Molecular electrostatic charge models: A topographical approach

Electrostatic charge models for molecules have been developed by employing the critical topographical features of the molecular electrostatic potential (MESP ) as the “fitting” criterion. These models include one or more spherical Gaussians for incorporating the continuous electron-charge distribution in addition to the positive valued point charges representing the nuclei. The model parameters (point charges, the orbital exponents, and Gaussian centers) are optimized so as to mimic the extremal characteristics of the corresponding quantum chemical MESP . The test cases reported here include methane, ethylene, and methanol molecules. The charge models developed using the present method are seen to satisfactorily reproduce the ab initio MESP and its extremal features. © 1994 John Wiley & Sons, Inc.     

Charge asymmetries in hydration of polar solutes

We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.     

Completely soft molecular electrostatic potentials (CoSMEP) and total density functions

Soft molecular electrostatic potentials (SMEP or SEMP) have been recently defined substituting the point-like proton by a Gaussian positive charge distribution. In the present paper an additional step is taken forward, transforming SMEP into a completely soft MEP (CoSMEP). Such transformation is carried out using a charge distributed proton as in SMEP and also a Gaussian positive nuclear charge distribution, instead of the classical point-like nuclear charges. The general form of MEP is roughly preserved, but new features can be noticed. Such new point of view is also associated to the possibility to redefine the molecular charge density. Definition of CoSMEP is thus connected to the definition of total molecular density functions (DF), where to the negative electronic DF is summed up the soft nuclear DF, made of linear combinations of Gaussian distributions of nuclear charges.     

Electrostatic water models

The possiblity of creating a useful model for the electrostatic potential around the water molecule is examined from two different starting points. It is suggested that the simplest and most accurate model will have three point charges on the nuclei together with a diffuse Gaussian charge centered near the nuclear center of the charge. This will represent the lone-pair cloud, include the penetration effects, and improve the representation of the electron density. The alternative use of atomic dipoles is explored but seen to be less effective.     

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

Summary Distributed Point Charge Models (PCM) for CO, (H₂O)₂, and HS-SH molecules have been computed from analytical expressions using multicenter multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.Dedicated to Prof. Alberte PullmanPacific Northwest Laboratory is operated for the US Department of Energy by Battelle Memorial Institute under contract DE-ACO6-76RLO 1830     

From dimer to condensed phases at extreme conditions: accurate predictions of the properties of water by a Gaussian charge polarizable model

Water exhibits many unusual properties that are essential for the existence of life. Water completely changes its character from ambient to supercritical conditions in a way that makes it possible to sustain life at extreme conditions, leading to conjectures that life may have originated in deep-sea vents. Molecular simulation can be very useful in exploring biological and chemical systems, particularly at extreme conditions for which experiments are either difficult or impossible; however this scenario entails an accurate molecular model for water applicable over a wide range of state conditions. Here, we present a Gaussian charge polarizable model (GCPM) based on the model developed earlier by Chialvo and Cummings [Fluid Phase Equilib. 150, 73 (1998)] which is, to our knowledge, the first that satisfies the water monomer and dimer properties, and simultaneously yields very accurate predictions of dielectric, structural, vapor-liquid equilibria, and transport properties, over the entire fluid range. This model would be appropriate for simulating biological and chemical systems at both ambient and extreme conditions. The particularity of the GCPM model is the use of Gaussian distributions instead of points to represent the partial charges on the water molecules. These charge distributions combined with a dipole polarizability and a Buckingham exp-6 potential are found to play a crucial role for the successful and simultaneous predictions of a variety of water properties. This work not only aims at presenting an accurate model for water, but also at proposing strategies to develop classical accurate models for the predictions of structural, dynamic, and thermodynamic properties.     

Potential energy surfaces for small alcohol dimers I: methanol and ethanol

Potential energy landscapes for homogeneous dimers of methanol and ethanol were calculated using counterpoise (CP) corrected energies at the MP26-311+G(2df,2pd) level. The landscapes were sampled at approximately 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of a relative monomer yaw, pitch, and roll and the spherical angles between the monomer centers (taken as the C atom attached to the O). The 19 different routes studied for methanol and the 22 routes examined for ethanol include 607 CP corrected energies. Both landscapes can be adequately represented by site-site, pairwise-additive models, suitable for use in molecular simulations. A modified Morse potential is used for the individual pair interactions either with or without point charges to represent the monomer charge distribution. A slightly better representation of the methanol landscape is obtained using point charges, while the potential energy landscape of ethanol is slightly better without point charges. This latter representation may be computationally advantageous for molecular simulations because it avoids difficulties associated with long-range effects of point-charge-type models.     

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials

A new method for performing molecular dynamics simulations with fluctuating charge polarizable potentials is introduced. In fluctuating charge models, polarizability is treated by allowing the partial charges to be variables, with values that are coupled to charges on the same molecule as well as those on other molecules. The charges can be efficiently propagated in a molecular dynamics simulation using extended Lagrangian dynamics. By making a coordinate change from the charge variables to a set of normal mode charge coordinates for each molecule, a new method is constructed in which the normal mode charge variables uncouple from those on the same molecule. The method is applied to the TIP4P-FQ model of water and compared to other methods for implementing the dynamics. The methods are compared using different molecular dynamics time steps.     

On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields

The Thole induced point dipole model is combined with three different point charge fitting methods, Merz–Kollman (MK), charges from electrostatic potentials using a grid (CHELPG), and restrained electrostatic potential (RESP), and two multipole algorithms, distributed multipole analysis (DMA) and Gaussian multipole model (GMM), which can be used to describe the electrostatic potential (ESP) around molecules in molecular mechanics force fields. This is done to study how the different methods perform when intramolecular polarizability contributions are self‐consistently removed from the fitting done in the force field parametrization. It is demonstrated that the polarizable versions of the partial charge models provide a good compromise between accuracy and computational efficiency in describing the ESP of small organic molecules undergoing conformational changes. For the point charge models, the inclusion of polarizability reduced the the average root mean square error of ESP over the test set by 4–10%. © 2015 Wiley Periodicals, Inc.     

A transferable classical potential for the water molecule

We developed a new model for the water molecule which contains only three Gaussian charges. Using the gas-phase geometry the dipole moment of the molecule matches, the quadrupole moment closely approximates the experimental values. The negative charge is connected by a harmonic spring to its gas-phase position. The polarized state is identified by the equality of the intermolecular electrostatic force and the spring force acting on the negative charge. In each timestep the instantaneous position of the massless negative charge is determined by iteration. Using the technique of Ewald summation, we derived expressions for the potential energy, the forces, and the pressure for Gaussian charges. The only properties to be fitted are the half-width values of the Gaussian charge distributions and the parameters of the nonelectrostatic repulsion-attraction potential. We determined the properties of gas-phase clusters up to six molecules, the internal energy and density of ambient water and hexagonal ice. We calculated the equilibrium density of ice VII as a function of pressure. As an additional test, we calculated the pair-correlation function, the isotherm compressibility, the heat capacity, and the self-diffusion coefficients for ambient water. As far as we know, this is the first classical model of water which is able to estimate both ends of the phase diagram, the high pressure ice VII, and the gas clusters of water with excellent accuracy.     

Topological analysis of the molecular charge density and impact sensitivy models of energetic molecules

Important explosives of practical use are composed of nitroaromatic molecules. In this work, we optimized geometries and calculated the electron density of 17 nitroaromatic molecules using the Density Functional Theory (DFT) method. From the DFT one-electron density matrix, we computed the molecular charge densities, thus the electron densities, which were then decomposed into electric multipoles located at the atomic sites of the molecules using the distributed multipole analysis (DMA). The multipoles, which have a direct chemical interpretation, were then used to analyze in details the ground state charge structure of the molecules and to seek for correlations between charge properties and sensitivity of the corresponding energetic material. The DMA multipole moments do not present large variations when the size of the Gaussian basis set is changed; the largest variations occurred in the range 10-15% for the dipole and quadrupole moments of oxygen atoms. The charges on the carbon atoms of the aromatic ring of each molecule become more positive when the number of nitro groups increases and saturate when there are five and six nitro groups. The magnitude and the direction of the dipole moments of the carbon atoms, indicators of site polarization, also depend on the nature of adjacent groups, with the largest dipole value being for C-H bonds. The total magnitude of the quadrupole moment of the aromatic ring carbon atoms indicates a decrease in the delocalized electron density due to an electron-withdrawing effect. Three models for sensitivity of the materials based on the DMA multipoles were proposed. Explosives with large delocalized electron densities in the aromatic ring of the component molecule, expressed by large quadrupole values on the ring carbon atoms, correspond to more insensitive materials. Furthermore, the charges on the nitro groups also influence the impact sensitivity.     

Surface properties of the polarizable Baranyai-Kiss water model

The water surface properties using the Baranyai-Kiss (BK) model [A. Baranyai and P. T. Kiss, J. Chem. Phys. 133, 144109 (2010)] are studied by molecular dynamics simulation, and compared to popular rigid water potentials, namely to the extended simple point charge (SPC/E) and the transferable interaction potential with 4 points (TIP4P) models. The BK potential is a polarizable model of water with three Gaussian charges. The negative charge is connected to its field-free position by a classical harmonic spring, and mechanical equilibrium is established between this spring force and the force due to the charge distribution of the system. The aim of this study is, on the one hand, to test the surface properties of the new model, and on the other hand, to identify differences between the models listed above. The obtained results reveal that the BK model reproduces very well a number of properties corresponding to liquid-vapor equilibrium, such as the coexisting liquid and vapor densities, saturated vapor pressure or surface tension. Further, this model reproduces excellently the critical point of water even in comparison with a large number of widely used polarizable and nonpolarizable models. The structural properties of the liquid surface of BK water turns out to be very similar to that of the SPC/E model, while the surface of TIP4P water is found to be somewhat less ordered. This finding is related to the fact that the critical temperature of the TIP4P model is lower than that of either SPC/E or BK.     

Polarizable contributions to the surface tension of liquid water

Surface tension, gamma, strongly affects interfacial properties in fluids. The degree to which polarizability affects gamma in water is thus far not well established. To address this situation, we carry out molecular dynamics simulations to study the interfacial forces acting on a slab of liquid water surrounded by vacuum using the Gaussian charge polarizable (GCP) model at 298.15 K. The GCP model incorporates both a fixed dipole due to Gaussian distributed charges and a polarizable dipole. We find a well-defined bulklike region forms with a width of approximately 31 A. The average density of the bulklike region agrees with the experimental value of 0.997 g/cm3. However, we find that the orientation of the molecules in the bulklike region is strongly influenced by the interfaces, even at a distance five molecular diameters from the interface. Specifically, the orientations of both the permanent and induced dipoles show a preferred orientation parallel to the interface. Near the interface, the preferred orientation of the dipoles becomes more pronounced and the average magnitude of the induced dipoles decreases monotonically. To quantify the degree to which molecular orientation affects gamma, we calculate the contributions to gamma from permanent dipolar interactions, induced dipolar interactions, and dispersion forces. We find that the induced dipole interactions and the permanent dipole interactions, as well as the cross interactions, have positive contributions to gamma, and therefore contribute stability to the interface. The repulsive core interactions result in a negative contribution to gamma, which nearly cancels the positive contributions from the dipoles. The large negative core contributions to gamma are the result of small oxygen-oxygen separation between molecules. These small separations occur due to the strong attractions between hydrogen and oxygen atoms. The final predicted value for gamma (68.65 m/Nm) shows a deviation of approximately 4% of the experimental value of 71.972 m/Nm. The inclusion of polarization is critical for this model to produce an accurate value.     

A non-polarizable model of water that yields the dielectric constant and the density anomalies of the liquid: TIP4Q

A four-site rigid water model is presented, whose parameters are fitted to reproduce the experimental static dielectric constant at 298 K, the maximum density of liquid water and the equation of state at low pressures. The model has a positive charge on each of the three atomic nuclei and a negative charge located at the bisector of the HOH bending angle. This charge distribution allows increasing the molecular dipole moment relative to four-site models with only three charges and improves the liquid dielectric constant at different temperatures. Several other properties of the liquid and of ice Ih resulting from numerical simulations with the model are in good agreement with experimental values over a wide range of temperatures and pressures. Moreover, the model yields the minimum density of supercooled water at 190 K and the minimum thermal compressibility at 310 K, close to the experimental values. A discussion is presented on the structural changes of liquid water in the supercooled region where the derivative of density with respect to temperature is a maximum.     

水在石墨(0001)面簇模型桥位上吸附的量子化学研究

用从头计算方法对水在石墨(0001)面桥位上的吸附进行了研究.用C₆H₈原子簇模拟石墨表面,在6-31G^*水平上计算了水在不同方向和位置上的吸附能量.研究表明:水在石墨面上的吸附很弱,属于物理吸附;在中性或带负电荷的石墨表面,当水分子中的氢原子靠近石墨面时,体系存在能量最小值,而在带正电荷的表面,当氧原子靠近石墨面时存在稳定的吸附点;不论表面带正电荷还是带负电荷,均对水分子的吸附起增强作用.     

Geometry-dependent atomic charges: Methodology and application to alkanes,aldehydes, ketones,and amides

A general methodology for deriving geometry-dependent atomic charges is presented. The main ingredient of the method is a model that describes the molecular dipole moment in terms of geometry-dependent point charges. The parameters of the model are determined from ab initio calculations of molecular dipole moments and their Cartesian derivatives at various molecular geometries. Transferability of the parameters is built into the model by fitting ab initio calculations for various molecules simultaneously. The results show that charge flux along the bonds is a major contributing factor to the geometry dependence of the atomic charges, with additional contributions from fluxes along valence angles and adjacent bonds. Torsion flux is found to be smaller in magnitude than the bond and valence angle fluxes but is not always unimportant. A set of electrostatic parameters is presented for alkanes, aldehydes, ketones, and amides. Transferability of these parameters for a host of molecules is established to within 3 ?5% error in the predicted dipole moments. A possible extension of the method to include atomic dipoles is outlined. With the inclusion of such atomic dipoles and with the set of transferable point charges and charge flux parameters, it is demonstrated that molecular electrostatic potentials as well as electrostatic forces on nuclei can be reproduced much better than is possible with other models (such as potential derived charges). © 1995 by John Wiley & Sons, Inc.     

基于静电效应的石墨烯纳米孔选择性渗透特性

Two-dimensional graphene nanopores have proved to be a very effective molecular sieve with ultra-high molecular permeance due to the atomic thickness of graphene sheets. The mechanism of graphene nanopores for molecular sieving is generally the size-sieving effect of different molecules. However, high-selective molecular separation is difficult to realize based only on the size-sieving effect. Therefore, graphene nanopore-based membranes usually present high permeance but a moderate selectivity, such that the separation performance cannot far exceed those of traditional separation membranes. In this study, the effects of charges on graphene surfaces on the selective permeation of CO₂/N₂ mixtures through a graphene nanopore is studied using molecular dynamics simulations; its purpose to realize electrostatic effect-based selective molecular permeation through graphene nanopores and find a promising method to improve the selectivity of molecular separation. The simulation results show that graphene nanopores with negative charges have higher CO₂ permeance and lower N₂ permeance and, thus, present a high selectivity for the separation of the CO₂/N₂ mixtures. The graphene nanopore with positive charges, however, does not improve the selectivity. The electrostatic effect-based selectivity of graphene nanopores is related to the different molecular adsorption abilities on the graphene surface with charges. For negative charges, the adsorption ability of CO₂ molecules increases and the number of permeated molecules via surface mechanism increases and the experience time during the permeation process also increases; ultimately the CO₂ permeance increases with increasing the charge density. For the molecules permeated through the surface mechanism, they are firstly adsorbed onto the graphene surface and then diffuse to the pore region for the ultimate permeation; thus, their experience time is longer than that of the molecules permeated through a direct mechanism. Therefore, a longer experience time means a more significant contribution of the surface flux to the total flux. At high surface charge densities, the contribution of surface flux is dominated and thus the experience time is longer. For CO₂ molecules, the permeation rates increase with increasing the surface charge density. Namely, a higher experience time corresponds to a higher permeation rate for CO₂ molecules. A decrease of N₂ permeance with increasing the charge density is correlated to the increasing CO₂ permeance via the inhibition effects of non-permeating components on the permeation of permeating components. For positive charges, the adsorption abilities of CO₂ and N₂ molecules have no obvious variation with the charge density and their permeance is constant; therefore, the graphene nanopore still has no electrostatic effect-based selectivity.     

Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set

We have recently developed a new class IV charge model for calculating partial atomic charges in molecules. The new model, called charge model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree–Fock theory and by hybrid density functional theory (HDFT) based on the modified Perdew–Wang density functional with several basis sets. In the present article, we extend CM3 for calculating partial atomic charges by Hartree–Fock theory with the economical but well balanced MIDI! basis set. Then, using a test set of accurate dipole moments for molecules containing nitramine functional groups (which include many high-energy materials), we demonstrate the utility of several parameters designed to improve the charges in molecules containing both N and O atoms. We also show that one of our most recently developed CM3 models that is designed for use with wave functions calculated at the mPWXPW91/MIDI! level of theory (where X denotes a variable percentage of Hartree–Fock exchange) gives accurate charge distributions in nitramines without additional parameters for N and O. To demonstrate the reliability of partial atomic charges calculated with CM3, we use these atomic charges to calculate polarization free energies for several nitramines, including the commonly used explosives 1,3,5-trinitro-s-triazine (RDX) and 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (HNIW), in nitromethane. These polarization energies are large and negative, indicating that electrostatic interactions between the charge distribution of the molecule and the solvent make a large contribution to the free energy of solvation of nitramines. By extension, the same conclusion should apply to solid-state condensation. Also, in contrast to some other charge models, CM3 yields atomic charges that are relatively insensitive to the presence of buried atoms and small conformational changes in the molecule, as well as to the level of treatment of electron correlation. This type of charge model should be useful in the future development of solvation models and force fields designed to estimate intramolecular interactions of nitramines in the condensed phase.     

Hydration force between model hydrophilic surfaces: computer simulations

We performed molecular dynamics simulations to study the interactions between model hydrophilic plates made of carbon atoms distributed on a hexagonal lattice. Although neutral, the plates carry equal amounts of positive and negative charges to represent physical dipoles. Using the thermodynamic perturbation theory we calculated the potential of mean force (PMF) acting between the plates as a function of the distance between these plates. We observed that, at distances when more than one water layer can be found between the plates, the contribution of water into the PMF can be either attractive or repulsive depending on the correlation between the charges situated on the plates.