DL_POLY: Application to molecular simulation

The fragmentation-recombination mechanism of the enzyme glutamate mutase studied by QM/MM simulations

The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 ( Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate.

Excess electron localization in solvated DNA bases

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Thermodynamic, diffusional, and structural anomalies in rigid-body water models

Structural, density, entropy, and diffusivity anomalies of the TIP4P/2005 model of water are mapped out over a wide range of densities and temperatures. The locus of temperatures of maximum density (TMD) for this model is very close to the experimental TMD locus for temperatures between 250 and 275 K. Four different water models (mTIP3P, TIP4P, TIP5P, and SPC/E) are compared with the TIP4P/2005 model in terms of their anomalous behavior. For all the water models, the density regimes for anomalous behavior are bounded by a low-density limit at around 0.85-0.90 g cm(-3) and a high-density limit at about 1.10-1.15 g cm(-3). The onset temperatures of the density anomaly in the various models show a much greater variation, ranging from 202 K for mTIP3P to 289 K for TIP5P. The order maps for the various water models are qualitatively very similar with the structurally anomalous regions almost superimposable in the q(tet)-τ plane. Comparison of the phase diagrams of water models with the region of liquid-state anomalies shows that the crystalline phases are much more sensitive to the choice of water models than the liquid state anomalies; for example, SPC/E and TIP4P/2005 show qualitatively similar liquid state anomalies but very different phase diagrams. The anomalies in the liquid in all the models occur at much lower pressures than those at which the melting line changes from negative to positive slope. The results in this study demonstrate several aspects of structure-entropy-diffusivity relationships of water models that can be compared with experiment and used to develop better atomistic and coarse-grained models for water.

A model for the strength of yarn-like carbon nanotube fibers

A model for the strength of pure carbon nanotube (CNT) fibers is derived and parametrized using experimental data and computational simulations. The model points to the parameters of the subunits that must be optimized in order to produce improvements in the strength of the macroscopic CNT fiber, primarily nanotube length and shear strength between CNTs. Fractography analysis of the CNT fibers reveals a fibrous fracture surface and indicates that fiber strength originates from resistance to nanotube pull-out and is thus proportional to the nanotube-nanotube interface contact area and shear strength. The contact area between adjacent nanotubes is determined by their degree of polygonization or collapse, which in turn depends on their diameter and number of layers. We show that larger diameter tubes with fewer walls have a greater degree of contact, as determined by continuum elasticity theory, molecular mechanics, and image analysis of transmission electron micrographs. According to our model, the axial stress in the CNTs is built up by stress transfer between adjacent CNTs through shear and is thus proportional to CNT length, as supported by data in the literature for CNT fibers produced by different methods and research groups. Our CNT fibers have a yarn-like structure in that rather than being solid, they are made of a network of filament subunits. Indeed, the model is consistent with those developed for conventional yarn-like fibers.

A computer simulation study of the interaction between passivated and bare gold nanoclusters

Molecular dynamics simulations have been performed with the objective of understanding the phenomenon of nanoparticle aggregation. We have attempted to calculate the free energy associated with the interaction between two 38-atom gold nanocores, with attached passivating thiol chains, in a supercritical ethane solvent and in the vacuum, and without passivating chains in ethane at the critical density and twice the critical density. Our model differs from those used by others in that each gold nanocore is bound by a realistic metal potential that is not formally rigid. In the case of the passivated nanoparticles, we observe profound structural changes in the nanocores, which radically affect the nature of the interaction between them—to the extent that fusion of the two gold nanocores cannot be prevented under the conditions examined. Bare nanocores, on the other hand, do not exhibit much structural change until close contact occurs. The fused nanocores in the passivated and bare nanocore systems have significantly different morphologies. There is evidence that at higher solvent density, the interaction between bare nanocores is slightly repulsive.

Glassy nature of water in an ultraconfining disordered material: the case of calcium-silicate-hydrate

We present the structural and dynamic nature of water ultraconfined in the quasi-two-dimensional nanopores of the highly disordered calcium-silicate-hydrate (C-S-H), the major binding phase in cement. Our approach is based on classical molecular simulations. We demonstrate that the C-S-H nanopore space is hydrophilic, particularly because of the nonbridging oxygen atoms on the disordered silicate chains which serve as hydrogen-bond acceptor sites, directionally orienting the hydrogen atoms of the interfacial water molecules toward the calcium-silicate layers. The water in this interlayer space adopts a unique multirange structure: a distorted tetrahedral coordination at short range up to 2.7 Å, a disordered structure similar to that of dense fluids and supercooled phases at intermediate range up to 4.2 Å, and persisting spatial correlations through dipole-dipole interactions up to 10 Å. A three-stage dynamics governs the mean square displacement (MSD) of water molecules, with a clear cage stage characteristic of the dynamics in supercooled liquids and glasses, consistent with its intermediate-range structure identified here. At the intermediate time scales corresponding to the β-relaxation of glassy materials, coincident with the cage stage in MSD, the non-Gaussian parameter indicates a significant heterogeneity in the translational dynamics. This dynamic heterogeneity is induced primarily because of the heterogeneity in the distribution of hydrogen bond strengths. The strongly attractive interactions of water molecules with the calcium silicate walls serve to constrain their motion. Our findings have important implications on describing the cohesion and mechanical behavior of cement from its setting to its aging.

Competitive entry of sodium and potassium into nanoscale pores

We have studied the competitive entry of potassium and sodium into carbon nanotubes using molecular dynamics simulations. Our results demonstrate how a combination of strong sodium hydration coupled with strong potassium-chlorine interaction leads to enhanced potassium selectivity at certain diameters. We detail the reasons behind this, and show how variation of nanotube diameter can cause a switch to sodium selectivity, or even cause a decrease in overall ion entry despite an increase in diameter. These results demonstrate the importance of considering inter-ion dependence in the theoretical study of pore selectivity and show that, with careful design, the practical separation of sodium and potassium is possible using diameter variation alone.

Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.

Relationship between structure, entropy, and diffusivity in water and water-like liquids

Anomalous behavior of the excess entropy (S(e)) and the associated scaling relationship with diffusivity are compared in liquids with very different underlying interactions but similar water-like anomalies: water (SPC/E and TIP3P models), tetrahedral ionic melts (SiO(2) and BeF(2)), and a fluid with core-softened, two-scale ramp (2SRP) interactions. We demonstrate the presence of an excess entropy anomaly in the two water models. Using length and energy scales appropriate for onset of anomalous behavior, we show the density range of the excess entropy anomaly to be much narrower in water than in ionic melts or the 2SRP fluid. While the reduced diffusivities (D*) conform to the excess-entropy-scaling relation, D* = A exp(alphaS(e)) for all the systems (Rosenfeld, Y. Phys. Rev. A 1977, 15, 2545), the exponential scaling parameter, alpha, shows a small isochore dependence in the case of water. Replacing S(e) by pair correlation-based approximants accentuates the isochore dependence of the diffusivity scaling. Isochores with similar diffusivity-scaling parameters are shown to have the temperature dependence of the corresponding entropic contribution. The relationship between diffusivity, excess entropy, and pair correlation approximants to the excess entropy are very similar in all the tetrahedral liquids.

Coarse-graining RNA nanostructures for molecular dynamics simulations

A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in full atomistic modeling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of RNA conformation classes.

Local order, energy, and mobility of water molecules in the hydration shell of small peptides

The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.

Transport properties of tetrahedral, network-forming ionic melts

Molecular dynamics simulations of liquid silica and beryllium fluoride are performed using the van Beest-Kramer-van Santen and transferable rigid ion model potentials, respectively, in order to compare transport properties. The ionic conductivity (sigma), shear viscosity (eta) and ionic self-diffusivities (D(+/-)) are computed over a fairly wide range of temperatures and densities and deviations from Arrhenius behavior along different isochores is studied. The Stokes-Einstein relation is shown to hold over the entire range of state points, though the effective hydrodynamic radius shows small variations due to thermal fluctuations, compression, and local tetrahedral order. Several alternative tests of the Nernst-Einstein relation are implemented which show that significant network-formation in the anomalous regime leads to a breakdown of this relationship. The relaxation times, tau(sigma) and tau(M), associated with the decay of the charge-flux and pressure ACFs respectively, are computed. In the anomalous regime, as the tetrahedral network formation progresses, tau(M) increases rapidly while tau(sigma) shows very little variation, indicating a decoupling of charge and momentum transport processes.

The DL_POLY molecular dynamics package

The DL_POLY package provides a set of classical molecular dynamics programs that have application over a wide range of atomic and molecular systems. Written for parallel computers they offer capabilities stretching from small systems consisting of a few hundred atoms running on a single processor, up to systems of several million atoms running on massively parallel computers with thousands of processors. In this article we describe the structure of the programs and some applications.

Rigid Molecule Approximation in Memory Function-based Models for Molecular Liquids: Application to Liquid Water

In the present article we show how models for simple liquids can be used to describe the dynamics of atoms in molecular liquids within the rigid molecule approximation. We show in particular that the atomic masses are to be replaced by the corresponding Sachs-Teller masses and we derive a formal expression for the so-called Einstein frequency. The approach is illustrated for a model which has been originally developed for simple liquids and which has been used in the past to analyze quasielastic neutron scattering data from pure water and dilute aqueous solutions of apolar molecules. We obtain a remarkable agreement with results from molecular dynamics simulations not only in the quasielastic, diffusive regime, but also in the inelastic regime corresponding to intermolecular vibrations and fast molecular librations.

Isomer separation and gas-phase configurations of organoruthenium anticancer complexes: ion mobility mass spectrometry and modeling

We have used ion mobility-mass spectrometry combined with molecular modeling for the separation and configurational analysis of three low-molecular-weight isomeric organoruthenium anticancer complexes containing ortho-, meta-, or para-terphenyl arene ligands. The isomers were separated using ion mobility based on traveling-wave technology and the experimentally determined collision cross sections were compared to theoretical calculations. Excellent agreement was observed between the experimentally and theoretically derived measurements.

Relationship between structure, entropy, and mobility in network-forming ionic melts

Diffusivity, ionic conductivity, and viscosity of network-forming ionic melts are examined using molecular dynamics simulations of BeF2 and SiO2 melts. These tetrahedral, network-forming ionic melts are shown to possess a conductivity anomaly, in addition to waterlike viscosity and diffusivity anomalies, corresponding to a striking breakdown of the Nernst-Einstein relation. The contrasting scaling behavior of the different mobility measures with different structural contributions to the excess entropy is demonstrated.

Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water

Spherical truncations of Coulomb interactions in standard models for water permit efficient molecular simulations and can give remarkably accurate results for the structure of the uniform liquid. However, truncations are known to produce significant errors in nonuniform systems, particularly for electrostatic properties. Local molecular field (LMF) theory corrects such truncations by use of an effective or restructured electrostatic potential that accounts for effects of the remaining long-ranged interactions through a density-weighted mean field average and satisfies a modified Poisson's equation defined with a Gaussian-smoothed charge density. We apply LMF theory to 3 simple molecular systems that exhibit different aspects of the failure of a naïive application of spherical truncations-water confined between hydrophobic walls, water confined between atomically corrugated hydrophilic walls, and water confined between hydrophobic walls with an applied electric field. Spherical truncations of 1/r fail spectacularly for the final system, in particular, and LMF theory corrects the failings for all three. Further, LMF theory provides a more intuitive way to understand the balance between local hydrogen bonding and longer-ranged electrostatics in molecular simulations involving water.