An intramolecular induction correction model of the molecular dipole moment

A model for intramolecular polarization is presented. It is used to describe the changes in the molecular charge distribution occurring as a response to changes of dihedral angles in the molecule. The model is based on a multicenter multipole distribution of the molecular charge distribution. The electric field from this charge distribution induce dipole moments in the same molecule. The model contains atom type parameters to describe the damping of the electric field. A total of four atom types are used. The parameters are fitted to a calibration set with various functional groups, and tested against a validation set. The error obtained for the calibration set is reduced by 92% and by 88% for the validation set, if compared to an accurate state-of-the-art force field. It is shown that rotating the non-polarizable multicenter multipole distribution for the equilibrium geometry gives too large dipole moments for dihedral angles deviating from the equilibrium geometry. This will lead to too large long-range attractions in simulations. This problem is overcome by using the dipole polarizability correction suggested here, which gives dipole moments very close to the Hartree-Fock dipole moments obtained from reference calculations.     

Gaussian induced dipole polarization model

A new induced dipole polarization model based on interacting Gaussian charge densities is presented. In contrast to the original induced point dipole model, the Gaussian polarization model is capable of finite interactions at short distances. Aspects of convergence related to the Gaussian model will be explored. The Gaussian polarization model is compared with the damped Thole-induced dipole model and the point dipole model. It will be shown that the Gaussian polarization model performs slightly better than the Thole model in terms of fitting to molecular polarizability tensors. An advantage of the model based on Gaussian charge distribution is that it can be easily generalized to other multipole moments and provide effective damping for both permanent electrostatic and polarization models. Finally, a method of parameterizing polarizabilities is presented. This method is based on probing a molecule with point charges and fitting polarizabilities to electrostatic potential. In contrast to the generic atom type polarizabilities fit to molecular polarizability tensors, probed polarizabilities are significantly more accurate in terms of reproducing molecular polarizability tensors and electrostatic potential, while retaining conformational transferability.     

Charge distributions for molecular dynamics simulations from self-consistent polarization method

Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly taken into account by distributing solvent molecules around the solute target. The performed analysis includes a few computational schemes (HF, MP2, B3LYP, and M026X), basis sets (cc-pvnz, n = 2, 3, …, 6), and electrostatically derived charge distributions (KS, CHELP, CHELPG, and HLY). It is demonstrated that the environment effect is very important and cannot be disregarded. The second solvation shell should be included to achieve the charge convergence. Huge corrections to charge distribution are due to induction and dispersion. The B3LYP/cc-pvqz level of theory is recommended for deriving the charges within self-consistent polarization scheme.     

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right phi angle) in the Y position.     

A simple electrostatic model of solvation for large molecules within the SCF MO theory

A very simple electrostatic model of solvation in which the solvent molecules are represented by point dipoles has been applied to simulate the hydration effect on molecular systems within the CNDO/2 method. The limitations of the model compared to the previous approaches as well as its feasible application to the study of tautomeric equilibria of cytosine and adenine in aqueous solution are discussed.     

Parameterization of electrostatic interactions for molecular dynamics simulations of heterocyclic polymers

The paper focuses on the problem of electrostatic interactions in molecular dynamics simulations of thermal properties of heterocyclic polymers. The study focuses on three thermoplastic polyimides synthesized on the basis of 1,3‐bis‐(3′,4‐dicarboxyphenoxy)benzene (dianhydride R) and three diamines: 4,4′‐bis‐(4″‐aminophenoxy) diphenylsulfone (diamine BAPS), 4,4′‐bis‐(4″‐aminophenoxy) biphenyl (diamine BAPB), and 4,4′‐bis‐(4''‐aminophenoxy) diphenyloxide (diamine BAPO). In the molecular dynamics simulations these polyimides were described by the Gromos53a5 force field. To parameterize the electrostatic interactions four methods of calculating the partial atomic charges were chosen: B3LYP/6–31G*(Mulliken), AM1(Mulliken), HF/6–31G*(Mulliken), and HF/6–31G*(ChelpG). As our parameterization is targeted to reproduce thermal properties of the thermoplastic polyimides, the choice of proper partial charges was finalized on a basis of the closest match between computational and experimental data for the thermal expansion coefficients of the polyimides below glass transition temperatures. Our finding clearly show that the best agreement with experimental data is achieved with the Mulliken partial atomic charges calculated by the Hartree‐Fock method with 6–31G* basis set. Furthermore, in addition to the thermal expansion coefficients this set of partial atomic charges predicts an experimentally observed relationship between glass transition temperatures of the three polyimides under study: . A mechanism behind the change in thermal properties upon the change in the chemical structure in considered polyimides may be related to an additional spatial ordering of sulfone groups due to dipole‐dipole interactions. Overall, the modified force‐field is proved to be suitable for accurate prediction of thermal properties of thermoplastic polyimides and can serve as a basis for building up atomistic theoretical models for describing other heterocyclic polymers in bulk. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 912–923     

Influence of polarization functions on molecular electrostatic potentials

We study the effects of d-polarization functions, centered on the heavy atoms, on the SCF molecular electrostatic potentials calculated for some molecules. The positions and energies of the minima found are very sensitive to the inclusion of polarization functions in the basis set used. The variations depend on the heavy atom involved and on the possible anisotropy of its charge distribution. These variations are particularly important for second-row atoms.     

Topography of approximate molecular electrostatic potentials

A new method is described for the approximation of the molecular electrostatic potential (MESP). This method is used for the study of the topography of small molecules. The critical points of the approximate and the exact MESP are compared. It is found that most of the critical points of the exact MESP are retained, but in regions where the exact MESP changes slowly near critical points the number of critical points of the approximate MESP can be reduced.     

Strategies to model the near-solute solvent molecular density/polarization

The solvent molecular distribution significantly affects the behavior of the solute molecules and is thus important in studying many biological phenomena. It can be described by the solvent molecular density distribution, g, and the solvent electric dipole distribution, p. The g and p can be computed directly by counting the number of solvent molecules/dipoles in a microscopic volume centered at r during a simulation or indirectly from the mean force F and electrostatic field E acting on the solvent molecule at r, respectively. However, it is not clear how the g and p derived from simulations depend on the solvent molecular center or the solute charge and if the g(F) and p(E) computed from the mean force and electric field acting on the solvent molecule, respectively, could reproduce the corresponding g and p obtained by direct counting. Hence, we have computed g, p, g(F), and p(E) using different water centers from simulations of a solute atom of varying charge solvated in TIP3P water. The results show that g(F) and p(E) can reproduce the g and p obtained using a given count center. This implies that rather than solving the coordinates of each water molecule by MD simulations, the distribution of water molecules could be indirectly obtained from analytical formulas for the mean force F and electrostatic field E acting on the solvent molecule at r. Furthermore, the dependence of the g and p distributions on the solute charge revealed provides an estimate of the change in g and p surrounding a biomolecule upon a change in its conformation.     

Influence of electrostatic interactions on the properties of cyanobiphenyl liquid crystals predicted from atomistic molecular dynamics simulations

The influence of force field details in all-atom molecular dynamics (MD) simulations on the predicted thermodynamic, structural, and dynamic properties of bulk 4-cyano-4?-pentylbiphenyl (5CB) systems have been investigated in the 292–368 K temperature range. The effect of the molecular dipole moment and the details of dihedral potential for biphenyl unit were investigated using both polarisable (POL) and non-polarisable (NP) versions of the quantum chemistry-based force field. The predicted densities for the nematic and isotropic phases of bulk 5CB were found to be in excellent agreement with available experimental data. The nematic-isotropic transition temperature (T_NI) showed strong sensitivity to the force field details, MD simulations with partial atomic charge distributions and molecular dipole moment corresponding to high-level quantum chemistry calculations predicted an overestimation of the T_NI by about 30 K. Rescaling the charges to allow the molecular dipole to be closer to experimentally reported values of 5CB dipole in condensed phases, significantly improved the prediction of T_NI as well as other thermodynamic and dynamic properties of 5CB. We also discuss how the structural, thermodynamic, and dynamic properties of bulk 5CB are affected by the flexibility of the central biphenyl dihedral and the inclusion of induced polarisation effects.     

Protonmotive force: development of electrostatic drivers for synthetic molecular motors

Ferrocene has been investigated as a platform for developing protonmotive electrostatic drivers for molecular motors. When two 3-pyridine groups are substituted to the (rapidly rotating) cyclopentadienyl (Cp) rings of ferrocene, one on each Cp, it is shown that the (Cp) eclipsed, pi-stacked rotameric conformation is preferred both in solution and in the solid state. Upon quaternization of both of the pyridines substituents, either by protonation or by alkylation, it is shown that the preferred rotameric conformation is one where the pyridinium groups are rotated away from the fully pi-stacked conformation. Electrostatic calculations indicate that the rotation is caused by the electrostatic repulsion between the charges. Consistently, when the pi-stacking energy is increased pi-stacked population increases, and conversely when the electrostatic repulsion is increased pi-stacked population is decreased. This work serves to provide an approximate estimate of the amount of torque that the electrostatically driven ferrocene platform can generate when incorporated into a molecular motor. The overall conclusion is that the electrostatic interaction energy between dicationic ferrocene dipyridyl systems is similar to the pi-stacking interaction energy and, consequently, at least tricationic systems are required to fully uncouple the pi-stacked pyridine substituents.     

Study of the molecular configuration and the dipole moment in fluorinated liquid crystals

We have investigated the relationship between the molecular configuration and dipole moment of some fluorinated liquid crystals (LCs). The geometries of the molecules were preliminarily optimized at empirical AM1 and then were further optimized at B3LYP/6‐31G(d) level. The dipole moment has been calculated. It is strongly influenced by the position and number of fluorine substituents in the benzene ring of the molecule. The polarizability, mean polarizabilities, and anisotropic polarizability of the phenylbicyclohexane (PBC) fluorine substituents are also given and discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions

The three-dimensional reference interaction site model integral equation theory (3D-RISM) combined with the ab initio molecular orbital method (3D-RISM-SCF) is applied to a solvated macromolecular system. The solvation structure around a solute molecule is obtained from the 3D-RISM integral equation under the electrostatic potential of the solute molecule, calculated by the ab initio molecular orbital theory. The electrostatic potential should be calculated on each grid point in the three-dimensional real space. Therefore, the calculation of the electrostatic potential is the most time consuming part in this method. In this article, we propose a new procedure to save the computational cost for calculating the electrostatic potential and the solvated fock matrix. The strategy of this procedure is to evaluate the electrostatic potential and the solvated fock matrix in different ways, depending on the distance between solute and solvent. Inside the repulsive cores of solute atoms, it is possible to avoid the calculation of electrostatic potential and solvated Fock matrix by assuming the potential to be infinity. In the region sufficiently far from solute, they are evaluated classically by putting the effective point charge on each atom. In the intermediate region, the electrostatic potential is evaluated directly by integrating the molecular orbitals of the solute molecule. The electronic structure and the energy gradient of Methionine-Enkephalin and solvation structure are estimated by using this procedure in aqueous solution, and are compared with the results from other procedures. The results are compared also with those from the continuum model.     

Off‐atomic site charges in some anions,metal cations,and complexes: Significance for electrostatic properties and binding

Electronic structures and properties of several anions, metal cations, and their complexes with neutral molecules were investigated at the HF/6‐31G** and B3LYP/6‐31G** levels of theory. Charges shifted from atomic sites due to atomic orbital hybridization called hybridization displacement charges (HDC) were investigated in detail. It has been found that many components of HDC are associated with each atom of ion that are shifted from the atomic sites, those associated with metal cations being shifted by large distances as found previously in electrically neutral systems. It is shown that atomic orbitals are appreciably rehybridized in going from neutral molecules to anions and cations. Molecular dipole moments and surface molecular electrostatic potentials (MEP) are obtained satisfactorily using HDC for the various types of species mentioned above. In the OH^?? H₂O complex, reversal of direction of shift of an HDC component associated with the hydrogen atom of H₂O involved in hydrogen bonding, indicates that the hydrogen bond between OH^? and H₂O would have some covalent character. Other atomic site‐based point charge models cannot provide such information about the nature of bonding. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem 2007     

A polarizable electrostatic model of the N‐methylacetamide dimer

Our previously developed polarizable electrostatic model is applied to isolated N‐methylacetamide (NMA) and to three hydrogen‐bonded configurations of the NMA dimer. Two versions of the model are studied. In the first one (POL1), polarizability along the valence bonds is described by induced bond charge increments, and polarizability perpendicular to the bonds is described by cylindrically isotropic induced atomic dipoles. In the other version (POL2), the induced bond charge increments are replaced by induced atomic dipoles along the bonds. The parameterization is done by fitting to ab initio MP2/6‐31++G(d,p) electric potentials. The polarizability parameters are determined by subjecting the NMA molecule to various external electric fields. POL1 turns out to be easier to optimize than POL2. Both models reproduce well the ab initio electric potentials, molecular dipole moments, and molecular polarizability tensors of the monomer and the dimers. Nonpolarizable models are also investigated. The results show that polarization is very important for reproducing the electric potentials of the studied dimers, indicating that this is also the case in hydrogen bonding between peptide groups in proteins. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1933–1943, 2001     

Nonexistence of local maxima in molecular electrostatic potential maps

It has been rigorously established by means of classical electrostatic arguments, that molecular electrostatic potential maps are devoid of local maxima. This forms a generalization of the earlier works of Politzer and co-workers which were restricted to the case of atoms.     

A surface site interaction point methodology for macromolecules and huge molecular databases

Determining the position and magnitude of Surface Site Interaction Points (SSIP) is a useful technique for understanding intermolecular interactions. SSIPs have been used for the prediction of solvation properties and for virtual co‐crystal screening. To determine the SSIPs for a molecule, the Molecular Electrostatic Potential Surface (MEPS) is first calculated using ab initio methods such as Density Functional Theory. This leads to a high cost in terms of computation time and is not compatible with the analysis of huge molecular databases. Herein, we present a method for the fast estimation of SSIPs, which is based on the MEPS calculated from MMFF94 atomic partial charges. The results show that this method can be used to calculate SSIPs for large molecular databases with a much higher speed than the original ab initio methodology. © 2017 Wiley Periodicals, Inc.