Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.

Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into ß-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.

Thermal transport in polyethylene and at polyethylene-diamond interfaces investigated using molecular dynamics simulation.

The thermal conductances across covalently bonded interfaces between oriented single crystal diamond and completely aligned polyethylene chains are determined for the three principal orientations of diamond. The calculated thermal conductances, which range over 690-930 MW m(-2) K(-1), are consistent with those of other strongly bonded interfaces. These results suggest that the experimental interfacial conductances across hard-soft interfaces can be quite large if the bonding across the interface is strong, a conclusion that could have important implications for thermal management in bioelectromechanical systems and other inorganic-organic structures. The effects of defects and cross-linking on the thermal conductivity of polyethylene are also analyzed.

Effect of filling on the compressibility of carbon nanotubes: predictions from molecular dynamics simulations.

The compressibility of filled and empty (10, 10) carbon nanotubes (CNTs) is examined using classical molecular dynamics simulations. The filled nanotubes contain C60, CH4, Ne, n-C4H10, and n-C4H7 molecules that are covalently cross-linked to the inner CNT walls. In addition, nanotubes filled with either a hydrogen-terminated carbon nanowire or a carbon nanotube of comparable diameter is also considered. The forces on the atoms are calculated using a many-body reactive empirical bond-order potential and the adaptive intermolecular reactive empirical bond-order potential for hydrocarbons. The butane-filled system shows a unique yielding behavior prior to buckling that has not been observed previously. Cross-linking the molecules to the inner CNT walls is not predicted to affect the stiffness of the filled nanotube systems and removes the yielding response. The mechanical response of the nanowire filled CNT is remarkably similar to the response of the similarly sized multiwalled CNT.

Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics.

The performance of the reaction-field method of electrostatics is tested in molecular dynamics simulations of protein human interleukin-4 and a short DNA fragment in explicit solvent. Two truncation schemes are considered: one based on the position of atomic charges in water molecules and the other on the position of groups of charges. The group-based truncation leads to the melting of the DNA double helix. In contrast, the atom-based truncation maintains the helical structure intact. Similarly for the protein, the group-based truncation leads to an unfolding at pH 2 while the atom-based truncation produces stable trajectories at low and normal pH, in agreement with experiment. Artificial repulsion between charged residues associated with the group-based truncation is identified as the microscopic reason behind unfolding of the protein. Implications of different truncation schemes in reaction-field simulations of biomolecules are discussed.

Displacement of Cu(II) by Ag(I) in solvated metal sulfides. A DFT and AIM computational study.

The substitution of Cu2+ by Ag+ in hydrated CuIIS and (CuII)3S3 was modeled computationally by density functional theory quantum theory of atoms in molecules, and solvent field methods. The coordination, first-shell and partly second-shell molecular structures, and thermochemical data for solvated Cu2+, Ag+, CuIIS, (CuII)3S3, AgCu2S3 and their reactions were obtained. The thermochemical data showed that displacement of Cu2+ and Cu+ from CuIIS and (CuII)3S3 by Ag+, while unfavorable in the gas phase, is facilitated in an aqueous environment. Several covalently bonded species were examined as intermediates in the substitution reactions.

Protonolysis of the Hg-C bond of chloromethylmercury and dimethylmercury. A DFT and QTAIM study.

Possible mechanisms for degrading chloromethylmercury (CH(3)HgCl) and dimethylmercury [(CH3)2Hg] involving thiol and ammonium residues were investigated by DFT and atoms-in-molecules (QTAIM) calculations. Using H2S and HS- as models for thiol and thiolate groups RSH and RS-, respectively, we obtained transition states and energy barriers for possible decomposition routes to Hg(SH)2 based on a model proposed by Moore and Pitts (Moore, M. J.; Distefano, M. D.; Zydowsky, L. D.; Cummings, R. T.; Walsh, C. T. Acc. Chem. Res. 1990, 23, 301. Pitts, K. E.; Summers, A. O. Biochemistry 2002, 41, 10287). Demethylation was found to be a multistep process that involved initial substitution of Cl- by RS-. We found that successive coordination of Hg with thiolates leads to increased negative charge on the methyl group and facilitates the protonolysis of the Hg-C bond by H-SH. This was also found to be the case for (CH3)2Hg. We found that NH4(+) readily protonolyzes the Hg-C bond of these thiolate complexes, suggesting that ammonium residues of protonated amino acids might also act as effective proton donors.

Density functional theory and QT atoms-in-molecules study on the hydration of CuI and AgI ions and sulfides.

The hydrates of Cu+, Ag+, CuS-, AgS-, Cu2S, and Ag2S were investigated with density functional theory (DFT), solvent field, and atoms-in-molecules (QTAIM) calculations. We found that covalent bonding of the first-shell water molecules to the metals plays a significant role in the total solvation energy. Molecular graphs were obtained and the bonding characterized by analysis of the electron density and its laplacian at bond critical points. Long-range electrostatic interactions between solute and the bulk solvent, quantified by solvent-field calculations, are more important for hydrated anions CuS- and AgS- than for Cu+ and Ag+ as well as for the neutral species Cu2S and Ag2S. Computed enthalpies of formation for hydrated Cu+ and Ag+ correlated well with experimentally determined values and allowed us to characterize the structures of several hydrates studied in the gas phase. We found that the stability of the hydrates is leveled in the water solvent field. The reactions of dissociation and substitution of metal sulfides in the gas phase and in solution were compared. A decrease in the of energy of the reactions in going from the gas phase to solution is explained on the basis of the higher coordination of metal atoms in the first hydration shell.

Compression of carbon nanotubes filled with C60, CH4, or Ne: predictions from molecular dynamics simulations.

The effect of filling nanotubes with C60, CH4, or Ne on the mechanical properties of the nanotubes is examined. The approach is classical molecular dynamics using the reactive empirical bond order (REBO) and the adaptive intermolecular REBO potentials. The simulations predict that the buckling force of filled nanotubes can be larger than that of empty nanotubes, and the magnitude of the increase depends on the density of the filling material. In addition, these simulations demonstrate that the buckling force of empty nanotubes depends on temperature. Filling the nanotube disrupts this temperature effect so that it is no longer present in some cases.