Spectroscopic and electronic structure of the CuIn,AgIn, CuGa and AgGa diatomics

Electronic, geometrical and spectroscopic properties of heteronuclear CuIn, AgIn, CuGa and AgGa diatomics have been investigated employing LCGTO-MP-LSD method. For all the molecules the ground state has been found to be the¹Σ one followed by³Π,¹Π and³Σ low-lying electronic state respectively. The geometric and electronic parameters are in reasonable agreement with the available experimental data. The chemical bond in the molecules has a single bond character due to the valence bond couplings between the Cu 4s (or Ag 5s) and the Ga 4p (or In 5p) electrons.     

Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling V(da) is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of V(da) for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a pi stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of V(da) are obtained with the standard 6-31G(*) and extended 6-31+ +G(**) basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of V(da) are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements V(da) for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.     

Understanding solvent effects on hyperfine coupling constants of cyclohexadienyl radicals

Quantum chemical calculations have been carried out to understand better solvent effects on the isotropic muon and proton hyperfine coupling constants in the C₆H₆Mu^• radical. Both polarizable continuum solvent models and explicit inclusion of water molecules into supermolecular complexes were used. Changes in the hyperfine couplings of in-plane hydrogen atoms are very small and difficult to discuss, partly due to relatively large experimental error bars. In contrast, the out-of-plane proton and muon hyperfine couplings exhibit more pronounced changes. These are partly due to structural changes of the radical and partly due to direct electronic polarization effects. Polarizable continuum solvent models agree well with experimental changes for benzene but overshoot the enhancement of the hyperfine couplings for water. Explicit inclusion of water molecules reduces this overestimated spin density increase and thereby tends to bring theory and experiment into closer agreement. The enhancement of the spin density on the out-of-plane hydrogen or muon atoms by the solvent environment is mainly due to an increased polarization of the singly occupied MO towards this side. Electronic Supplementary Material: Supplementary material is available in the online version of this article at dx.doi.org/10.1007/s00214-005-0680-x     

Excitation energy transfer pathways in light‐harvesting proteins: Modeling with PyFREC

Excitation energy transfer (EET) determines the fate of sunlight energy absorbed by light‐harvesting proteins in natural photosynthetic systems and photovoltaic cells. As previously reported (D. Kosenkov, J. Comput. Chem. 2016, 37(19), 1847), PyFREC software enables computation of electronic couplings between organic molecules with a molecular fragmentation approach. The present work reports implementation of direct fragmentation‐based computation of the electronic couplings and EET rates in pigment–protein complexes within the Förster theory in PyFREC. The new feature enables assessment of EET pathways in a wide range of photosynthetic complexes, as well as artificial molecular architectures that include light‐harvesting proteins or tagged fluorescent biomolecules. The developed methodology has been tested analyzing EET in the Fenna–Matthews–Olson (FMO) pigment–protein complex. The pathways of excitation energy transfer in FMO have been identified based on the kinetics studies. © 2017 Wiley Periodicals, Inc.     

Does Förster theory predict the rate of electronic energy transfer for a model dyad at low temperature?

The use of the F?rster model to predict the dynamics of resonant electronic energy transfer (RET) in a model donor-acceptor dyad (a terphenyl-bridged perylene diimide (PDI)-terrylene diimide (TDI) dyad molecule) embedded at low temperature in a PMMA matrix is tested against experiment. The relevant ingredients involved in the F?rster rate for RET, namely electronic coupling, spectral overlap, and screening effects, are accounted for in a quantitative manner. Electronic couplings are obtained from time-dependent density functional theory calculations, and the effect of the PMMA environment is included both on the transition densities and on their interaction through the IEFPCM model. We find that the presence of the terphenyl bridge induces a slight delocalization of the PDI and TDI transition densities over the bridge originating in a 56% increase in the coupling and in the breakdown of the dipole-dipole approximation. The spectral overlap is determined on the basis of a detailed simulation of the homogeneously broadened donor emission and acceptor absorption line shapes determined by fitting the single molecule spectra measured at 1.2 K. The corresponding distribution of spectral overlap throughout the ensemble is then estimated by assuming an uncorrelated inhomogeneous line broadening for the donor and acceptor. Combining the calculated electronic couplings and spectral overlaps sampled from Monte Carlo realizations of the energetic disorder, we obtain a mean RET time (approximately 8 ps) and a distribution in reasonable agreement with experiment.     

The Impact of Interlayer Electronic Coupling on Charge Transport in Organic Semiconductors: A Case Study on Titanylphthalocyanine Single Crystals

Traditionally, it is believed that three‐dimensional transport networks are preferable to those of lower dimensions. We demonstrate that inter‐layer electronic couplings may result in a drastic decrease of charge mobilities by utilizing field‐effect transistors (FET) based on two phases of titanyl phthalocyanine (TiOPc) crystals. The α‐phase crystals with electronic couplings along two dimensions show a maximum mobility up to 26.8 cm² V^?1 s^?1. In sharp contrast, the β‐phase crystals with extra significant inter‐layer electronic couplings show a maximum mobility of only 0.1 cm² V^?1 s^?1. Theoretical calculations on the bulk crystals and model slabs reveal that the inter‐layer electronic couplings for the β‐phase devices will diminish remarkably the device charge transport abilities owing to the coupling direction perpendicular to the current direction. This work provides new insights into the impact of the dimensionality and directionality of the packing arrangements on charge transport in organic semiconductors.     

Exciton Migration in Conjugated Dendrimers: A Joint Experimental and Theoretical Study

We report a joint experimental and theoretical investigation of exciton diffusion in phenyl‐cored thiophene dendrimers. Experimental exciton diffusion lengths of the dendrimers vary between 8 and 17 nm, increasing with the size of the dendrimer. A theoretical methodology is developed to estimate exciton diffusion lengths for conjugated small molecules in a simulated amorphous film. The theoretical approach exploits Fermi’s Golden Rule to estimate the energy transfer rates for a large ensemble of bimolecular complexes in random relative orientations. Utilization of Poisson’s equation in the evaluation of the Coulomb integral leads to very efficient calculation of excitonic couplings between the donor and the acceptor chromophores. Electronic coupling calculations with delocalized transition densities revealed efficient coupling pathways in the bulk of the material, but do not result in strong couplings between the chromophores which are calculated for more localized transition densities. The molecular structures of dendrimers seem to be playing a significant role in the magnitude of electronic coupling between chromophores. Simulated diffusion lengths correlate well with the experimental data. The chemical structure of the chromophore, the shape of the transition densities and the exciton lifetime are found to be the most important factors in determining the size of the exciton diffusion length in amorphous films of conjugated materials.     

Modelling charge transfer reactions with the frozen density embedding formalism

The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5'-GG-3' and 5'-GT-3'. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.     

Electronic couplings in DNA pi-stacks: multistate effects

In this study, we employ a multistate generalized Mulliken-Hush approach for calculating electronic couplings V(da) for charge transfer (CT) in DNA pi-stacks consisting of three, four, and five base pairs. In these systems the guanine donor and acceptor sites are separated by several (AT) pairs. The Hartree-Fock calculations of the stacks are carried out with the standard 6-31G basis sets. All possible superexchange pathways are accounted for. We examine electronic couplings estimated using the two-state and multistate models. Although for some systems the two-state scheme provides reasonable estimates of V(da), in general this simple model fails to reproduce the electronic couplings calculated with the multistate approach. The two-state treatment of pi-stacks with a tunneling gap less than 0.3 eV, for instance, GAAG and GAAAG, may lead to invalid estimates of V(da). We consider the dependence of V(da) on the length and composition of the bridge. The calculations show that V(da) is less sensitive to the arrangement of nucleobases in the bridge, as can be predicted on the basis of electronic couplings between adjacent base pairs.     

Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD

We describe the new Pathways plugin for the molecular visualization program visual molecular dynamics. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules, and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU's Not Unix (GNU) public license. © 2012 Wiley Periodicals, Inc.     

Ecoupling server: A tool to compute and analyze electronic couplings

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user‐friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI‐python using Apache and it is accessible at http://ecouplingserver.bsc.es . Ecoupling server is free and open to all users without login. © 2016 Wiley Periodicals, Inc.     

A fast scheme to calculate electronic couplings between P3HT polymer units using diabatic orbitals for charge transfer dynamics simulations

We propose a fast and accurate calculation method to compute the electronic couplings between molecular units in a thiophene-ring-based polymer chain mimicking a real organic semiconducting polymer, poly(3-hexylthiophene). Through a unit block diabatization scheme, the method employed minimal number of diabatic orbitals to compute the site energies and electronic couplings, which were validated by comparing with benchmark density functional theory calculations. In addition, by using the obtained electronic couplings, a quantum dynamics simulation was carried out to propagate a hole initially localized in a thiophene-ring unit of the polymer chain. This work establishes a simple, efficient, and robust means for the simulation of electron or hole transfer processes in organic semiconducting materials, an important capability for study and understanding of the class of organic optoelectronic and photovoltaic materials. © 2018 Wiley Periodicals, Inc.     

Influence of the alkyl and alkoxy side chains on the electronic structure and charge-transport properties of polythiophene derivatives

Density Functional Theory has been used to study the structural, electronic and charge-transport properties of two regio-regular head-to-tail polythiophene derivatives, i.e. poly(3-hexyl-thiophene), P3HT, and poly(3-oxyhexyl-thiophene), P3OHT. The effect of substituents on the electronic structure was analyzed by means of bandwidth, bandgap, effective mass, total and partial densities of states and crystal orbital overlap populations. Electronic couplings were estimated from band diagrams as the splitting of the valence band. The neutral and cationic states of isolated oligomers were optimized using the supercell approximation. The hole-transfer rates and mobilities were evaluated according to Marcus's theory. Results provide a compelling illustration of the effect of side chains on the crystal packing, electronic structure and charge-transport properties. Thus, the hole mobility calculated for the alkyl derivative was 0.15 cm(2) V(-1) s(-1) (experimental mobility is 0.10 cm(2) V(-1) s(-1)), while the alkoxy derivative has a theoretical mobility of 0.49 cm(2) V(-1) s(-1). The obtained results hopefully could motivate experimentalists to try out P3OHT for an improved charge carrier mobility.     

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.     

Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance

We present a method for analytically calculating the derivative couplings between a pair of configuration-interaction-singles (CIS) excited states obtained in an atom-centered basis. Our theory is exact and has been derived using two completely independent approaches: one inspired by the Hellmann-Feynman theorem and the other following from direct differentiation. (The former is new, while the latter is in the spirit of existing approaches in the literature.) Our expression for the derivative couplings incorporates all Pulay effects associated with the use of an atom-centered basis, and the computational cost is minimal, roughly comparable to that of a single CIS energy gradient. We have validated our method against CIS finite-difference results and have applied it to the lowest lying excited states of naphthalene; we find that naphthalene derivative couplings include Pulay contributions sufficient to have a qualitative effect. Going beyond standard problems in analytic gradient theory, we have also constructed a correction, based on perturbative electron-translation factors, for including electronic momentum and eliminating spurious components of the derivative couplings that break translational symmetry. This correction is general and can be applied to any level of electronic structure theory.     

Electronic couplings in organic mixed-valence compounds: the contribution of photoelectron spectroscopy

We show that the electronic coupling in strongly coupled organic mixed-valence systems can be effectively probed by means of gas-phase ultraviolet photoelectron spectroscopy (UPS). Taking six diamines as examples, the UPS estimates for the electronic couplings H(ab) are compared with the corresponding values determined from the intervalence charge-transfer absorption bands and from electronic structure calculations. Similar trends are observed for the H(ab) values estimated from UPS and optical spectra; this provides support for the applicability of Hush theory to strongly coupled organic mixed-valence systems. The UPS electronic couplings are found to be somewhat smaller than those from optical spectroscopy, which is attributed to the role of vibronic coupling to symmetrical modes; when corrected for this vibronic coupling, the UPS H(ab) estimates confirm that triarylamine-based mixed-valence systems are close to the class-II/class-III borderline.     

Evidence of Long-Range 13C-31P Couplings: A 13C NMR Investigation of Some Aryl Esters of Phosphor-Amidochloridic Acid and the Related Compounds

Abstract

In ¹³ NMR study organophosphorus compounds, sign and magnitude of ¹³ C-³¹ P spin-spin couplings has been of great interest to elucidate stereochemistry and electronic state of phosphorus central atom. However, a discussion about the mechanisms of carbon-phosphorus couplings is still complicated specially in the case of long-range couplings that also are not frequently observed. In this study, ¹³ C NMR chemical shifts and coupling constants have been determined for a series of aryl esters of phosphoramidochloridic acid with the general formula: R₂NP(O)(OAr)Cl, in which R = methyl and/or benzyl, Ar = p-tolyl. p-nitrophenyl, and phenyl. Besides usual W-couplings that could be found in these systems, we detected long-range couplings through five and six bonds. It has been shown that, these couplings are highly dependent on substituents on phosphorus nuclei. The data for some related compounds have been also obtained for a comparison.     

Stereoselectivity in Autoionization Reactions of Hydrogenated Molecules by Metastable Noble Gas Atoms: The Role of Electronic Couplings

Focus in the present paper is on the analysis of total and partial ionization cross sections, measured in absolute value as a function of the collision energy, representative of the probability of ionic product formation in selected electronic states in Ne*?H₂O, H₂S, and NH₃ collisions. In order to characterize the imaginary part of the optical potential, related to electronic couplings, we generalize a methodology to obtain direct information on the opacity function of these reactions. Such a methodology has been recently exploited to test the real part of the optical potential (S. Falcinelli et al., Chem. Eur. J., 2016 , 22, 764–771). Depending on the balance of noncovalent contributions, the real part controls the approach of neutral reactants, the removal of ionic products, and the structure of the transition state. Strength, range, and stereoselectivity of electronic couplings, triggering these and many other reactions, are directly obtained from the present investigation.