Molecular mechanics of organic halides. V. Conformational equilibria in solution

With a view of using data on solutions and liquids for parameter fitting in molecular mechanical force fields, Abraham's theory of solvation is incorporated in the force field procedure. Geometries and bond moments are estimated internally, partial account being taken of bond–bond induction, and used to calculate the intramolecular electrostatic energy, dipole moment, and the dipole and quadrupole terms in the solvation energy. Three dielectric constants are used, one for the solute in the vapor, one for the solution, and one for the intramolecular space through which dipole–dipole interactions take place. Examples are given, including such where computation differs with measurement, to illustrate the performance of the scheme.     

A Hirshfeld-I interpretation of the charge distribution, dipole and quadrupole moments of the halogenated acetylenes FCCH, ClCCH, BrCCH, and ICCH

We report the dipole and quadrupole moments of the halogenated acetylenes calculated using large basis sets and the SCF, DFT(B3LYP), and CCSD methods, and we analyze the charge density using the Hirshfeld and Hirshfeld-I techniques. The atomic charges, dipoles, and quadrupoles resulting from the Hirshfeld-I analysis are used to interpret the unusually small molecular dipole moments in the sequence as well as the molecular quadrupole moments. The very small dipoles obtain for two reasons. First, the dipole moment associated with the σ and π electron densities is comparable in magnitude and opposite in direction. Second, the charge and induced dipole contributions for ClCCH, BrCCH, and ICCH have opposite signs further reducing the molecular dipoles. The molecular quadrupole moments are the sum of a charge, atomic dipole, and in situ quadrupole terms, and are dominated by the atomic dipoles and in situ quadrupoles with the charge contributions playing an unexpectedly minor role.     

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 ?. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.     

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Condensed‐phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur‐containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur‐containing molecules including cysteine and methionine residues in proteins. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Conformational energy analysis of substituted diphenylethanes: Part VI. Calculations of the solvent dependence of the conformational equilibria in stilbene dihalogenides. Intramolecular interactions in the PCILO fr

As part of a theoretical analysis of the conformational equilibria of stilbene dihalogenides, the free energy at 300 K of each stable conformational isomer of these molecules has been estimated for a solvent of dielectric constant 3.5. Classical empirical potential functions were used. Interaction with the solvent was considered only in terms of a continuous dielectric medium interacting with the local dipoles and quadrupoles of the molecule. Simulation of the experimental conditions (i.e. appropriate values for the dielectric constant of the solvent) yielded better agreement with the available experimental data, which were mainly dipole moments and optical rotation values. The quadrupole energy term has a very small influence on the calculated conformational populations and can be neglected when dibenzyl derivatives are considered. The mechanism of the intramolecular interactions is discussed within the PCILO framework.     

On the interplay between CH...O and OH...O interactions in determining crystal packing and molecular conformation: an experimental and theoretical charge density study of the fungal secondary metabolite austdiol (C12H12O5)

The total experimental electron density rho(r), its Laplacian inverted delta(2)rho(r), the molecular dipole moment, the electrostatic potential phi(r), and the intermolecular interaction energies have been obtained from an extensive set of single-crystal X-ray diffracted intensities, collected at T = 70(1) K, for the fungal metabolite austdiol (1). The experimental results have been compared with theoretical densities from DFT calculations on the isolated molecule and with fully periodic calculations. The crystal structure of (1) consists of zigzag ribbons extended along one cell axis and formed by molecules connected by both OH...O and CH...O interactions, while in a perpendicular direction, adjacent molecules are linked by short CH...O intermolecular contacts. An extensive, quantitative study of all the intra- and intermolecular H...O interactions, based not only on geometrical criteria, but also on the topological analysis of rho(r), as well as on the evaluation of the pertinent energetics, allowed us (i) to assess the mutual role of OH...O and CH...O interactions in determining molecular conformation and crystal packing; (ii) to identify those CH...O contacts which are true hydrogen bonds (HBs); (iii) to determine the relative hydrogen bond strengths. An experimental, quantitative evidence is given that CH...O HBs are very similar to the conventional OH...O HBs, albeit generally weaker. The comparison between experimental and theoretical electric dipole moments indicates that a noticeable charge rearrangement occurs upon crystallization and shows the effects of the mutual cooperation of HBs in the crystal. The total intermolecular interaction energies and the electrostatic energy contribution obtained through different theoretical methods are reported and compared with the experimental results. It is found that the new approach proposed by Spackman, based on the use of the promolecular charge density to approximate the penetration contribution to intermolecular electrostatic energies, predicts the correct relative electrostatic interaction energies in most of the cases.     

On the representation of molecular quadrupole moments in terms of atomic moments

The magnitude and algebraic sign of the molecular quadrupole moments of the homonuclear diatomic molecules N2, O2, F2, P2, S2 and Cl2 are analyzed by expressing them as a sum of the quadrupole moments of the free atoms and an induced molecular quadrupole due to bond formation. This induced molecular quadrupole is further analyzed in terms of in situ atomic dipole and quadrupole moments constructed following the electron partitioning method suggested by Hirshfeld. These in situ moments are interpreted in terms of the sigma and pi character of the chemical bonds and are compared with those predicted by the DMA method of Stone (The Theory of Intermolecular Forces; Clarendon: Oxford, 1996).     

A new insight on the structural changes of linear quadrupole liquids

Molecular-dynamics simulations for linear quadrupole liquids are presented. The study is carried out for two different molecular lengths at constant density and a number of temperatures and quadrupole moments. All the simulated thermodynamic states correspond to the condensed phases and some of them show typical features of a solid structure. Furthermore, a change on the preferred intermolecular orientation in the liquid phase is observed from a shifted parallel molecular arrangement to a perpendicular orientation as the quadrupole raises. This change depends on the quadrupole moment as well as on the molecular length and is put in relation with the solid structure of different "diatomic" molecules such as nitrogen, ethane, and acetylene. The appearance of a plastic solid phase at low quadrupole moment and density is also justified. A thoroughly discussion about the availability of classical perturbation theories for this kind of systems is presented.     

三氟甲基磺酰氟绝缘介质理化特性的分子动力学模拟

采用分子动力学模拟方法, 研究了新型绝缘介质三氟甲基磺酰氟(CF₃SO₂F)的理化特性, 为高压电气设备应用CF₃SO₂F替代SF₆气体提供了理论依据. 基于量子化学计算的分子结构、 内转动、 偶极矩和振动频率等优化设计了mPCFF力场模型, 计算了243~323 K温度范围内CF₃SO₂F的各种气-液相平衡性质(饱和蒸汽压、 密度、 热容、 蒸发焓和临界参数等)与关键输运特性(扩散系数、 介电常数、 黏度和热导率等)基础参数, 并考察了CF₃SO₂F与N₂或CO₂形成混合气体的理化特性. 通过对比SF₆以及C4/CO₂混合环保绝缘气体, 针对混合比、 液化温度、 扩散和热导等因素提出了CF₃SO₂F的电气设备应用建议.     

Atomic dipole moments calculated using analytical molecular second-moment gradients

We have implemented analytical second-moment gradients for Hartree-Fock and multiconfigurational self-consistent-field wave functions. The code is used to calculate atomic dipole moments based on the generalized atomic polar tensor (GAPT) formalism [Phys. Rev. Lett. 62, 1469 (1989)], and the proposal of Dinur and Hagler (DH) for the calculation of atomic multipoles [J. Chem. Phys. 91, 2949 (1989)]. Both approaches display smooth basis-set convergence toward a well-defined basis-set limit and give reasonable electron correlation effects on the calculated atomic properties. However, the atomic charges and atomic dipole moments obtained from the GAPT partitioning scheme are unable to provide even qualitatively meaningful molecular quadrupole moments for some molecules, and thus the atomic multipole moments calculated in this scheme cannot be considered well suited for analyzing the electron density in molecules and for calculating intermolecular interaction energies. In contrast, the DH approach gives atomic charges and dipole moments that by definition exactly reproduce the molecular quadrupole moments. The approach of DH is, however, restricted to planar molecules and thus suffers from not being applicable to molecules of arbitrary shape. Both the GAPT and DH approaches give rather poor results for octupole and hexadecapole moments, indicating that at least atomic quadrupole moments are required for an accurate representation of the molecular charge distribution in terms of atomic electric moments.     

介电法研究萃取过程中分子间的络合作用

用介电法测定若干重要萃取剂的摩尔极化度和偶极矩，研究协萃体系中萃取剂之间的络合作用和协同萃了现象，求得缔合物、萃合物的摩尔极化度、偶极矩及缔合常数。     

Excess electron in water at different thermodynamic conditions

A hydrated electron in water at different densities and temperatures is studied via a set of density functional based molecular dynamics simulations, showing that a localization of an excess electron is still present even at very low densities. Space variations of the molecular dipole moments are analyzed, proposing a simple algorithm to identify the region of localization of the wavefunction relative to the solvated electron in terms of orientation of the H2O molecular dipole moments. Finally, the effects of the self-interaction corrections on the optical absorption spectra are analyzed and compared with both available experimental data and path integral molecular dynamics calculations, showing that a weighted subtraction of the self-interaction yields a systematic improvement in the position of the absorption peak.     

Dipole and quadrupole moments of molecules in crystals: a novel approach based on integration over Hirshfeld surfaces

Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%-40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.     

Calculation of molecular quadrupole moments and a demonstration of the importance of overlap densities in the theory of polyatomic molecules

A computational method for calculating quadrupole moments from molecular wave functions in a Slater orbital basis set is described. Using both IEHT and CNDO wave functions quadrupole moments for a series of polyatomic molecules are calculated. They are compared with experimental results and the IEHT wave functions are found to give agreement with experiment while CNDO wave functions do not. The importance of bicentric densities (overlap densities) in the calculation of multipole moments is shown. This is followed by a discussion of the usefulness of these wave functions for a quantitative characterization of the electronic structure of large molecules.     

The impact of the multipolar distribution on chiral discrimination in racemates

This article explores the impact of the multipolar distribution on chiral discrimination in a series of racemic fluids. Discrimination is measured via the difference between the like-like (LL) and the like-unlike (LU) radial distributions in the liquid. We have found previously that the magnitude and orientation of the molecular dipole have a decisive impact on the short-ranged enantiomeric imbalance in racemates. Although quadrupolar and octupolar interactions decrease more rapidly with intermolecular separation, they can be significant at small separations, where enantiomeric imbalances occur. We have carefully selected a number of models in which we isolate the effects of the molecular quadrupole and octupole. We find that discrimination can be greatly enhanced by changes in the quadrupole moments. However, for octupole moments, changes in discrimination are small and some octupoles inhibit discrimination. We identify the quadrupole moment closest to the plane perpendicular to the direction of the molecular dipole as the moment that has the greatest favorable effect on chiral discrimination in racemates. In racemates where this moment is large, we have found differences of up to 40% between the LL and the LU radial distributions.     

Comparison of rigid and flexible simple point charge water models at supercritical conditions

This study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773–1073 K and densities in the range 115–659 kg/m³. We present thermodynamic data, pair correlation functions, self-diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self-diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.     

The Role of Computational Chemistry in the Experimental Determination of the Dipole Moment of Molecules in Solution

The methods for the experimental determination of electric dipole moment of molecules in solution from measurements of dielectric permittivity and refractive index are traditionally based on the classical Onsager model. In this model the molecular solute is approximated as a simple polarizable point dipole inside a spherical or ellipsoidal cavity of a dielectric medium representing the solvent. However, the inadequacies of the model resulting from the assumption of a simple shape of the cavity, for the evaluation of the cavity field effect, and from the uncertainty of the polarizability of the molecular solute influences the results and hampers the comparison with the electric dipole moments computed from quantum chemical solvation models. In this article we propose a new method for the experimental determination of the electric dipole moment in solution in which information from the Polarizable Continuum Model calculations are used in place of the Onsager model. The new method overcomes the limitations of this latter model regarding both the cavity field effect and the polarizability of the molecular solutes, and thus allows a coherent comparison between experimental and computed dipole moments of solvated molecules. © 2019 Wiley Periodicals, Inc.     

Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: a molecular dynamics study

The dynamical properties of the soft sticky dipole-quadrupole-octupole (SSDQO) water model using SPC/E moments are calculated utilizing molecular dynamics simulations. This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Phys. 124, 134504 (2006)]. The forces and torques of SSDQO water for the dipole-quadrupole, quadrupole-quadrupole, and dipole-octupole interactions are derived here. The simulations are carried out at 298 K in the microcanonical ensemble employing the Ewald method for the long-range dipole-dipole interactions. Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. The dielectric constant of SSDQO:SPC/E is essentially identical to SPC/E, and both are slightly lower than experiment. Also, molecular dynamics simulations of the SSDQO water model are found to be about twice as fast as three-site models such as SPC/E.     

Effect of flexibility on surface tension and coexisting densities of water

Molecular dynamics simulations of pure water at the liquid-vapor interface are performed using direct simulation of interfaces in a liquid slab geometry. The effect of intramolecular flexibility on coexisting densities and surface tension is analyzed. The dipole moment profile across the liquid-vapor interface shows different values for the liquid and vapor phases. The flexible model is a polarizable model. This effect is minor for liquid densities and is large for surface tension. The liquid densities increase from 2% at 300 K to 9% at 550 K when the force field is changed from a fully rigid simple point charge extended (SPCE) model to that of a fully flexible model with the same intermolecular interaction parameters. The increases in surface tension at both temperatures are around 11% and 36%, respectively. The calculated properties of the flexible models are closer to the experimental data than those of the rigid SPCE. The effect of the maximum number of reciprocal vectors (h(z) (max)) and the surface area on the calculated properties at 300 K is also analyzed. The coexiting densities are not sensitive to those variables. The surface tension fluctuates with h(z) (max) with an amplitude larger than 10 mN m(-1). The effect of using small interfacial areas is slightly larger than the error in the simulations.     

Comparative characteristics of a tryptophan molecule in the gas phase and water

The L and D isomers of the tryptophan (Trp) molecule and the (Trp)⁺ cation in the gas phase and water are calculated at the DFT level to reveal the effect of water considered in the dielectric continuum approximation on the electronic characteristics of the molecule. The distribution of effective atomic charges and bond lengths enables the prediction of the most probable parts of the chemical bond cleavage during the fragmentation of the molecule under the ionizing particle flux. These data are supplemented with a calculation of fragmentation energies. Zwitterionic structures characterized by the appearance of considerable dipole moments and a change in their orientation with respect to the ground state are distinguished among the possible isomeric forms in water.