Abstract: A specific methodology was developed to collate the interlayer configurations resulting from Grand-Canonical Monte Carlo (GCMC) simulations with experimental X-ray and neutron diffraction data for two synthetic Na-saturated saponites having contrasting layer charge. Numerical simulations were performed assuming different existing sets of atomic partial charge and Lennard-Jones parameters for clay and water. For each parameter set and for the two samples in both the mono- and bihydrated states, the water contents resulting from GCMC simulations were first compared to water vapor desorption gravimetry data. The density distributions of interlayer species were then used to generate 00l intensities that were compared to X-ray and neutron diffraction data, the latter being recorded on both hydrogenated and deuterated specimens. The CLAYFF model [Cygan et al. J. Phys. Chem. B2004, 108, 1255] is shown to better account for water content and organization compared to the model developed by Skipper et al. (Clays Cl...

Abstract: We present a scaling theory for charge transport in disordered molecular semiconductors that extends percolation theory by including bonds with conductances close to the percolating one in the random-resistor network representing charge hopping. A general and compact expression is given for the charge mobility for Miller-Abrahams and Marcus hopping on different lattices with Gaussian energy disorder, with parameters determined from numerically exact results. The charge-concentration dependence is universal. The model-specific temperature dependence can be used to distinguish between the hopping models.

Abstract: We discuss the origin of an additional dip other than the charge neutrality point observed in the transfer characteristics of graphene-based field-effect transistors with a Si/SiO2 substrate used as the back-gate. The double dip is proved to arise from charge transfer between the graphene and the metal electrodes, while charge storage at the graphene/SiO2 interface can make it more evident. Considering a different Fermi energy from the neutrality point along the channel and partial charge pinning at the contacts, we propose a model which explains all the features observed in the gate voltage loops. We finally show that the double dip enhanced hysteresis in the transfer characteristics can be exploited to realize graphene-based memory devices.

Abstract: Ordinary least-squares (OLS) regression has been used widely for constructing the scoring functions for protein–ligand interactions. However, OLS is very sensitive to the existence of outliers, and models constructed using it are easily affected by the outliers or even the choice of the data set. On the other hand, determination of atomic charges is regarded as of central importance, because the electrostatic interaction is known to be a key contributing factor for biomolecular association. In the development of the AutoDock4 scoring function, only OLS was conducted, and the simple Gasteiger method was adopted. It is therefore of considerable interest to see whether more rigorous charge models could improve the statistical performance of the AutoDock4 scoring function. In this study, we have employed two well-established quantum chemical approaches, namely the restrained electrostatic potential (RESP) and the Austin-model 1-bond charge correction (AM1-BCC) methods, to obtain atomic partial charges, and we...

Abstract: We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-a-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp.

Abstract: Ab initio studies on molecular hydrogen adsorption in lithium-doped hexaborane(6) (B6H6Li2) have been carried out. Our calculated results show that the lithium sites in the complex carry a partial positive charge, and the binding energy of Li to the borane framework, as calculated at the MP2/aug-cc-pVTZ level of theory, is found to be −196.467 kcal/mol per lithium, which is large enough to ensure the stability toward recyclability. This charged surface created around the metal atom is found to interact with molecular hydrogen through charge-induced dipole interaction. Each lithium site is found to adsorb a maximum of three hydrogen molecules which corresponds to a gravimetric density of 12 wt %. We have also verified the possibility of constructing a three-dimensional solid using the dilithium-doped B6 unit as a building block and −C≡C− units as a linking agent. The hydrogen adsorption properties of this designed structure show that it can adsorb hydrogen with a gravimetric density of 7.3 wt %, and bindin...

Abstract: The electronic coupling between adjacent molecules is an important parameter for the charge transport properties of organic semiconductors. In a previous paper, a semiclassical generalized nonadiabatic transition state theory was used to investigate the nonperturbative effect of the electronic coupling on the charge transport properties, but it is not applicable at low temperatures due to the presence of high-frequency modes from the intramolecular conjugated carbon–carbon stretching vibrations [G. J. Nan et al., J. Chem. Phys., 2009, 130, 024704]. In the present paper, we apply a quantum charge transfer rate formula based on the imaginary-time flux–flux correlation function without the weak electronic coupling approximation. The imaginary-time flux–flux correlation function is then expressed in terms of the vibrational-mode path average and is evaluated by the path integral approach. All parameters are computed by quantum chemical approaches, and the mobility is obtained by kinetic Monte-Carlo simulation. We evaluate the intra-layer mobility of sexithiophene crystal structures in high- and low-temperature phases for a wide range of temperatures. In the case of strong coupling, the quantum charge transfer rates were found to be significantly smaller than those calculated using the weak electronic coupling approximation, which leads to reduced mobility especially at low temperatures. As a consequence, the mobility becomes less dependent on temperature when the molecular packing leads to strong electronic coupling in some charge transport directions. The temperature-independent charge mobility in organic thin-film transistors from experimental measurements may be explained from the present model with the grain boundaries considered. In addition, we point out that the widely used Marcus equation is invalid in calculating charge carrier transfer rates in sexithiophene crystals.

Abstract: A recent study of the interaction of a lithium atom with the thiophene molecule found a large disagreement between high-level coupled cluster (CCSD(T)/AVTZ) and quantum Monte Carlo (fixed-node diffusion Monte Carlo, or FNDMC) calculations. We address this "lithium-thiophene riddle" by analyzing the influence of crucial FNDMC simulation parameters, namely, the one-electron models, basis sets, and pseudopotentials used for the generation of the trial wave function. These are shown to have a significant impact on the calculated FNDMC interaction energies, and good agreement between CCSD(T) and FNDMC is found when nodal hypersurfaces of sufficient quality are used. On the basis of our proposed consensus reference value, we go on to benchmark the standard toolbox of lower-level quantum chemistry methods for this model interaction. Newly developed dispersion-corrected DFT methods perform reasonably well despite the partial charge transfer character of the interaction and might well be worthy of further study in larger lithium-thiophene systems.

Abstract: This paper presents an analytical study of the distribution of charge on the particles in a complex plasma; the study is based on statistical mechanics and ensures that the charge on the particles is an integral multiple of the electronic charge. The formulation incorporates both the number and energy balance of electrons/ions. Three specific cases of charging of particles have been considered, namely (i) in a plasma in the absence of electron emission from the particles, (ii) in a complex plasma in thermal equilibrium and (iii) in a complex plasma irradiated by monochromatic radiation, causing photoelectric emission of electrons from the particles. The effect of various parameters on the charge distribution has also been investigated. This paper is in reasonably good agreement with the fluctuation theory for large values of Z (Ze is the charge on a particle). It is seen that under certain conditions, a significant number of oppositely charged particles occur in the complex plasma.

Abstract: A one-site and a five-site polarizable model for liquid carbon tetrachloride (CCl4) is presented. They are based on a non-polarizable model consisting of five van der Waals sites not carrying any partial charges. In the one-site model, a charge on a spring with a polarizability of 11.1 nm3 was attached to the carbon to make the model polarizable, while in the five-site model polarizabilities nm3 and nm3 were added to the carbon and chlorine atoms, respectively. Both models exactly reproduce the experimental static dielectric permittivity of 2.24 at 293 K and 1 atm. This quantity was calculated by applying a homogeneous external electric field of varying strength. The one-site polarizable model is only about 1.7 times more computationally expensive than the non-polarizable one and is compatible with the GROMOS force field. A selected set of thermodynamic, dynamic and structural quantities was calculated and compared to experiment.

Abstract: Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi–Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi–Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred.

Abstract: In this work, we analyzed the influence of the charge model on the magnitudes of atomic charges and electrostatic energies for the binding of aromatic drug molecules with DNA. The dependence of the charge and energy on the level of theory (HF, DFT (B3LYP), MP2, semi-empirical methods), basis set (STO-3G, 3-21G, 6-31G, 6-31G*, 6-31G**), method of charge computation (Mulliken, Natural Population Analysis, CHelpG, Merz–Kollman), and force field charge (CHARMM27, AMBER99) has been tracked for typical aromatic drugs of different structure and charge state. Recommendations and restrictions have been formulated for the use of particular approaches in charge/electrostatic energy calculations.

Abstract: The inventory of the single-crystal X-ray structures of aliphatic and aromatic 2-oxazolines, namely 2-nonyl-2-oxazoline, 2,2′-tetramethylenebis(2-oxazoline) and 2-phenyl-2-oxazoline, reveals significant delocalization of π-electrons along the NCO segment. The delocalization of π-electrons is stabilized by inductive and resonance contributions of the side-chains; in 2-phenyl-2-oxazoline, also π-arene interactions between the benzene ring and the CN and the CO bond stabilize the crystalline phase. This delocalization gives a partial negative charge to the nitrogen atom and a partial positive charge to the oxygen atom. The partial negative charge of the nitrogen atom makes this atom the exclusive reaction partner also for highly reactive non-selective cations, which explains the regioselectivity of electrophilic attacks in cationic ring-opening polymerizations. Copyright © 2011 Society of Chemical Industry

Abstract: By using Mulliken and Natural Bond Orbital (NBO) methods based on the density functional theory (DFT), partial charges of exocyclic nitrogen atoms were calculated for nitrenium ions formed from 201 known drugs and 50 Ames positive (mutagenic) compounds containing aryl amine and nitro moieties. The statistical difference of the partial charges was analysed based on the hypothesis that the mutagens have a more negative charge on their exocyclic nitrogen atom resulting in stable nitrenium ions, and thus a longer lifetime to react selectively with DNA; whereas known drugs are not in general mutagenic and therefore have a relatively more positive partial charge. The nitrenium ions with 1° amine parent compounds did not show a statistical difference between drugs and mutagens based on the Mulliken charges. A slight difference was observed in the NBO data where the drugs have more negative partial charge on their exocyclic nitrogen atoms compared with the mutagens. Interestingly, nitrenium ions with aryl nitro drugs as their parent compounds have more negative charge on the exocyclic nitrogen compared with the other drug classes. Aryl nitro drugs are relatively scarce and are often linked to genotoxicity, which fits with the hypotheses proposed. These results indicate that other physical properties besides the stability of the nitrenium ions are important to determine the mutagenic potential of aryl amine and nitro containing compounds.

Abstract: The nature and strength of the interactions occurring between epoxides and CO2 have been investigated by combining infrared spectroscopy with quantum chemistry calculations. A series of infrared absorption experiments on four model epoxide molecules highly diluted in supercritical CO2 have been performed at constant temperature T = 40 °C for various CO2 pressures varying from 1 to 30 MPa. Then, we carried out a theoretical analysis based on quantum chemistry calculations using Density Functional Theory (B3PW91 and CAM-B3LYP) and ab initio (MP2) computational methods. A very good agreement between experimental and calculated vibrational frequency shifts of the epoxide ring vibrations group was obtained using the CAM-B3LYP functional, hence validating the calculated optimized geometries of the epoxide–CO2 complexes. Whatever the epoxide considered, CO2 is found to be on average above the oxygen atom of the epoxy ring and interacts with the carbon atom of CO2 through a Lewis acid–Lewis base type of interaction. The substituents on the epoxide ring are found to influence the stability of the epoxide–CO2 complexes mainly because of the partial charge on the oxygen atom that is sensitive to the nature of the substituent.

Abstract: A classical, polarizable, electrostatic theory of short-ranged atom−atom interactions, incorporating the smeared nature of atomic partial charges, is presented. Detailed models are constructed for CO monomer and for CO interacting with an iron atom, as a first step toward heme proteins. A good representation is obtained of the bond-length-dependent dipole of CO monomer from fitting at the equilibrium distance only. Essential features of the binding of CO to myoglobin (Mb) and model heme compounds, including the binding energy, the position of the minimum in the Fe−C potential, the Fe−C frequency, the bending energy, the linear geometry of FeCO, and the increase of the Stark tuning rate and IR intensity, are obtained, suggesting that a substantial part of the Fe−CO interaction consists of a classical, noncovalent, “electrostatic bond ”. The binding energy is primarily polarization energy, and the polarization energy of an OH pair in water is shown to be comparable to the experimental hydrogen bond energy.

Abstract: The replacement of a point dipole and a point quadrupole by a corresponding linear arrangement of two point charges (+q, −q) and accordingly three point charges (+q, −2q, +q) is studied with respect to vapour–liquid equilibria. The dependence of saturated liquid density, vapour pressure and heat of vaporization on the choice of the distance d between the charges in the point charge arrangement is analysed. For the studied dipolar two-centre Lennard-Jones (2CLJD) and quadrupolar two-centre Lennard-Jones (2CLJQ) models, d/σ between 1/15 and 1/20 is a reasonable compromise between numerical and physical accuracy, where σ is the Lennard-Jones size parameter. The results are used to derive validated partial charge based models of 59 real fluids from previously published point dipole and point quadrupole based models.

Abstract: Continuum solvent models have shown to be very efficient for calculating solvation energy of biomolecules in solution. However, in order to produce accurate results, besides atomic radii or volumes, an appropriate set of partial charges of the molecule is needed. Here, a set of partial charges produced by a fluctuating charge model—the atom-bond electronegativity equalization method model (ABEEMσπ) fused into molecular mechanics is used to fit for the analytical continuum electrostatics model of generalized-Born calculations. Because the partial atomic charges provided by the ABEEMσπ model can well reflect the polarization effect of the solute induced by the continuum solvent in solution, accurate and rapid calculations of the solvation energies have been performed for series of compounds involving 105 small neutral molecules, twenty kinds of dipeptides and several protein fragments. The solvation energies of small neutral molecules computed with the combination of the GB model with the fluctuating charge protocol (ABEEMσπ/GB) show remarkable agreement with the experimental results, with a correlation coefficient of 0.97, a slope of 0.95, and a bias of 0.34 kcal/mol. Furthermore, for twenty kinds of dipeptides and several protein fragments, the results obtained from the analytical ABEEMσπ/GB model calculations correlate well with those from ab initio and Poisson-Boltzmann calculations. The remarkable agreement between the solvation energies computed with the ABEEMσπ/GB model and PB model provides strong motivation for the use of ABEEMσπ/GB solvent model in the simulation of biochemical systems.

Abstract: We present a simple and practical method to include ligand electronic polarization in molecular dynamics (MD) simulation of biomolecular systems The method involves periodically spawning quantum mechanical (QM) electrostatic potential (ESP) calculations on an extra set of computer processors using molecular coordinate snapshots from a running parallel MD simulation The QM ESPs are evaluated for the small-molecule ligand in the presence of the electric field induced by the protein, solvent, and ion charges within the MD snapshot Partial charges on ligand atom centers are fit through the multi-conformer restrained electrostatic potential (RESP) fit method on several successive ESPs The RESP method was selected since it produces charges consistent with the AMBER/GAFF force-field used in the simulations The updated charges are introduced back into the running simulation when the next snapshot is saved The result is a simulation whose ligand partial charges continuously respond in real-time to the short-term mean electrostatic field of the evolving environment without incurring additional wall-clock time We show that (1) by incorporating the cost of polarization back into the potential energy of the MD simulation, the algorithm conserves energy when run in the microcanonical ensemble and (2) the mean solvation free energies for 15 neutral amino acid side chains calculated with the quantum polarized fluctuating charge method and thermodynamic integration agree better with experiment relative to the Amber fixed charge force-field

Abstract: The literature data on substituent influence on the g factors, hyperfine coupling (hfc) constants (a) of the EPR signals and the spin densities (ρ) have been analyzed for 25 series of the organic radical cations and radical anions as well as of the transition metal complexes. The g, a, and ρ values were first established to depend not only on the inductive and resonance effects but also on the polarizability of substituents which can be characterized by the σα constants. The polarizability effect is caused by the partial charge on the radical center. This effect consists in an electrostatic attraction between the charge and the dipole moments induced by this charge in the substituents. The polarizability contribution ranges up to 92%. Copyright © 2011 John Wiley & Sons, Ltd.

Abstract: Surface charge density and distribution dependence of a nanochannel electro-osmotic flow was examined using a Molecular Dynamics (MD) model. Systems consisting of Na+ and Cl? ions in water confined between crystalline walls with varying negative charge on inner surfaces in an external electric field were investigated. At low surface charge densities, water flows as expected by common interpretations of electro-osmosis. At intermediate surface charge density, the flow exhibits a maximum. Strongly charged surfaces cause adsorption of counterions, immobilisation of the near-wall fluid layers, and subsequent flow reversal. An effect of increase in the viscosity of water near the strongly charged surface was demonstrated. When the discrete ?1 e charge was distributed on a subgrid of surface atoms, the flow deteriorated and reversed at much lower surface charge densities than when all the surface atoms carried equal partial charge.

Abstract: We developed three-dimensional quantitative structure activity relationship (3D-QASR) models for 17 adamantyl derivatives as P-glycoprotein (P-gp) inhibitors. Eighteen different partial charge calculation methods were tested to check the feasibility of the 3D-QSAR models. Best predictive comparative molecular field analysis (CoMFA) model was obtained with the Austin Model 1-Bond Charge Correction (AM1-BCC) atomic charge. The 3D-QSAR models were derived with CoMFA and comparative molecular similarity indices analysis (CoMSIA). The final CoMFA model ( = 0.764, = 0.988) was calculated with an AM1-BCC charge and electrostatic parameter, whereas the CoMSIA model ( = 0.655, = 0.964) was derived with an AM1-BCC charge and combined steric, electrostatic, hydrophobic and HB-acceptor parameters. Leave-five-out (LFO) cross-validation was also performed, which yielded good correlation coefficient for both CoMFA (0.801) and CoMSIA (0.656) models. Robustness of the developed models was checked further with 1000 run bootstrapping analyses, which gave an acceptable correlation coefficient for CoMFA (BS- = 0.997, BS-SD = 0.003) and CoMSIA (BS- = 0.996, BS-SD = 0.018).

Abstract: A variety of combinations of oppositely charged ions have been reacted to examine the role of the charge state from a multiply protonated or multiply deprotonated reagent ion on the efficiency of conversion of a singly charged ion of opposite polarity to a singly charged ion of the same polarity as the reagent. Maximum efficiencies on the order of tens of percent were observed. A threshold for charge inversion was noted in all cases and, with one exception, a clear decrease in efficiency was also noted at high charge states. A model was developed to predict charge inversion efficiency based on charge states, cross-sections of the reactants, and relevant thermodynamic ion affinity values for the reactants and products. The model predicts a threshold for charge inversion, although the prediction does not match the observed threshold quantitatively. This discrepancy is likely due to a simplifying assumption that is not justified on a quantitative basis but which does reproduce the qualitative trend. The model does not predict the major decrease in efficiency at high charge states. However, calculations show that the kinetic energies of the charge inversion products can lead to significant scattering losses at high charge states of the ion-ion collision complex.

Abstract: Equilibrium charge state fractions have been measured for 3–7 MeV lithium, boron and carbon ions passing through thin foils of copper, silver, and gold. The current results are combined with other low-Z ion data from the literature to give the relative influence of different target materials on charge exchange processes. The mean charge of the projectile, the functional form of the charge state distribution, and the charge state distribution width are parameters used to examine the effects of the electronic structure on charge exchange for various target-projectile combinations. Projectile shell structure is found to have a large influence on the widths of the charge state.

Abstract: The spectral and kinetic properties of 5-(4,5-diphenyl-1,3-oxazol-2-yl)spiro[indoline-naphthopyran] derivatives were studied by experimental and theoretical methods. The additional long-wavelength maximum in the absorption spectra of compounds studied is due to the introduction of a diphenyloxazole fragment and corresponds to a π-π* electronic transition with a partial charge transfer character. Substituents have little effect on the kinetic parameters of the spironaphthopyrans studied.

Abstract: Potential models which include charge transfer are used to study ice/water coexistence properties and properties of the ice Ih phase. Two charge transfer models are used, one which is non-polarizable and one which is polarizable. These models transfer a discreet amount of charge for each hydrogen bond made and the net charge of a molecule is determined by the difference in the number of hydrogen bonds a molecule makes as a donor and as an acceptor. In ice Ih, this difference is very near zero and the net amount of charge transfer is correspondingly essentially zero. This differs from the amount of charge transfer in the liquid phase. The results for the polarizable charge transfer model confirm other studies that suggest the importance of polarizability in reproducing the high dielectric constant of ice Ih.