Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models

A polarizable model for simulation of liquid methanol, compatible with the COS/G2 water model, has been developed using the Charge-on-Spring (COS) technique. The model consists of three point charges, with one polarizable center on the oxygen atom. The Lennard-Jones parameters on the oxygen atom together with the molecular polarizability were varied to reproduce the experimental heat of vaporization and density of liquid methanol at ambient conditions. We examined the energies of various methanol dimers in the gas phase and compared them with values obtained from ab initio calculations. The model was then used to study the thermodynamic, dynamic, structural, and dielectric properties of liquid methanol as well as of a methanol-water mixture. A microscopic picture of the structure of pure liquid methanol and of the methanol-water mixture is provided. Good agreement was found between the results from our model simulations and available experimental and ab initio calculation data. In particular, the experimental dielectric permittivity of 32 could be reproduced, which had been shown to be difficult when using nonpolarizable models.     

Molecular dynamics simulations of transport and separation of carbon dioxide-alkane mixtures in carbon nanopores

The configurational-bias Monte Carlo method, which is used for efficient generation of molecular models of n-alkane chains, is combined for the first time with the dual control-volume grand-canonical molecular-dynamics simulation, which has been developed for studying transport of molecules in pores under an external potential gradient, to investigate transport and separation of binary mixtures of n-alkanes, as well as mixtures of CO2 and n-alkanes, in carbon nanopores. The effect of various factors, such as the temperature of the system, the composition of the mixture, and the pore size, on the separation of the mixtures is investigated. We also report the preliminary results of an experimental study of transport and separation of some of the same mixtures in a carbon molecular-sieve membrane with comparable pore sizes. The results indicate that, for the mixtures considered in this paper, even in very small carbon nanopores the energetic effects still play a dominant role in the transport and separation properties of the mixtures, whereas in a real membrane they are dominated by the membrane's morphological characteristics. As a result, for the mixtures considered, a single pore may be a grossly inadequate model of a real membrane, and hence one must resort to three-dimensional molecular pore network models of the membrane.     

Molecular dynamics simulations of bilayers containing mixtures of sphingomyelin with cholesterol and phosphatidylcholine with cholesterol

We performed six molecular dynamics simulations: three on hydrated bilayers containing pure phospholipids and three on hydrated bilayers containing mixtures of these phospholipids with cholesterol. The phospholipids in our simulations were SSM (sphingomyelin containing a saturated 18:0 acyl chain), OSM (sphingomyelin with an unsaturated 18:1 acyl chain), and POPC (palmitoyloleoylphosphatidylcholine containing one saturated and one unsaturated chain). Data from our simulations were used to study systematically the effect of cholesterol on phospholipids that differed in their headgroup and tail composition. In addition to the structural analysis, we performed an energetic analysis and observed that energies of interaction between cholesterol and neighboring SM molecules are similar to the energies of interaction between cholesterol and POPC. We also observed that the interaction energy between cholesterol and neighboring lipids cannot be used for the determination of which lipids are involved in the creation of a complex.     

Molecular dynamics simulations of halide glasses

Summary Halide glasses have been extensively studied in recent years because of their potential application as infrared transmitting fibre optic materials. They are believed to be more ionic than glasses based on silica and should therefore be more amenable to molecular dynamics simulation using simple two-body potentials. Here the main features of structural models derived using such techniques are described and compared with available structural data. Possible future applications of this approach are outlined.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Molecular dynamics simulations of lipid bilayers

Computer simulation methods are becoming increasingly widespread as tools for studying the structure and dynamics of lipid bilayer membranes. The length scale and time scale accessible to atomic-level molecular dynamics simulations are rapidly increasing, providing insight into the relatively slow motions of molecular reorientation and translation and demonstrating that effects due to the finite size of the simulation cell can influence simulation results. Additionally, significant advances have been made in the complexity of membrane systems studied, including bilayers with cholesterol, small solute molecules, and lipid-protein and lipid-DNA complexes. Especially promising is the progress that continues to be made in the comparison of simulation results with experiment, both to validate the simulation algorithms and to aid in the interpretation of existing experimental data.     

Molecular dynamics simulations of polyelectrolyte adsorption

We have performed molecular dynamics simulations of polyelectrolyte adsorption at oppositely charged surfaces from dilute polyelectrolyte solutions. In our simulations, polyelectrolytes were modeled by chains of charged Lennard-Jones particles with explicit counterions. We have studied the effects of the surface charge density, surface charge distribution, solvent quality for the polymer backbone, strength of the short-range interactions between polymers and substrates on the polymer surface coverage, and the thickness of the adsorbed layer. The polymer surface coverage monotonically increases with increasing surface charge density for almost all studied systems except for the system of hydrophilic polyelectrolytes adsorbing at hydrophilic surfaces. In this case the polymer surface coverage saturates at high surface charge densities. This is due to additional monomer-monomer repulsion between adsorbed polymer chains, which becomes important in dense polymeric layers. These interactions also preclude surface overcharging by hydrophilic polyelectrolytes at high surface charge densities. The thickness of the adsorbed layer shows monotonic dependence on the surface charge density for the systems of hydrophobic polyelectrolytes for both hydrophobic and hydrophilic surfaces. Thickness is a decreasing function of the surface charge density in the case of hydrophilic surfaces while it increases with the surface charge density for hydrophobic substrates. Qualitatively different behavior is observed for the thickness of the adsorbed layer of hydrophilic polyelectrolytes at hydrophilic surfaces. In this case, thickness first decreases with increasing surface charge density, then it begins to increase.     

Molecular dynamics simulations of biotin carboxylase

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As a consequence the structure with ATP bound lacked key structural information such as for the Mg2+ ions and contained altered conformations of key active-site residues. Therefore, nanosecond molecular dynamics studies of the wild-type biotin carboxylase were undertaken to supplant and amend the results of the crystal structures. Specifically, the protein-metal interactions of the two catalytically critical Mg2+ ions bound in the active site are presented along with a reevaluation of the conformations of active-site residues bound to ATP. In addition, the regions of the polypeptide chain that serve as hinges for the large conformational change were identified. The results of the hinge analysis complemented a covariance analysis that identified the individual structural elements of biotin carboxylase that change their conformation in response to ATP binding.     

Molecular dynamics simulations of cardiolipin bilayers

Cardiolipin is a key lipid component in the inner mitochondrial membrane, where the lipid is involved in energy production, cristae structure, and mechanisms in the apoptotic pathway. In this article we used molecular dynamics computer simulations to investigate cardiolipin and its effect on the structure of lipid bilayers. Three cardiolipin/POPC bilayers with different lipid compositions were simulated: 100, 9.2, and 0% cardiolipin. We found strong association of sodium counterions to the carbonyl groups of both lipid types, leaving in the case of 9.2% cardiolipin virtually no ions in the aqueous compartment. Although binding occurred primarily at the carbonyl position, there was a preference to bind to the carbonyl groups of cardiolipin. Ion binding and the small headgroup of cardiolipin gave a strong ordering of the hydrocarbon chains. We found significant effects in the water dipole orientation and water dipole potential which can compensate for the electrostatic repulsion that otherwise should force charged lipids apart. Several parameters relevant for the molecular structure of cardiolipin were calculated and compared with results from analyses of coarse-grained simulations and available X-ray structural data.     

Molecular dynamics simulations for human CAR inverse agonists

Constitutive androstane receptor (CAR), along with pregnane x receptor (PXR), is an important metabolic sensor in the hepatocytes. Like all other nuclear receptors (NRs), CAR works in concert with coregulator proteins, coactivators, and corepressors which bind to the NRs. The main basis for the receptor to distinguish between coactivators and corepressors is the position of the C-terminal helix 12 (H12), which is determined by the bound NR ligand. CAR, having constitutive activity, can be repressed or further activated by its ligands. Crystal structure of human CAR bound to an agonist and a coactivator peptide is available, but no structural information on an inverse agonist-bound human CAR and a corepressor exists. In our previous molecular dynamics (MD) studies, no corepressor peptide was included. Therefore, probably due to the strong interactions which keep the relatively short H12 of CAR in the active position, the structural changes elicited by inverse agonists were very subtle, and H12 of CAR seemed to more or less retain its active conformation. Here, we have run a series of MD simulations to study the movement of H12 in the presence of both activating and repressing ligands as well as a corepressor peptide. The presence of the corepressor on the coregulator surface of CAR induced a clear shift of H12 of the inverse agonists-bound CAR. In general, H12 moved toward H10 and not away from the ligand binding domain, as seen in some other NRs. However, H12 of CAR is short enough that this movement seems to be adequate to accommodate the binding of the corepressor.     

Molecular dynamics simulations of lithium alkyl carbonates

A quantum chemistry-based many-body polarizable force field has been developed for two model solid-electrolyte interphase (SEI) components: dilithium ethylene dicarbonate (Li(2)EDC) and lithium methyl carbonate (LiMC). Molecular dynamics (MD) simulations of amorphous Li(2)EDC and LiMC were performed at temperatures from 393 to 600 K. Simulations reveal that Li(+) is coordinated by approximately 4.6 oxygen atoms from -COO(-) groups coming from different alkyl carbonate molecules. Charge transport in Li(2)EDC was found to be almost entirely due to Li(+). The temperature dependence of the ionic conductivity of the SEI model compounds Li(2)EDC and LiMC was found to be significantly stronger than that of liquid electrolytes (e.g., ethylene carbonate + LiTFSI), yielding extrapolated conductivities of the Li(2)EDC on order of 10(-10) S/cm at -30 degrees C.     

Molecular dynamics simulations of supramolecular polymer rheology

Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.     

Molecular dynamics simulations of peptide carboxylate hydration

Aqueous solvation of carboxylate groups, as present in the glycine zwitterion and the dipeptide aspartylalanine, is studied employing a force-field that includes distributed multipole electrostatics and induction contributions (Amoebapro: P. Ren and J. W. Ponder, J. Comput. Chem., 2002, 23, 1497; P. Ren and J. W. Ponder, J. Phys. Chem. B, 2003, 107, 5933; J. W. Ponder and D. A. Case, Adv. Protein Chem., 2003, 66, 27). Radial and orientation distribution functions, as well as hydration numbers, are calculated and compared with existing simulation data derived from Car-Parrinello molecular dynamics (CPMD), and also distributed-charge force-fields. Connections are also made with experimental data for solvation of carboxylates in water. Our findings show that Amoebapro yields carboxylate solvation properties in very good agreement with CPMD results, significantly closer agreement than can be obtained from traditional force-fields. We also demonstrate that the influence of solvation on the conformation of the dipeptide is markedly different using Amoebapro compared with the other force-fields.     

Molecular dynamics simulations of local field factors

In the present work, the authors evaluate a scheme based on molecular dynamics to derive local field factors. These are given without any assumption of a cavity by fitting the Langevin functions to the order parameters obtained from the molecular dynamics simulations. The local field factors so obtained, with the detailed chromophore-solvent interactions and solvent structures taken into account, are much smaller than those calculated from the conventional Onsager and Lorentz models. A numerical demonstration is given for two typical organic chromophore molecules, p-nitroaniline and p-nitro-N,N-dimethylaniline dissolved in chloroform.     

Molecular dynamics simulations of the oxidation of aluminum nanoparticles

The oxidation of aluminum nanoparticles is studied with classical molecular dynamics and the Streitz-Mintmire (Streitz, F. H.; Mintmire, J. W. Phys. Rev. B 1994, 50, 11996) electrostatic plus (ES+) potential that allows for the variation of electrostatic charge on all atoms in the simulation. The structure and charge distributions of bulk crystalline alpha-Al(2)O(3), a surface slab of alpha-Al(2)O(3) with an exposed (0001) basal plane, and an isolated Al(2)O(3) nanoparticle are studied. Constant NVT simulations of the oxidation of aluminum nanoparticles are also performed with different oxygen exposures. The calculations simulate a thermostated one-time exposure of an aluminum nanoparticle to different numbers of surface oxygen atoms. In the first set of oxidation studies, the overall approximate ratios of Al to O in the nanoparticle are 1:1 and 2:1. The nanoparticles are annealed to 3000 K and are then cooled to 500, 1000, or 1500 K. The atomic kinetic energy is scaled during the simulation to maintain the desired temperature. The structure and charge distributions in the oxidized nanoparticles differ from each other and from those of the bulk Al(2)O(3) phases. In the Al(1)O(1) simulation, an oxide shell forms that stabilizes the shape of the particle, and thus the original structure of the nanoparticle is approximately retained. In the case of Al(1)O(0.5), there is insufficient oxygen to form a complete oxide shell, and the oxidation results in particles of irregular shapes and rough surfaces. The particle surface is rough, and the nanoparticle is deformed.     

Molecular dynamics simulations of the melting of 1,3,3-trinitroazetidine

Physical properties of condensed-phase 1,3,3-trinitroazetidine (TNAZ) have been computed with molecular dynamics (MD) and a nonreactive, fully flexible force field formulated by combining the intramolecular interactions obtained from the Generalized AMBER Force Field and the rigid-molecule force field developed by Sorescu-Rice-Thompson [J. Phys. Chem. B 1997, 101, 798] (AMBER-SRT). The results are compared with MD calculations, using the AMBER force field. The predicted densities of crystalline TNAZ from both force fields are about 10% lower than the experimental value. The calculated thermodynamic melting point at 1 atm from the AMBER-SRT force field is 390 K, in good agreement with the measured value of 374 K, while the AMBER force field predicts a thermodynamic melting point of 462 K. The lattice parameters and the molecular and crystal structures calculated with the AMBER-SRT force field are in excellent agreement with experiment. Simulations with the AMBER-SRT force field were also used to generate the isotherm of TNAZ up to 4 GPa and the bulk modulus and its pressure derivative.     

Molecular dynamics simulations of the melting of aluminum nanoparticles

Molecular dynamics simulations are performed to determine the melting points of aluminum nanoparticles of 55-1000 atoms with the Streitz-Mintmire [Phys. Rev. B 1994, 50, 11996] variable-charge electrostatic plus potential. The melting of the nanoparticles is characterized by studying the temperature dependence of the potential energy and Lindemann index. Nanoparticles with less than 850 atoms show bistability between the solid and liquid phases over temperature ranges below the point of complete melting. The potential energy of a nanoparticle in the bistable region alternates between values corresponding to the solid and liquid phases. This bistability is characteristic of dynamic coexistence melting. At higher temperatures, only the liquid state is stable. Nanoparticles with more than 850 atoms undergo a sharp solid-liquid-phase transition characteristic of the bulk solid phase. The variation of the melting point with the effective nanoparticle radius is also determined.