Computer simulation study of water using a fluctuating charge model

Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Ricket al (S W Rick, S J Stuart and B J Berne 1994J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to fluctuate as a function of time, depending on their local environment. The charge flow is driven by the difference in the electronegativity of the atoms within the water molecule, thus effectively mimicking the effects of polarization of the charge density. The potential model is thus transferable across all phases of water. Using this model, we have obtained the minimum energy structures of water clusters up to a size often. The cluster structures agree well with experimental data. In addition, we are able to distinctly identify the hydrogens that form hydrogen bonds based on their charges alone, a feature that is not possible in simulations using fixed charge models. We have also studied the structure of liquid water at ambient conditions using this fluctuating charge model.     

Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation

Proteins often undergo changes in internal conformation upon interacting with a surface. We investigate the thermodynamics of surface induced conformational change in a lattice model protein using a multicanonical Monte Carlo method. The protein is a linear heteropolymer of 27 segments (of types A and B) confined to a cubic lattice. The segmental order and nearest neighbor contact energies are chosen to yield, in the absence of an adsorbing surface, a unique 3x3x3 folded structure. The surface is a plane of sites interacting either equally with A and B segments (equal affinity surface) or more strongly with the A segments (A affinity surface). We use a multicanonical Monte Carlo algorithm, with configuration bias and jump walking moves, featuring an iteratively updated sampling function that converges to the reciprocal of the density of states 1/Omega(E), E being the potential energy. We find inflection points in the configurational entropy, S(E)=k ln Omega(E), for all but a strongly adsorbing equal affinity surface, indicating the presence of free energy barriers to transition. When protein-surface interactions are weak, the free energy profiles F(E)=E-TS(E) qualitatively resemble those of a protein in the absence of a surface: a free energy barrier separates a folded, lowest energy state from globular, higher energy states. The surface acts in this case to stabilize the globular states relative to the folded state. When the protein surface interactions are stronger, the situation differs markedly: the folded state no longer occurs at the lowest energy and free energy barriers may be absent altogether.     

Transitions of tethered polymer chains: a simulation study with the bond fluctuation lattice model

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density-of-states results have been evaluated for interaction parameters spanning the range from good- to poor-solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and two-dimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.     

Computer simulation of different modes of ACE based on the dynamic complexation model

Several modes of the often used ACE processes are simulated based on the principle of dynamic complexation of interacting species in a capillary column. The model is built on the mass transfer equation, to provide insight into the detailed analyte migration and interaction processes in CE. Normal ACE, Hummel-Dreyer method, vacancy affinity CE, vacancy peak method, and CE frontal analysis are simulated based on typical ACE conditions, and the results are compared with the detector responses of real CE processes using BSA and warfarin as a model system. Remarkable resemblance between the simulated results and the experimental observations was demonstrated for well-buffered ACE systems.     

Nonbonded potential energy functions based on the dumbbell model of diatomic molecules

Summary The potential energy functions commonly used in calculating crystal packing are in poor agreement when applied to the interaction of a spherically symmetric atom and diatomic molecule or to the interaction of two diatomic molecules. The attractive components of potential energy functions of these interactions, however, are known from quantum mechanics. New potential energy functions for these interactions, based on a dumbbell model, are proposed. In addition, the goodness of fit of the repulsion term is discussed.

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Zusammenfassung Potentielle Energiefunktionen, die gewöhnlich bei der Berechnung der Packung von Molekülen in Kristalliten Verwendung finden, stimmen nicht mit der bekanntenvan der W aals-Wechselwirkung eines kugelsymmetrischen Atoms und eines zweiatomigen Moleküls oder der Wechselwirkung zweier zweiatomigen Moleküle überein. Neue potentielle Energiefunktionen für die Atom-Atom-Wechselwirkung von Molekülen werden vorgeschlagen und die Güte der Anpassung des abstoßenden Terms einesBuckingham-Potentials diskutiert.

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Dedicated to Prof.R. Hosemann on the occasion of his 60th birthday.     

Computer simulation on the energy transfer processes in allophycocyanins

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Molecular dynamics simulation of the reaction of hydration of formaldehyde using a potential based on solute-solvent interaction energy components

Molecular dynamics simulations of aqueous solutions at infinite dilution of the reaction of water with formaldehyde, H(2)O + H(2)CO --> H(2)C(OH)(2), were performed using Lennard-Jones 12-6-1 potentials to describe the solute-solvent interactions, and TIP3P to describe the water-water interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the dispersion component at MP2 level were used to reproduce the molecular parameters of the solute-water interaction potential. The results show that the functions that use the EX-PL-DIS-ES interaction model to describe the solvation of the reactant and product systems lead to good values of the reaction (DeltaG) and activation (DeltaG(#)) free energy as compared with those from using AMBER-derived parameters, and with the available theoretical and experimental data.     

A molecular model of water based on the lattice gas model

A lattice gas model is used to describe the vapor-liquid state of water molecules. The orientationally directed interaction of the water molecules via their tetrahedral structure and dipole-dipole interaction are considered in the theory, along with the Lennard-Jones contributions to the potential of molecular interaction, which stabilize the system with dipole interaction. We studied how the radius of the molecular interaction potential affects the equilibrium characteristics of the system (the phase separation curves of the vapor-liquid system, and the relationship between the fluid density and the chemical potential value).     

Monte Carlo simulation of a lattice model for ternary polymer mixtures

Monte Carlo studies of symmetrical polymer mixturesAB, modelled by selfavoiding walks withN _A =N _B =N steps on a simple cubic lattice, are presented for arbitrary concentrations of vacancies _v in the range from _v =0.2 to _v =0.8 and chain lengthsN64. We obtained the phase diagrams and the equation of state for three choices of the ratio / _AB ( being the energy between monomers of the same kind, _AB being the energy between different monomers). Flory-Huggins theory provides only a qualitative understanding of these results. If the equation of state is fitted with an effective Flory-Huggins parameter _eff , the latter turns out to be strongly dependent on both concentration and temperature.Contributed paper delivered at the Tagung der Deutschen Physikalischen Gesellschaft, Fachausschuß Polymerphysik, Berlin, March 30–April 3, 1987.     

Molecular pair potential of chiral amino acid amphiphile in Langmuir monolayers on the basis of an atomistic model

In the present work, the pair potential of enantiomeric N-palmitoyl aspartic acid amphiphile monolayer at the air/water interface is calculated based on an atomistic model. The molecular structure and partial charges are calculated using two semi empirical (PM3, AM1) and one empirical (Gasteiger and Marcili) methods. A distance-dependent dielectric function is used to represent the interfacial dielectric constant at the aqueous subphase. The present study indicates that a pair of molecules have favorable interaction at specific ranges of mutual orientations. Other orientations are favorable but at larger separations. Favorable electrostatic interaction at a specific combination of orientation and short separations of the head groups significantly contribute to the total energy. The curvature of the domain boundary is suggested to be driven by the favorable arrangement which is dependent on the pair potential of molecules. The use of charges obtained by the PM3 and GM do not lead to a significant variation of the orientation-dependent features, while the AM1 predicts higher partial charges and interactions are stronger than the former two methods. However, orientation-dependent features remain the same. The variations in the LJ parameters and charges indicate that the conclusions made are insensitive to the choice of parameters. The mutual favorable interaction predicted by calculation agree with the handedness of curvature of domains.     

Computer simulation of polypeptide adsorption on model biomaterials

When biomaterials are inserted in a biological environment, for instance in a body implant, proteins do quickly adsorb on the exposed surface. Such process is of fundamental importance, since it directs the subsequent cell adhesion. Here we review recent advances in this field obtained with molecular simulations. While coarse-grained models can provide important general results, as it has long been recognized in polymer science, the hierarchical structure of a very complex copolymer such as a protein, together with the nature of the biomaterial surface suggest that atomistic models are better suited to investigate these phenomena. Thus, after briefly mentioning some common features of coarse-grained and atomistic force fields, we first discuss early theoretical and coarse-grained simulation results about protein adsorption, and then we highlight the main results recently obtained by us with atomistic models. In particular, we discuss some conformational and energetic aspects of the adsorption of protein fragments with different secondary structure on surfaces of different wettability, including hydrophobic graphite and hydrophilic poly(vinylalcohol). We also consider other features, such as the simulation of the materials wettability, the hydration of the adsorbed fragments, their kinetics of spreading, and the sequential adsorption of two protein fragments on top of each other, highlighting the results of general interest.     

Mapping the interaction energy surfaces of cyclic alkanes: evaluating the transferability of an ab initio based potential model

Detailed interaction energy maps are computed for symmetric cyclopropane and tetrahedrane dimer systems using ab initio methods. Interaction energies of cubane and cyclohexane dimers are also reported. The global minimum energy structures of cyclopropane and tetrahedrane systems are both D(3d) structures with energies of -1.850 and -2.171 kcal mol(-1). The ability of NIPE potential model, based on ab initio nonbonding data of neopentane (N), isobutane (I), propane (P), ethane (E) and all their combinations to predict the pair interaction energies of these strained cyclic hydrocarbons is also investigated. The difference between the energies predicted by NIPE and those obtained from the ab initio calculations increases with ring strain In general, NIPE values are in close agreement with the ab initio results for alkane ring structures having low ring strain.     

A Monte Carlo simulation of the inhomogeneous Lebwohl-Lasher lattice model

A Monte Carlo computer simulation of a modified Lebwohl-Lasher model is presented. The model consists of a set of interaction centres placed at the sites of a cubic lattice. The angular part of the pair potential is a second Legendre polynomial of the relative orientation between the two particles, like that of the Lebwohl-Lasher model. Each particle interacts with its six nearest neighbours with an attractive anisotropic potential differing in strength for the four horizontal and the two vertical neighbours. Various values of the in-plane to out-of-plane coupling ratio δ have been considered, i.e. δ = 0.75, 0.5, 0.1, 0.0. The latter case corresponds to the limiting situation of a two-dimensional lattice. Systems with a 1000 particles have been simulated for δ = 0.75, 0.5 and 0.1 while a sample of 3600 particles has been investigated for the two-dimensional lattice. Comparisons are made with available simulations and with mean field theory. We find that the molecular field theory predictions worsen as the effective coordination number is decreased. Energy, specific heat, second and fourth rank order parameters have been evaluated for the various models. We also present, for the first time, a way of approximately reconstructing the pair distribution, G(r₁₂, ω₁₂), using maximum entropy and second and fourth rank two particle order parameters.     

Molecular dynamics simulation study of superhydrated perdeuterated natrolite using a new interaction potential model

To test a new interaction potential, molecular dynamics simulations of zeolite natrolite were performed for the structures under ambient conditions hydrated by perdeuterated water and at high pressure (1.87 GPa) in the superhydrated phase, which were recently studied by neutron diffraction. The experimental structures were reproduced with reasonable accuracy, and the hydrogen bond features are discussed. As in ordinary natrolite, a flip motion of water molecules around the HOH bisector is found, which, together with translational oscillations, gives rise to transient hydrogen bonds between water molecules, which do not appear from experimental equilibrium coordinates. The dynamics of water molecules can explain some problems encountered in refining the experimental structure. Vibrational spectra of natrolite containing perdeuterated water, which are not yet measured, were simulated, and their qualitative trend is discussed.     

Thermodynamic properties of the Cu-Au system using a face-centered-cubic lattice model with a renormalized potential

A Monte Carlo simulation is carried out to study thermodynamic properties of Cu-Au alloys using a face-centered-cubic (fcc) lattice-gas model. To obtain quantitatively accurate results, a Finnis-Sinclair-type potential, which has been widely used for molecular dynamics (MD) simulations, is employed. To overcome some shortcomings of lattice-gas models such as neglecting vibrational entropy, the potential is mapped onto the fcc lattice using the renormalization technique. The renormalized potential gives an improved Cu-Au phase diagram compared to the original MD potential applied directly on the lattice.     

Computer simulation study on the structural-optical related properties of a pyrene-functionalized fluorescent film

Molecular dynamics simulations were carried out to investigate the structural properties and the structure related optical properties of a pyrene-functionalized film and also the film in the presence of nitrobenzene. It has been shown that at equilibrium (1) the pyrene molecules of the film, of which the fluorophore molecules have been attached to a glass plate surface via relatively long flexible spacers, adopt quasi-coplanar structures; (2) the distance between a pair of pyrene rings populates from 4 A to longer than 10 A, but quite a large number of pyrene molecules populate within distances between 4 and 5 A, indicating that the fluorescence of the film should be characterized by both monomer emission and excimer emission; (3) introduction of nitrobenzene into the system results in a decrease of the population of pyrene molecules within the distances suitable for the formation of excimers, suggesting that excimer emission of the film would be decreased; and (4) the incoming nitrobenzene molecules insert themselves in between the previously formed coplanar structures of pyrene rings and form a complex with one of them. Considering that nitrobenzene is an electron-poor compound and nonfluorescent and that pyrene is an electron-rich one, it is expected that the formation of the complex must result in an excitation transfer from pyrene to nitrobenzene, provided that the distance between them and the orientations of them are reasonable. This indicates that the introduction of nitrobenzene not only decreases the number of excimers of pyrene but also quenches the monomer emission of the fluorophore. All the expectations from the simulation studies are basically consistent with the experimental observations.     

Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus

Summary Molecular dynamics simulations have been used to study the free energy of binding of an antiviral agent to the human rhinovirus HRV-14 and to a mutant in which a valine residue in the antiviral binding pocket is replaced by leucine. The simulations predict that the antiviral should bind to the two viruses with similar affinity, in apparent disagreement with experimental results. Possible origins of this discrepancy are outlined. Of particular importance is the apparent need for methods to systematically sample all significant conformations of the leucine side chain.     

Natural convection of composite nanofluids based on a two-phase lattice Boltzmann model

Journal of Thermal Analysis and Calorimetry - A two-phase lattice Boltzmann method (LBM) is used to study the natural convection heat exchange characteristics of Al2O3–H2O nanofluids and...