Class IV charge models: A new semiempirical approach in quantum chemistry

Summary We propose a new criterion for defining partial charges on atoms in molecules, namely that physical observables calculated from those partial charges should be as accurate as possible. We also propose a method to obtain such charges based on a mapping from approximate electronic wave functions. The method is illustrated by parameterizing two new charge models called AM1-CM1A and PM3-CM1P, based on experimental dipole moments and, respectively, on AM1 and PM3 semiempirical electronic wave functions. These charge models yield rms errors of 0.30 and 0.26 D, respectively, in the dipole moments of a set of 195 neutral molecules consisting of 103 molecules containing H, C, N and O, covering variations of multiple common organic functional groups, 68 fluorides, chlorides, bromides and iodides, 15 compounds containing H, C, Si or S, and 9 compounds containing C-S-O or C-N-O linkages. In addition, partial charges computed with this method agree extremely well with high-level ab initio calculations for both neutral compounds and ions. The CM1 charge models provide a more accurate point charge representation of the dipole moment than provided by most previously available partial charges, and they are far less expensive to compute.     

Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane

The molecular structures of cycloalkanes (from cyclopropane to cyclodecane) and tetrahedrane were optimized at the Hartree–Fock/6–31G** level and their molecular electric potentials (MEPs) were calculated using a geodesic grid. The MEPs were fitted using net atomic charges and several site charge models. The net atomic charge model gave very poor fits to the MEPs in every case. A model with additional methylene bisector charge sites, similar to one successfully used previously for linear alkanes, greatly improved the fits to the MEPs of these cycloalkanes. The MEPs of the highly strained molecules cyclopropane and tetrahedrane were further studied using ring center and displaced bond charge sites. The fitting of the MEP of cyclopropane was consistent with a banana bond model with asymmetrically displaced electron density in the C C bonds. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 579–585, 1999     

Molecular cluster building algorithm: electrostatic guidelines and molecular tailoring approach

Nano-sized clusters of various materials are recent experimental targets, since they exhibit size-dependent physico-chemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interaction energies of large molecular clusters of zinc sulfide, benzene, and water are presented.     

Toward accurate transferable electrostatic models for polypeptides: A distributed multipole study of blocked amino acid residue charge distributions

We have developed a method for building up accurate electrostatic models for polypeptides, based on a distributed multipole representation of the SCF charge densities for the dipeptides (CH₃.CO.NH.CHR.CO.NH.CH₃) of the naturally occurring amino acids. It is based on the observation that each peptide residue has almost the correct formal charge (0, ±1). We find that the variations in the backbone charge distributions (excluding proline) with sidechain have a negligible effect on the predicted electrostatic potential around the residue. However changes in the atomic multipoles with the torsion angles (?, ψ, χ) are more significant, and may need to be taken into account if electrostatic potential close to the residue is required to high accuracy. This type of DMA peptide library provides more accurate, more theoretically based, estimates of the electrostatic potential around polypeptides than current models.     

Development of spherical gaussian-based point charge models for the evaluation of electrostatic potentials

A set of charge- and dipole moment-conserving point charge models of the electron density of a spherical Gaussian-based wavefunction is described. A particular model may be chosen to satisfy the computational and/or accuracy requirements of a given application. Criteria for selection of models for the evaluation of electrostatic potentials are detailed and tested in an application to the porphyrin molecule.     

Molecular dynamics simulations of beta-SiC using both fixed charge and variable charge models

In this paper, molecular dynamics simulations have been performed using both fixed charge and variable charge models. In the fixed charge model, partial charges are introduced to Si and C atoms to model the charge transfer observed in first principles studies. The calculated phonon dispersions, elastic constants, and lattice constants are in good accuracy. Variable charge model is also used to obtain geometry and connectivity dependent atomic charges. Our results show that although the variable charge model may not be advantageous in the study of ordered structures, it is important in describing structural disorders such as vacancies.     

A numerically stable restrained electrostatic potential charge fitting method

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)‐based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill‐conditioning is alleviated. This charge fitting method can be used in quantum mechanical/molecular mechanical (QM/MM) simulations and similar studies, where QM calculated electronic properties are frequently mapped to partial atomic charges. © 2012 Wiley Periodicals, Inc.     

Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models

To generate reduced point charge models of proteins, we developed an original approach to hierarchically locate extrema in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions. A charge fitting program was used to assign charge values to the so-obtained reduced representations. In continuation to a previous work, the Amber99 force field was selected. To easily generate reduced point charge models for protein structures, a library of amino acid templates was designed. Applications to four small peptides, a set of 53 protein structures, and four KcsA ion channel models, are presented. Electrostatic potential and solvation free energy values generated by the reduced models are compared with the corresponding values obtained using the original set of atomic charges. Results are in closer agreement with the original all-atom electrostatic properties than those obtained with a previous reduced model that was directly built from the smoothed MEP functions [Leherte and Vercauteren in J Chem Theory Comput 5:3279–3298, 2009].     

A novel approach for designing simple point charge models for liquid water with three interaction sites

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard-Jones and Coulomb interaction functions and without including a self-energy correction in the effective pair-potential as is done in the SPC/E model. Here, a different approach to circumvent this problem is presented. A short-range interaction term, which corrects the oxygen-oxygen energy at small distances by small amounts of energy, was introduced in the nonbonded interaction function. This additional force-field term allows to derive new parameter sets for SPC-like water models that yield better agreement with experimental data on liquid water. Based on previous investigations of the force-field parameter dependence of the water properties of SPC-like models, the necessary parameter changes to obtain a lower diffusion coefficient and a larger dielectric permittivity were specified and accordingly six new models were developed. They all represent an improvement over SPC in terms of structural and diffusional properties, four of them show better dielectric properties also. One model, SPC/S, has been characterized in more detail, and represents most properties of liquid water better than SPC while avoiding the larger discrepancies with experimental values regarding density, thermal compressibility, energy, and free energy of the SPC/E model. We conclude that the use of a simple, short-ranged additional oxygen-oxygen interaction term makes a simultaneous improvement of the diffusion coefficient and the dielectric properties of water feasible.     

Molecular electrostatic potential studies on antiepileptic drug: Troxidone

Ab initio SCF -MO -LCAO calculations of the molecular electrostatic potential (MEP ) have been carried out on a seven-member series related to the antiepileptic drug troxidone. The effect of the substituted alkyl groups on the bioactivity of these molecules is discussed. The substituted alkyl groups increase the negative potential found near the oxygen atoms in the molecular plane.     

Molecular electrostatic potential approach to determining the steric effect of phosphine ligands in organometallic chemistry

A two-layer ONIOM(B3LYP/6-31G(d,p):UFF) quantum mechanics (QM)-molecular mechanics (MM) optimization of PR3 ligands, where the QM layer is always constructed as PH3, followed by molecular electrostatic potential (MESP) analysis of the QM layer is suggested as a simple and effective method for evaluating the steric effect of PR3 ligands. The subtle variations in the electron distribution that arise as a result of the steric bulkiness as well as the conformational changes in the substituent groups is well reflected in the value of the MESP minimum (Vmin) located in the QM region. In general, a sterically bulky group has always shown a more negative Vmin than a sterically less bulky group. The difference between the Vmin value of free PH3 and the Vmin value at the QM region of PR3 is used as a measure of the steric effect of the PR3 ligand. This value, designated as MESPsteric, showed a good linear correlation with the cone angle values as well as the average of the intervalence HPH angles found in the QM layer. Further, the difference between the Vmin value at the QM region of PR3 (an indicator of the steric effect) and the Vmin value of the completely optimized PR3 ligand (an indicator of the combined effect of steric and electronic effects) showed a good linear correlation with the Hammett Sigmasigmap constants, which further confirmed the present approach to understanding the steric effect separately from the electronic effect.     

Python implementation of the restrained electrostatic potential charge model

The restrained electrostatic potential (RESP) charge model is widely used in molecular dynamics simulations, especially for the AMBER and GAFF force fields. We have implemented the RESP scheme using the accessible and widely used Python language and the NumPy numerical library. This article provides a programming-oriented introduction to the RESP scheme and highlights some of the features of NumPy that are useful in scientific computing.     

Avoidance of the weighing problem arising from electrostatic charge

Summary A simple method for avoiding the difficulty of weighing an object carrying an electrostatic charge has been proposed by which the correct weight can be obtained.

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Zusammenfassung Ein einfaches Verfahren wird beschrieben, mit dessen Hilfe sich die beim Wägen elektrostatisch geladener Objekte ergebenden Schwierigkeiten vermieden und korrekte Gewichtsangaben ermittelt werden können.

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Résumé Pour éviter la difficulté de peser un objet portant une charge électrostatique, on a proposé une méthode simple qui permet d'obtenir le poids correct.

     

Molecular electrostatic fields from bond fragments

We apply completely transferable, strictly localized molecular orbitals for the calculation of molecular electrostatic fields. This approach, derived from our previous bond fragment method for the calculation of molecular electrostatic potentials, reduces computational efforts drastically. The fields around small molecules containing first- and second-row atoms are systematically overestimated as compared with ab initio calculations with a minimal STO -3G basis set. However, deviations can be corrected by a simple multiplicative factor, which means that the overall shape of the potential and field around the molecule is correctly reproduced. Our approximate field can be used to determine possible hydration sites around molecules as proposed earlier by Peinel and coworkers. Application of the method is illustrated on the formamide molecule.     

Insight into the chemical bonding and electrostatic potential: A charge density study on a quinazoline derivative

2,3-Trimethylene-3,4-dihydroquinazoline shares the heterocyclic core with natural compounds and synthetic drugs. The hydrochloride of the compound forms excellent dihydrate crystals which have allowed us to collect high-resolution X-ray diffraction data and obtain the experimental charge density. The solid may be understood as built up from pairs of heterocyclic cations and chloride anions; a direct hydrogen bond links the halide to the formally cationic pyrimidine NH group. The hydrate water molecules interact with the anions, forming an infinite chain along the crystallographic a axis between the stacks of the heterocyclic cations. Based on the experimental charge density, a dipole moment of 16.1 Debye is calculated for a pair of the hydrogen-bonded quinazolinium cation and the chloride anion in the extended crystal structure.