Infuence of New Interaction Potential on MD Simulation of MgSiO3 Perovskite Thermodynamic Properties

The interaction potential plays an important role in molecular dynamics (MD) simulations. Pair potentialhas been used to simulate the melting temperature of MgSiO3 perovskite in previous studies, but considerablediscrepancy of melting temperature exists between these simulations. Comparisons of potential energy curvesare performed to explain the discrepancy. To further investigate the infuence of the interaction potentialparameters on the MD simulation result, a new set of potential parameters is developed based on two fitting potential parameters of previous studies, and is applied in the present study. The simulated molar volume MgSiO3 perovskite agrees well with the study by Belonoshko and Dubrovinsky at ambient condition. The equations of state, constant-pressure heating capacity and the constant-pressure thermal expansivity of MgSiO3 perovskite are close to the experimental data. Calculated melting temperatures are also comparable with those derived from previous studies.     

Isothermalisobaric molecular dynamics simulation of diatomic liquids and their mixtures

Isothermalisobaric ensemble molecular dynamics simulations have been performed for systems of two-center Lennard-Jones molecules for pure fluids as well as binary mixtures. The results obtained from various ensemble averages have been compared for pure fluid simulations of Lennard-Jones model diatomic fluids. The excess enthalpy and excess volume of three equimolar mixtures (argonnitrogen, argonoxygen, and nitrogenoxygen) have been calculated and compared with values obtained from previous NVT molecular dynamics and perturbation theory. Pair distribution functions obtained from various methods are compared for the equimolar mixture of nitrogen and oxygen and used to study the effect of attractive forces on the local structure. For four other systems (argonethane, methaneethane, carbon disulfidecarbon tetrachloride, and carbon disulfidetetrachloroethylene), excess enthalpies and excess volumes from NPT simulations are used to test the ability of perturbation theory to predict these properties and are also compared with experimental data. The comparison of simulation and experiment clearly shows the need to improve the available parameters for cross interactions in binary mixtures.     

NMR solvent shifts of acetonitrile from frozen density embedding calculations

We present a density functional theory (DFT) study of solvent effects on nuclear magnetic shielding parameters. As a test example we have focused on the sensitive nitrogen shift of acetonitrile immersed in a selected set of solvents, namely water, chloroform, and cyclohexane. To include the effect of the solvent environment in an accurate and efficient manner, we employed the frozen-density embedding (FDE) scheme. We have included up to 500 solvent molecules in the NMR computations and obtained the cluster geometries from a large set of conformations generated with molecular dynamics. For small solute-solvent clusters comparison of the FDE results with conventional supermolecular DFT calculations shows close agreement. For the large solute-solvent clusters the solvent shift values are compared with experimental data and with values obtained using continuum solvent models. For the water --> cyclohexane shift the obtained value is in very good agreement with experiments. For the water --> chloroform NMR solvent shift the classical force field used in the molecular dynamics simulations is found to introduce an error. This error can be largely avoided by using geometries taken from Car-Parrinello molecular dynamics simulations.     

Computer simulations of the refolding of sperm whale apomyoglobin from high-temperature denaturated state

The refolding mechanism of apomyoglobin (apoMb) subsequent to high-temperature unfolding has been examined using computer simulations with atomic level detail. The folding of this protein has been extensively studied experimentally, providing a large database of folding parameters which can be probed using simulations. In the present study, 4-folding trajectories of apoMb were computed starting from coiled structures. A crystal structure of sperm whale myoglobin taken from the Protein Data Bank was used to construct the final native conformation by removal of the heme group followed by energy optimization. The initial unfolded conformations were obtained from high-temperature molecular dynamics simulations. Room-temperature refolding trajectories at neutral pH were obtained using the stochastic difference equation in length algorithm. The folding trajectories were compared with experimental results and two previous molecular dynamics studies at low pH. In contrast to the previous simulations, an extended intermediate with large helical content was not observed. In the present study, a structural collapse occurs without formation of helices or native contacts. Once the protein structure is more compact (radius of gyration<18 A) secondary and tertiary structures appear. These results suggest that apoMb follows a different folding pathway after high-temperature denaturation.     

Use of Cartesian Rotation Vectors in Brownian Dynamics Algorithms: Theory and Simulation Results

Summary: We have shown that the components of Cartesian rotation vectors can be used successfully as generalized coordinates describing angular orientation in Brownian dynamics simulations of non‐spherical nanoparticles. For this particular choice of generalized coordinates, we rigorously derived the conformation‐space diffusion equations from kinetic theory for both free nanoparticles and nanoparticles interconnected by springs or holonomic constraints into polymer chains. The equivalent stochastic differential equations were used as a foundation for the Brownian dynamics algorithms. These new algorithms contain singularities only for points in the conformation‐space where both the probability density and its first coordinate derivative equal zero (weak singularities). In addition, the coordinate values after a single Brownian dynamics time step are throughout the conformation‐space equal to the old coordinate values plus the respective increments. For some parts of the conformation‐space these features represent a major improvement compared to the situation when Eulerian angles describe rotational dynamics. The presented simulation results of the equilibrium probability density for free nanoparticles are in perfect agreement with the results from kinetic theory.

Simulation of p^(eq)(Φ) for free nanoparticles.     

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set of parameters that reproduces the correct pucker preference. Our molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen-like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation (and thus the right phi angle) in the Y position.     

Quantum effects on adsorption and diffusion of hydrogen and deuterium in microporous materials

Monte Carlo and molecular dynamics simulations and neutron scattering experiments are used to study the adsorption and diffusion of hydrogen and deuterium in zeolite Rho in the temperature range of 30-150 K. In the molecular simulations, quantum effects are incorporated via the Feynman-Hibbs variational approach. We suggest a new set of potential parameters for hydrogen, which can be used when Feynman-Hibbs variational approach is used for quantum corrections. The dynamic properties obtained from molecular dynamics simulations are in excellent agreement with the experimental results and show significant quantum effects on the transport at very low temperature. The molecular dynamics simulation results show that the quantum effect is very sensitive to pore dimensions and under suitable conditions can lead to a reverse kinetic molecular sieving with deuterium diffusing faster than hydrogen.     

Comparison of aqueous molecular dynamics with NMR relaxation and residual dipolar couplings favors internal motion in a mannose oligosaccharide.

An investigation has been performed to assess how aqueous dynamical simulations of flexible molecules can be compared against NMR data. The methodology compares state-of-the-art NMR data (residual dipolar coupling, NOESY, and (13)C relaxation) to molecular dynamics simulations in water over several nanoseconds. In contrast to many previous applications of residual dipolar coupling in structure investigations of biomolecules, the approach described here uses molecular dynamics simulations to provide a dynamic representation of the molecule. A mannose pentasaccharide, alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->2)-D-Manp, was chosen as the model compound for this study. The presence of alpha-linked mannan is common to many glycopeptides, and therefore an understanding of the structure and the dynamics of this molecule is of both chemical and biological importance. This paper sets out to address the following questions. (1) Are the single structures which have been used to interpret residual dipolar couplings a useful representation of this molecule? (2) If dynamic flexibility is included in a representation of the molecule, can relaxation and residual dipolar coupling data then be simultaneously satisfied? (3) Do aqueous molecular dynamics simulations provide a reasonable representation of the dynamics present in the molecule and its interaction with water? In summary, two aqueous molecular dynamics simulations, each of 20 ns, were computed. They were started from two distant conformations and both converged to one flexible ensemble. The measured residual dipolar couplings were in agreement with predictions made by averaging the whole ensemble and from a specific single structure selected from the ensemble. However, the inclusion of internal motion was necessary to rationalize the relaxation data. Therefore, it is proposed that although residual dipolar couplings can be interpreted as a single-structure, this may not be a correct interpretation of molecular conformation in light of other experimental data. Second, the methodology described here shows that the ensembles from aqueous molecular dynamics can be effectively tested against experimental data sets. In the simulation, significant conformational motion was observed at each of the linkages, and no evidence for intramolecular hydrogen bonds at either alpha(1-->2) or alpha(1-->3) linkages was found. This is in contrast to simulations of other linkages, such as beta(1-->4), which are often predicted to maintain intramolecular hydrogen bonds and are coincidentally predicted to have less conformational freedom in solution.     

Water absorption in polyaniline emeraldine base

Atomistic classical molecular dynamics simulations have been used to investigate the water absorption behavior of polyaniline emeraldine base. Results derived from simulations, which were performed considering polymeric systems with different concentrations of water (3%, 10%, 15%, 20%, 50%, and 100% w/w), have been compared with experimental evidences obtained for both powder and films. Calculation of the Hildebrand solubility parameters explains not only the insolubility of polyaniline in water but also the requirements, in terms of intermolecular interactions, needed by solvents to be compatibles with this polymer. The maximum content of absorbed water predicted for hygroscopic polyaniline is 15% w/w. The effects of the absorbed water in both the organization and conformation of the polymer chains have been examined at the microscopic level by analyzing the microstructures derived from simulations, while the role of the moisture in the morphology of powder and film samples has been investigated using atomic force microscopy. The overall of the results provides a complete and understandable view of the polyaniline·water interactions, and explains the influence of the water molecules in the structural properties of the polymer. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1322–1331, 2011     

Constrained proper sampling of conformations of transition state ensemble of protein folding

Characterizing the conformations of protein in the transition state ensemble (TSE) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al. [Nature (London) 409, 641 (2001)] to study TSE is to generate conformations that satisfy all constraints imposed by the experimentally measured φ values that provide information about the native likeness of the transition states. Fai?sca et al. [J. Chem. Phys. 129, 095108 (2008)] generated conformations of TSE based on the criterion that, starting from a TS conformation, the probabilities of folding and unfolding are about equal through Markov Chain Monte Carlo (MCMC) simulations. In this study, we use the technique of constrained sequential Monte Carlo method [Lin et al., J. Chem. Phys. 129, 094101 (2008); Zhang et al. Proteins 66, 61 (2007)] to generate TSE conformations of acylphosphatase of 98 residues that satisfy the φ-value constraints, as well as the criterion that each conformation has a folding probability of 0.5 by Monte Carlo simulations. We adopt a two stage process and first generate 5000 contact maps satisfying the φ-value constraints. Each contact map is then used to generate 1000 properly weighted conformations. After clustering similar conformations, we obtain a set of properly weighted samples of 4185 candidate clusters. Representative conformation of each of these cluster is then selected and 50 runs of Markov chain Monte Carlo (MCMC) simulation are carried using a regrowth move set. We then select a subset of 1501 conformations that have equal probabilities to fold and to unfold as the set of TSE. These 1501 samples characterize well the distribution of transition state ensemble conformations of acylphosphatase. Compared with previous studies, our approach can access much wider conformational space and can objectively generate conformations that satisfy the φ-value constraints and the criterion of 0.5 folding probability without bias. In contrast to previous studies, our results show that transition state conformations are very diverse and are far from nativelike when measured in cartesian root-mean-square deviation (cRMSD): the average cRMSD between TSE conformations and the native structure is 9.4 A? for this short protein, instead of 6 A? reported in previous studies. In addition, we found that the average fraction of native contacts in the TSE is 0.37, with enrichment in native-like β-sheets and a shortage of long range contacts, suggesting such contacts form at a later stage of folding. We further calculate the first passage time of folding of TSE conformations through calculation of physical time associated with the regrowth moves in MCMC simulation through mapping such moves to a Markovian state model, whose transition time was obtained by Langevin dynamics simulations. Our results indicate that despite the large structural diversity of the TSE, they are characterized by similar folding time. Our approach is general and can be used to study TSE in other macromolecules.     

Identification of active sites of biomolecules. 1. Methyl-alpha-mannopyranoside and Fe(III)

Car-Parrinello molecular dynamics (CPMD) simulations, DFT chemical reactivity index calculations, and mass spectrometric measurements are combined in an integrated effort to elucidate the details of the coordination of a transition-metal ion to a carbohydrate. The impact of the interaction with the FeIII ion on the glycosidic linkage conformation of methyl-alpha-d-mannopyranoside is studied by classical molecular dynamics (MD) and CPMD simulations. This study shows that FeIII interacts with specific hydroxyl oxygen atoms of the carbohydrate, affecting the ground state carbohydrate conformation. These conformational details are discussed in terms of a set of supporting experiments involving electrospray ionization mass spectrometry, and CPMD simulations clearly indicate that the specific conformational preference is due to intramolecular hydrogen bonding. Classical MD simulations proved insensitive to these important chemical properties. Thus, we demonstrate the importance of chemical reactivity calculations and CPMD simulations in predicting the active sites of biological molecules toward metal cations.     

Comparison between theoretical values and simulation results of viscosity for the dissipative particle dynamics method

In order to investigate the validity of the dissipative particle dynamics method, which is a mesoscopic simulation technique, we have derived an expression for viscosity from the equation of motion of dissipative particles. In the concrete, we have shown the Fokker-Planck equation in phase space, and macroscopic conservation equations such as the equation of continuity and the equation of momentum conservation. The basic equations of the single-particle and pair distribution functions have been derived using the Fokker-Planck equation. The solutions of these distribution functions have approximately been solved by the perturbation method under the assumption of molecular chaos. The expressions of the viscosity due to momentum and dissipative forces have been obtained using the approximate solutions of the distribution functions. Also, we have conducted nonequilibrium dynamics simulations to investigate the influence of the parameters, which have appeared in defining the equation of motion in the dissipative particle dynamics method. The theoretical values of the viscosity due to dissipative forces in the Hoogerbrugge-Koelman theory are in good agreement with the simulation results obtained by the nonequilibrium dynamics method, except in the range of small number densities. There are restriction conditions for taking appropriate values of the number density, number of particles, time interval, shear rate, etc., to obtain physically reasonable results by means of dissipative particle dynamics simulations.     

Temperature dependence of NMR order parameters and protein dynamics

The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the temperature dependence of internal motions of the backbone amide moieties of HP36. The potential of mean force (PMF) for the N-H bond vector, determined from the constrained simulations, is found to be temperature dependent. A simple analytical expression is derived that describes the temperature dependence of the PMF. The parameters of this model are obtained from the PMF, from the unconstrained molecular dynamics simulations, or from experimental values of the generalized order parameter. The results provide a linkage between experimental and theoretical measures of the temperature dependence of protein motions.     

Determination of molecular vibrational state energies using the ab initio semiclassical initial value representation: application to formaldehyde

We have demonstrated the use of ab initio molecular dynamics (AIMD) trajectories to compute the vibrational energy levels of molecular systems in the context of the semiclassical initial value representation (SC-IVR). A relatively low level of electronic structure theory (HF/3-21G) was used in this proof-of-principle study. Formaldehyde was used as a test case for the determination of accurate excited vibrational states. The AIMD-SC-IVR vibrational energies have been compared to those from curvilinear and rectilinear vibrational self-consistent field/vibrational configuration interaction with perturbation selected interactions-second-order perturbation theory (VSCF/VCIPSI-PT2) and correlation-corrected vibrational self-consistent field (cc-VSCF) methods. The survival amplitudes were obtained from selecting different reference wavefunctions using only a single set of molecular dynamics trajectories. We conclude that our approach is a further step in making the SC-IVR method a practical tool for first-principles quantum dynamics simulations.     

Anisotropic united-atoms (AUA) potential for alcohols

An anisotropic united-atom (AUA4) intermolecular potential has been derived for the family of alkanols by first optimizing a set of charges to reproduce the electrostatic potential of the isolated molecules of methanol and ethanol and then by adjusting the parameters of the OH group to fit selected equilibrium properties. In particular, the proposed potential includes additional extra-atomic charges in order to improve the matching to the electrostatic field. Gibbs ensemble Monte Carlo simulations were performed to determine the phase equilibria, while the critical region was explored by means of grand canonical Monte Carlo simulations combined with histogram reweighting techniques. In order to increase the transferability of the model, only the parameters of the Lennard-Jones OH group have been fitted, the parameters of the other AUA groups are taken from previous works. Nevertheless, a good level of agreement was obtained for all compounds considered in this work. In particular, excellent results were obtained for the Henry constants calculation of different gases in alkanols.     

Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k

Calbindin D_9k is a member of the S100 subfamily of EF-hand calcium binding proteins, and has served as an important model system for biophysical studies. The fast timescale dynamics of the calcium-free (apo) state is characterized using molecular dynamics simulations. Order parameters for the backbone NH bond vectors are determined from the simulations and compared with experimentally derived values, with a focus on the dynamics of calcium-binding site I. There is a significant discrepancy between simulated and experimental order parameters for site I residues in the case of no ion bound in site I. However, it was found in the simulations that a Na⁺ ion can bind in site I, and the resulting order parameters determined from the simulations are in excellent agreement with experiment. Comparisons are made to X-ray structures of other S100 family members in which Na⁺ ions were observed or suggested to be bound in site I. © 2019 Wiley Periodicals, Inc.     

New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).     

Force-field parametrization and molecular dynamics simulations of p-menthan-3,9-diols: a family of amphiphilic compounds derived from terpenoids

A set of amphiphilic p-menthan-3,9-diols have been investigated by molecular dynamics simulations. These are four stereoisomers than can be specifically obtained from two terpenoids widely used in biorganic chemistry. For this purpose, the p-menthan-3,9-diols have been explicitly parametrized using both semiempirical and ab initio quantum mechanical calculations. The reliability of these parameters has been validated by predicting different molecular and thermodynamic properties. Molecular dynamics simulations in aqueous solution have been performed with the new parameters. The results provide useful insights about the conformational properties of this family of compounds and the formation of intra- and intermolecular hydrogen bonds.     

Transannular Diels-Alder reactivities of 14-membered macrocylic trienes and their relationship with the conformational preferences of the reactants: a combined quantum chemical and molecular dynamics study

Transannular Diels-Alder (TADA) reactions that occur between the diene and dienophile moieties located on a single macrocyclic triene molecule have been recognized as effective synthetic routes toward realizing complex tricyclic molecules in a single step. In this paper, we report a comprehensive study on the TADA reactions of 14-membered cyclic triene macrocycles to yield A.B.C[6.6.6] tricycles using quantum chemical methods and using classical molecular dynamics simulations. A benchmark study has been performed to examine the reliability of the commonly used ab initio methods and hybrid density functional levels of theory in comparison with results from CCSD(T) calculations to accurately model TADA reactions. The energy barriers obtained using the M06-2X functional were found to be in quantitative agreement with the CCSD(T) level of theory using a reasonably large basis set. Conformational properties of the reactants have been systematically studied using extensive molecular dynamics (MD) simulations. For this purpose, model systems were conceived, and force field parameters corresponding to the dihedral terms in the potential energy function were obtained. Linear relationship between the activation energies corresponding to the TADA reactions and the probability of finding the reactant in certain conformational states was obtained. A clustering method along with optimizations at the molecular mechanics and density functional M06-2X levels has been used to locate the most stable conformation of each of the trienes.