Use of thermodynamic integration to calculate the hydration free energies of n-alkanes

Molecular Mechanisms of the Generation and Accumulation of Gas at the Interface

Gas-evolving reactions are widespread in chemical and energy fields. However, the generated gas will accumulate at the interface, which reduces the rate of gas generation. Understanding the microscopic processes of the generation and accumulation of gas at the interface is crucial for improving the efficiency of gas generation. Here, we develop an algorithm to reproduce the process of catalytic gas generation at the molecular scale based on the all-atom molecular dynamics simulations and obtain the quantitative evolution of the gas generation, which agrees well with the experimental results. In addition, we demonstrate that under an external electric field, the generated gas molecules do not accumulate at the electrode surface, which implies that the electric field can significantly increase the rate of the gas generation. The results suggest that the external electric field changes the structure of the water molecules near the electrode surface, making it difficult for gas molecules to accumulate on the electrode surface. Furthermore, it is found that gas desorption from the electrode surface is an entropy-driven process, and its accumulation at the electrode surface depends mainly on the competition between the entropy and the enthalpy of the water molecules under the influence of the electric field. These results provide deep insight into gas generation and inhibition of gas accumulation.

Structural and thermodynamic properties of bulk triglycerides and triglyceride/water mixtures reproduced using a polarizable coarse-grained model

Triglycerides (TGs) play important roles in renewable energies, food production, medicine, and metabolism in organisms. Here, we developed a novel coarse-grained (CG) force field (FF) for triglycerides to reproduce both the structural and thermodynamic properties of bulk TGs, TG/air interfaces, and TG/water mixtures using molecular dynamics (MD) simulations. We rigorously optimized the bonded and nonbonded force parameters between the CG beads of TGs and nonbonded force parameters between TG beads and polarizable CG water beads by employing an efficient meta-multilinear interpolation parameterization algorithm recently developed by us. This CG FF performs very well in reproducing the percolating network of the TG bulk phase self-assembled in water and a variety of molecular conformations predicted by all-atom MD simulations. More importantly, it also correctly reproduces multiple experimentally measurable macroscopic thermodynamic properties, including the density and surface tensions of both the TG/air and TG/water interfaces. This paves the way for studying more complicated systems involving TGs on a large scale.

A top-down and bottom-up combined strategy for parameterization of coarse-grained force fields for phospholipids

Coarse-graining (CG) molecular dynamics (MD) simulations are widely used in interpreting experimental observations and predicting assembly morphology as well as collective behaviour but also face the problem of poor accuracy. A main issue is that cross-termed interactions between different CG beads are inadequately parameterized. This work proposes a novel top-down and bottom-up combined strategy to parameterize both self- and cross-termed interactions of zwitterionic phospholipids in water solution based on a piecewise Morse potential describing nonbonded van der Waals interactions. The self-interacting force parameters were optimized by matching experimental density, heat vapourization, and surface tension in a top-down manner, while the cross-termed interactions were optimized by fitting pseudo properties obtained from atomistic simulations in a bottom-up way, including mixing density, intermolecular energy, and radial mixing coefficient. The transferability of the CG force field (FF) was confirmed by reproducing a variety of structural and thermodynamic properties of lipid membranes in both liquid and gel phases. This FF can well depict vesicle self-assembly and vesicle fusion processes. Matching pseudo properties opens a new way to develop CG FF with increased accuracy and transferability.

Development of accurate coarse-grained force fields for weakly polar groups by an indirect parameterization strategy

Coarse-grained (CG) molecular dynamics simulations are widely used to predict morphological structures and interpret mechanisms of mesoscopic behavior between the scope of traditional experiments and all-atom simulations. However, most current CG force fields (FFs) are not precise enough, especially for polar molecules or functional groups. A main obstacle in developing accurate CG FFs for polar molecules is the freezing problem met at room temperature. In this work, we introduce an indirect parametrization strategy for weakly polar groups by considering their short-chain homologs to avoid freezing. Here, a polar group containing three to four heavy atoms is mapped into one CG bead that is connected to one alkyl bead composed of three or four carbons. The CG beads interact via 4-parameter nonbonded Morse potentials and harmonic bonded potentials. An efficient meta-multilinear interpolation parameterization algorithm, as recently developed by us, is used to rigorously optimize the force parameters. Satisfactory accuracy is witnessed in terms of the density, heat of vaporization, surface tension, and solvation free energy of the homologs of twelve polar molecules, all deviating from the experiment by less than 5%. The transferability of the current FF is indicated by the predicted density, heat of vaporization, and end-to-end distance distributions of fatty acid methyl esters composed of multiple functional groups parameterized in this work.

Development of coarse-grained force field for alcohols: an efficient meta-multilinear interpolation parameterization algorithm

Coarse-grained (CG) molecular dynamics are powerful tools to access a mesoscopic phenomenon and simultaneously record microscopic details, but currently the CG force fields (FFs) are still limited by low parameterization efficiency and poor accuracy especially for polar molecules. In this work, we developed a Meta-Multilinear Interpolation Parameterization (Meta-MIP) algorithm to optimize the CG FFs for alcohols. This algorithm significantly boosts parameterization efficiency by constructing on-the-fly local databases to cover the global optimal parameterization path. In specific, an alcohol molecule is mapped to a heterologous model composed of an OH bead and a hydrocarbon portion which consists of alkane beads representing two to four carbon atoms. Non-bonded potentials are described by soft Morse functions that have no tail-corrections but can still retain good continuities at truncation distance. Nearly all of the properties in terms of density, heat of vaporization, surface tension, and solvation free energy for alcohols predicted by the current FFs deviate from experimental values by less than 7%. This Meta-MIP algorithm can be readily applied to force field development for a wide variety of molecules or functional groups, in many situations including but not limited to CG FFs.

Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning

In this review we will discuss how computational methods, and in particular classical molecular dynamics simulations, can be used to calculate solubility of pharmaceutically relevant molecules and systems. To the extent possible, we focus on the non-technical details of these calculations, and try to show also the added value of a more thorough and detailed understanding of the solubilization process obtained by using computational simulations. Although the main focus is on classical molecular dynamics simulations, we also provide the reader with some insights into other computational techniques, such as the COSMO-method, and also discuss Flory-Huggins theory and solubility parameters. We hope that this review will serve as a valuable starting point for any pharmaceutical researcher, who has not yet fully explored the possibilities offered by computational approaches to solubility calculations.

Confinement Effect on Molecular Conformation of Alkanes in Water-Filled Cavitands: A Combined Quantum/Classical Density Functional Theory Study

The depletion force exerted on an alkane molecule from surrounding solvent may greatly alter its conformation. Such a behavior is closely related to the selective molecular recognition, molecular sensors, self-assembly, and so on. Herein, we report a multiscale theoretical study on the conformational change of a single alkane molecule confined in water-filled cavitands, in which the quantum and classical density functional theories (DFTs) are combined to determine the grand potential of alkane-water system. Specifically, the intrinsic free energy of the alkane molecule is tackled by quantum DFT, while the solvent effect arising from the solvent density inhomogeneity in confined space is addressed by classical DFT. By varying the alkane chain length, pore size, and wettability of inner pore surface, we find that pore confinement and hydrophilic inner surface facilitate the alkane conformational change from extended state to helical state, which becomes more significant as the alkane chain length increases. Our findings, which are in line with previous experimental observations, provide not only the microscopic mechanism but also theoretical guidance for elaborately manipulating molecular conformation at the nanoscale.

PFC and Triglyme for Li-Air Batteries: A Molecular Dynamics Study

In this work, we present an all-atom molecular dynamics (MD) study of triglyme and perfluorinated carbons (PFCs) using classical atomistic force fields. Triglyme is a typical solvent used in nonaqueous Li-air battery cells. PFCs were recently reported to increase oxygen availability in such cells. We show that O2 diffusion in two specific PFC molecules (C6F14 and C8F18) is significantly faster than in triglyme. Furthermore, by starting with two very different initial configurations for our MD simulation, we demonstrate that C8F18 and triglyme do not mix. The mutual solubility of these molecules is evaluated both theoretically and experimentally, and a qualitative agreement is found. Finally, we show that the solubility of O2 in C8F18 is considerably higher than in triglyme. The significance of these results to Li-air batteries is discussed.

The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration

We propose a novel, anisotropic rigid-body intermolecular potential model to predict the properties of water and the hydration free energies of neutral organic solutes. The electrostatic interactions of water and the solutes are modeled using atomic multipole moments up to hexadecapole; these are obtained from distributed multipole analysis of the quantum mechanically computed charge densities and include average polarization effects in solution. The repulsion-dispersion water-water interactions are modeled with a three-site, exp-6 model fitted to the experimental liquid water density and oxygen-oxygen radial distribution function at ambient conditions. The proposed water model reproduces well several water properties not used in its parametrization, including vapor-liquid coexistence densities, the maximum in liquid water density at atmospheric pressure, the structure of ordered ice polymorphs, and the liquid water heat capacity. The model is used to compute the hydration free energy of 10 neutral organic solutes using explicit-solvent free energy perturbation. The solute-solute repulsion-dispersion intermolecular potential is obtained from previous parametrizations on organic crystal structures. In order to calculate the free energies of hydration, water-solute repulsion-dispersion interactions are modeled using Lorenz-Berthelot combining rules. The root-mean-square error of the predicted hydration free energies is 1.5 kcal mol(-1), which is comparable to the error found using a continuum mean-field quantum mechanical approach parametrized using experimental free energy of hydration data. The results are also contrasted with explicit-solvent hydration free energies obtained with an atomic charge representation of the solute's charge density computed at the same level of theory used to compute the distributed multipoles. Replacing the multipole description of the solute's charge density with an atomic charge model changes the free energy of hydration by as much as 3 kcal mol(-1) and provides an estimate for the effect of the modeling quality of the intermolecular electrostatic forces in free energy of solvation calculations.

Association of alkanes with the aqueous liquid-vapor interface: a reference system for interpreting hydrophobicity generally through interfacial fluctuations

We report free energy calculations and fluctuation profiles of single alkanes (from methane to pentane) along the direction normal to the air-water interface. The induced fluctuations and the interfacial stabilities of alkanes are found to be correlated and similar to the results of inorganic monovalent ions (Ou et al., J. Phys. Chem. B, 2013, 117, 11732). This suggests that hydrophobic solvation of solutes and ions is important in determining the adsorption behavior.

Density functional theory for protein transfer free energy

We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible surface area, and temperature dependence of the transfer free energy all emerge naturally within this formalism, and may be compared with simplified "back of the envelope" models, which are also developed here. Depletion contributions to osmolyte induced stability range from 5 to 10 kBT for typical protein lengths. The general DFT transfer theory developed here may be simplified to reproduce a Langmuir isotherm condensation mechanism on the protein surface in the limits of short-ranged interactions, and dilute solute. Extending the equation of state to higher solute densities results in non-monotonic behavior of the free energy driving protein or polymer collapse. Effective interaction potentials between protein backbone or side chains and TMAO are obtained, assuming a simple backbone/side chain two-bead model for the protein with an effective 6-12 potential with the osmolyte. The transfer free energy δg shows significant entropy: d(δg)/dT ≈ 20 kB for a 100-residue protein. The application of DFT to effective solvent forces for use in implicit-solvent molecular dynamics is also developed. The simplest DFT expressions for implicit-solvent forces contain both depletion interactions and an "impeded-solvation" repulsive force at larger distances.

Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations

The 1-octanol-water partition coefficient log K(ow) of a solute is a key parameter used in the prediction of a wide variety of complex phenomena such as drug availability and bioaccumulation potential of trace contaminants. In this work, adaptive biasing force molecular dynamics simulations are used to determine absolute free energies of hydration, solvation, and 1-octanol-water partition coefficients for n-alkanes from methane to octane. Two approaches are evaluated; the direct transfer of the solute from 1-octanol to water phase, and separate transfers of the solute from the water or 1-octanol phase to vacuum, with both methods yielding statistically indistinguishable results. Calculations performed with the TIP4P and SPC∕E water models and the TraPPE united-atom force field for n-alkanes show that the choice of water model has a negligible effect on predicted free energies of transfer and partition coefficients for n-alkanes. A comparison of calculations using wet and dry octanol phases shows that the predictions for log K(ow) using wet octanol are 0.2-0.4 log units lower than for dry octanol, although this is within the statistical uncertainty of the calculation.

Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models

We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for fixed-charge force fields. The implications of such behavior pertain to the modeling of polar and charged solutes in lipidic environments.

Molecular dynamics study of the behavior of selected nanoscale building blocks in a gel-phase lipid bilayer

The cellular membrane functions as a regulating barrier between the intracellular and extracellular regions. For a molecule to reach the interior of the cell from the extracellular fluid, it must diffuse across the membrane, via either active or passive transport. The rigid structure of lipid bilayers, which are a key component of cellular membranes, prohibit simple diffusion of most particles, while vital nutrients are transported to the interior by specific mechanisms, such as ion channels and transport proteins. Although the cellular membrane provides the cell with protection against unwanted toxins that may be in the extracellular medium, some foreign particles can reach the interior of the cell, resulting in irregularities in cellular function. This behavior is particularly noted for permeants with compact molecular structure, suggesting that common nanoscale building blocks, such as fullerenes, may enter into the interior of a cell. To gauge the propensity for such particles to cross the membrane, we have computed the Gibbs free energy of transfer along the axis normal to the bilayer surface for two nanoscale building blocks, C(60) and a hydrogen-terminated polyhedral oligomeric silsequioxane (H-POSS) monomer, in a hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer using molecular dynamics simulations and potential of mean force calculations. The studies show that C(60) has a substantial energetic preference for the soft polymer region of the lipid bilayer system, below the water/bilayer interface, with a transition energy from bulk water of -19.8 kcal/mol. The transition of C(60) from the bulk water to the center of the bilayer, while also energetically favorable, has to overcome a +5.9 kcal/mol energetic barrier in the hydrophobic lipid tail region. The H-POSS simulations indicate an energy minimum at the water-bilayer interface, with an energy of -10.9 kcal/mol; however, a local minimum of -2.7 kcal/mol is also observed in the hydrophobic dense aliphatic region. The energy barrier seen in the hydrophobic core region of the C(60) study is likely due to the significant penalty associated with inserting the relatively large particle into such a dense region. In contrast, whereas H-POSS is found to be subject to an energetic penalty upon insertion into the bilayer, the relatively small size of the H-POSS solute renders this penalty less significant. The energy barrier seen in the soft polymer region for the H-POSS monomer is primarily attributed to the lack of favorable solute-bilayer electrostatic interactions, which are present in the interfacial region, and fewer van der Waals interactions in the soft polymer region than the dense aliphatic region. These results indicate that C(60) may partition into the organic phase of the DPPC/water system, given the favorable free energies in the soft polymer and dense aliphatic regions of the bilayer, and H-POSS is likely to partition near the water-bilayer interface, where the particle has low-energy electrostatic interactions with the polar head groups of the bilayer.

A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes

In order to extend the time and distance scales of molecular dynamics simulations, it is essential to create accurate coarse-grained force fields, in which each particle contains several atoms. Coarse-grained force fields that utilize the Lennard-Jones potential form for pairwise nonbonded interactions have been shown to suffer from serious inaccuracy, notably with respect to describing the behavior of water. In this paper, we describe a coarse-grained force field for water, in which each particle contains four water molecules, based on the Morse potential form. By molecular dynamics simulations, we show that our force field closely replicates important water properties. We also describe a Morse potential force field for alkanes and a simulation method for alkanes in which individual particles may have variable size, providing flexibility in constructing complex molecules comprised partly or solely of alkane groups. We find that, in addition to being more accurate, the Morse potential also provides the ability to take larger time steps than the Lennard-Jones, because the short distance repulsion potential profile is less steep. We suggest that the Morse potential form should be considered as an alternative for the Lennard-Jones form for coarse-grained molecular dynamics simulations.

Molecular dynamics simulations of functional group effects on solvation thermodynamics of model solutes in decane and tricaprylin

Triglycerides and related fatty acid esters constitute a large percentage of the lipid excipients employed in the development of lipid-based drug formulations. Computer simulations can provide useful information on the structural, dynamic, and thermodynamic properties of these systems and may ultimately be valuable in predicting relative drug solubilities in lipid vehicles. This study utilized all-atom molecular dynamics simulations to explore the solvation of several model solutes in lipid vehicles. First, a combined thermodynamic perturbation and integration approach was employed to calculate functional group contributions to the free energy of transfer from n-decane to tricaprylin for a set of polar substituents attached to the 9-position of anthracene. A scaling factor of 0.79 for all atomic charges in the dry lipid (where the unscaled charges were obtained at the level of the HF/6-31G* basis set) was necessary in order to match the calculated group contributions to the free energies of transfer with their experimental values at 37 degrees C. A second set of simulations was performed in water-saturated tricaprylin containing a single molecule of benzamide to explore the state of organization of solvent molecules, the distribution of water molecules, and the local environment surrounding the solute. Radial distribution functions revealed evidence of local structure in the liquid triglyceride. The dissolved water was found to exist approximately 50% as monomers and 50% as self-associated species. Substantial hydrogen-bonding of benzamide with ester carbonyl oxygen atoms was observed.

Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: An assessment of simulation methodology and force field performance and transferability

Hydration free energies of nonpolarizable monovalent atomic ions in transferable intermolecular potential four point fluctuating charge (TIP4P-FQ) are computed using several commonly employed ion-water force fields including two complete model sets recently developed for use with the simple water model with four sites and Drude polarizability and TIP4P water models. A simulation methodology is presented which incorporates a number of finite-system free energy corrections within the context of constant pressure molecular dynamics simulations employing the Ewald method and periodic boundary conditions. The agreement of the computed free energies and solvation structures with previously reported results for these models in finite droplet systems indicates good transferability of ion force fields from these water models to TIP4Q-FQ even when ion polarizability is neglected. To assess the performance of the ion models in TIP4P-FQ, we compare with consensus values for single-ion hydration free energies arising from recently improved cluster-pair estimates and a reevaluation of commonly cited, experimentally derived single-ion hydration free energies; we couple the observed consistency of these energies with a justification of the cluster-pair approximation in assigning single-ion hydration free energies to advocate the use of these consensus energies as a benchmark set in the parametrization of future ion force fields.

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

Quantitative free energy computation involves both using a model that is sufficiently faithful to the experimental system under study (accuracy) and establishing statistically meaningful measures of the uncertainties resulting from finite sampling (precision). In order to examine the accuracy of a range of common water models used for protein simulation for their solute/solvent properties, we calculate the free energy of hydration of 15 amino acid side chain analogs derived from the OPLS-AA parameter set with the TIP3P, TIP4P, SPC, SPC/E, TIP3P-MOD, and TIP4P-Ew water models. We achieve a high degree of statistical precision in our simulations, obtaining uncertainties for the free energy of hydration of 0.02-0.06 kcal/mol, equivalent to that obtained in experimental hydration free energy measurements of the same molecules. We find that TIP3P-MOD, a model designed to give improved free energy of hydration for methane, gives uniformly the closest match to experiment; we also find that the ability to accurately model pure water properties does not necessarily predict ability to predict solute/solvent behavior. We also evaluate the free energies of a number of novel modifications of TIP3P designed as a proof of concept that it is possible to obtain much better solute/solvent free energetic behavior without substantially negatively affecting pure water properties. We decrease the average error to zero while reducing the root mean square error below that of any of the published water models, with measured liquid water properties remaining almost constant with respect to our perturbations. This demonstrates there is still both room for improvement within current fixed-charge biomolecular force fields and significant parameter flexibility to make these improvements. Recent research in computational efficiency of free energy methods allows us to perform simulations on a local cluster that previously required large scale distributed computing, performing four times as much computational work in approximately a tenth of the computer time as a similar study a year ago.

Molecular-dynamics evaluation of fluid-phase equilibrium properties by a novel free-energy perturbation approach: Application to gas solubility and vapor pressure of liquid hexane

A novel free-energy perturbation method is developed for the computation of the free energy of transferring a molecule between fluid phases. The methodology consists in drawing a free-energy profile of the target molecule moving across a binary-phase structure built in the computer. The novelty of the method lies in the difference of the definition of the free-energy profile from the common definition. As an important element of the method, the process of making a correction to the transfer free energy with respect to the cutoff of intermolecular forces is elucidated. In order to examine the performance of the method in the application to fluid-phase equilibrium properties, molecular-dynamics computations are carried out for the evaluation of gas solubility and vapor pressure of liquid n-hexane at 298.15 K. The gas species treated are methane, ethane, propane, and n-butane, with the gas solubility expressed as Henry's constant. It is shown that the method works fine and calculated results are generally in good agreement with experiments. It is found that the cutoff correction is strikingly large, constituting a dominant part of the calculated transfer free energy at the cutoff of 8 A.

Hybrid integral equation/simulation model for enhancing free energy computations

Integral equation theory is used for extrapolating free energy data from molecular simulations of a reference state with respect to a modification of the interaction potential. The methodology is applied to the correction of artefacts arising from potential shifting and truncation. Corrective contributions for the hydration free energy with respect to the full potential are analysed for the case that both the solute-solvent as well as the solvent-solvent potentials are truncated and modified by a shifted-force term, reaching beyond the range of the dielectric continuum approximation and simple long-range correction expressions. The model systems argon in water and pure water are used as examples for apolar and polar solutes, revealing significant correction contributions even for the short-ranged dispersive interactions and the magnitude of solute-solvent and solvent-solvent components. In comparison with simulation-based extrapolation techniques the integral equation method is shown to be capable of quantitatively predicting truncation artefacts at negligible computational overhead.

Solubility of Methane in Water: The Significance of the Methane−Water Interaction Potential

The influence of the methane-water interaction potential on the value of the Henry constant obtained from molecular dynamics simulations was investigated. The SPC, SPC/E, MSPC/E, and TIP3P potentials were used to describe water and the OPLS-UA and TraPPE potentials for methane. Nonbonding interactions between unlike atoms were calculated both with one of four mixing rules and with our new methane-water interaction potential. The Henry constants obtained from simulations using any of the mixing rules differed significantly from the experimental ones. Good agreement between simulation and experiment was achieved with the new potential over the whole temperature range.

Direct calculation of the binding free energies of FKBP ligands

Direct calculations of the absolute free energies of binding for eight ligands to FKBP protein were performed using the Fujitsu BioServer massively parallel computer. Using the latest version of the general assisted model building with energy refinement (AMBER) force field for ligand model parameters and the Bennett acceptance ratio for computing free-energy differences, we obtained an excellent linear fit between the calculated and experimental binding free energies. The rms error from a linear fit is 0.4 kcal/mol for eight ligand complexes. In comparison with a previous study of the binding energies of these same eight ligand complexes, these results suggest that the use of improved model parameters can lead to more predictive binding estimates, and that these estimates can be obtained with significantly less computer time than previously thought. These findings make such direct methods more attractive for use in rational drug design.

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.

Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field

We calculated the free energy of solvation of the neutral analogs of 18 amino acid side-chains (not including glycine and proline) using the OPLS all-atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid.