Bonding and excitation in COCu(001) from a cluster model and density functional treatments

The bonding properties and charge distributions of the COCu(001) system have been studied within density functional theory (DFT) with several density functionals. A Cu18(9,4,5)CO three layer cluster was found to give bond distances and energies in agreement with previous experimental and theoretical results for low coverage systems, provided the atomic basis set includes diffuse orbitals and d-orbitals at the Cu atoms. Charge distributions give insight on the nature of the localized adsorbate bonding. Time-dependent DFT results on excitation energies and on transition and average electric dipoles, relevant to photodesorption, are also presented.     

Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water

A combination of the polarizable continuum model (PCM) and the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology, PCM-MM/QM, is used to include the solute electronic polarization and then study the solvent effects on the low-lying n→π(?) excitation energy and the (15)N nuclear magnetic shielding of pyrazine and pyridazine in aqueous environment. The results obtained with PCM-MM/QM are compared with two other procedures, i.e., the conventional PCM and the iterative and sequential QM/MM (I-QM/MM). The QM calculations are made using density functional theory in the three procedures. For the excitation energies, the time-dependent B3LYP/6-311+G(d) model is used. For the magnetic shielding, the B3LYP/aug-pcS2(N)/pcS2(C,O,H) is used with the gauge-including atomic orbitals. In both cases, i.e., PCM-MM/QM and I-QM/MM, that use a discrete model of the solvent, the solute is surrounded by a first shell of explicit water molecules embedded by an electrostatic field of point charges for the outer shells. The best results are obtained including 28 explicit water molecules for the spectral calculations and 9 explicit water molecules for the magnetic shielding. Using the PCM-MM/QM methodology the results for the n→π(?) excitation energies of pyridazine and pyrazine are 32,070 ± 80 cm(-1) and 32,675 ± 60 cm(-1), respectively, in good agreement with the corresponding I-MM/QM results of 32,540 ± 80 cm(-1) and 32,710 ± 60 cm(-1) and the experimental results of 33,450-33,580 cm(-1) and 32,700-33,300 cm(-1). For the (15)N magnetic shielding, the corresponding numbers for the gas-water shifts obtained with PCM-MM/QM are 47.4 ± 1.3 ppm for pyridazine and 19.7 ± 1.1 ppm for pyrazine, compared with the I-QM/MM values of 53.4?±?1.3 ppm and 19.5 ± 1.2 ppm and the experimental results of 42-54 ppm and 17-22 ppm, respectively. The agreement between the two procedures is found to be very good and both are in agreement with the experimental values. PCM-MM/QM approach gives a good solute polarization and could be considered in obtaining reliable results within the expected QM/MM accuracy. With this electronic polarization, the solvent effects on the electronic absorption spectra and the (15)N magnetic shielding of the diazines in water are well described by using only an electrostatic approximation. Finally, it is remarked that the experimental and theoretical results suggest that the (15)N nuclear magnetic shielding of any diazine has a clear dependence with the solvent polarity but not directly with the solute-solvent hydrogen bonds.     

Polarization energy gradients in combined quantum mechanics, effective fragment potential, and polarizable continuum model calculations

A method that combines quantum mechanics (QM), typically a solute, the effective fragment potential (EFP) discrete solvent model, and the polarizable continuum model is described. The EFP induced dipoles and polarizable continuum model (PCM) induced surface charges are determined in a self-consistent fashion. The gradients of these two energies with respect to molecular coordinate changes are derived and implemented. In general, the gradients can be formulated as simple electrostatic forces and torques among the QM nuclei, electrons, EFP static multipoles, induced dipoles, and PCM induced charges. Molecular geometry optimizations can be performed efficiently with these gradients. The formulas derived for EFPPCM can be generally applied to other combined molecular mechanics and continuum methods that employ induced dipoles and charges.     

Intermolecular coulomb couplings from ab initio electrostatic potentials: application to optical transitions of strongly coupled pigments in photosynthetic antennae and reaction centers

An accurate and numerically efficient method for the calculation of intermolecular Coulomb couplings between charge densities of electronic states and between transition densities of electronic excitations is presented. The coupling of transition densities yields the F?rster type excitation energy transfer coupling, and from the charge density coupling, a shift in molecular excitation energies results. Starting from an ab initio calculation of the charge and transition densities, atomic partial charges are determined such as to fit the resulting electrostatic potentials of the different states and the transition. The different intermolecular couplings are then obtained from the Coulomb couplings between the respective atomic partial charges. The excitation energy transfer couplings obtained in the present TrEsp (transition charge from electrostatic potential) method are compared with couplings obtained from the simple point-dipole and extended dipole approximations and with those from the ab initio transition density cube method of Krüger, Scholes, and Fleming. The present method is of the same accuracy as the latter but computationally more efficient. The method is applied to study strongly coupled pigments in the light-harvesting complexes of green sulfur bacteria (FMO), purple bacteria (LH2), and higher plants (LHC-II) and the "special pairs" of bacterial reaction centers and reaction centers of photosystems I and II. For the pigment dimers in the antennae, it is found that the mutual orientation of the pigments is optimized for maximum excitonic coupling. A driving force for this orientation is the Coulomb coupling between ground-state charge densities. In the case of excitonic couplings in the "special pairs", a breakdown of the point-dipole approximation is found for all three reaction centers, but the extended dipole approximation works surprisingly well, if the extent of the transition dipole is chosen larger than assumed previously. For the "special pairs", a large shift in local transition energies is found due to charge density coupling.     

Electronic excitation spectrum of the photosensitizer [Ir(ppy)2(bpy)]+

The vertical singlet-singlet and singlet-triplet electronic excitation energies of bis(2-phenylpyridinato-)(2,2'-bipyridine)iridium(III) ([Ir(ppy)(2)(bpy)](+)) are calculated on the basis of a comparative quantum chemical study using wave function methods such as CASSCF∕CASPT2 and density functional theory (TDDFT) with local and range-separated functionals. The TDDFT results show a strong dependence of the charge-transfer transition energies on the amount of the exact exchange in the functional. In general, TDDFT with range-separated functionals provides a good agreement with the experimental spectra. As a result a new assignment of the absorption spectrum of the title compound is proposed.     

Theoretical investigation of the mechanism and dynamics of intramolecular coherent resonance energy transfer in soft molecules: a case study of dithia-anthracenophane

A computational study is conducted on dithia-anthracenophane (DTA), for which there is experimental evidence for coherent resonance energy transfer dynamics, and on dimethylanthracene (DMA), a molecule representing the energy donor and the acceptor in DTA. Electronic excitation energies are calculated by configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) methods and are compared to experimental ones. Electronic coupling constants are calculated between two DMAs embedded into the ground-state structure of DTA employing methods based on transition densities. The resulting values of electronic coupling provide a more consistent interpretation of experiments than those based on one-half the level spacing of DTA excitation energies. Solvation effects are studied based on the polarizable continuum model (PCM). Solvent-induced polarization and screening effects are shown to make opposite contributions, and the net electronic coupling is little different from the value in a vacuum. The likelihood of coherent population transfer is assessed on the basis of a recently developed theory of coherent resonance energy transfer. The time scale of bath is shown to have an important role in sustaining the quantum coherence. The combination of quantum chemical and dynamical data suggests that the electronic coupling in DTA is in the range of 50-100 cm(-1). The presence of oscillatory excitation population dynamics can be understood from the picture of polaronic excitation moderately dressed with dispersive vibrational modes. The effect of torsional modulation on the excitation energies of DTA and electronic coupling is examined on the basis of optimized structures with the torsional angle constrained. The result suggests that inelastic effect due to torsional motion cannot be disregarded in DTA.     

Chlorophyll excitation energies and structural stability of the CP47 antenna of photosystem II: a case study in the first-principles simulation of light-harvesting complexes

Natural photosynthesis relies on light harvesting and excitation energy transfer by specialized pigment–protein complexes. Their structure and the electronic properties of the embedded chromophores define the mechanisms of energy transfer. An important example of a pigment–protein complex is CP47, one of the integral antennae of the oxygen-evolving photosystem II (PSII) that is responsible for efficient excitation energy transfer to the PSII reaction center. The charge-transfer excitation induced among coupled reaction center chromophores resolves into charge separation that initiates the electron transfer cascade driving oxygenic photosynthesis. Mapping the distribution of site energies among the 16 chlorophyll molecules of CP47 is essential for understanding excitation energy transfer and overall antenna function. In this work, we demonstrate a multiscale quantum mechanics/molecular mechanics (QM/MM) approach utilizing full time-dependent density functional theory with modern range-separated functionals to compute for the first time the excitation energies of all CP47 chlorophylls in a complete membrane-embedded cyanobacterial PSII dimer. The results quantify the electrostatic effect of the protein on the site energies of CP47 chlorophylls, providing a high-level quantum chemical excitation profile of CP47 within a complete computational model of “near-native” cyanobacterial PSII. The ranking of site energies and the identity of the most red-shifted chlorophylls (B3, followed by B1) differ from previous hypotheses in the literature and provide an alternative basis for evaluating past approaches and semiempirically fitted sets. Given that a lot of experimental studies on CP47 and other light-harvesting complexes utilize extracted samples, we employ molecular dynamics simulations of isolated CP47 to identify which parts of the polypeptide are most destabilized and which pigments are most perturbed when the antenna complex is extracted from PSII. We demonstrate that large parts of the isolated complex rapidly refold to non-native conformations and that certain pigments (such as chlorophyll B1 and β-carotene h1) are so destabilized that they are probably lost upon extraction of CP47 from PSII. The results suggest that the properties of isolated CP47 are not representative of the native complexed antenna. The insights obtained from CP47 are generalizable, with important implications for the information content of experimental studies on biological light-harvesting antenna systems.

Advanced QM/MM simulations explore the excited states of a photosynthetic light-harvesting antenna in its physiologically complexed state and model the consequences of extraction on conformational and electronic properties.     

High-resolution inner-shell excitation spectroscopy of H2-phthalocyanine

We report on a combined experimental and theoretical carbon and nitrogen K-edge near-edge x-ray absorption fine structure investigation on condensed metal-free phthalocyanine (H2Pc). Based on the results from improved virtual orbital calculations, all resonances in the experimental high-resolution data can be assigned to various electronic transitions. The comparison between experiments and calculations further shows that a significant influence of the core hole, which affects both the transition energies and the cross sections, is present and must be considered in theoretical approaches. Moreover, additional fine structure is clearly resolved for the first N 1s-->pi* transition, which can be interpreted as vibronic coupling to the electronic core excitation.     

Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems

Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.     

Spin-orbit relativistic long-range corrected time-dependent density functional theory for investigating spin-forbidden transitions in photochemical reactions

A long-range corrected (LC) time-dependent density functional theory (TDDFT) incorporating relativistic effects with spin-orbit couplings is presented. The relativistic effects are based on the two-component zeroth-order regular approximation Hamiltonian. Before calculating the electronic excitations, we calculated the ionization potentials (IPs) of alkaline metal, alkaline-earth metal, group 12 transition metal, and rare gas atoms as the minus orbital (spinor) energies on the basis of Koopmans' theorem. We found that both long-range exchange and spin-orbit coupling effects are required to obtain Koopmans' IPs, i.e., the orbital (spinor) energies, quantitatively in DFT calculations even for first-row transition metals and systems containing large short-range exchange effects. We then calculated the valence excitations of group 12 transition metal atoms and the Rydberg excitations of rare gas atoms using spin-orbit relativistic LC-TDDFT. We found that the long-range exchange and spin-orbit coupling effects significantly contribute to the electronic spectra of even light atoms if the atoms have low-lying excitations between orbital spinors of quite different electron distributions.     

Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins

The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.     

TD-CI simulation of the electronic optical response of molecules in intense fields II: comparison of DFT functionals and EOM-CCSD

Time-dependent configuration interaction (TD-CI) simulations can be used to simulate molecules in intense laser fields. TD-CI calculations use the excitation energies and transition dipoles calculated in the absence of a field. The EOM-CCSD method provides a good estimate of the field-free excited states but is rather expensive. Linear-response time-dependent density functional theory (TD-DFT) is an inexpensive alternative for computing the field-free excitation energies and transition dipoles needed for TD-CI simulations. Linear-response TD-DFT calculations were carried out with standard functionals (B3LYP, BH&HLYP, HSE2PBE (HSE03), BLYP, PBE, PW91, and TPSS) and long-range corrected functionals (LC-ωPBE, ωB97XD, CAM-B3LYP, LC-BLYP, LC-PBE, LC-PW91, and LC-TPSS). These calculations used the 6-31G(d,p) basis set augmented with three sets of diffuse sp functions on each heavy atom. Butadiene was employed as a test case, and 500 excited states were calculated with each functional. Standard functionals yield average excitation energies that are significantly lower than the EOM-CC, while long-range corrected functionals tend to produce average excitation energies slightly higher. Long-range corrected functionals also yield transition dipoles that are somewhat larger than EOM-CC on average. The TD-CI simulations were carried out with a three-cycle Gaussian pulse (ω = 0.06 au, 760 nm) with intensities up to 1.26 × 10(14) W cm(-2) directed along the vector connecting the end carbons. The nonlinear response as indicated by the residual populations of the excited states after the pulse is far too large with standard functionals, primarily because the excitation energies are too low. The LC-ωPBE, LC-PBE, LC-PW91, and LC-TPSS long-range corrected functionals produce responses comparable to EOM-CC.     

Theoretical and experimental study of the vertical excitation energies in the ionic and tautomeric forms of 4-aminomethylpyridine

4-Aminomethylpyridine (4-PAM) has been widely used as a model compound to elucidate the mechanisms of biological and biomedical action of the amino derivatives of vitamin B₆. By virtue of the presence of two ionizable groups (viz. a pyridine nitrogen and an amino function) in its structure, 4-PAM in solution occurs as various ionic and tautomeric forms in equilibrium. In this work, we optimized the geometries of such forms and found the protonation status of the ionizable groups in 4-PAM to affect the molecular geometry and frontier orbitals. In addition, we determined the experimental electronic excitation energies for each molecular species of 4-PAM from deconvoluted UV–vis spectra. The results thus obtained were compared with their theoretical counterparts as determined from TD-DFT calculations. Based on the outcome, the theoretical methodology used affords correct simulation of electronic excitation energies. The theoretical and experimental results showed that the deprotonation of the pyridine nitrogen has no effect on the energy of the first electronic transition, however it affects its intensity. Additionally, the deprotonation of both pyridine nitrogen and methylamino group increases the number of bands, by increasing the n–π^* transitions.     

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the pi stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares V(2) and the energies of basepair triplets XG(+)Y and XA(+)Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15,000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, approximately 0.07 eV, while the interstrand couplings are quite different. The energies of hole states G(+) and A(+) in the stack depend on the nature of the neighboring pairs. The XG(+)Y are by 0.5 eV more stable than XA(+)Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.     

UV-vis spectra of <Emphasis Type="Italic">p</Emphasis>-benzoquinone anion radical in solution by a TD-DFT/PCM approach

Excited electronic states of the anion radical of para-benzoquinone were studied by time dependent density functional theory (TD-DFT) including bulk solvent effects by the polarizable continuum model (PCM). The computed vertical excitation energies for the first four low-lying doublet states are in good agreement with previous post-Hartree–Fock computations. Geometry optimization of excited states and inclusion of solvent effects lead to a remarkable agreement between computed adiabatic transition energies and experimental band maxima. Together with their specific interest, the results point out the reliability of TD-DFT/PCM approach for valence excitations and the need to take geometry relaxation and solvent effects into the proper account for a meaningful comparison between computed and experimental absorption spectra.