The shoving model for the glass-former LiCl center dot 6H(2)O: A molecular dynamics simulation study

Molecular dynamics (MD) simulations of LiCl center dot 6H(2)O Showed that the diffusion coefficient D, and also I lie structural relaxation time <tau >, follow a power law at high temperatures, D(-1) proportional to (T - T(0))(-mu), with the same experimental parameters for viscosity (T(0) = 207 K, mu = 2.08). Decoupling between D and <tau > occurs at T(x) similar to 1.1 T(0). High frequency acoustic excitations for the LiCl center dot 6H(2)O model were obtained by the calculation of time correlation functions of mass current fluctuations. The temperature dependence of the instantaneous shear modulus, G,(T), was considered in the shoving model for supercooled liquids [J.C. Dyre, T. Christensen, N.B. Olsen, J. Non-Cryst. Solids 352 (2006) 4635] resulting in a linear relationship log (D(-1)) vs. G root T. (C) 2009 Elsevier B.V. All rights reserved.

Prigogine-Defay Ratio for an Ionic Glass-Former: Molecular Dynamics Simulations

The pressure dependence of the glass-transition temperature, T(g)(P), of the ionic glass-former 2Ca(NO(3))(2) center dot 3KNO(3), CKN, has been obtained by molecular dynamics (MD) simulations The liquid-glass difference of thermal expansivity, Delta alpha, heat capacity, Delta C(p), and isothermal compressibility, Delta kappa, have been calculated as a function of pressure. It has been found that the Ehrenfest relation dT(g)/dP = TV Delta alpha/Delta C(p) predicts the pressure dependence of T, but the other Ehrenfest relation, dT(g)/dP = Delta kappa/Delta alpha, does not. Consequently, the Prigogine-Defay ratio, Pi = Delta C(p)Delta kappa/TV Delta alpha(2), is Pi similar to 1.2 at low pressures, but increases 1 order of magnitude at high pressures. The pressure dependence of the Prigogine-Defay ratio is interpreted in light of recent explanations for the finding Pi > 1.

Alkoxy Chain Effect on the Viscosity of a Quaternary Ammonium Ionic Liquid: Molecular Dynamics Simulations

The viscosity of ionic liquids based on quaternary ammonium cations is reduced when one of the alkyl chains is replaced by an alkoxy chain (Zhou et al. Chem. Eur. J. 2005, 11, 752.). A microscopic picture of the role played by the ether function in decreasing the viscosity of quaternary ammonium ionic liquids is provided here by molecular dynamics (MD) simulations. A model for the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM(2)E TFSI, is compared to the tetraalky-lammonium counterpart. The alkoxy derivative has lower viscosity, higher ionic diffusion coefficients, and higher conductivity than the tetraalkyl system at the same density and temperature. A clear signature of the ether function on the liquid structure is observed in cation-cation correlations, but not in anion-anion or anion-cation correlations. In both the alkyl and the alkoxy ionic liquids, there is aggregation of long chains of neighboring cations within micelle-like structures. The MD simulations indicate that the less effective assembly between the more flexible alkoxy chains, in comparison to alkyl chains, is the structural reason for higher ionic mobility in MOENM(2)E TFSI.

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Preferential location of prilocaine and etidocaine in phospholipid bilayers: A molecular dynamics study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular dynamics simulation on devitrification: Isothermal devitrification and thermodynamics of PbF2 glasses

The vitrification and devitrification features of lead fluoride are investigated by means of molecular dynamic simulations. The influence of heating rate on the devitrification temperature as well as the dependence of the glass properties on its thermal history, i.e., the cooling rate employed, is identified. As expected, different glasses are obtained when the cooling rates differ. Diffusion coefficient analysis during heating of glass and crystal, indicates that the presence of defects on the glassy matrix favors the transition processes from the ionic to a superionic state, with high mobility of fluorine atoms, responsible for the high anionic conduction of lead fluoride. Nonisothermal and isothermal devitrification processes are simulated in glasses obtained at different cooling rates and structural organizations occurring during the heat treatments are clearly observed. When a fast cooling rate is employed during the glass formation, the devitrification of a single crystal (limited by the cell dimensions) is observed, while the glass obtained with slower cooling rate, allowing relaxations and organization of various regions on the glass bulk during the cooling process, devitrifies in more than one crystalline plane. (C) 2004 American Institute of Physics.

Molecular dynamics simulations on devitrification: the PbF2 case

In this work molecular dynamics simulations were performed to reproduce the kinetic and thermodynamic transformations occurring during melt crystallization, vitrification, and glass crystallization (devitrification) of PbF2. Two potential parameters were analyzed in order to access the possibility of modeling these properties. These interionic potentials are models developed to describe specific characteristic of PbF2, and thermodynamic properties were well reproduced by one of them, while the other proved well adapted to simulate the crystalline structure of this fluoride. By a modeled nonisothermal heat treatment of the glass, it was shown that the devitrification of a cubic structure in which the Pb-Pb distances are in good agreement with theory and experiment. (C) 2002 American Institute of Physics.

Molecular Dynamics simulations of track formation at different ensembles

A series of Molecular Dynamics simulations of thermal spikes has been run in zircon. For two different ensembles: microcanonical one and a combination of microcanonical one acting on the simulation core with Langevin one on the side walls of simulation. Depending on the used ensemble, different track-formation threshold energies were found. When the combined ensemble is carried out, the total energy of the simulations varies with the temperature which can influence how annealing fission-track models should deal with the lattice recovery. A fission-track annealing model is tested with the simulation results. © 2012 Elsevier Ltd. All rights reserved.

Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (k cat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. © 2013 Elsevier B.V. All rights reserved.

Amorphous ZrF4-a molecular dynamics study

Using an effective two-body interaction potential, a molecular dynamics study of the structural properties of amorphous ZrF4 phase is presented. The effective pair potential includes steric repulsion, Coulomb interaction due to charge transfer, and charge-dipole interaction due to the large electronic polarizability of anions. The results for structural correlations, such as pair distribution functions, coordination numbers, and bond angle distributions are presented. Excellent agreement is obtained by comparing experimental X-ray diffraction and the simulated static X-ray structure factor. © 1993.

A novel set of ss-N-biaryl ether sulfonamide hydroxamates as potential MMPs inhibitors: Molecular dynamics simulations and molecular properties evaluation

Matrix metalloproteinases (MMPs) constitute a family of zinc-dependent proteases involved in the extracellular matrix degradation. MMP-2 and MMP9 are overexpressed in several human cancer types, including melanoma, thus the development of new compounds to inhibit MMPs' activity is desirable. Molecular dynamic simulation and molecular properties calculations were performed on a set of novel beta-N-biaryl ether sulfonamide-based hydroxamates, reported as MMP-2 and MMP-9 inhibitors, for providing data to develop an exploratory analysis. Thermodynamic, electronic, and steric descriptors have significantly discriminated highly active from moderately and less active inhibitors of MMP-2 whereas apparent partition coefficient at pH 1.5 was also significant for the MMP-9 data set. Compound 47 was considered an outlier in all analysis, indicating the presence of a bulky substituent group in R3 is crucial to this set of inhibitors for the establishment of molecular interactions with the S1 subsite of both enzymes, but there is a limit. (C) 2012 Wiley Periodicals, Inc.

Influence of Molecular Dynamics on the Dielectric Properties of Poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) -Based Devices

This paper uses Nuclear Magnetic Resonance (NMR) and Differential Scanning Calorimetry (DSC) techniques to study the molecular relaxations and phase transitions in poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT), which has been extensively studied as the active thin film in organic devices. Besides the identification of the glass transition, beta relaxation and crystal-to-crystal phase transition, we correlate such phenomena with dielectric and transport mechanisms in diodes with F8BT as the active layer. The beta relaxation has been assigned to a transition at about 210 K measured by H-1 and C-13 solid state NMR, and can be attributed to local motions in the side chains. The glass transition has been detected by DSC and H-1 NMR. Dielectric spectroscopy (DS) carried out at low frequencies on diodes made from F8BT show two peaks which are coincident with the above transitions. This allowed us to correlate the electrical changes in the film with the onset of specific molecular motions. In addition, DS indicates a third peak related with a crystal-to-crystal phase transition. Finally, these transitions were correlated with changes in the carrier mobility recorded in thin films and published recently.

Characterization of suramin binding sites on the human group IIA secreted phospholipase A(2) by site-directed mutagenesis and molecular dynamics simulation

Suramin is a polysulphonated naphthylurea with inhibitory activity against the human secreted group IIA phospholipase A(2) (hsPLA2GIIA), and we have investigated suramin binding to recombinant hsPLA2GIIA using site-directed mutagenesis and molecular dynamics (MD) simulations. The changes in suramin binding affinity of 13 cationic residue mutants of the hsPLA2GIIA was strongly correlated with alterations in the inhibition of membrane damaging activity of the protein. Suramin binding to hsPLA2GIIA was also studied by MD simulations, which demonstrated that altered intermolecular potential energy of the suramin/mutant complexes was a reliable indicator of affinity change. Although residues in the C-terminal region play a major role in the stabilization of the hsPLA2GIIA/suramin complex, attractive and repulsive hydrophobic and electrostatic interactions with residues throughout the protein together with the adoption of a bent suramin conformation, all contribute to the stability of the complex. Analysis of the h5PLA2GIIA/suramin interactions allows the prediction of the properties of suramin analogues with improved binding and higher affinities which may be candidates for novel phospholipase A(2) inhibitors. (C) 2012 Elsevier Inc. All rights reserved.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).

Comparison of model potentials for molecular dynamics simulation of crystalline silica

Simulationen von SiO2 mit dem von van Beest, Kramer und vanSanten (BKS) entwickelten Paarpotenzial erzeugen vielezufriedenstellende Ergebnisse, aber auch charakteristischeSchwachstellen. In dieser Arbeit wird das BKS-Potenzial mitzwei kürzlich vorgeschlagenen Potenzialen verglichen, dieeffektiv Mehrteilchen-Wechselwirkungen beinhalten. Der ersteAnsatz erlaubt dazu fluktuierende Ladungen, der zweiteinduzierbare Polarisierungen auf den Sauerstoffatomen. Die untersuchten Schwachstellen des BKS Potenzialsbeinhalten das Verhältnis der zwei Gitterkonstanten a und cim Quarzübergang, das von BKS falsch beschrieben wird.Cristobalit und Tridymit erscheinen instabil mit BKS.Weiterhin zeigt die BKS-Zustandsdichte charakteristischeAbweichungen von der wahren Zustandsdichte. DerÜbergangsdruck für den Stishovit I-II Übergang wird deutlichüberschätzt. Das Fluktuierende-Ladungs-Modell verbesserteinige der genannten Punkte, reproduziert aber viele andereEigenschaften schlechter als BKS. DasFluktierende-Dipol-Modell dagegen behebt alle genanntenArtefakte. Zusätzlich wird der druckinduzierte Phasenübergang imalpha-Quarz untersucht. Alle Potentiale finden die selbeStruktur für Quarz II. Bei anschliessender Dekompressionerzeugt BKS eine weitere Phase, während die beiden anderenPotentiale wieder zum alpha-Quarz zurückkehren. Weiterhinwerden zwei Methoden entwickelt, um die piezoelektrischenKonstanten bei konstantem Druck zu bestimmen. Die Ergebnissegeben Hinweise auf eine möglicherweisenicht-elektrostatische Natur der Polarisierungen imFluktuierende-Dipole-Modell. Mit dieser Interpretation scheint das Fluktuierende-DipolPotential alle verfügbaren experimentellen Daten am bestenvon allen drei untersuchten Ansätzen zu reproduzieren.