A periodic ab initio Hartree-Fock calculation on corundum

The electronic structure of corundum (α-Al₂O₃) is calculated at the ab initio Hartree-Fock level. Cohesive energy, total and projected densities of states, atomic multipoles, bond populations and electron charge density distribution maps are given. The oxygen-aluminium bond is found to be partially covalent in nature; the atomic charges are −0.73 e and +1.09 e for O and Al respectively.     

Atomic charges derived from semiempirical methods

It is demonstrated that semiempirical methods give electrostatic potential (ESP) derived atomic point charges that are in reasonable agreement with ab initio ESP charges. Furthermore, we find that MNDO ESP charges are superior to AM1 ESP charges in correlating with ESP charges derived from the 6-31G* basis set. Thus, it is possible to obtain 6-31G* quality point charges by simply scaling MNDO ESP charges. The charges are scaled in a linear (y = Mx) manner to conserve charge. In this way researchers desiring to carry out force field simulations or minimizations can obtain charges by using MNDO, which requires much less computer time than the corresponding 6-31G* calculation.     

The effects of charge transfer on the aqueous solvation of ions

Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and -0.775 for Na(+), K(+), and Cl(-), respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.     

Accurate modeling of the intramolecular electrostatic energy of proteins

The (?, ψ) energy surface of blocked alanine (N-acetyl–N′-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization-induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization-induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.     

Critical and phase-equilibrium properties of an ab initio based potential model of methanol and 1-propanol using two-phase molecular dynamics simulations

Two-phase molecular dynamics simulations employing a Monte Carlo volume sampling method were performed using an ab initio based force field model parameterized to reproduce quantum-mechanical dimer energies for methanol and 1-propanol at temperatures approaching the critical temperature. The intermolecular potential models were used to obtain the binodal vapor-liquid phase dome at temperatures to within about 10 K of the critical temperature. The efficacy of two all-atom, site-site pair potential models, developed solely from the energy landscape obtained from high-level ab initio pair interactions, was tested for the first time. The first model was regressed from the ab initio landscape without point charges using a modified Morse potential to model the complete interactions; the second model included point charges to separate Coulombic and dispersion interactions. Both models produced equivalent phase domes and critical loci. The model results for the critical temperature, density, and pressure, in addition to the sub-critical equilibrium vapor and liquid densities and vapor pressures, are compared to experimental data. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here.     

室温离子液体BMIGaCl4热力学性质研究

An ionic liquid （IL） BMIGaCh was prepared by directly mixing GaCl3 and 1-methyl-3-butylimidazolium chloride with molar ratio of 1/1 under argon atmosphere. The densities and surface tensions of this pure ionic liquid were determined in the temperature range of 268.15 to （338.15±0.1） K. A new theoretical model of ionic liquids, an interstice model, was applied to calculate the thermal expansion coefficient of IL BMIGaCh, a, and the magnitude order of its value calculated by the theory was the same as experimental one. Both Raman scattering and ab initio calculations indicate that GaCl4^- is the only species containing Ga in the ionic liquid BMIGaCl4.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Parameterization and evaluation of a flexible water model

The thermodynamic, dielectric, and dynamic properties of a newly parameterized flexible water model are studied using molecular dynamics simulations. The potential function developed is based on the popular simple point charge (SPC) rigid model with the addition of appropriate harmonic and anharmonic energy terms for stretching and bending. Care was taken to account for the self-polarization and gas-phase monomer energy corrections during the parameterization, which have typically been ignored in past studies. The results indicate that an increased Lennard-Jones repulsive coefficient and slightly scaled partial charges are required when adding flexibility to the rigid model potential to reliably reproduce the experimental density, energy, and O ? O radial distribution function of water at 298 K and 1 atm. Analysis of the power spectrum derived from the H-velocity autocorrelation function allowed the water potential to be evaluated further and refined by adjusting the valence forces to fit the vibrational frequencies of the gas and liquid. Once a consistent set of parameters was determined, the static dielectric properties of the water model were calculated at two temperatures using the reaction field method to treat long-range forces and correlations. The dielectric constant of 75 ± 7 calculated at 300 K is in good agreement with the experimental value of 78.5. The Kirkwood g factor was also examined for temperature dependence and showed the correct increasing behavior with decreasing T. As a final check of the water potential, the free energies of solvation of a flexible water molecule and neon were predicted using thermodynamic perturbation methods. The calculated solvation energies of ?7.0 ± 0.8 for water and 2.7 ± 0.7 for neon are both consistent with the experimental values of ?6.3 and 2.7 kcal/mol. Comparisons are made throughout the study with the results of previous rigid and flexible model simulations. © 1995 by John Wiley & Sons, Inc.     

Molecular simulation of guanidinium-based ionic liquids

A new systematic all-atom force field was developed for cyclic guanidinium-based ionic liquids (ILs) based on the AMBER force field. Optimized molecular geometries and equilibrium bond lengths and angles were obtained by ab initio calculations, and charges were allocated to each atom center by fitting the ab initio electrostatic potential. Molecular dynamics simulations were performed for eleven kinds of ILs that are comprised of NO3(-) anions and cyclic guanidinium-based cations. Validation was carried out by comparing our simulated densities with experimental and calculated data from the literature. Transport properties such as self-diffusion coefficients, viscosities, and conductivities were calculated by molecular dynamic simulation, and their dependence on the length of the alkyl chains of cyclic guanidinium-based cations are discussed. Radial distribution functions and spatial distribution functions were investigated to depict the microscopic structures of the ILs, and the relationship between their properties and microstructures is also discussed.     

Effect of charge distribution on electrostatic chromophore—protein interactions in Bacteriorhodopsin

Charge distributions of a protonated and unprotonated Schiff base model compound are determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between the model molecule and protein are calculated. Interaction energies as well as the calculated pK_1/2 values of the model molecule are shown to depend considerably on the chosen charge distribution. Electrostatic potential derived partial charges determined at different ab initio levels reveal interaction energies between the model molecule and nearby residues such as ARG-82, ASP-85, and ASP-212, which are relatively method independent. Consequently, such charge distributions also result in pK_1/2 values for the model molecule that are very similar. Larger deviations in the electrostatic interaction energies, however, are found in the case of charge distributions derived according to the Mulliken population analysis. Nevertheless, some sets of Mulliken derived partial charges predicted pK_1/2 values for the model molecule that are close to those determined with electrostatic potential derived partial charges. This agreement, however, is only achieved because the individual errors of the contributing terms are approximately compensated. The use of the extended atom model is shown to be problematic. Although potential derived charges can correctly describe electrostatic interaction energies, they fail to predict pK_1/2 values. On the basis of the present investigation a new set of partial charges for the protonated and unprotonated retinal Schiff base is proposed to be used in molecular dynamics simulations and electrostatics calculations. © 1997 by John Wiley & Sons, Inc.     

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.     

Simulation of liquid imidazole using a high-rank quantum topological electrostatic potential

Rigid body molecular dynamics simulations were carried out on pure liquid imidazole at four different temperatures and at 1 atm. Imidazole, which is important both in life science and materials science, is one of the simplest molecules to possess both a lone pair and a π system. These two features are known to benefit from multipolar electrostatics. Here the electrostatic interaction is governed by atomic multipole moments obtained from topologically partitioned ab initio electron densities. The non-electrostatic terms are modeled with Lennard-Jones parameters adjusted to fit the experimental liquid density. All σ values are incrementally increased by one single scaling factor. We report on how the presence of multipolar electrostatics influences the local structure, dynamics and thermodynamics of the liquid compared to electrostatics by atomic point charges. The point charge force field exaggerates the number of π-stacked dimers in the liquid, and underestimates the number of hydrogen-bonded dimers. The effect of the temperature on the local structure of liquid imidazole was analysed using radial and spatial distribution functions.     

Determination of the atomic charge on sodium in sodium salts by numerical integration — a theoretical investigation

The electron density difference in a NaSCN crystal is set up from the ab initio densities of Na⁺ and SCN^? ions and compared to the experimental counterpart based on X-ray diffraction measurements. Numerical integration over the electron density difference is executed around the Na⁺ ion. The atomic charge (+0.20e) derived in this way is in good agreement with the analogous experimental charge (+0.27e) The low experimental value cannot therefore be taken as an indication for a predominantly non-ionic structure of NaSCN and similar sodium salts     

离子液体BMIBF4性质的研究

用最大气泡法和韦氏天平法, 在278.15～343.15 K范围内测定了离子液体BMIBF₄的表面张力和密度; 讨论了这个离子液体的体积性质和表面性质; 根据离子个头大又极不对称的特点, 提出了离子液体的空隙模型. 根据空隙模型计算的离子液体恒压热膨胀系数与实验值相比, 偏差在10%左右.     

A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation

To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge‐distribution model based on a promolecule augmented with point charges (aug‐PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug‐PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug‐PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol^?1 to DFT‐SAPT with B3LYP/aug‐cc‐pVTZ).     

Molecular dynamics simulations of aqueous solutions of ethanolamines

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.     

Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors

Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon—carbon rather than carbon—nitrogen bonds. © 1997 by John Wiley & Sons, Inc.     

Theoretical calculation of electrode potentials: Electron-withdrawing compounds

The electrode potential of 2,3-dicyanobenzoquinone in aqueous solution has been calculated relative to parabenzoquinone using a thermodynamic cycle approach that includes accurate gasphase ab initio calculations and calculation of differences in free energies of hydration using the free-energy perturbation method. The discrepancy between the calculated and experimental electrode potential is disappointingly large (99 mV) compared to previous studies using this approach. This, along with the experimental evidence, suggests that the experimental value itself is too large and that theoretical approaches may indeed be as reliable as experimental ones for determining redox properties of molecules such as 2,3-dicyanobenzoquinone. In the light of this discrepancy we have examined the variation of the results with the basis set, inclusion of electron correlation and changes in the parameters used in the molecular dynamics free-energy simulations. The results are shown to be dependent upon the torsional parameters and especially dependent upon the basis set or semiempirical method used to obtain the electrostatic potential-derived charges. The best charge set was determined using the ab initio criteria of completeness—as far as it can be applied to large molecules—and also by studying the effect of hydration on these charges. This was done by allowing the solvent to perturb the wave function prior to the electrostatic potential determination. Thus, 3-21G and 6-31G * basis sets were found to give satisfactory results. Similar results were obtained using semiempirical and ab initio geometries.