ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models.     

Phase transitions of methane using molecular dynamics simulations

Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.     

Characterization of titanium dioxide nanoparticles using molecular dynamics simulations

Molecular dynamics simulations of titanium dioxide nanoparticles in the three commonly occurring phases (anatase, brookite, and rutile) are reported. The structural properties inferred by simulated X-ray diffraction patterns of the nanoparticles were investigated. The titanium-oxygen bond length as a function of size, phase, and temperature was determined and was found to be dependent on the coordination environment of the titanium and independent of phase and size. The equilibrium Ti-O bond length is 1.86 A for a four-coordinated titanium ion, 1.92 A for a five-coordinated titanium ion, and 1.94 A for an octahedral titanium ion. Smaller nanoparticles are characterized by a higher fraction of titanium ions that are four and five coordinated, due to the larger surface area-to-volume ratios. The surface energies for anatase, rutile, and brookite particles were reported. The surface energy of the nanoparticle increases and approaches a constant value as the particle gets bigger. The surface energies of small rutile particles are higher than that for anatase particles of a similar size, consistent with anatase being the more stable phase of nanocrystalline titanium dioxide.     

Interpreting NMR data for beta-peptides using molecular dynamics simulations

NMR is one of the most used techniques to resolve structure of proteins and peptides in solution. However, inconsistencies may occur due to the fact that a polypeptide may adopt more than one conformation. Since the NOE distance bounds and (3)J-values used in such structure determination represent a nonlinear average over the total ensemble of conformers, imposition of NOE or (3)J-value restraints to obtain one unique conformation is not an appropriate procedure in such cases. Here, we show that unrestrained MD simulation of a solute in solution using a high-quality force field yields a conformational ensemble that is largely compatible with the experimental NMR data on the solute. Four 100 ns MD simulations of two forms of a nine-residue beta-peptide in methanol at two temperatures produced conformational ensembles that were used to interpret the NMR data on this molecule and resolve inconsistencies between the experimental NOEs. The protected and unprotected forms of the beta-peptide adopt predominantly a 12/10-helix in agreement with the qualitative interpretation of the NMR data. However, a particular NOE was not compatible with this helix indicating the presence of other conformations. The simulations showed that 3(14)()-helical structures were present in the ensemble of the unprotected form and that their presence correlates with the fulfillment of the particular NOE. Additionally, all inter-hydrogen distances were calculated to compare NOEs predicted by the simulations to the ones observed experimentally. The MD conformational ensembles allowed for a detailed and consistent interpretation of the experimental data and showed the small but specific conformational differences between the protected and unprotected forms of the peptide.     

Overcoming free energy barriers using unconstrained molecular dynamics simulations

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate xi is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of xi is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method.     

Study of hydrogen adsorption on FeTi using molecular dynamics simulations

We have used molecular dynamics simulation to study the adsorption isotherms of molecular hydrogen on FeTi at several temperatures ranging from 60 to 100 K. Adsorption coverage, isosteric heat, and binding energy were calculated at different temperatures and pressures. The results indicated that FeTi can be used as an ideal hydrogen storage material. The surface coverage or total amount of hydrogen adsorbed on FeTi is between 0.28 to 0.35.     

Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations

Classical molecular dynamics is a convenient method for computing anharmonic infrared spectra of polyatomic molecules and condensed phase systems. However it does not perform well for predicting accurate intensities and it lacks nuclear quantization, two deficiencies that are usually accounted for by empirical scaling factors. In this paper we show on the examples of the trans isomer of nitrous acid and naphthalene that both issues can be alleviated by preparing the initial conditions according to semiclassical quantization based on a normal mode representation. The method correctly reproduces fundamental frequencies obtained with quantum mechanical methods. At increasing temperatures, the effective frequencies are found to follow the same trends as path-integral based methods. In the low-temperature limit, the band intensities predicted by the method are also found to agree with quantum mechanical considerations.     

Coarse-grained protein molecular dynamics simulations

A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.     

Multibaric-multithermal ensemble molecular dynamics simulations

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.     

Ab initio folding of helix bundle proteins using molecular dynamics simulations

We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.     

Looking inside the entanglement “tube” using molecular dynamics simulations

For 30 years, the dynamics of entangled polymers have been explained using the phenomenological “tube” model, where the “tube” represents the confining effects of surrounding chains, but the tube properties, such as its length and diameter, could only be inferred indirectly by fitting the tube model to rheological data. Now, however, molecular simulations are allowing these properties to be directly computed. The computational advances in molecular dynamics and related methods that have made this possible are here reviewed. In addition, it is discussed how new findings, such as an apparent time dependence of the tube diameter and direct observation of “hopping” of branch points along the tube, are helping to refine the tube model. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 3240–3248, 2007     

Potential energy constrained molecular dynamics simulations

A method for carrying out molecular dynamics simulations in which the potential energy U of the molecular system is constrained at its initial value is developed and thoroughly tested. The constraint is not introduced within the framework of the Lagrange multipliers technique, rather it is fulfilled in a natural way by carrying out the simulations in terms of suitable sets of delocalized coordinates. Such coordinates are defined by an appropriate tuning of the Baker, Kessi, and Delley internal delocalized nonredundant coordinates technique [J. Chem. Phys. 105, 192 (1996)]. The proposed method requires multiple evaluations of energy and gradients in each step of the molecular dynamics simulation, so that constant U simulations suffer some overhead compared to ordinary simulations. But the particular formulation of the delocalized coordinates and of the equations of motion greatly simplifies all the various steps required by the Baker's technique, thus allowing for the efficient implementation of the method itself. The technique is reliable and allows for very high accuracy in the potential energy conservation during the whole simulation. Moreover, it proved to be free of drift troubles which can occur when standard constraint methods are straightforwardly implemented without the application of appropriate correcting techniques.     

Vesicle shapes from molecular dynamics simulations

Lipid bilayer membranes are known to form various structures such as large sheets or vesicles. When the two leaflets of the bilayer have an equal composition, the membrane preferentially forms a flat sheet or a spherical vesicle. However, a difference in the composition of the two leaflets may result in a curved bilayer or in a wide variety of vesicle shapes. Vesicles with different shapes have already been shown in experiments and diverse vesicle shapes have been predicted theoretically from energy minimization of continuous curves. Here we present a molecular dynamics study of the effect of small changes in the phospholipid headgroups on the spontaneous curvature of the bilayer and on the resulting vesicle shape transformations. Small asymmetries in the bilayers already result in high spontaneous curvature and large vesicle deformations. Vesicle shapes that are formed include ellipsoids, discoids, pear-shaped vesicles, cup-shaped vesicles, as well as budded vesicles. Comparison of these vesicles with theoretically derived vesicle shapes shows both resemblances and differences.     

Estimating entropies from molecular dynamics simulations

While the determination of free-energy differences by MD simulation has become a standard procedure for which many techniques have been developed, total entropies and entropy differences are still hardly ever computed. An overview of techniques to determine entropy differences is given, and the accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated using liquid water as a test system. Reasonably accurate entropy differences are obtained through thermodynamic integration in which many copies of a solute are desolvated. When only one solute molecule is involved, only two methods seem to yield useful results, the calculation of solute-solvent entropy through thermodynamic integration, and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference. One-step perturbation methods seem unsuitable to obtain entropy estimates.     

Resolution of discordant HIV-1 protease resistance rankings using molecular dynamics simulations

The emergence of drug resistance is a major challenge for the effective treatment of HIV. In this article, we explore the application of atomistic molecular dynamics simulations to quantify the level of resistance of a patient-derived HIV-1 protease sequence to the inhibitor lopinavir. A comparative drug ranking methodology was developed to compare drug resistance rankings produced by the Stanford HIVdb, ANRS, and RegaDB clinical decision support systems. The methodology was used to identify a patient sequence for which the three rival online tools produced differing resistance rankings. Mutations at only three positions ( L10I , A71IV, and L90M ) influenced the resistance level assigned to the sequence. We use ensemble molecular dynamics simulations to elucidate the origin of these discrepancies and the mechanism of resistance. By simulating not only the full patient sequences but also systems containing the constituent mutations, we gain insight into why resistance estimates vary and the interactions between the various mutations. In the same way, we also gain valuable knowledge of the mechanistic causes of resistance. In particular, we identify changes in the relative conformation of the two beta sheets that form the protease dimer interface which suggest an explanation of the relative frequency of different amino acids observed in patients at residue 71.     

A comparison of methods for melting point calculation using molecular dynamics simulations

Accurate and efficient prediction of melting points for complex molecules is still a challenging task for molecular simulation, although many methods have been developed. Four melting point computational methods, including one free energy-based method (the pseudo-supercritical path (PSCP) method) and three direct methods (two interface-based methods and the voids method) were applied to argon and a widely studied ionic liquid 1-n-butyl-3-methylimidazolium chloride ([BMIM][Cl]). The performance of each method was compared systematically. All the methods under study reproduce the argon experimental melting point with reasonable accuracy. For [BMIM][Cl], the melting point was computed to be 320 K using a revised PSCP procedure, which agrees with the experimental value 337-339 K very well. However, large errors were observed in the computed results using the direct methods, suggesting that these methods are inappropriate for large molecules with sluggish dynamics. The strengths and weaknesses of each method are discussed.     

Structures and properties of Newton black films characterized using molecular dynamics simulations

We used molecular dynamics (MD) simulations to investigate the structures and properties of Newton black films (NBF) for several surfactants: sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (C16TAB), and surfactin using film thicknesses up to 10 nm. By calculating the interface formation energy for various packing conditions on the surface pressure-area isotherm, we found that the most probable surface concentration is approximately 42 A(2)/molecule for SDS and C16TAB and approximately 170 A(2)/molecule for surfactin. We then used this most probable concentration of each surfactant to simulate NBF with various film thicknesses. From analyzing the disjoining pressure-film thickness isotherms with the density profiles and the solvation coordination number, we found that the increase of the disjoining pressure during the film thinning was coupled with the change in inner structure of the NBF (i.e., density profile and the solvation of ionic entities). In the range of film thicknesses less than approximately 30 A, the disjoining pressures for the SDS and C16TAB were found to be larger than that of the surfactin. We predicted the Gibbs elasticity (175 dyn/cm for surfactin; 109 dyn/cm for C16TAB; 38 dyn/cm for SDS) required to assess the stability of NBF against surface concentration fluctuations, and the shear modulus (6.5 GPa for the surfactin; 6.1 GPa for the C16TAB; 3.5 GPa for the SDS) and the yield stress (approximately 0.8 GPa for surfactin; approximately 0.8 GPa for C16TAB; approximately 0.4 GPa for the SDS) to assess the mechanical stability against the externally imposed mechanical perturbation.     

Enthalpies of mixing predicted using molecular dynamics simulations and OPLS force field

Enthalpy of mixing (EOM) is one of the most basic thermodynamic properties of mixtures. To assess feasibility of predicting EOM using force field simulation methods, fifteen (15) representative binary mixtures were investigated using MD simulations based on OPLS and TIP4P force fields. The simulation conditions and errors were carefully examined. The precision level of 0.04 kJ/mol was obtained for calculated EOM data. However, the predictions, measured by deviations from experimental data, were only qualitatively correct. Among various factors influencing the accuracy of predictions, force field quality representing interactions among different molecules plays the most significant role. Using methanol/benzene and ethanol/benzene as examples, we demonstrated that non-additive interaction terms between polarizable atoms can be used to significantly improve the quality of predictions. In addition, it appears that charge-dependent LJ parameters are required in order to represent the polarization effects accurately.     

Hybrid molecular dynamics simulations of living filaments

We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.     

Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…