Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents.

Recently, the GROMOS biomolecular force field parameter set 53A6--which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side-chain analogs--was presented. To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in different solvents (methanol, dimethyl sulfoxide (DMSO), acetonitrile, and acetone) from molecular dynamics simulations using the GROMOS 53A6 force field. For methanol and DMSO, parameters were used that are available in the 53A6 parameter set. For acetonitrile, a recently developed model was taken and for acetone, two models available in literature were used. We found that trends in and values for the solvation free enthalpies are in satisfactory agreement with experiment, except for the solvation in acetone for which deviations from experiment can be explained in terms of the properties of the models used.     

Atomistic detailed free‐energy landscape of intrinsically disordered protein studied by multi‐scale divide‐and‐conquer molecular dynamics simulation

Calcineurin (CaN) is a eukaryotic serine/threonine protein phosphatase activated by both Ca²⁺ and calmodulin (CaM), including intrinsically disordered region (IDR). The region undergoes folding into an α‐helix form in the presence Ca²⁺‐loaded CaM. To sample the ordered structure of the IDR by conventional all atom model (AAM) molecular dynamics (MD) simulation, the IDR and Ca²⁺‐loaded CaM must be simultaneously treated. However, it is time‐consuming task because the coupled folding and binding should include repeated binding and dissociation. Then, in this study, we propose novel multi‐scale divide‐and‐conquer MD (MSDC‐MD), which combines AAM‐MD and coarse‐grained model MD (CGM‐MD). To speed up the conformation sampling, MSDC‐MD simulation first treats the IDR by CGM to sample conformations from wide conformation space; then, multiple AAM‐MD in a limited area is initiated using the resultant CGM conformation, which is reconstructed by homology modeling method. To investigate performance, we sampled the ordered conformation of the IDR using MSDC‐MD; the root‐mean‐square distance (RMSD) with respect to the experimental structure was 2.23 Å.     

New approach to free energy of solvation applying continuum models to molecular dynamics simulation

A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.     

Hierarchical atom type definitions and extensible all‐atom force fields

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom‐type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined. The computed Debye-Waller factors and simulated FTIR spectra are in good agreement with the experimental data. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves which should lead to a better understanding of the catalytic processes and the crucial role played by templating molecules.     

Cracking of n‐octadecane: A molecular dynamics simulation

Despite the extensive research studies, the understanding of the fundamental mechanisms of chemical transformations at the cracking of hydrocarbons remains unexplored. In the present study, the initial stages of both thermal and catalytic cracking of n‐octadecane C₁₈H₃₈ (with a nickel Ni₄₉ particle as a catalyst) were investigated using the ReaxFF force field (the ReaxFF software package). The initial cracking mechanism of n‐octadecane was simulated at four different temperatures 1,800, 1,900, 2,000, and 2,200 K on a large interface system (2,849 atoms) consisting of 49 nickel atoms surrounded by 50 hydrocarbon molecules. Analysis of trajectories, according to the simulations, reveals a complex mechanism for initiating thermal and catalytic cracking of C₁₈H₃₈. Thermal cracking of C₁₈H₃₈ is initiated by breaking the C–C bond and proceeds via a free‐radical mechanism, whereas catalytic cracking is preferentially activated by deprotonation and protonation of the C–C bond. This work demonstrates that the ReaxFF force field can be actively used in the study of complex chemical transformations that occur at the cracking of hydrocarbons.     

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

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

Atomistic insight into chondroitin‐6‐sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation

Chondroitin‐6‐sulfate (C6S) is a glycosaminoglycan (GAG) constituent in the extracellular matrix, which participates actively in crucial biological processes, as well as in various pathological conditions, such as atherosclerosis and cancer. Molecular interactions involving the C6S chain are therefore of considerable interest. A computational model for atomistic simulation was built. This work describes the design and validation of a force field for a C6S dodecasaccharide chain. The results of an extensive molecular dynamics simulation performed with the new force field provide a novel insight into the structure and dynamics of the C6S chain. The intramolecular H‐bonds in the disaccharide linkage region are suggested to play a major role in determining the chain structural dynamics. Moreover, the unravelling of an additional H‐bond involving the sulfate groups in C6S is interesting as changes in sulfation have been claimed to be an important factor in several diseases. The force field will prove useful for future studies of crucial interactions between C6S and various nanoassemblies. It can also be used as a basis for modeling of other GAGs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Electrostatic component of solvation: comparison of SCRF continuum models

We report a systematic comparison of the electrostatic contributions to the free energy of solvation from three different kinds of quantum mechanical self-consistent reaction field (SCRF) methods. We also compare the liquid-phase dipole moments as a measure of the solute's response to the reaction field of the solvent. In particular, we compare these quantities for the generalized Born model as implemented in the SM5.42R method, the multipolar expansion model developed at Nancy, and the MST version of the polarizable continuum model. All calculations are carried out at the HF/6-31G(d) level. The effects of various choices of solute cavities and representations of the charge density are examined. The test set consists of 18 molecules containing prototypical polar groups, and three different values of the dielectric permittivity are considered.     

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.     

Effects of system net charge and electrostatic truncation on all‐atom constant pH molecular dynamics

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all‐atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force‐shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt‐bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini‐protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK_a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation‐state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge‐compensating background plasma. © 2014 Wiley Periodicals, Inc.     

Structural characteristics of p‐t‐Octylphenol formaldehyde resole resins using molecular simulation

p‐t‐Octylphenol formaldehyde resole resins have two linkage types of methylene‐ and dimethylene ether‐linkages and have three terminal types of hydrogen, methylol, and o‐methylene quinone. Variation of structural characteristics of the resins due to different types of linkages and terminals were studied using molecular dynamics and molecular mechanics. The structural characteristics of the methylene‐bridged resins were intramolecular hydrogen bonds between hydroxyl groups of the adjacent p‐t‐octylphenols. In the dimethylene ether‐bridged resin, the intramolecular hydrogen bonds between oxygen atoms of the dimethylene ether‐linkages and hydroxyl groups of the neighboring phenolic units were found. For the resins with both methylol terminals, one of both terminals of the resins was hidden at the center of the molecule when the resin size is large. The number of hydrogen bonds in the resins with the methylol terminal was larger than for the resins with the o‐methylene quinone terminal. Variation of the structural characteristics of the resins by dehydration of the terminal methylol was discussed. Using the calculated results, dissociation of the dimethylene ether linkage and crosslinking reaction of rubber chains by the resin were explained. Copyright © 2002 John Wiley & Sons, Ltd.     

United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system

We refined the united atom field for the simulations of phospholipid membranes. To validate this potential we performed 1000-ps constant pressure simulation of a dipalmitoylphosphatidicholine (DPPC) bilayer at T=50° C. The average area per head group (61.6±0.6) Ų obtained in our simulation agrees well with the measured one of (62.9±1.3) Ų. The calculated S_CD order parameters for the Sn-2 hydrocarbon tail also display a good agreement with the experiment. The conformations of head groups in our simulations of the liquid crystal phase are different than the ones observed in the crystal structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20, 531–545, 1999     

Calculation of relative solvation free energy differences by thermodynamic perturbation method: Dependence of free energy results on simulation length

Molecular dynamics (MD) simulations in conjunction with the thermodynamic cycle perturbation approach has been used to calculate relative solvation free energies for acetone to acetaldehyde, acetone to pyruvic acid, acetone to 1,1,1-trifluoroacetone, acetone to 1,1,1-trichloroacetone, acetone to 2,3-butanedione, acetone to cyclopropanone, and formaldehyde hydrate to formaldehyde. To evaluate the dependence of relative solvation free energy convergence on MD simulation length and starting configuration two studies were performed. In the first study, each simulation started from the same well-equilibrated configuration and the length was varied from 153 to 1530 ps. In the second study, the relative solvation free energy differences were calculated starting from three different configurations and using 510 ps of MD simulation for each mutation. These results clearly indicate that, even for molecules with limited conformational flexibility, a simulation length of 510 ps or greater is required to obtain satisfactory convergence and, for the mutations of large structural changes between reactant and product, such as cyclopropanone to acetone, require much longer simulation lengths to achieve satisfactory convergence. These results also show that performing one long simulation is better than averaging results from three shortest simulations of the same length using different starting conformations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1018–1027, 1999