene dihedral angles. Finally, our calculations suggest that the transitions in the lower energy region (550-750 nm) can be assigned to the excitations originating from the porphyrin subunit; the mid-energy region transitions (450-550 nm) are assigned to the perylene-centered excitations, while the high-energy transitions (350-450 nm) involve contributions from both porphyrin and perylene subunits.}, number={38}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={High, Judah S. and Virgil, Kyle K. and Jakubikova, Elena}, year={2015}, month={Sep}, pages={9879–9888} }
 @misc{jakubikova_bowman_2015, title={Fe(II)-Polypyridines as Chromophores in Dye-Sensitized Solar Cells: A Computational Perspective}, volume={48}, ISSN={["1520-4898"]}, DOI={10.1021/ar500428t}, abstractNote={Over the past two decades, dye-sensitized solar cells (DSSCs) have become a viable and relatively cheap alternative to conventional crystalline silicon-based systems. At the heart of a DSSC is a wide band gap semiconductor, typically a TiO2 nanoparticle network, sensitized with a visible light absorbing chromophore. Ru(II)-polypyridines are often utilized as chromophores thanks to their chemical stability, long-lived metal-to-ligand charge transfer (MLCT) excited states, tunable redox potentials, and near perfect quantum efficiency of interfacial electron transfer (IET) into TiO2. More recently, coordination compounds based on first row transition metals, such as Fe(II)-polypyridines, gained some attention as potential sensitizers in DSSCs due to their low cost and abundance. While such complexes can in principle sensitize TiO2, they do so very inefficiently since their photoactive MLCT states undergo intersystem crossing (ISC) into low-lying metal-centered states on a subpicosecond time scale. Competition between the ultrafast ISC events and IET upon initial excitation of Fe(II)-polypyridines is the main obstacle to their utilization in DSSCs. Suitability of Fe(II)-polypyridines to serve as sensitizers could therefore be improved by adjusting relative rates of the ISC and IET processes, with the goal of making the IET more competitive with ISC. Our research program in computational inorganic chemistry utilizes a variety of tools based on density functional theory (DFT), time-dependent density functional theory (TD-DFT) and quantum dynamics to investigate structure-property relationships in Fe(II)-polypyridines, specifically focusing on their function as chromophores. One of the difficult problems is the accurate determination of energy differences between electronic states with various spin multiplicities (i.e., (1)A, (1,3)MLCT, (3)T, (5)T) in the ISC cascade. We have shown that DFT is capable of predicting the trends in the energy ordering of these electronic states in a set of structurally related complexes with the help of appropriate benchmarks, based either on experimental data or higher-level ab initio calculations. Models based on TD-DFT and quantum dynamics approaches have proven very useful in understanding IET processes in Fe(II)-polypyridine-TiO2 assemblies. For example, they helped us to elucidate the origin of "band selective" sensitization in the [Fe(bpy-dca)2(CN)2]-TiO2 assembly (bpy-dca = 2,2'-bipyridine-4,4'-dicarboxylic acid), first observed by Ferrere and Gregg [ Ferrere , S. ; Gregg , B. A. J. Am. Chem. Soc. 1998 , 120 , 843 . ]. They also shed light on the relationship between the linker group that anchors Fe(II)-polypyridines onto the TiO2 surface and the speed of IET in Fe(II)-polypyridine-TiO2 assemblies. More interestingly, our results show that the IET efficiency is strongly correlated with the amount of electron density on the linker group and that one can obtain insights into the IET in dye-semiconductor assemblies based on ground state electronic structure calculations alone. This may be useful for quick screening of a large number of complexes for use as potential sensitizers in DSSCs, especially if followed up by TD-DFT and quantum dynamics simulations for selected target compounds to confirm efficient sensitization. While our focus over the past few years has been exclusively on Fe(II)-polypyridines, the computational strategies outlined in this Account are applicable to a wide variety of sensitizers.}, number={5}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Jakubikova, Elena and Bowman, David N.}, year={2015}, month={May}, pages={1441–1449} }
 @article{shrestha_jakubikova_2015, title={Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method}, volume={119}, ISSN={["1089-5639"]}, DOI={10.1021/acs.jpca.5b05644}, abstractNote={Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.}, number={33}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Shrestha, Kushal and Jakubikova, Elena}, year={2015}, month={Aug}, pages={8934–8943} }
 @article{nance_bowman_mukherjee_kelley_jakubikova_2015, title={Insights into the Spin-State Transitions in [Fe(tpy)2]2+: Importance of the Terpyridine Rocking Motion}, volume={54}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/acs.inorgchem.5b01747}, DOI={10.1021/acs.inorgchem.5b01747}, abstractNote={Iron(II) polypyridine complexes have the potential for numerous applications on a global scale, such as sensitizers, sensors, and molecular memory. The excited-state properties of these systems, particularly the intersystem crossing (ISC) rates, are sensitive to the choice of ligands and can be significantly altered depending on the coordination environment. We employ density functional theory and Smolyak's sparse grid interpolation algorithm to construct potential energy surfaces (PESs) for the photophysically relevant states ((1)A, (3,5)MC, and (1,3)MLCT) of the [Fe(tpy)2](2+) (tpy = 2,2':6',2"-terpyridine) complex, with the goal of obtaining a deeper understanding of the ground- and excited-state electronic structure of this system. The three dimensions that define our adiabatic PESs consist of equatorial and axial metal-ligand bond length distortions and a terpyridine ligand "rocking angle", which has not previously been investigated. The intersection crossing seams and minimum energy crossing points (MECPs) between surfaces are also determined. Overall, we find that the PESs of all electronic excited states investigated are characterized by low-energy valleys along the tpy rocking-angle coordinate. This results in the presence of large low-energy areas around the MECPs on the intersection seams of different electronic states and indicates that inclusion of this third coordinate is crucial for an adequate description of the PESs and surface crossing seams of the [Fe(tpy)2](2+) complex. Finally, we suggest that tuning the energetics of the tpy ligand rocking motion could provide a way to control the ISC process in this complex.}, number={23}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Nance, James and Bowman, David N. and Mukherjee, Sriparna and Kelley, C. T. and Jakubikova, Elena}, year={2015}, month={Nov}, pages={11259–11268} }
 @inbook{bowman_chan_jakubikova_2015, place={Washington, DC}, series={ACS Symposium Series}, title={Investigating Interfacial Electron Transfer in Highly Efficient Porphyrin-Sensitized Solar Cells}, DOI={10.1021/bk-2015-1196.ch008}, abstractNote={The YD2-o-C8 complex based on zinc tetraphenylporphyrin (ZnTPP) is among the most efficient sensitizers for DSSCs to date, reaching over 12% in power conversion efficiency when paired with an organic co-sensitizer on a TiO2 surface. To understand the link between the structure and light-harvesting properties of ZnTPP dyes, four sensitizers based on ZnTPP are investigated, with a systematic addition of structural features found in YD2-o-C8. Density functional theory (DFT) and time-dependent DFT are utilized to obtain the ground and excited state electronic structure of each chromophore. Quantum dynamics simulations are also employed to investigate interfacial electron transfer between the electronically excited ZnTPP dyes and the TiO2 semiconductor. Overall, we find that substitution of the strongly coupled ethynyl bridged benzoic acid and diarylamine at the meso position of the porphyrin ring have the most significant impact on the absorption properties and IET efficiencies of Zn TPP based dyes. The addition of the alkoxy groups and long chain alkanes onto the meso substituted phenyl groups to produce YD2-o-C8 have little impact on the ground and excited state properties of the sensitizer. The structural modifications that do not impact the chromophore electronic structure are, however, likely to impact intermolecular interactions (chromophore-chromophore and chromophore-electrolyte). Overall, our results shed light on the origins of the sensitization efficiency of the YD2-o-C8 dye and support the conclusions of previous experimental and computation work on this system.}, booktitle={Photoinduced Processes at Surfaces and in Nanomaterials}, publisher={American Chemical Society}, author={Bowman, D.N. and Chan, J. and Jakubikova, E.}, year={2015}, pages={168–188}, collection={ACS Symposium Series} }
 @article{bowman_chan_jakubikova_2015, title={Investigating interfacial electron transfer in highly efficient porphyrin-sensitized solar cells}, volume={1196}, journal={Photoinduced processes at surfaces and in nanomaterials}, author={Bowman, D. N. and Chan, J. and Jakubikova, E.}, year={2015}, pages={169–188} }
 @article{bowman_mukherjee_barnes_jakubikova_2015, title={Linker dependence of interfacial electron transfer rates in Fe(II)-polypyridine sensitized solar cells}, volume={27}, ISSN={0953-8984 1361-648X}, url={http://dx.doi.org/10.1088/0953-8984/27/13/134205}, DOI={10.1088/0953-8984/27/13/134205}, abstractNote={Dye-sensitized solar cells (DSSCs) convert solar energy to electricity employing dye molecules attached to a semiconductor surface. Some of the most efficient DSSCs use Ru-based chromophores. Fe-based dyes represent a cheaper and more environmentally friendly alternative to these expensive and toxic dyes. The photoactive state of Fe-based chromophores responsible for charge-separation at the dye-semiconductor interface is, however, deactivated on a sub-picosecond time scale via the intersystem crossing (ISC) into a manifold of low-lying photo-inactive quintet states. Therefore, development of Fe-based dyes capable of fast interfacial electron transfer (IET) leading to efficient charge separation on a time scale competitive with the ISC events is important. This work investigates how linker groups anchoring a prototypical Fe-based dye [Fe(bpy-L)2(CN)2] (bpy = 2,2′-bipyridine, L = linker group) onto the TiO2 semiconductor surface influence the IET rates in the dye–semiconductor assemblies. Linker groups investigated include carboxylic acid, phosphonic acid, hydroxamate, catechol, and acetylacetonate. We employ time-dependent density functional theory (TD-DFT) to obtain absorption spectra of [Fe(bpy-L)2(CN)2] with each linker, and quantum dynamics simulations to investigate the IET rates between the dye and the (101) TiO2 anatase surface. For all attachments, TD-DFT calculations show similar absorption spectra with two main bands corresponding to the metal-to-ligand charge transfer transitions. The quantum dynamics simulations predict that the utilization of the hydroxamate linker instead of the commonly used carboxylic acid linker will lead to a more efficient IET and better photon-to-current conversion efficiencies in Fe(II)-polypyridine sensitized solar cells.}, number={13}, journal={Journal of Physics: Condensed Matter}, publisher={IOP Publishing}, author={Bowman, David N and Mukherjee, Sriparna and Barnes, Lyndsay J and Jakubikova, Elena}, year={2015}, month={Mar}, pages={134205} }
 @article{bowman_bondarev_mukherjee_jakubikova_2015, title={Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study}, volume={54}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.5b01409}, abstractNote={Fe(II) polypyridines are an important class of pseudo-octahedral metal complexes known for their potential applications in molecular electronic switches, data storage and display devices, sensors, and dye-sensitized solar cells. Fe(II) polypyridines have a d(6) electronic configuration and pseudo-octahedral geometry and can therefore possess either a high-spin (quintet) or a low-spin (singlet) ground state. In this study, we investigate a series of complexes based on [Fe(tpy)2](2+) (tpy = 2,2';6',2″-terpyridine) and [Fe(dcpp)2](2+) (dcpp = 2,6-bis(2-carboxypyridyl)pyridine). The ligand field strength in these complexes is systematically tuned by replacing the central pyridine with five-membered (N-heterocyclic carbene, pyrrole, furan) or six-membered (aryl, thiazine-1,1-dioxide, 4-pyrone) moieties. To determine the impact of ligand substitutions on the relative energies of metal-centered states, the singlet, triplet, and quintet states of the Fe(II) complexes were optimized in water (PCM) using density functional theory at the B3LYP+D2 level with 6-311G* (nonmetals) and SDD (Fe) basis sets. It was found that the dcpp ligand scaffold allows for a more ideal octahedral coordination environment in comparison to the tpy ligand scaffold. The presence of six-membered central rings also allows for a more ideally octahedral coordination environment relative to five-membered central rings, regardless of the ligand scaffold. We find that the ligand field strength in the Fe(II) polypyridines can be tuned by altering the donor atom identity, with C donor atoms providing the strongest ligand field.}, number={17}, journal={INORGANIC CHEMISTRY}, author={Bowman, David N. and Bondarev, Alexey and Mukherjee, Sriparna and Jakubikova, Elena}, year={2015}, month={Sep}, pages={8786–8793} }
 @article{shrestha_gonzalez-delgado_blew_jakubikova_2014, title={Electronic Structure of Covalently Linked Zinc Bacteriochlorin Molecular Arrays: Insights into Molecular Design for NIR Light Harvesting}, volume={118}, ISSN={["1520-5215"]}, DOI={10.1021/jp507749c}, abstractNote={Pigment-based molecular arrays, especially those based on porphyrins, have been extensively studied as viable components of artificial light harvesting devices. Unlike porphyrins, bacteriochlorins absorb strongly in the NIR, yet little is known of the applicability of covalently linked bacteriochlorin-based arrays in this arena. To lay the foundation for future studies of excited state properties of such arrays, we present a systematic study of the ground state electronic structure of zinc bacteriochlorin (ZnBC) molecular arrays with various linkers and linker attachment sites (meso vs β) employing density functional theory in combination with the energy-based fragmentation (EBF) method, and the EBF with molecular orbitals (EBF-MO) method. We find that the level of steric hindrance between the ZnBC and the linker is directly correlated with the amount of ground sate electronic interactions between the ZnBCs. Low steric hindrance between the ZnBC and the linker found in alkyne-linked arrays results in strongly interacting arrays that are characterized by a decrease in the HOMO-LUMO energy gaps, large orbital energy dispersion in the frontier region, and low ZnBC-linker rotational barriers. In contrast, sterically hindered linkers, such as aryl-based linkers, result in weakly interacting arrays characterized by increased orbital energy degeneracy in the frontier region and high ZnBC-linker rotational barriers. For all linkers studied, the level of steric hindrance decreases when the ZnBCs are linked at the β position. Hence, ZnBC arrays that exhibit strong, weak, or intermediate ground-state electronic interactions can be realized by adjusting the level of steric hindrance with a judicious choice of the linker type and linker attachment site. Such tuning may be essential for design of light harvesting arrays with desired spectral properties.}, number={42}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Shrestha, Kushal and Gonzalez-Delgado, Jessica M. and Blew, James H. and Jakubikova, Elena}, year={2014}, month={Oct}, pages={9901–9913} }
 @article{nance_jakubikova_kelley_2014, title={Reaction Path Following with Sparse Interpolation}, volume={10}, ISSN={1549-9618 1549-9626}, url={http://dx.doi.org/10.1021/ct5004669}, DOI={10.1021/ct5004669}, abstractNote={Computing the potential energy of an N-atom molecule is an expensive optimization process of 3N - 6 molecular coordinates, so following reaction pathways as a function of all 3N - 6 coordinates is unfeasible for large molecules. In this paper, we present a method that isolates d < 3N - 6 molecular coordinates and continuously follows reaction paths on d-dimensional potential energy surfaces approximated by a Smolyak's sparse grid interpolation algorithm.1 Compared to dense grids, sparse grids efficiently improve the ratio of invested storage and computing time to approximation accuracy and thus allow one to increase the number of coordinates d in molecular reaction path following simulations. Furthermore, evaluation of the interpolant is much less expensive than the evaluation of the actual energy function, so our technique offers a computationally efficient way to simulate reaction paths on ground and excited state potential energy surfaces. To demonstrate the capabilities of our method, we present simulation results for the isomerization of 2-butene with two, three, and six degrees of freedom.}, number={8}, journal={Journal of Chemical Theory and Computation}, publisher={American Chemical Society (ACS)}, author={Nance, James and Jakubikova, Elena and Kelley, C. T.}, year={2014}, month={Jul}, pages={2942–2949} }
 @article{seaman_pedrick_tsuchiya_wu_jakubikova_hayton_2013, title={Comparison of the Reactivity of 2-Li-C6H4CH2NMe2 with MCl4 ( M = Th, U): Isolation of a Thorium Aryl Complex or a Uranium Benzyne Complex}, volume={52}, ISSN={["1521-3773"]}, DOI={10.1002/anie.201303992}, abstractNote={Why do U react like that? Reaction of 2-Li-C6H4CH2NMe2 with [MCl4(DME)n] (M=Th, n=2; M=U, n=0) results in the formation of a thorium aryl complex, [Th(2-C6H4CH2NMe2)4] or a uranium benzyne complex, [Li][U(2,3-C6H3CH2NMe2)(2-C6H4CH2NMe2)3]. A DFT analysis suggests that the formation of a benzyne complex with U but not with Th is a kinetic and not thermodynamic effect.}, number={40}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Seaman, Lani A. and Pedrick, Elizabeth A. and Tsuchiya, Takashi and Wu, Guang and Jakubikova, Elena and Hayton, Trevor W.}, year={2013}, month={Sep}, pages={10589–10592} }
 @article{bowman_blew_tsuchiya_jakubikova_2013, title={Correction to Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO2 Assemblies}, volume={52}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/IC402856J}, DOI={10.1021/IC402856J}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO2 AssembliesDavid N. Bowman, James H. Blew, Takashi Tsuchiya, and Elena Jakubikova*Cite this: Inorg. Chem. 2013, 52, 24, 14449Publication Date (Web):December 4, 2013Publication History Published online4 December 2013Published inissue 16 December 2013https://doi.org/10.1021/ic402856jCopyright © 2013 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views329Altmetric-Citations8LEARN 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 PDF (190 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts}, number={24}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Bowman, David N. and Blew, James H. and Tsuchiya, Takashi and Jakubikova, Elena}, year={2013}, month={Dec}, pages={14449–14449} }
 @article{bowman_blew_tsuchiya_jakubikova_2013, title={Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO2 Assemblies}, volume={52}, ISSN={["1520-510X"]}, DOI={10.1021/ic4007839}, abstractNote={Iron(II) polypyridines represent a cheaper and nontoxic alternative to analogous Ru(II) polypyridine dyes successfully used as photosensitizers in dye-sensitized solar cells (DSSCs). We employ density functional theory (DFT) and time-dependent DFT (TD-DFT) to study ground and excited state properties of [Fe(bpy)(CN)4](2-), [Fe(bpy-dca)(CN)4](2-), and [Fe(bpy-dca)2(CN)2] complexes, where bpy = 2,2'-bipyridine and dca = 4,4'-dicarboxylic acid. Quantum dynamics simulations are further used to investigate the interfacial electron transfer (IET) between the excited Fe(II) dyes and a TiO2 nanoparticle. All three dyes investigated display two bands in the visible region of the absorption spectrum, with the major transitions corresponding to the metal-to-ligand charge transfer states. The calculated IET rates from the particle states created by the excitation of the lower-energy absorption band are comparable to or slower than the rate of the excited state decay into the nonemissive, metal-centered states of the Fe(II) dyes (∼100 fs), indicating that the IET upon the excitation of this band is unlikely. Several particle states in the higher-energy absorption band display IET rates at or below 100 fs, suggesting the possibility of the IET between the Fe(II)-sensitizer and TiO2 nanoparticle upon excitation with visible light. Our results are consistent with the previous experimental work on Fe(II) sensitizers (Ferrere, S. Chem. Mater. 2000, 12, 1083) and elucidate the band-selective nature of the IET in these compounds.}, number={15}, journal={INORGANIC CHEMISTRY}, author={Bowman, David N. and Blew, James H. and Tsuchiya, Takashi and Jakubikova, Elena}, year={2013}, month={Aug}, pages={8621–8628} }
 @article{tsuchiya_shrestha_jakubikova_2013, title={Orbital Analysis and Excited-State Calculations in an Energy-Based Fragmentation Method}, volume={9}, ISSN={["1549-9626"]}, DOI={10.1021/ct400025a}, abstractNote={Covalently bound molecular arrays composed of porphyrins or related pigments have gained a lot of interest as components of artificial light-harvesting systems and molecular photonic devices. The large size of these arrays, however, makes their theoretical investigation employing the ab initio or density functional methodologies difficult. Energy-based fragmentation methods (EBF) represent a set of conceptually simple approaches to theoretical investigation of large systems and were therefore chosen as a tool to study these systems. Here a new approach to EBF, EBF-MO, is introduced that enables one to obtain orbitals and orbital energies and to perform population analysis and excited-state calculations of large systems composed of hundreds of atoms. This approach was implemented into a parallel program, JETT, and the benchmark calculations have shown its accuracy and applicability to the ground- and excited-state calculations of systems containing transition metals and extended π-conjugation. EBF-MO was then applied to the density functional theory (DFT) and the time-dependent density functional theory (TDDFT) calculations of ground- and excited-state properties of a porphyrin-based molecular photonic wire composed of 472 atoms and 4265 basis functions at the B3LYP/LANL08,6-31G* level. The TDDFT calculations have revealed the character of the excited states, and the unidirectionality of the excitation energy transfer across the array relevant to its signal transfer function. The computational approaches introduced here have widened the applicability of the ab initio and density functional methodologies to calculations of extended systems such as natural and artificial light-harvesting systems and molecular photonic devices.}, number={8}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, author={Tsuchiya, Takashi and Shrestha, Kushal and Jakubikova, Elena}, year={2013}, month={Aug}, pages={3350–3363} }
 @article{bowman_jakubikova_2012, title={Low-Spin versus High-Spin Ground State in Pseudo-Octahedral Iron Complexes}, volume={51}, ISSN={["1520-510X"]}, DOI={10.1021/ic202344w}, abstractNote={Pseudo-octahedral complexes of iron find applications as switches in molecular electronic devices, materials for data storage, and, more recently, as candidates for dye-sensitizers in dye-sensitized solar cells. Iron, as a first row transition metal, provides a weak ligand-field splitting in an octahedral environment. This results in the presence of low-lying (5)T excited states that, depending on the identity of iron ligands, can become the ground state of the complex. The small energy difference between the low-spin, (1)A, and high-spin, (5)T, states presents a challenge for accurate prediction of their ground state using density functional theory. In this work, we investigate the applicability of the B3LYP functional to the ground state determination of first row transition metal complexes, focusing mainly on Fe(II) polypyridine complexes with ligands of varying ligand field strength. It has been shown previously that B3LYP artificially favors the (5)T state as the ground state of Fe(II) complexes, and the error in the energy differences between the (1)A and (5)T states is systematic for a set of structurally related complexes. We demonstrate that structurally related complexes can be defined as pseudo-octahedral complexes that undergo similar distortion in the metal-ligand coordination environment between the high-spin and low-spin states. The systematic behavior of complexes with similar distortion can be exploited, and the ground state of an arbitrary Fe(II) complex can be determined by comparing the calculated energy differences between the singlet and quintet electronic states of a complex to the energy differences of structurally related complexes with a known, experimentally determined ground state.}, number={11}, journal={INORGANIC CHEMISTRY}, author={Bowman, David N. and Jakubikova, Elena}, year={2012}, month={Jun}, pages={6011–6019} }
 @article{tsuchiya_jakubikova_2012, title={Role of Noncoplanar Conformation in Facilitating Ground State Hole Transfer in Oxidized Porphyrin Dyads}, volume={116}, ISSN={["1520-5215"]}, DOI={10.1021/jp307285z}, abstractNote={We employ density functional theory to investigate ground state hole transfer in covalently linked oxidized zinc-zinc porphyrin ([ZnZn](+)) and zinc-free-base porphyrin ([ZnFb](+)) dyads in both coplanar and noncoplanar (tilted) conformations. We obtain reactant, product, and transition state (TS) for the hole transfer reaction in the [ZnZn](+) system. The hole is localized on a single porphyrin unit in the reactant and product states while delocalized in the TS, implying the dominance of superexchange mechanism in the hole transfer reaction. A metastable as well as stable states are located for the [ZnFb](+) system while no TS is found, indicating a barrierless hole transfer reaction. The hole lifetimes are calculated to be 15.80 and 0.034 ns for [ZnZn](+) in the coplanar and tilted conformation, respectively, and 14.45 and 0.313 ns for [ZnFb](+). The hole transfer rates are found to be several orders of magnitude faster in the tilted conformation than in the coplanar conformation for both dyads, showing the importance of noncoplanar conformation between the two porphyrin pigments in facilitating the hole transfer process. We also show that inclusion of solvent effects in calculations plays an important role in the proper ground state hole localization in oxidized dyads. These results provide an unconventional insight into the hole transfer mechanism in porphyrin arrays and are relevant to design of artificial photoharvesting materials.}, number={41}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Tsuchiya, Takashi and Jakubikova, Elena}, year={2012}, month={Oct}, pages={10107–10114} }
 @article{jakubikova_campbell_martin_2011, title={Effects of Peripheral and Axial Substitutions on Electronic Transitions of Tin Naphthalocyanines}, volume={115}, ISSN={["1520-5215"]}, DOI={10.1021/jp205705e}, abstractNote={Tin naphthalocyanine molecules display strong absorption in the infrared region (IR), making them ideal as components of organic photodiodes and solar cells. We use density functional theory and time-dependent density functional theory (TD-DFT) at the B3LYP level to study the influence of axial and peripheral ligands on the absorption wavelength of tin naphthalocyanines. We find that TD-DFT is successful at reproducing the experimental absorption spectra of free base naphthalocyanine and tin naphthalocyanine molecules and can be used as a reliable tool to predict absorption spectra of substituted naphthalocyanines. Functional groups attached axially to tin (-F, -Cl, -Br, -I) and peripherally to the inner ring (-F, -Cl, -Br, -Ph, -OH, -COCH(3), -O(CH(2))(3)CH(3)) of the tin naphthalocyanine molecule tune the excitation wavelength in the near-infrared region between 770 and 940 nm. While substituents to the outer naphthalocyanine ring (-Cl, -Br) affect the intensity of the absorption peaks in the NIR region, they do not influence their absorption wavelength. Asymmetric substitution of naphthalocyanine pendant arms can be employed to decrease intensity of the absorption peaks in the visible region with respect to the intensity of the peaks in the NIR.}, number={33}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Jakubikova, Elena and Campbell, Ian H. and Martin, Richard L.}, year={2011}, month={Aug}, pages={9265–9272} }
 @article{jakubikova_martin_batista_2010, title={Systematic Study of Modifications to Ruthenium(II) Polypyridine Dyads for Electron Injection Enhancement}, volume={49}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/ic902504y}, DOI={10.1021/ic902504y}, abstractNote={Spatial localization of excited-state electrons in transition-metal complexes used as photocatalysts or dye sensitizers in solar cells is important for efficient electron injection into the metal oxide nanoparticles. We use density functional theory to investigate the excited states in a prototype catalyst-chromophore assembly [(bpy)(H(2)O)Ru(tpy-tpy)Ru(tpy)](4+) ([Ru(tpy)(bpy)(H(2)O)](2+) = catalyst, [Ru(tpy)(2)](2+) = chromophore, tpy = 2,2':6',2''-terpyridine, and bpy = 2,2'-bipyridine) and a series of related compounds. We explore several bridging ligand and terminal tpy ligand modifications of the prototype assembly, with the aim of inducing electronic excitations into the terminal tpy ligand upon irradiation with visible light. The excitations into the terminal ligand (i.e., ligand covalently attached to the semiconductor in the photocatalytic synthetic cell) should, in turn, enhance electron injection into the semiconductor. Our results suggest that both introduction of a spacer group (such as phenylene or alkane) into the tpy-tpy bridge and replacement of the terminal tpy group by a more extended pi-conjugated ligand are necessary to shift the electronic excitations from the bridging ligand into the terminal ligand. These results have implications for the design of photocatalysts and dye-sensitizer assemblies based on ruthenium(II) terpyridine compounds.}, number={6}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Jakubikova, Elena and Martin, Richard L. and Batista, Enrique R.}, year={2010}, month={Mar}, pages={2975–2982} }
 @article{roy_jakubikova_guthrie_batista_2009, title={Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?}, volume={113}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/jp811388w}, DOI={10.1021/jp811388w}, abstractNote={Density Functional calculations have been performed to calculate the one-electron oxidation potential for ferrocene and the redox couples for a series of small transition metal compounds of the first-, second-, and third-row elements. The solvation effects are incorporated via a self-consistent reaction field (SCRF), using the polarized continuum model (PCM). From our study of seven different density functionals combined with three different basis sets for ferrocene, we find that no density functional method can reproduce the redox trends from experiment when referencing our results to the experimental absolute standard hydrogen electrode (SHE) potential. In addition, including additional necessary assumptions such as solvation effects does not lead to any conclusion regarding the appropriate functional. However, we propose that if one references their transition metal compounds results to the calculated absolute half-cell potential of ferrocene, they can circumvent the additional assumptions necessary to predict a redox couple. Upon employing this method on several organometallic and inorganic complexes, we obtained very good correlation between calculated and experimental values (R(2) = 0.97), making it possible to predict trends with a high level of confidence. The hybrid functional B3LYP systematically underestimates the redox potential; however, the linear correlation between DFT and experiment is good (R(2) = 0.96) when including a baseline shift. This protocol is a powerful tool that allows theoretical chemists to predict the redox potential in solution of several transition metal complexes a priori and aids in the rational design of redox-active catalysts.}, number={24}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={Roy, Lindsay E. and Jakubikova, Elena and Guthrie, M. Graham and Batista, Enrique R.}, year={2009}, month={Jun}, pages={6745–6750} }
 @article{jakubikova_chen_dattelbaum_rein_rocha_martin_batista_2009, title={Electronic Structure and Spectroscopy of [Ru(tpy)2]2+, [Ru(tpy)(bpy)(H2O)]2+, and [Ru(tpy)(bpy)(Cl)]+}, volume={48}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/ic901477m}, DOI={10.1021/ic901477m}, abstractNote={We use a combined, theoretical and experimental, approach to investigate the spectroscopic properties and electronic structure of three ruthenium polypyridyl complexes, [Ru(tpy)(2)](2+), [Ru(tpy)(bpy)(H(2)O)](2+), and [Ru(tpy)(bpy)(Cl)](+) (tpy = 2,2':6',2''-terpyridine and bpy = 2,2'-bipyridine) in acetone, dichloromethane, and water. All three complexes display strong absorption bands in the visible region corresponding to a metal-to-ligand-charge-transfer (MLCT) transition, as well as the emission bands arising from the lowest lying (3)MLCT state. [Ru(tpy)(bpy)(Cl)](+) undergoes substitution of the Cl(-) ligand by H(2)O in the presence of water. Density functional theory (DFT) calculations demonstrate that the triplet potential energy surfaces of these molecules are complicated, with several metal-centered ((3)MC) and (3)MLCT states very close in energy. Solvent effects are included in the calculations via the polarizable continuum model as well as explicitly, and it is shown that they are critical for proper characterization of the triplet excited states of these complexes.}, number={22}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Jakubikova, Elena and Chen, Weizhong and Dattelbaum, Dana M. and Rein, Francisca N. and Rocha, Reginaldo C. and Martin, Richard L. and Batista, Enrique R.}, year={2009}, month={Nov}, pages={10720–10725} }
 @article{jakubikova_snoeberger_batista_martin_batista_2009, title={Interfacial Electron Transfer in TiO2 Surfaces Sensitized with Ru(II)−Polypyridine Complexes}, volume={113}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/jp903966n}, DOI={10.1021/jp903966n}, abstractNote={Studies of interfacial electron transfer (IET) in TiO(2) surfaces functionalized with (1) pyridine-4-phosphonic acid, (2) [Ru(tpy)(tpy(PO(3)H(2)))](2+), and (3) [Ru(tpy)(bpy)(H(2)O)-Ru(tpy)(tpy(PO(3)H(2)))](4+) (tpy = 2,2':6,2''-terpyridine; bpy = 2,2'-bipyridine) are reported. We characterize the electronic excitations, electron injection time scales, and interfacial electron transfer (IET) mechanisms through phosphonate anchoring groups. These are promising alternatives to the classic carboxylates of conventional dye-sensitized solar cells since they bind more strongly to TiO(2) surfaces and form stable covalent bonds that are unaffected by humidity. Density functional theory calculations and quantum dynamics simulations of IET indicate that electron injection in 1-TiO(2) can be up to 1 order of magnitude faster when 1 is attached to TiO(2) in a bidentate mode (tau approximately 60 fs) than when attached in a monodentate motif (tau approximately 460 fs). The IET time scale also depends strongly on the properties of the sensitizer as well as on the nature of the electronic excitation initially localized in the adsorbate molecule. We show that IET triggered by the visible light excitation of 2-TiO(2) takes 1-10 ps when 2 is attached in a bidentate mode, a time comparable to the lifetime of the excited electronic state. IET due to visible-light photoexcitation of 3-TiO(2) is slower, since the resulting electronic excitation remains localized in the tpy-tpy bridge that is weakly coupled to the electronic states of the conduction band of TiO(2). These results are particularly valuable to elucidate the possible origin of IET efficiency drops during photoconversion in solar cells based on Ru(II)-polypyridine complexes covalently attached to TiO(2) thin films with phosphonate linkers.}, number={45}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={Jakubikova, Elena and Snoeberger, Robert C., III and Batista, Victor S. and Martin, Richard L. and Batista, Enrique R.}, year={2009}, month={Jul}, pages={12532–12540} }
 @article{he_xie_dong_heinbuch_jakubikova_rocca_bernstein_2008, title={Reactions of Sulfur Dioxide with Neutral Vanadium Oxide Clusters in the Gas Phase. II. Experimental Study Employing Single-Photon Ionization}, volume={112}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/jp805744g}, DOI={10.1021/jp805744g}, abstractNote={Single-photon ionization through vacuum ultraviolet (VUV, 10.5 eV) and soft X-ray (extreme ultraviolet, EUV, 26.5 eV) laser radiation is successfully employed for the study of the reactions of neutral vanadium oxide clusters (V(m)O(n)) with sulfur dioxide (SO2) in the gas phase. V(m)O(n) clusters are generated by reaction of a laser-generated vanadium plasma with O2 in a supersonic expansion. The clusters are cooled in the expansion and are reacted with SO2 in a fast-flow reactor. Detection of neutral clusters and products is through ionization employing VUV and EUV laser radiation and time-of-flight mass spectrometry. Many association reaction intermediates [V(m)O(n)SO2 and V2O4(SO2)2] are observed. Isolated SO is also observed, as a product as predicted by theoretical studies presented in part I (J. Phys. Chem. A 2007, 111, 13339). A weak feature at the SO3 mass channel (80 amu) is suggested to be present in the product mass spectra. Further reactions of the intermediates with O2 are positively identified for VO2SO2, V3O7SO2, and V5O10SO2. Reaction mechanisms are interpreted on the basis of the observations and preliminary theoretical calculations. Molecular level reaction mechanisms for oxidation of SO2 to SO3 facilitated by condensed-phase vanadium oxides as catalysts are suggested.}, number={44}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={He, Sheng-Gui and Xie, Yan and Dong, Feng and Heinbuch, Scott and Jakubikova, Elena and Rocca, J. J. and Bernstein, Elliot R.}, year={2008}, month={Nov}, pages={11067–11077} }
 @article{jakubikova_rappé_bernstein_2007, title={Density Functional Theory Study of Small Vanadium Oxide Clusters†}, volume={111}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/jp0745844}, DOI={10.1021/jp0745844}, abstractNote={Density functional theory is employed to study structure and stability of small neutral vanadium oxide clusters in the gas phase. BPW91/LANL2DZ level of theory is used to obtain structures of VOy (y=1-5), V2Oy (y=2-7), V3Oy (y=4-9), and V4Oy (y=7-12) clusters. Enthalpies of growth and fragmentation reactions of the lowest energy isomers of vanadium oxide molecules are also obtained to study the stability of neutral vanadium oxide species under oxygen saturated gas-phase conditions. Our results suggest that cyclic and cage-like structures are preferred for the lowest energy isomers of neutral vanadium oxide clusters, and oxygen-oxygen bonds are present for oxygen-rich clusters. Clusters with an odd number of vanadium atoms tend to have low spin ground states, while clusters with even number of vanadium atoms have a variety of spin multiplicities for their ground electronic state. VO2, V2O5, V3O7, and V4O10 are predicted to be the most stable neutral clusters under the oxygen saturated conditions. These results are in agreement with and complement previous gas-phase experimental studies of neutral vanadium oxide clusters.}, number={50}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={Jakubikova, Elena and Rappé, Anthony K. and Bernstein, Elliot R.}, year={2007}, month={Dec}, pages={12938–12943} }
 @article{jakubikova_bernstein_2007, title={Reactions of Sulfur Dioxide with Neutral Vanadium Oxide Clusters in the Gas Phase. I. Density Functional Theory Study†}, volume={111}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/jp076439w}, DOI={10.1021/jp076439w}, abstractNote={Thermodynamics of reactions of vanadium oxide clusters with SO2 are studied at the BPW91/LANL2DZ level of theory. BPW91/LANL2DZ is insufficient to properly describe relative V-O and S-O bond strengths of vanadium and sulfur oxides. Calibration of theoretical results with experimental data is necessary to compute reliable enthalpy changes for reactions between VxOy and SO2. Theoretical results indicate SO2 to SO conversion occurs for oxygen-deficient clusters and SO2 to SO3 conversion occurs for oxygen-rich clusters. Stable intermediate structures of VOy (y = 1 - 4) clusters with SO2 are also obtained at the BPW91/TZVP level of theory. Some possible mechanisms for SO3 formation and catalyst regeneration for condensed-phase systems are suggested. These results are in agreement with, and complement, gas-phase experimental studies of neutral vanadium oxide clusters.}, number={51}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={Jakubikova, Elena and Bernstein, Elliot R.}, year={2007}, month={Dec}, pages={13339–13346} }
 @article{jakubikova_rappé_bernstein_2006, title={Exploration of Basis Set Issues for Calculation of Intermolecular Interactions}, volume={110}, ISSN={1089-5639 1520-5215}, url={http://dx.doi.org/10.1021/jp0680239}, DOI={10.1021/jp0680239}, abstractNote={The ab initio calculation of intermolecular interactions requires a large basis set to describe systems with dominant dispersion interaction accurately. This paper focuses on calculation of intermolecular bonding energies of weakly bound systems within the supermolecular method and on issues related to the choice of a basis set for these calculations, in particular size of the basis set, efficiency of 2-electron integral codes, basis set superposition error (BSSE), and the linear dependence of basis functions. In an attempt to find more efficient basis sets for calculations of intermolecular interactions, standard basis sets (10s Huzinaga, 6-311G**, cc-pV6Z), or their parts, are extended (tessellated) by a set of off-centered, s or p functions, symmetrically placed around the nuclei. Standard basis sets (10s Huzinaga, 6-311G**, cc-pVXZ, aug-cc-pVXZ, X = D, T, Q, 5, 6) are also augmented by sets of atom-centered, higher angular momentum functions (p, d, f). The distance from the nucleus of tessellating functions and orbital exponents of tessellating and augmenting functions are optimized with respect to the BSSE-corrected bonding energy at the MP2 or UCCSD level of theory. The two approaches are tested on the model systems with dominant dispersion interactions (3)H(2), (CH(4))(2), and Ne(2), and their efficiency is compared. Both tessellation and augmentation are successful in describing the intermolecular interactions of these model systems, with augmentation being more efficient. Our results draw attention to the linear dependence problems inevitably present in accurate calculations and confirm the need for underlying standard basis sets that provide good descriptions of core and valence electrons for the tessellation and augmentation approaches to be reliable.}, number={31}, journal={The Journal of Physical Chemistry A}, publisher={American Chemical Society (ACS)}, author={Jakubikova, Elena and Rappé, Anthony K. and Bernstein, Elliot R.}, year={2006}, month={Aug}, pages={9529–9541} }
 @article{babinec_jakubı́ková elena_leszczynski_2004, title={Erratum to: “Recurrence plot analysis of nonlinear vibrational dynamics in H3+ molecule” [Chaos, Solitons and Fractals 17 (5) (2003) 981–984]}, volume={21}, ISSN={0960-0779}, url={http://dx.doi.org/10.1016/j.chaos.2003.12.002}, DOI={10.1016/j.chaos.2003.12.002}, number={2}, journal={Chaos, Solitons & Fractals}, publisher={Elsevier BV}, author={Babinec, Peter and Jakubı́ková Elena and Leszczynski, Jerzy}, year={2004}, month={Jul}, pages={513–514} }
 @article{babinec_jakubíková_leszczynski_2000, title={Transition from Regular to Stochastic Vibrational Motion in H+3 Molecule: An ab initio Classical Trajectory Study}, volume={55}, ISSN={1865-7109 0932-0784}, url={http://dx.doi.org/10.1515/zna-2000-3-417}, DOI={10.1515/zna-2000-3-417}, abstractNote={Abstract An ab initio classical trajectory study of intramolecular vibrational dynamics in H+3 molecule revealed a transition from regular quasiperiodic to stochastic motion at an energy slightly higher than the zero point vibrational energy}, number={3-4}, journal={Zeitschrift für Naturforschung A}, publisher={Walter de Gruyter GmbH}, author={Babinec, P. and Jakubíková, E. and Leszczynski, J.}, year={2000}, month={Apr}, pages={478–480} }
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