Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AM1 atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino- s -triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, m 1.4, m 6.4 and 0.0 kcal/mol for PCB14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of m 5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM+ force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and m 0.7 (PPDDT) kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by m 3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.     

Enthalpies of solution and solvation of amides in N,N-dimethylformamide: Application of the random contact point approach

Calorimetrically determined molar enthalpies of solution at infinite dilution in N,N-dimethylformamide and densities of several amides at 25°C are reported. Some of the enthalpies are combined with literature data for enthalpies of vaporization to obtain molar enthalpies of solvation. Relations are found between the enthalpies of solution and the size, and between these enthalpies and the enthalpic pair interaction coefficients of the solute molecules. These relations are quantified by an extension of the random contact point approach. This additivity scheme is also applied to enthalpies of solvation, vaporization and cavity formation. With this approach thermodynamic quantities of solution, solvation, vaporization, and pair interaction of different solutes and solvents are correlated with a single consistent set of group interaction parameters. In addition, the random contact point model provides a simple method to calculate thermodynamics of cavity formation which appear to be as reliable as those of the much more complicated scaled particle theory.     

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.     

X-ray photoelectron study of electron density distribution in palladium(II) β-diketonate complexes

This work is devoted to experimental (X-ray photoelectron) and theoretical investigations of electron density distribution in Pd(II) β-diketonate complexes. Data about the electronic structure (effective charges, core level energies) of the compounds are compared with their thermodynamic parameters (thermal stability, vaporization enthalpy). In molecular crystals of Pd(II) β-diketonates, the volatility of the complexes and vaporization enthalpy ΔH _T ⁰ depend not only on van der Waals interactions, but also on electrostatic interactions of molecules in crystal.     

A novel united-atom force field for imidazolium-based ionic liquids

A novel united-atom (UA) force field is proposed from our previously developed all-atom (AA) force field for the imidazolium-based ionic liquids by the introduction of a coarse-grained method. The Lennard-Jones parameters for CH(2) and CH(3) in alkyls are fitted to match the AA force field, and the partial atomic charges are re-fitted by the one conformation two-step RESP method. The force field is verified by molecular dynamics simulations of pure ionic liquids and the mixture of [bmim][BF(4)] and acetonitrile. The densities, self-diffusion coefficients, vaporization enthalpies, cohesive energy densities, and microscopic structures of both the pure components and mixtures are simulated. The simulated results from the UA force field agree well with those from the AA force field. In addition, the predictive capability of the UA force field for the liquid densities of [C(n)mim][PF(6)] is tested. The UA force field proposed in this work provides a useful tool with good accuracy and much less computational intensity for future molecular design of ionic liquids.     

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization

Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their "ideal" values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization can significantly reduce the prediction errors. We believe that GAFF can greatly improve its performance in predicting liquid properties of organic molecules after a systematic vdW parameterization, which will be reported in a separate paper.     

GEMC和GDI方法计算流体气液相平衡的比较

考察采用TraPPE联合原子和OPLS全原子力场两种分子力场, Gibbs系综蒙特卡罗(GEMC)方法和Gibbs-Duhem积分(GDI)方法计算流体气液相平衡的适用性、计算速度、计算精度等问题. 结果表明, 在采用全原子力场情况下, GDI方法比GEMC方法极大地节省了计算时间. 从计算结果来看, 两种方法各有适用范围, 在使用时可互为补充. 在给定力场的前提下, 两种方法所得到的液相密度、蒸发焓、临界温度和临界密度相差不大, 而当力场中的缺陷导致蒸发焓的计算不够准确时, 两种计算方法得到的气体的压力和密度明显不同,进而导致预测的临界压力也明显不同.     

Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be -5.6 +/- 0.2 kcal/mol, in respectable agreement with the experimental value of -5.1 kcal/mol. With respect to solution microstructure, the present cluster analysis suggests that the microscale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bipercolating network structure.     

Gas‐phase and liquid‐state properties of esters,nitriles, and nitro compounds with the OPLS‐AA force field

Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1340–1352, 2001     

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.     

Optimization of a molecular mechanics force field for type-II polyoxometalates focussing on electrostatic interactions: a case study

In this study, we have focussed on type-II polyanions such as [M(7)O(24)](6-), and we have developed and validated optimized force fields that include electrostatic and van der Waals interactions. These contributions to the total steric energy are described by the nonbonded term, which encompasses all interactions between atoms that are not transmitted through the bonds. A first validation of a stochastic technique based on genetic algorithms was previously made for the optimization of force fields dedicated to type-I polyoxometalates. To describe the new nonbonded term added in the functional, a fixed-charged model was chosen. Therefore, one of the main issues was to analyze that which partial atomic charges could be reliably used to describe these interactions in such inorganic compounds. Based on several computational strategies, molecular mechanics (MM) force field parameters were optimized using different types of atomic charges. Moreover, the influence of the electrostatic and van der Waals buffering constants and 1,4-interactions scaling factors used in the force field were also tested, either being optimized as well or fixed with respect to the values of CHARMM force field. Results show that some atomic charges are not well adapted to CHARMM parameters and lead to unrealistic MM-optimized structures or a MM divergence. As a result, a new scaling factor has been optimized for Quantum Theory of Atoms in Molecules charges and charges derived from the electrostatic potential such as ChelpG. The force fields optimized can be mixed with the CHARMM force field, without changing it, to study for the first time hepta-anions interacting with organic molecules.     

The influence of discrete surface charges on the force between charged surfaces

The force between two parallel charged flat surfaces, with discrete surface charges, has been calculated with Monte Carlo simulations for different values of the electrostatic coupling. For low electrostatic coupling (small counterion valence, small surface charge, high dielectric constant, and high temperature) the total force is dominated by the entropic contribution and can be described by mean field theory, independent of the character of the surface charges. For moderate electrostatic coupling, counterion correlation effects lead to a smaller repulsion than predicted by mean field theory. This correlation effect is strengthened by discrete surface charges and the repulsive force is further reduced. For large electrostatic coupling the total force for smeared out surface charges is known to be attractive due to counterion correlations. If discrete surface charges are considered the attractive force is weakened and can even be turned into a repulsive force. This is due to the counterions being strongly correlated to the discrete surface charges forming effective, oppositely directed, dipoles on the two walls.     

Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side‐chain analogues

A previously introduced polarizable simulations with second‐order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side‐chains. Parameters have been fitted to permit reproducing many‐body energies, gas‐phase dimerization energies, and geometries and liquid‐phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second‐order approximation of the full‐scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins. © 2012 Wiley Periodicals, Inc.     

Lattice energetics and thermochemistry of phenyl acridine-9-carboxylates and 9-phenoxycarbonyl-10-methylacridinium trifluoromethanesulphonates

The melting points and melting enthalpies of nine phenyl acridine-9-carboxylates—nitro-, methoxy- or halogen-substituted in the phenyl fragment—and their 9-phenoxycarbonyl-10-methylacridinium trifluoromethanesulphonate derivatives were determined by DSC. The volatilisation temperatures and enthalpies of phenyl acridine-9-carboxylates were either measured by DSC or obtained by fitting TG curves to the Clausius–Clapeyron relationship. For the compounds whose crystal structures are known, crystal lattice energies and enthalpies were determined computationally as the sum of electrostatic, dispersive and repulsive interactions. By combining the enthalpies of formation of gaseous phenyl acridine-9-carboxylates or 9-phenoxycarbonyl-10-methylacridinium trifluoromethanesulphonate ions, obtained by the DFT method, and the corresponding enthalpies of sublimation and/or crystal lattice enthalpies, the enthalpies of formation of the compounds in the solid phase were predicted. In the case of the phenyl acridine-9-carboxylates, the computationally predicted crystal lattice enthalpies correspond reasonably well with the experimentally obtained enthalpies of sublimation. The crystal lattices of phenyl acridine-9-carboxylates are stabilised predominantly by dispersive interactions between molecules, whilst the crystal lattices of their quaternary salts are stabilised by electrostatic interactions between ions.     

Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpy of vaporization

Three-dimensional Quantitative Structure-Property Relationship (QSPR) models have been derived using Comparative Molecular Field Analysis (CoMFA) to correlate the vaporization enthalpies of a representative set of polychlorinated biphenyls (PCBs) at 298.15 K with their CoMFA-calculated physicochemical properties. Various alignment schemes, such as inertial, as is, and atom fit, were employed in this study. The CoMFA models were also developed using different partial charge formalisms, namely, electrostatic potential (ESP) charges and Gasteiger-Marsili (GM) charges. The most predictive model for vaporization enthalpy (Delta(vap)H(m)(298.15 K)), with atom fit alignment and Gasteiger-Marsili charges, yielded r2 values 0.852 (cross-validated) and 0.996 (conventional). The vaporization enthalpies of PCBs increased with the number of chlorine atoms and were found to be larger for the meta- and para-substituted isomers. This model was used to predict Delta(vap)H(m)(298.15 K) of the entire set of 209 PCB congeners.     

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.