Showing papers in "Molecular Simulation in 2002"

DL_POLY: Application to molecular simulation

Abstract: DL_POLY is a general-purpose molecular dynamics simulation package, which was developed by Daresbury Laboratory in the mid-1990s for the molecular simulation community in the United Kingdom. The package now has a world-wide user base and applications in many areas of molecular simulation. In this article we briefly review the history and design of the package and highlight some recent applications in the areas of; liquids and solutions; spectroscopy; ionic solids; molecular crystals; polymers; glasses; membranes; proteins; solid and liquid interfaces; catalysis; liquid crystals; intercalation and clathrates; and novel systems. The strengths and weaknesses of the code and its future in the near term are also discussed.

Calculating Free Energies Using a Scaled-Force Molecular Dynamics Algorithm

Abstract: We propose and test a family of methods to calculate the free energy along a generalized coordinate, , based on computing the force acting on this coordinate. First, we derive a formula that connec...

A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations

Abstract: One of the long-standing problems in free energy calculations that involve the annihilation of particles is the choice of how to scale the non-bonded interactions of the disappearing particle. We make use of a "null transformation" (converting naphthalene to naphthalene) to extensively test and compare a number of scaling approaches, including simple linear, quadratic, mixed non-linear and separation-shifted ("soft-core") scaling. While any protocol that involves some sort of non-linear scaling yields reasonable free energy results, only the "soft-core" scaling methods yield completely stable dynamics near the simulation end-points. Additional advantages of this method in the context of complex molecular conversions are also discussed.

Hybrid approach for generating realistic amorphous carbon structure using metropolis and reverse Monte Carlo

Abstract: An improved method for the modelling of carbon structures based on a hybrid reverse Monte Carlo (HRMC) method is presented. This algorithm incorporates an accurate environment dependent interaction potential (EDIP) in conjunction with the commonly used constraints derived from experimental data. In this work, we compare this new method with other modelling results for a small system of 2.9 g/cc amorphous carbon. We find that the new approach greatly improves the structural description, alleviating the common problem in standard reverse Monte Carlo method (RMC) of generating structures with a high proportion of unphysical small rings. The advantage of our method is that larger systems can now be modelled, allowing the incorporation of mesoscopic scale features.

Free Energy Calculations. The Long and Winding Gilded Road

Abstract: The fourth workshop on free energy calculations held at the Centre Europeen de Calcul Atomique et Moleculaire (CECAM) in Lyon, last June 19-21, 2000, presented an opportunity for a critical look at the past successes and failures of simulations targeted at the estimation of free energies, and for a glimpse into their promising future. In an abridged historical background, the methodological milestones paving the road for today's free energy simulations are summarized. The continuing difficulties encountered when attempting to obtain accurate free energy estimates are then discussed, with an emphasis on the potential usefulness of such large-scale calculations in non-academic environments. Finally, current strategies for improving the reliability of free energy calculations, while at the same time making them more affordable (and thus more compatible with the constraints of the industrial environment) are discussed.

Multiscale simulation in polymer science

Abstract: The paper gives a short overview on recent approaches to link several time and length scales in soft matter simulations. Special attention is given to the fact that in contrast to low molecular weight compounds, intramolecular entropy is as important as the energetic contribution. First applications to industrially relevant problems are mentioned.

Monte Carlo simulation of branched alkanes and long chain n -alkanes with anisotropic united atoms intermolecular potential

Abstract: The anisotropic united atoms potential for linear alkanes proposed by Ungerer (J. Chem. Phys. , 112 , 5499, 2000), called AUA4, has been used to predict several equilibrium properties (vapour pressure, vaporisation enthalpies, and liquid densities) of alkanes by Gibbs ensemble Monte Carlo simulation. In order to extend the potential to branched alkanes, potential parameters for the CH group have been determined by optimisation on the basis of equilibrium properties of isobutane, keeping the same parameters as AUA4 for the CH 3 groups. The resulting CH parameters form a regular sequence with those previously determined for CH 3 and CH 2 groups, so that a physically consistent parameter set is obtained. Simulations have been performed at temperatures ranging from 450 to 800 u K for long n -alkanes (C20, C25 and C30) and from 350 to 450 u K for four heptane isomers (n -heptane, 2-methylhexane, 2,4-dimethylpentane and 2-ethylpentane). In order to achieve internal relaxation of long chains with a good efficien...

An adiabatic molecular dynamics method for the calculation of free energy profiles

Abstract: A new molecular dynamics method for calculating free energy profiles for rare events is presented. The new method is based on the creation of an adiabatic separation between the reaction coordinate subspace and the remaining degrees of freedom within a molecular dynamics run. This is achieved by associating with the reaction coordinate(s) a high temperature and large mass, thereby allowing the activated process to occur while permitting the remaining degrees of freedom to respond adiabatically. In this limit, by applying a formal multiple time scale Liouville operator factorization, it can be rigorously shown that the free energy profiles are obtained directly from the probability distribution of the reaction coordinate subspace and, therefore, require no postprocessing of the output data. The new method is applied to a variety of model problems and its performance tested against free energy calculations using the "bluemoon ensemble" approach. The comparison shows that free energy profiles can be calculat...

Investigation of Lignin-water interactions by molecular simulation

Abstract: The results of molecular dynamics simulations of three lignin-water systems are presented. Static and dynamic properties of each system are compared to a benchmark system consisting entirely of water molecules. The significantly reduced mobility of water molecules local to lignin hydroxyl regions is attributed to hydrogen bond formation, while the slightly reduced mobility of water molecules in the vicinity of lignin methoxyl groups results from a hydrophobic effect that causes water molecules to structure themselves around these groups. The average diffusion of water in each system correlates with the number of methoxyl groups present in the system. As the number of methoxyls in the system increases, so too does the average diffusion constant of water in that system. The bulky methoxyl groups obstruct water from accessing lignin hydroxyl regions where hydrogen bond formation is anticipated and the hydrogen-bonded water lowers the average diffusion constant.

Atomistic models of carbonate minerals: bulk and surface structures, defects, and diffusion

Abstract: 3 anion group, are used to evaluate the lattice, elastic, dielectric, and vibrational data for calcite and aragonite. The resulting potential parameters for the carbonate group were then successfully transferred to models of the structures of rhombohedral carbonates of Mn, Fe, Mg, Ni, Zn, Co, and Cd. Simulations of the (1014) cleavage surface of calcite, magnesite, and dolomite show that these surfaces undergo relaxation leading to the rotation and distortion of the carbonate group with associated movement of cations. The influence of water on the surface structure has been investigated for monolayer coverage. The extent of carbonate group distortion is greater for the dry surfaces compared to the hydrated surfaces, and for the dry calcite relative to that for dry dolomite or magnesite. Point defect calculations for the doping of calcite indicate an increase in defect formation energy with increasing size of the substituting divalent ion. Migration energies for Ca, Mg, and Mn in calcite suggest a strong preference for diffusion along pathways roughly parallel to the c-axis rather than along the ab-plane.

Hydrous calcium magnesium carbonate, a possible precursor to the formation of sedimentary dolomite

Abstract: Material of composition Ca1.056 Mg0.944 (SO4)0.035 (CO3)1.965 ⋅0.26H2O has been synthesised from solutions of Ca(NO3)2, MgSO4 and Na2CO3. X-ray diffraction and infrared spectroscopy show this to be identical to "protodolomite" found in nature, and that the structure is related to dolomite but is hydrous, retaining water to beyond 200°C on heating. This hydrous magnesium calcium carbonate grows as spherules, with a distinct core-rim structure apparent in optical microscopy. It seems likely that in low-temperature environments (around 80°C) a dolomite crystal grows in nature via this or a similar hydrous intermediate phase, which may hold the solution to the "dolomite problem".

Selective attachment of monovalent background electrolyte ions and growth inhibitors to polar steps on sulfates as studied by molecular simulations and AFM observations

Abstract: Molecular simulations and in situ atomic force microscopy (AFM) experiments are used to demonstrate the influence of the ionic strength of the solution and the mechanism of growth inhibitors on growth and dissolution of barite with some comparative experiments on celestite. Growth and dissolution rates, as determined from monolayer step edge velocities, increase with increasing background electrolyte (NaCl) concentration. The electrolyte effect is analyzed in terms of changes of the bulk solution, physicochemical properties of the near-surface region and the mechanisms on the sulfate surfaces at a molecular scale. Bulk solution effects are mainly based on changes in the activity coefficient of dissolved species whereas increased growth and dissolution rates are partly due to a decreased interfacial tension between barite and supersaturated aqueous solution at high ionic strength. We have also found possible mechanisms from molecular simulations that explain the rate changes and also the significant change...

Reversibility of Free Energy Simulations∶ Slow Growth May Have a Unique Advantage. (With a Note on Use of Ewald Summation)

Abstract: We review the slow-growth method for computing free energy changes for processes in conformation space or in "chemical" space, in which a system parameter, h is changed at each integration time step, and the free energy, j A is approximated by accumulating the work performed at each step. The method is simple to implement and use, convergence can be monitored by performing longer simulations and by performing the simulations changing h in both directions, and statistical error can be evaluated by performing multiple independent simulations. Because slow growth simulates a continuous process, it closely approximates the ideal isothermal quasi-static process used in defining the free energy in thermodynamics, and thus a small hysteresis in slow-growth results practically guarantees that the process is reversible, which is of course a prerequisite for the results to represent a free energy change. Whenever hysteresis is not negligible (which happens when the required long simulation times are unattainable), ...

The Role of Bonded Energy Terms in Free Energy Simulations - Insights from Analytical Results

Abstract: A statistical mechanical analysis of the role of bond stretching and angle bending terms, as well as of dummy atoms, in alchemical free energy simulations is presented. It allows one to resolve several ambiguities concerning their treatment from first principles. The relative importance of vibrational, Jacobian factor and potential-of-mean-force-like contributions from bonded energy terms to single and dual free energy differences is compared. Additional conclusions can be drawn for dummy atoms. In particular, it is shown that double free energy differences obtained in thermodynamic cycle calculations can always be made independent of the treatment of dummy atoms. Further, the equivalence of single and dual topology calculations in such applications is demonstrated. The theoretical considerations are accompanied and illustrated by simulation results for the free energy difference of solvation between iso-butane and propane.

Fast-growth Thermodynamic Integration∶ Results for Sodium Ion Hydration

Abstract: Slow-growth thermodynamic integration (TI) is a simple method to calculate free energy differences in fluid and macromolecular systems. A recently derived identity (Jarzynski, C. Phys. Rev. Lett. 78, 2690, 1997) permits the calculation of free energy differences from repeated TIs at arbitrary growth rates. Here, I investigate the quantitative accuracy of the resulting 'fast-growth' TI for the charging of a sodium ion in water. To estimate the corresponding free energy of hydration, I use simple expressions involving the means and variances of the non-equilibrium work.

Calcium hydration on montmorillonite clay surfaces studied by Monte Carlo simulation

Abstract: Monte Carlo computer simulations were used to investigate the interlayer structure of Ca-montmorillonite for hydration levels ranging from the dry clay to a three-layer system. Our model of montmorillonite consists of negative charge sites in both the octahedral and tetrahedral layers. Our results are compared with X-ray diffraction data from Ca-clays, which have suggested an interlayer structure similar to Mg-clays. However, the Ca 2+ co-ordination number in these systems and in bulk liquid is a subject of ongoing debate. Our results support an eightfold water solvation shell for calcium, even within the confines of a clay pore. The Ca 2+ co-ordination number decreased at lower water content, as the water layer became constrained and less like bulk liquid. Additionally, Ca 2+ solvation shells included surface oxygen atoms at low water content, although this may be a result of the Ca-O interaction potentials.

Adsorption of methanoic acid onto the low-index surfaces of calcite and aragonite

Abstract: We have employed atomistic simulation techniques to investigate the effect of the adsorption of methanoic acid on the surfaces of calcite and aragonite. We have calculated surface energies and adsorption energies for all the surfaces considered, and compared the surface energies with those of the pure surfaces. Generally the methanoic acid molecules coordinate via their doubly bonded oxygen atom to surface calcium atoms, with the hydroxyl hydrogen atom directed towards oxygen atoms of surface carbonate groups. The hydrogen bonded to the carbon atom of the methanoic acid is usually pointing away from the surface, which is of considerable significance since we are using methanoic acid as a model adsorbate for long chain carboxylic acids, that are used extensively in the process of flotation. We suggest that the replacement of the hydrogen atom of the methanoic acid with a long chain hydrocarbon would not result in significantly different interactions and, thus, would give similar adsorption energies ( m 54 ...

Modelling of hydrated ca-rich zeolites

Abstract: The successful modelling of the structure of two hydrated calcium-rich natural zeolites is described, showing how modelling can reproduce their complex structure, in excellent agreement with experiment. Furthermore, we demonstrate how such methods are able to determine the preferred Al ordering in the mineral Goosecreekite. The dehydration behaviour of Goosecreekite is also predicted. The interatomic potentials for water, evaluated here, are found to be robust and transferable to zeolitic materials.

Modelling oxide thin films

Abstract: Three simulation methodologies have been employed to investigate the growth, nucleation, and structure of oxides supported on oxide substrates, these are atom-by-atom deposition, layer-by-layer deposition and finally amorphisation of a structure followed by recrystallisation. The materials which have been investigated include the rocksalt-structured oxides; MgO, CaO, SrO, and BaO, the perovskite structured SrTiO 3 and also fluorite structured CeO 2 and ZrO 2. The work has shown that the substrate influences critically the structure of the supported thin film by determining the nature and interactions of defects, dislocations and grain-boundaries, as well as influencing the interfacial ion densities and various epitaxial relationships. In addition, graphical techniques have been employed to show the three-dimensional atomistic structure of each structural and epitaxial feature. Moreover, by considering large simulation cell sizes (approaching the mesoscale, 18 nm square), it has been possible to accommodat...

Where the bulk terminates: Experimental evidence for restructuring, chemibonded OH − and H + , adsorbed water and hydrocarbons on calcite surfaces

Abstract: Better understanding of mineral surface reactivity can improve control of crystal growth and dissolution which is central to biomineralisation, design of advanced materials and preventing transport of toxic substances in the environment. Some experimental observations of fundamental processes on calcite using high-resolution techniques (AFM, XPS, TOF-SIMS, LEED) are summarised. Surfaces, cleaved in ultrahigh vacuum (UHV) in the absence of reactive species, relax. Cleavage in air results in hydration and hydrolysis, covering the surface with chemisorbed CaOH and CO 3 H. Water adsorbed from air promotes recrystallisation on apparently dry surfaces. Organic components can inhibit dissolution and precipitation; even in the cleanest laboratory, surfaces have at least a monolayer of hydrocarbons. On commercial calcite powders contaminated by organic additives during manufacture, we do not see layer-by-layer and atom-by-atom growth or dissolution and behaviour contradicts the theoretical models developed from ma...

Representation of Coarse-grained Potentials for Polymer Simulations

Abstract: In order to be able to simulate long time and large space scale properties of polymer melts one has to resort to coarse grained models, for example by subdividing all polymers into parts and restricting attention to the center of mass positions and velocities of these parts. The dynamics of these variables is governed by Langevin equations in which the free energy obtained by integrating the remaining variables provides the potential of the conservative forces. In general this leads to many particle interactions on the coarse-grained level. Methods suggested in the literature to represent these many particle interactions by effective two body interactions are reviewed and a new method, based on the Gibbs-Bogoliubov inequality, is proposed. The reason why none of these methods is able to reproduce the pressure of the underlying atomistic model is discussed.

Cation distribution in faujasite-type zeolites: A test of semi-empirical force fields for Na cations

Abstract: (N,V,T) Monte Carlo (MC) simulations have been performed in order to test three available force fields for sodium cations in faujasite-type zeolites. A rigid framework faujasite model, using an average T atom scheme and the cation force field proposed by [Jaramillo, E. and Auerbach, S.M. J. Phys. Chem. 103 (1999) 9589] was found to reproduce quite well the experimentally observed cation location in NaY and could thus be used in future works for predicting cation distributions and possible cation migration upon adsorption in faujasites.

Simulation of diffusion of O 2 and CO 2 in amorphous poly(ethylene terephthalate) and related alkylene and isomeric polyesters

Abstract: The diffusion of small molecules through polymers is important in many areas of polymer science, such as gas barrier and separation membrane materials, polymeric foams, and in the processing and properties of polymers. Molecular simulation techniques have been applied to study the diffusion of oxygen and carbon dioxide as small molecule penetrants in models of bulk amorphous poly(ethylene terephthalate) (PET) and related alkylene and isomeric polyesters. A bulk amorphous configuration with periodic boundary conditions made into a unit cell whose dimensions were determined for each of the simulated polyesters in the cell having the experimental density. The diffusion coefficients for O 2 and CO 2 were determined via NVE molecular dynamics simulations using the Dreiding 2.21 molecular mechanics force field over a range of temperatures (300, 500 and 600 K) using up to 3 ns simulation time. We have focussed on the influence of the temperature, polymer dynamics, number of CH 2 groups, density and free volume d...

The calculation of structural, elastic and phase stability properties of minerals using first principles techniques: A comparison of HF, DFT and Hybrid functional treatments of exchange and correlation

Abstract: We benchmark the performance of four treatments of electron exchange and correlation in the prediction of structural and elastic properties of a range of minerals. The treatments used are the Hartree-Fock (HF) theory, the local density approximation (LDA) and the generalised gradient approximation (GGA) to the density functional theory (DFT) and Becke's three parameter hybrid functional (B3LYP). We find that the hybrid functional, B3LYP method yields computed elastic properties in significantly better agreement to experiment than HF or DFT-LDA and performs at least as well, if not better than the most successful DFT-GGA functionals. We suggest that B3LYP is a simple, reliable and computationally efficient tool for the ab initio simulation of mineral systems.

Molecular dynamics simulations of the incorporation of Mg 2+ , Cd 2+ and Sr 2+ at calcite growth steps: Introduction of a SrCO 3 potential model

Abstract: Molecular dynamics simulations were used to model the incorporation of magnesium, cadmium and strontium ions at two stepped (10 1 4) surfaces of the calcium carbonate polymorph calcite. The potential model used in the simulations was derived to reproduce experimental enthalpies of CaCO 3 , MgCO 3 , CdCO 3 and SrCO 3 formation and dissolution and the effect of solvent was modelled by the addition of a layer of water molecules. From the calculated energies we expect that, in a solution containing all four cations, MgCO 3 and SrCO 3 grow onto the calcite steps in preference to CdCO 3 and especially CaCO 3 . Growth of complete rows of MgCO 3 and CdCO 3 occurs at either step edge, while growth of a row of SrCO 3 at the acute edge releases a large amount of energy ( m 420 kJ mol m 1 ), which should, therefore, be the preferential step for incorporation of complete SrCO 3 edges.

An atomistic simulation study of cylindrical ultrathin Cu nanowires

Abstract: In order to understand the structure and properties of cylindrical ultrathin copper nanowires, we have simulated the growth of cylindrical copper nanowires using the steepest descent method, and investigated the energy per atom from changing the diameter, from spreading sheets, from the angular correlation function, and from the radial distribution function. The stable structure of the cylindrical ultrathin copper nanowires was found to be multi-shell packs composed of coaxial cylindrical shells with a {111} facet. As the diameter of the nanowire increases, the structural properties of nanowire becomes close to those of the bulk.

Computer simulation of calcite growth inhibition: A study of monophosphonate interaction with calcite

Abstract: We have performed atomistic surface simulations of the interaction of monophosphonate growth inhibitor ions with the planar and obtuse stepped { 10 1 ¥ 4 } surfaces of calcium carbonate. We show that phosphonate inhibitor ions have a smaller adsorption energy on the planar { 10 1 ¥ 4 } surface compared to the obtuse stepped { 10 1 ¥ 4 } surface in accordance with experiment; and that the binding energy of the inhibitor with the surface is dominated by electrostatic forces. We find that replacement processes which simulate the irreversible incorporation of monophosphonate ions at terrace and step sites are energetically more favourable than those calculated for the diphosphonate ion. The inhibition mechanism proposed to operate for the deprotonated monophosphonate/calcite system is via the binding or incorporation of monophosphonate ions to the calcite obtuse step sites and kink sites thus slowing step flow and thereby destroying and/or delaying the formation of potential kink sites and step assembly.

Molecular modelling studies of calcium carbonate and its nanoparticles

Abstract: Molecular dynamics (MD), simulations have been carried out of crystalline aragonite and calcite, and of finely dispersed calcium carbonate in the form of nanosized inorganic core- organic shell particles. The latter, called overbased detergents commercially, are used as acid-consuming components in automotive and marine engine oils. We have modelled several types of these particles using different surfactant types. We compare the internal structure of the calcium carbonate in these particles with calcite and aragonite crystalline forms using MD in each case. The atomic force-field adopted accounts reasonably well for the crystalline phases, although under unconstrained (constant stress) conditions some distortion of the aragonite structure was noticed. The microstructure of the nanoparticles appears to be quite different to the crystals, and seemingly amorphous. For these small clusters it appears that there is probably no thermodynamic benefit in forming local crystalline order in the cores. The relative...

DFT modelling of hydrogen on Cu (110)- and (111)- type clusters

Abstract: Density Functional Theory (DFT) calculations using gaussian 98 have been performed on hydrogen adsorbed on clusters representing the (110) and (111) surfaces of Cu. Clusters were constructed to model different adsorption sites, and at least two different size clusters were used for each site. On the (111) surface, hydrogen prefers to adsorb in a hollow site, though with the hcp variant being favoured by the adsorption energy, and the fcc alternative by the vibrational frequencies. On the (110) surface, the "fcc" site on a (1 2 2) reconstructed surface is preferred.

Calculation of the Affinity of the λ Repressor-Operator Complex Based on Free Energy Component Analysis

Abstract: A calculation of the binding free energy of the u repressor-operator complex is described based on free energy component analysis. The calculations are based on a thermodynamic cycle of seven steps decomposed into a total of 24 individual components. The values of these terms are estimated using a combination of empirical potential functions from AMBER, generalized Born - solvent accessibility calculations, elementary statistical mechanics and semiempirical physicochemical properties. Two alternative approaches are compared, one based on the crystal structure of the complex and the other based on the molecular dynamics simulation of the u repressor-operator complex. The calculated affinity is m 19.7 kcal/mol from the crystal structure calculation and m 17.9 kcal/mol from the MD method. The corresponding experimental affinity of the complex is about m 12.6 kcal/mol, indicating reasonable agreement between theory and experiment, considering the approximations involved in the computational methodology. The r...