Abstract: 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 Forster 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 Kruger, 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.

Abstract: Electron pairs in the valence shell of an atom that do not participate in the bonding of a molecule (“lone pairs”) give rise to a concentrated electron density away from the atom center. To account for the asymmetry in the electron charge density that arises from lone pairs, an electrostatic model is developed that is parametrically anisotropic at the atomic level. The model uses virtual interaction sites with partial charges that are associated but not coincident with the nuclei. In addition, the model incorporates anisotropic atomic polarizabilities. The protocol previously outlined in Anisimov et al. [J. Chem. Theory Comput. 2005, 1, 153] for parametrizing the electrostatic potential energy of a polarizable force field using classical Drude oscillators is extended to incorporate additional lone pair parameters. To probe the electrostatic environment around the lone pairs, the static (molecule alone) and perturbed (molecule in the presence of a test charge) electrostatic potential (ESP) are evaluated an...

Abstract: Effects of nanoscale confinement and partial charges that stem from quantum calculations are investigated in silica slit channels filled with 1 M KCl at the point of zero charge by using a hierarch...

Abstract: Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter model of KcsA of about 300 atoms at the Hartree-Fock level of theory. Partial charges were derived from the quantum mechanically determined electrostatic potential either with Merz-Kollman or Hinsen-Roux schemes. Large polarization and/or charge transfer occur on potassium ions located in the filter, while the charges on sodium ions remain closer to unity. As a result, a weaker binding is obtained for K+ ions. Using a simplified version of a permeation model based on the concerted-motion mechanism for ion translocation within the single-file ion channel [P. H. Nelson, J. Chem. Phys. 117, 11396 (2002)], we discuss how differences in polarization effects in the adducts with K+ and Na+ can play a role as for ionic selectivity and conductance.

Abstract: An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjusting Rappe and Goddard's atomic electronegativity values. Using a test set of compounds for which experimental solvation energies are available and a rather small number of parameters, very good agreement was obtained with experiment, with a mean unsigned error of about 0.5 kcal/mol. The QEq atomic partial charge assignment method can reflect the effects of the conformational changes and solvent induction on charge distribution in molecules. In the second section of the paper we examined this feature with a study of the alanine dipeptide conformations in water solvent. The different contributions to the energy surface of the dipeptide were examined and compared with the results from fixed CHARMm charge potential, which is widely used for molecular dynamics studies.

Abstract: The charge distribution of taurine (2-aminoethane-sulfonic acid) is revisited by using an orbital-based method that describes the density in a fixed molecular orbital basis with variable orbital occupation numbers. A new neutron data set is also employed to explore whether this improves the deconvolution of thermal motion and charge density. A range of molecular properties that are novel for experimentally determined charge densities are computed, including Weinhold population analysis, Mayer bond orders, and local kinetic energy densities, in addition to charge topological analysis and quantum theory of atoms-in-molecules (QTAIM) integrated properties. The ease with which a distributed multipole analysis can be performed on the fitted density matrix makes it straightforward to compute molecular moments, the lattice energy, and the electrostatic interaction energies of molecules removed from the crystal. Results are compared with high-level (QCISD) gas-phase calculations and band structure calculations employing density functional theory. Finally, the avenues available for extending the range of molecular properties that can be calculated from experimental charge densities still further using this approach are discussed.

Abstract: Charge form factors for N=82 and N=126 isotonic nuclei are calculated with the relativistic eikonal approximation, in which the charge density distributions are from the relativistic mean-field theory. The variations of charge form factors with proton number are discussed in detail. It is found that the most sensitive parts of the charge form factors are those around the minimums and maximums. For an increasing proton number, the charge form factors near the extrema have an upward shift. As the protons increase and occupy a new shell, the minimums and maximums of the charge form factors could also have a significant inward shift. The results can be useful for the study of behaviors of valence-proton wave functions for such nuclei as can be considered as a core plus proton(s), and thus the proton-halo phenomenon. In addition, the results can also be useful for future electron-unstable nucleus scattering experiments and provide tests of the reliability of the relativistic mean-field theory for the unstable nuclei.

Abstract: A theoretical description of photoinduced charge transfer involves explicit treating both the optical formation of the nuclear wave packet on the excited free energy surface and its ensuing dynamics. The reaction pathway constitutes two-stage charge transfer between three centers. Manifestations of fractional charge transfer at first stage are explored. An expression for time dependent rate constant of photoinduced charge transfer is found in the framework of the linear dielectric continuum model of the medium. The model involves both the intramolecular vibrational reorganization and the Coulombic interaction of the transferred charge with the medium polarization fluctuations and allows to express the rate in terms of intramolecular reorganization parameters and complex dielectric permittivity. The influence of the vibrational coherent motion in the locally excited state on the charge transfer dynamics has been explored. The dependence of the ultrafast photoinduced charge transfer dynamics on the excitation pulse carrier frequency (spectral effect) has been investigated. The spectral effect has been shown to depend on quantity of the fractional charge.

Abstract: Ab initio plane-wave-based density functional calculations for the molecules Zn 2 L 2 with the ligands L = H, CH 3 , F, η 5 -C 5 H 5 (cyclopentadienyl Cp) show how the ZnZn and ZnL bonds evolve to dimetallocene from simple H to the electronically and spatially extended Cp ligand. The metal–metal bond distances (pm) decrease in the order: 240.2 (H), 239 (CH 3 ), 230.4 (F), 230 (Cp) compared to distances: 266 (Zn metal), 246 (Zn 2 2+ ), 230.5 (crystalline Zn 2 [C 5 (CH 3 ) 5 ] 2 ). Analysis is supported by calculation of the total charge and partial charge density distributions and the electron localization function (ELF). In the dizinc region, the ELF consists of a separate ring (torus) and mid-bond axis basin. For molecules with the ligands H, CH 3 , and F, the mid-bond basin attractor appears on the bond axis at higher ELF followed at lower values by the ring. For Cp, the reverse is true. In the Cp compound, the bonding from ring to metal atom involves both sigma σ -contributions with s-, p-, and d-components and π -contributions with p- and d-components. In the Cp compound, the ELF shows some differentiation in the CC bonding within the C 5 ring towards three single C–C and two double C C bonds.

Abstract: First principles density functional calculations are performed on a number of square planar hydroxamate chelates of several divalent metal ions in order to determine their respective affinities for some biologically important ligands. The structures of the complexes are discussed, and the calculated binding mode is in agreement with experimental results. Extensive calculations have shown that, although the interactions are dominated mainly by electrostatic forces, there is a covalent contribution as well that introduces subtle variations in binding affinities of various metal ions. Thus, although a reasonable correlation is found between the complexation energies and reciprocals of the ionic radii of the metal ions, deviations may be attributed to some covalent character of the metal–ligand bonds, which modify a ligand's affinity for a metal ion and introduce subtle variations that are ultimately responsible for their biological action. A linear relationship between the partial charge on the metal ion and the LUMO energy shows that metal ions with lower lying vacant orbitals are able to form covalent coordination with the ligand. The affinity of the formohydroxamate ion for Ni(II) is satisfactorily explained on this basis. The bonding characteristics of the investigated complexes are discussed, as is the optimum size of the metal binding site. Some other hydroxamic acids are also investigated in this work. The electronic structures of urease from two microorganisms, and their acetohydroxamate complexes are also investigated in order to understand the inhibition mechanism. This study should prove useful not only for the understanding of coordination bonding, but also in the investigation of metalloenzymes and their inhibition.

Abstract: Post form of “boundary corrected continuum intermediate state (BCIS)” approximation has been employed to study charge transfer cross-sections in collision of Cq+, Nq+ and Oq+ (q=1–5) with ground state atomic hydrogen in the energy range of 50–200 keV/amu. In this formalism we have adopted model potential for the interaction of the active electron with the projectile ion. Calculated results for total charge transfer cross-sections have significant improvement over other existing theoretical results in their comparison to the available experimental findings except for singly charge ions. Sub-shell distribution for total charge transfer cross-section has also been reported in graphical form. Predictions suggested by Olson in connection with the sub-shell distribution of total charge transfer cross-section has been reaffirmed. However, an oscillatory structure of charge state dependence of the total charge transfer cross-sections has not been found in the present investigation.

Abstract: Charge optimization as a tool for both analyzing and enhancing binding electrostatics has become an attractive approach over the past few years. An interesting feature of this method for molecular design is that it provides not only the optimal charge magnitudes, but also the selectivity of a particular atomic center for its optimal charge. The current approach to compute the charge selectivity at a given atomic center of a ligand in a particular binding process is based on the binding-energy cost incurred upon the perturbation of the optimal charge distribution by a unit charge at the given atomic center, while keeping the other atomic partial charges at their optimal values. A limitation of this method is that it does not take into account the possible concerted changes in the other atomic charges that may incur a lower energetic cost than perturbing a single charge. Here, we describe a novel approach for characterizing charge selectivity in a concerted manner, taking into account the coupling between the ligand charge centers in the binding process. We apply this novel charge selectivity measure to the celecoxib molecule, a nonsteroidal anti-inflammatory agent binding to cyclooxygenase 2 (COX2), which has been recently shown to also exhibit cross-reactivity toward carbonic anhydrase II (CAII), to which it binds with nanomolar affinity. The uncoupled and coupled charge selectivity profiles over the atomic centers of the celecoxib ligand, binding independently to COX2 and CAII, are analyzed comparatively and rationalized with respect to available experimental data. Very different charge selectivity profiles are obtained for the uncoupled versus coupled selectivity calculations.

Abstract: We study a model of charge transfer in alloys proposed by Bruno, Zingales, and Wang Phys. Rev. Lett. 91, 166401 2003 and show its connection with electron-electron correlations. We then investigate in detail the properties of Madelung and related matrices, the mechanism leading to the screening of the electrostatic interactions between atomic net charges in random alloys, and calculate the screened interactions. Furthermore, we derive an expression for the total energy and show that the fluctuation contributions to the local and Madelung energy mutually cancel. We then derive and discuss the probability distribution function of local charges and make a comparison with calculations for large supercells. Finally, we discuss the relation of the present approach to other theories aimed at the description of Coulomb effects in alloys.

Abstract: The Ca* + CH3F --> CaF + CH3 reaction was photoinduced in 1:1 Ca...CH3F complexes formed in a supersonic expansion. The transition state of the reaction was explored by monitoring the electronically excited product, CaF, while scanning the laser that turns on the reaction. Moreover, the electronic structure of the Ca...FCH3 system was studied using ab initio methods by associating a pseudopotential description of the [Ca2+] and [F7+] cores, a core polarization operator on calcium, an extensive Gaussian basis and a treatment of the electronic problem at the CCSD(T) (ground state) and RSPT2 (excited states) level. In this contribution we present experimental results for the free complex and a comparison with the results of a previous experiment where the Ca...CH3F complexes are deposited at the surface of large argon clusters. The ab initio calculations allowed an interpretation of the experimental data in terms of two reaction mechanisms, one involving a partial charge transfer state, the other involving the excitation of the C-F stretch in the CH3F moiety prior to charge transfer.

Abstract: Thirty-one thermodynamical and quantum-chemical descriptors were used to characterize all 209 chloro trans-azobenzenes (Ct-ABs, PCt-ABs) in terms of their environmental stability and specific dioxin-like toxicity. Some of the PCt-ABs are produced as a by-side impurity during the manufacture of 3,4-dichloroaniline (DCA) and its derivatives and thus can be found in technical products of certain chloroaniline herbicides. A prepared basic thermodynamic and quantum-chemical property data matrix of PCt-ABs was interpreted using Principal Component Analysis (PCA). The PCA of the thermodynamic and quantum-chemical data matrix created a three-dimensional model that explained 78% (68% + 6% + 4%) of the total variance in the data set. The loading plot shows that the first Principal Component (PC) is influenced by variables describing molecular weight, polarizability and lipophilicity. The second PC was strongly influenced by the most positive partial charge on atoms and the most negative partial charge on atoms. The third PC depends on energy of the highest occupied molecular orbital. Next, factors extracted from PCA were used for selection of a representative set of eight trans-chloroazobenzene congeners, which seemed in the best way reflect a diverse property of all 209 PCt-ABs.

Abstract: We observed the memory effect, the working voltage lowering, which occurred due to the repeated partial charge-discharge cycling of a Ni-capacity-limited alkaline cell, for example 50–70% state of charge, and γ-NiOOH in the Ni electrode was identified as the cause of the memory effect. During this condition, γ-NiOOH is proposed to be formed by partial overcharging due to the heterogeneity of the conductive materials such as cobalt compounds in the Ni electrode. Using nano-sized conductive materials homogeneously dispersed in the electrode leads to a significant effect on the suppression of the memory effect occurring due to the repeated partial charge-discharge cycling.

Abstract: Redox-active hollow spheres were prepared through extracting a polystyrene core from the latex particle (PSPAAFc) composed of the core and the polyallylamine shell including ferrocenyl carboxylic amide. The suspension of the hollow spheres showed anodic and cathodic voltammetric peaks, which were nearly reversible and diffusion-controlled. The current was 3 times as large as the current for the suspension of the filled PSPAAFc. This value agreed with the theoretical one evaluated from the diameter (1.28 μm), the number of ferrocenyl moieties per particle, 1.2 × 108, by UV spectroscopy, and the diffusion coefficient obtained from the Stokes−Einstein equation. This fact indicates the reaction of the whole loaded charge, in contrast to the partial charge transfer of PSPAAFc. The dynamic flattening motion was observed to support the reaction of the whole charge.

Abstract: In associative charge transfer (ACT) reactions, a core ion activates ligand molecules by partial charge transfer. The activated ligand polymerizes, and the product oligomer takes up the full charge from the core ion. In the present system, benzene+• (Bz+•) reacts with two propene (Pr) molecules to form a covalently bonded ion, C6H6+• + 2 C3H6 → C6H12+• + C6H6. The ACT reaction is activated by a partial charge transfer from Bz+• to Pr in the complex, and driven to completion by the formation of a covalent bond in the polymerized product. An alternative channel forms a stable association product (Bz·Pr)+•, with an ACT/association product ratio of 60:40% that is independent of pressure and temperature. In contrast to the Bz+•/propene system, ACT polymerization is not observed in the Bz+•/ethylene (Et) system since charge transfer in the Bz+•(Et) complex is inefficient to activate the reaction. The roles of charge transfer in these complexes are verified by ab initio calculations. The overall reaction of Bz+•...

Abstract: We have set up a model for the energy-dependent lifetime, including the effects of the charge carrier collisions with ionized impurities, polar optical phonons, and space charge. The model is then used to compute the mobility spectrum at each temperature, which used to compute the pertinent magnetic-field-dependent Hall parameters. The computed Hall parameters compared can then be measured values to estimate the validity of the lifetime model and parameters. The method has been applied to two n-GaAs∕SI–GaAs epitaxial layers containing two types of carriers. The magnetic field dependence of the Hall voltage has been observed in the studied GaAs layers. We present the numerical solution of the neutrality equation, which contains all sources of charges present in the sample, and numerical integration of the total relaxation times ⟨τ⟩ so combined that is possible to obtain the mobility of the partial charges and their part in the whole conductivity of the layer.

Abstract: The profile of injected charges in a C60-based field-effect transistor (FET) is considered. A simple scheme for calculations of the charge distribution between the 2D layers of C60 molecules is founded on a small magnitude of the interball electron hopping. Analytical solutions of the equations for the charge distributions are obtained in the limits of thick and thin crystals. The charge density is shown to drop exponentially with the crystal depth. The calculations predict the relative part of induced charges involved in the surface layer to be 3∕4 and 2∕3 in the cases of electron and hole injection, respectively.

Abstract: Motivated by the charge order (CO) and superconductivity (SC) in θ - ( ET ) 2 X salts, we study the extended Hubbard model in a two-dimensional triangular lattice with variational Monte Carlo method. We show that the nearest-neighbor Coulomb interaction V induces charge fluctuation and the 3-fold CO state is stabilized. We also discuss the possibility of next-nearest-neighbor f-wave SC induced by charge fluctuation.