Temperature dependence of protein dynamics simulated with three different water models

The effect of variation of the water model on the temperature dependence of protein and hydration water dynamics is examined by performing molecular dynamics simulations of myoglobin with the TIP3P, TIP4P, and TIP5P water models and the CHARMM protein force field at temperatures between 20 and 300 K. The atomic mean-square displacements, solvent reorientational relaxation times, pair angular correlations between surface water molecules, and time-averaged structures of the protein are all found to be similar, and the protein dynamical transition is described almost indistinguishably for the three water potentials. The results provide evidence that for some purposes changing the water model in protein simulations without a loss of accuracy may be possible.

Shear banding in molecular dynamics of polymer melts

In order to establish constitutive equations for a viscoelastic fluid uniform shear flow is usually required. However, in the last 10 years S. Q. Wang and co-workers have demonstrated that some entangled polymers do not flow with the uniform shear rate as usually assumed, but instead choose to separate into fast and slow flowing regions. This phenomenon, known as shear banding, causes flow instabilities and in principle invalidates all rheological measurements when it occurs. In this Letter we report the first observation of shear banding in molecular dynamics simulations of entangled polymer melts. We show that our observations are in a very good agreement with the phenomenology developed by Fielding and Olmsted. Our findings provide a simple way of validating the empirical macroscopic phenomenology of shear banding. © 2012 American Physical Society

Mg/Ca partitioning between aqueous solution and aragonite mineral: a molecular dynamics study

We have calculated the concentrations of Mg in the bulk and surfaces of aragonite CaCO3 in equilibrium with aqueous solution, based on molecular dynamics simulations and grand-canonical statistical mechanics. Mg is incorporated in the surfaces, in particular in the (001) terraces, rather than in the bulk of aragonite particles. However, the total Mg content in the bulk and surface of aragonite particles was found to be too small to account for the measured Mg/Ca ratios in corals. We therefore argue that most Mg in corals is either highly metastable in the aragonite lattice, or is located outside the aragonite phase of the coral skeleton, and we discuss the implications of this finding for Mg/Ca paleothermometry.

Computer simulations of the structure of colloidal ferrofluids

The structure of a ferrofluid under the influence of an external magnetic field is expected to become anisotropic due to the alignment of the dipoles into the direction of the external field, and subsequently to the formation of particle chains due to the attractive head to tail orientations of the ferrofluid particles. Knowledge about the structure of a colloidal ferrofluid can be inferred from scattering data via the measurement of structure factors. We have used molecular-dynamics simulations to investigate the structure of both monodispersed and polydispersed ferrofluids. The results for the isotropic structure factor for monodispersed samples are similar to previous data by Camp and Patey that were obtained using an alternative Monte Carlo simulation technique, but in a different parameter region. Here we look in addition at bidispersed samples and compute the anisotropic structure factor by projecting the q vector onto the XY and XZ planes separately, when the magnetic field was applied along the z axis. We observe that the XY- plane structure factor as well as the pair distribution functions are quite different from those obtained for the XZ plane. Further, the two- dimensional structure factor patterns are investigated for both monodispersed and bidispersed samples under different conditions. In addition, we look at the scaling exponents of structure factors. Our results should be of value to interpret scattering data on ferrofluids obtained under the influence of an external field.

Structure and magnetic properties of polydisperse ferrofluids: a molecular dynamics study

We study by Langevin molecular dynamics simulations systematically the influence of polydispersity in the particle size, and subsequently in the dipole moment, on the physical properties of ferrofluids. The polydispersity is in a first approximation modeled by a bidisperse system that consists of small and large particles at different ratios of their volume fractions. In the first part of our investigations the total volume fraction of the system is fixed, and the volume fraction phi(L) of the large particles is varied. The initial susceptibility chi and magnetization curve of the systems show a strong dependence on the value of phi(L). With the increase of phi(L), the magnetization M of the system has a much faster increment at weak fields, and thus leads to a larger chi. We performed a cluster analysis that indicates that this is due to the aggregation of the large particles in the systems. The average size of these clusters increases with increasing phi(L). In the second part of our investigations, we fixed the volume fraction of the large particles, and increased the volume fraction phi(S) of the small particles in order to study their influence on the chain formation of the large ones. We found that the average aggregate size formed by large particles decreases when phi(S) is increased, demonstrating a significant effect of the small particles on the structural properties of the system. A topological analysis of the structure reveals that the majority of the small particles remain nonaggregated. Only a small number of them are attracted to the ends of the chains formed by large particles.

Molecular dynamics study on the equilibrium magnetization properties and structure of ferrofluids

We investigate in detail the initial susceptibility, magnetization curves, and microstructure of ferrofluids in various concentration and particle dipole moment ranges by means of molecular dynamics simulations. We use the Ewald summation for the long-range dipolar interactions, take explicitly into account the translational and rotational degrees of freedom, coupled to a Langevin thermostat. When the dipolar interaction energy is comparable with the thermal energy, the simulation results on the magnetization properties agree with the theoretical predictions very well. For stronger dipolar couplings, however, we find systematic deviations from the theoretical curves. We analyze in detail the observed microstructure of the fluids under different conditions. The formation of clusters is found to enhance the magnetization at weak fields and thus leads to a larger initial susceptibility. The influence of the particle aggregation is isolated by studying ferro-solids, which consist of magnetic dipoles frozen in at random locations but which are free to rotate. Due to the artificial suppression of clusters in ferrosolids the observed susceptibility is considerably lowered when compared to ferrofluids.

Mode-specific chemisorption of CH4 on Pt{110}-(1 x 2) explored by first-principles molecular dynamics

The chemisorption of CH4 on Pt{110}-(1 x 2) has been studied by vibrational analysis of the reaction pathway defined by the potential energy surface and, in time reversal, by first-principles molecular dynamics simulations of CH4 associative desorption, with the electronic structure treated explicitly using density functional theory. We find that the symmetric stretch vibration ν1 is strongly coupled to the reaction coordinate; our results therefore provide a firm theoretical basis for recently reported state-resolved reactivity measurements, which show that excitation of the ν1 normal mode is the most efficient way to enhance the reaction probability

Bond-selective energy redistribution in the chemisorption of CH3D and CD3H on Pt{1 1 0}-(1 2): a first-principles molecular dynamics study

We have investigated the chemisorption of CH3D and CD3H on Pt{11 0}-(1 2) by performing first-principles molecular dynamics simulations of the recombinative desorption of CH3D (from adsorbed methyl and deuterium) and of CD3H (from adsorbed trideuteromethyl and hydrogen). Vibrational analysis of the symmetry adapted internal coordinates of the desorbing molecules shows that excitation of the single C– D (C–H) bond in the parent molecule is strongly correlated with energy excess in the reaction coordinate. The results of the molecular dynamics simulations are consistent with observed mode- and bond-specific reactivity measurements for chemisorption of methane and its isotopomers on platinum and nickel surfaces.

Significance of cross correlations in the stress relaxation of polymer melts

According to linear response theory, all relaxation functions in the linear regime can be obtained using time correlation functions calculated under equilibrium. In this paper, we demonstrate that the cross correlations make a significant contribution to the partial stress relaxation functions in polymer melts. We present two illustrations in the context of polymer rheology using (1) Brownian dynamics simulations of a single chain model for entangled polymers, the slip-spring model, and (2) molecular dynamics simulations of a multichain model. Using the single chain model, we analyze the contribution of the confining potential to the stress relaxation and the plateau modulus. Although the idea is illustrated with a particular model, it applies to any single chain model that uses a potential to confine the motion of the chains. This leads us to question some of the assumptions behind the tube theory, especially the meaning of the entanglement molecular weight obtained from the plateau modulus. To shed some light on this issue, we study the contribution of the nonbonded excluded-volume interactions to the stress relaxation using the multichain model. The proportionality of the bonded/nonbonded contributions to the total stress relaxation (after a density dependent "colloidal" relaxation time) provides some insight into the success of the tube theory in spite of using questionable assumptions. The proportionality indicates that the shape of the relaxation spectrum can indeed be reproduced using the tube theory and the problem is reduced to that of finding the correct prefactor. (c) 2007 American Institute of Physics

Hierarchical modeling of entangled polymers

We demonstrate that it is possible to link multi-chain molecular dynamics simulations with the tube model using a single chain slip-links model as a bridge. This hierarchical approach allows significant speed up of simulations, permitting us to span the time scales relevant for a comparison with the tube theory. Fitting the mean-square displacement of individual monomers in molecular dynamics simulations with the slip-spring model, we show that it is possible to predict the stress relaxation. Then, we analyze the stress relaxation from slip-spring simulations in the framework of the tube theory. In the absence of constraint release, we establish that the relaxation modulus can be decomposed as the sum of contributions from fast and longitudinal Rouse modes, and tube survival. Finally, we discuss some open questions regarding possible future directions that could be profitable in rendering the tube model quantitative, even for mildly entangled polymers

Deforming glassy polystyrene: Influence of pressure, thermal history, and deformation mode on yielding and hardening

The toughness of a polymer glass is determined by the interplay of yielding, strain softening, and strain hardening. Molecular-dynamics simulations of a typical polymer glass, atactic polystyrene, under the influence of active deformation have been carried out to enlighten these processes. It is observed that the dominant interaction for the yield peak is of interchain nature and for the strain hardening of intrachain nature. A connection is made with the microscopic cage-to-cage motion. It is found that the deformation does not lead to complete erasure of the thermal history but that differences persist at large length scales. Also we find that the strain-hardening modulus increases with increasing external pressure. This new observation cannot be explained by current theories such as the one based on the entanglement picture and the inclusion of this effect will lead to an improvement in constitutive modeling.

Microscopic Mechanisms of Strain Hardening in Glassy Polymers

The mechanisms underlying the increase in stress for large mechanical strains of a polymer glass, quantified by the strain-hardening modulus, are still poorly understood. In the present paper we aim to elucidate this matter and present new mechanisms. Molecular-dynamics simulations of two polymers with very different strain-hardening moduli (polycarbonate and polystyrene) have been carried out. Nonaffine displacements occur because of steric hindrances and connectivity constraints. We argue that it is not necessary to introduce the concept of entanglements to understand strain hardening, but that hardening is rather coupled with the increase in the rate of nonaffine particle displacements. This rate increases faster for polycarbonate, which has the higher strain-hardening modulus. Also more nonaffine chain stretching is present for polycarbonate. It is shown that the inner distances of such a nonaffinely deformed chain can be well described by the inner distances of the worm-like chain, but with an effective stiffness length (equal to the Kuhn length for an infinite worm-like chain) that increases during deformation. It originates from the finite extensibility of the chain. In this way the increase in nonaffine particle displacement can be understood as resulting from an increase in the effective stiffness length of the perturbed chain during deformation, so that at larger strains a higher rate of plastic events in terms of nonaffine displacement is necessary, causing in turn the observed strain hardening in polymer glasses.

Binding studies of a protonated dioxatetraazamacrocycle with carboxylate substrates

The tetraprotonated form of the dioxatetraazamacrocycle, 6,19-dioxa-3,9,16,22-tetraaza[22.2.2.2(11,14)]-triaconta-1(26),11,13,24, 27,29-hexaene, (H4L1)(4+), was used as the receptor for binding studies with carboxylate anionic substrates of different shapes, sizes, and charges [succinate (suc(2-)), cyclo- hexanetricarboxylate (cta(3-)), phthalate (ph(2-)), isophthalate (iph(2-)), terephthalate (tph(2-)), and benezenetricarboxylate (btc(3-))]. Association constants were determined by potentiometry in aqueous solution at 298.2 K and 0.10 M KCl and by H-1 NMR titration in D2O. The strongest association was found for the btc3- anion at 5-7 pH region. From both techniques it was possible to establish the binding preference trend of the receptor for the different substrates, and the H-1 NMR spectroscopy gave important suggestions about the type of interactions between partners and the location of the substrates in the supramolecular entities formed. The effective binding constants at pH 6 follow the order: btc(3-)>iph(2-)>cta(3-) =ph(2-)>tph(2-)>suc(2-). All the studies suggest that the anionic substrates bind to the receptor via N-H center dot center dot center dot O = C hydrogen bonds and electrostatic interactions, and the aromatic substrates can also establish pi-pi stacking interactions. The crystal structures of (H4L1)(4+) and its supramolecular assemblies with ph(2-) and tph(2-) were determined by X-ray diffraction. The last two structures showed that the association process in solid state occurs via multiple N-H center dot center dot center dot O = C hydrogen bonds with the anionic substrate located outside the macrocyclic cavity of the receptor. Molecular dynamics simulations carried out for the association of (H4L1)(4+) with tph(2-) and btC(3-) in water solution established at atomic level the existence of all interactions suggested by the experimental studies, which act cooperatively in the binding process. Furthermore, the binding free energies were estimated and the values are in agreement with the experimental ones, indicating that the binding of these two anionic substrates occurs into the receptor cavity. However, the tph(2-) has also propensity to leave the macrocyclic cavity and its molecular recognition can also happen at the top of the receptor. (C) 2008 Elsevier Ltd. All rights reserved.

Thallium pi-cation complexation by calix[4]tubes: Tl-205 NMR and X-ray evidence

Thallium cation complexation by calix[4]tubes has been investigated by a combination of (TI)-T-205, H-1 NMR and ES MS demonstrating the solution formation of a dithallium complex in which the cations are held in the calix[4]arene cavities. In addition, the structure of the complex has been determined in the solid state revealing the cations to be held exclusively by pi-cation interactions. Furthermore, this crystal structure has been used as the basis for molecular dynamics simulations to confirm that binding of the smaller K+ cation in the calix[4]tube cryptand like array occurs via the axial route featuring a g-cation intermediate.

Development of novel brush-type chiral stationary phases based on terpenoid selectors: HPLC evaluation and theoretical investigation of enantioselective binding interactions

The terpenoid chiral selectors dehydroabietic acid, 12,14-dinitrodehydroabietic acid and friedelin have been covalently linked to silica gel yielding three chiral stationary phases CSP 1, CSP 2 and CSP 3, respectively. The enantiodiscriminating capability of each one of these phases was evaluated by HPLC with four families of chiral aromatic compounds composed of alcohols, amines, phenylalanine and tryptophan amino acid derivatives and beta-lactams. The CSP 3 phase, containing a selector with a large friedelane backbone is particularly suitable for resolving free alcohols and their derivatives bearing fluorine substituents, while CSP 2 with a dehydroabietic architecture is the only phase that efficiently discriminates 1, 1'-binaphthol atropisomers. CSP 3 also gives efficient resolution of the free amines. All three phases resolve well the racemates of N-trifluoracetyl and N-3,5-dinitrobenzoyl phenylalanine amino acid ester derivatives. Good enantioseparation of beta-lactams and N-benzoyl tryptophan amino acid derivatives was achieved on CSP 1. In order to understand the structural factors that govern the chiral molecular recognition ability of these phases, molecular dynamics simulations were carried out in the gas phase with binary diastereomeric complexes formed by the selectors of CSP 1 and CSP 2 and several amino acid derivatives. Decomposition of molecular mechanics energies shows that van der Waals interactions dominate the formation of the diastereomeric transient complexes while the electrostatic binding interactions are primarily responsible for the enantioselective binding of the (R)- and (S)-analytes. Analysis of the hydrogen bonds shows that electrostatic interactions are mainly associated with the formation of N-(HO)-O-...=C enantio selective hydrogen bonds between the amide binding sites from the selectors and the carbonyl groups of the analytes. The role of mobile phase polarity, a mixture of n-hexane and propan-2-ol in different ratios, was also evaluated through molecular dynamics simulations in explicit solvent. (c) 2006 Elsevier Ltd. All rights reserved.