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ABSTRACTS

INDEX

Plumbing the depths with ab initio thermodynamics

M. J. Gillan
Physics and Astronomy Department, University College London, Gower Street, London WC1E 6BT

Recently, it has become possible to make very precise calculations of the free energy and chemical potentials of liquid and solid mixtures using ab initio simulation methods based on density functional theory. I will outline how the new methods work, and I will describe how they are giving a completely new way of determining the temperature and chemical composition of the Earth's core [1 - 4] .

References

1
D. Alfe, M. J. Gillan and G. D. Price, 'Thermodynamics of hexagonal close-packed iron under Earth's core conditions', Phys. Rev. B 64 , 1-16 (2001).
2
D. Alfe, M. J. Gillan and G. D. Price, 'Temperature and composition of the Earth's core constrained by combining ab initio calculations and seismic data', Earth Planet. Sci. Lett. submitted.
3
D. Alfe, M. J. Gillan and G. D. Price, 'Constraints on the composition of the Earth's core from ab initio calculations', Nature 405 , 172 (2000).
4
D. Alfe, M. J. Gillan and G. D. Price, 'Melting curve of iron from ab initio calculations', Nature 401 , 462 (1999).
Index of talks

Biomolecules at Soft Interfaces

M. Klein
Laboratory for Research on the Structure of Matter, University of Pennsylvania, 3231 Walnut Street, Philadelphia, USA

This talk reviews recent work using classical simulation techniques to probe the behaviour of biomembranes and their interaction with small peptides and proteins.

Index of talks

Hard particles between hard walls

A. Chrzanowska 1, P. I. C. Teixeira 2, H. Ehrentraut 1 and D. J. Cleaver 3

  1. Institut fur Mechanik (AG3) Technische Universität Darmstadt Hochschulstraße 1, D-64289 Darmstadt, Germany
  2. Departamento de Engenharia de Materiais e ICEMS Instituto Superior Tecnico Avenida Rovisco Pais P-1049-001 Lisbon Portugal
  3. Materials Research Institute Sheffield Hallam University Pond Street Sheffield S1 1WB United Kingdom

The structure of a fluid of hard Gaussian overlap particles of elongation , κ=5, confined between two hard walls, has been calculated from density-functional theory and Monte Carlo simulations. By using the exact expression for the excluded volume kernel [1] and solving the appropriate Euler-Lagrange equation entirely numerically, we have been able to extend our theoretical predictions into the nematic phase, which had up till now remained relatively unexplored due to the high computational cost. Simulation reveals a rich adsorption behaviour with increasing bulk density, which is described semi-quantitatively by the theory without any adjustable parameters. Furthermore, we discuss the extension of this approach to model the recently-simulated hybrid films [2].

References

1
E. Velasco and L. Mederos, J. Chem. Phys. 109 2361 (1998)
2
D. J. Cleaver and P. I. C. Teixeira, Chem. Phys. Lett. 1 (2001)
Index of talks

Thermal diffusion in simple binary mixture in bulk fluid and in nanoporous medium, a NonEquilibrium Molecular dynamics approach.

G. Galliéro 1@, B. Duguay 2, J.-P. Caltagirone 1, and F. Montel 3

  1. Laboratoire MASTER-ENSCPB, Université de Bordeaux I, Avenue Pey Berland, F-33402 Talence CEDEX, France.
  2. Laboratoire LPCM (UMR-5803), Université de bordeaux I, 351, Cours de la Libération, F-33405 Talence CEDEX, France.
  3. Total-Fina-Elf EP, CSTJF, Avenue Larribau, F-64018 Pau, France.

@
To whom correspondence should be addressed:
galliero@lmaster.u-bordeaux.fr

It is now established that, at a microscopic scale, the diffusion coefficients are affected by the introduction of a porous medium [1] . The difference with the bulk fluid is strongly linked to the attractiveness of the studied surface. Therefore the thermal diffusion, that characterize a cross effect that coupled mass flux and thermal gradient, is likely to be affected too [2] .

To study this possible influence we have created a parallel program of molecular dynamics. With boundary driven NonEquilibrium Molecular Dynamics (NEMD) we can evaluate directly the Soret coefficient, transport coefficient associated to the thermal diffusion [3] . The fluids studied are binary mixtures of Lennard-Jones (LJ) particles in and near the supercritical region.

In a first step we have compared the different approaches that exist and drawn the more stable and the less dependent of the system size in order to compute as properly as possible the various transport coefficients [4] . Then, in bulk fluid, we have separately changed the ratio of one of the LJ parameters mass, atomic diameter and interaction strength [5] . We have obtained two linear relations for the last two parameters ratio and one more complex for the mass ratio. Additionally the superposition of the influence of the parameters ratio was investigated. The results shown that the different contributions are nearly additive for a majority of mixtures.

To describe the porous media, we have adopted models that rely on integrated potentials: the interaction between the fluid and the solid is treated as a Steele potential [6] . The geometry is based on two simple approaches, the slit pore (specular or diffusive) and the composite spheres. As we expected, the influence of the porous medium is not negligible. The size of the pore as well as the wall-fluid potential affect the Soret effect in such a way that for larger pores the influence of the porous medium become negligible and for the thinner pores the thermal diffusion can hardly occur. Another major point appeared: the imposed temperature gradient generates near the walls a microscopic convection phenomena known as thermal creep. These small currents appear, unlike theoretical prediction, even with specular condition of reflection. Moreover as the characteristic time of convection and diffusion are of the same order for the huge heat fluxes used, it seems that a coupling between these two phenomena occur.

References

1
L. Bocquet et J.-L Barrat, Hydrodynamic properties of confined fluids, J. Phys. Cond. Matter 8 , 9297, (1996).
2
I. Wold, Nonequilibrium Molecular Dynamics Simulations of Porous Media, Phd Thesis, University of science and Technology of Trondheim, 1997.
3
J.M. Kincaïd et B.Hafskjold, Thermal diffusion for the Lennard Jones/spline system, Mol. Phys. 82 , 1099, (1994).
4
G. Galliéro, B. Duguay, J.-P. Caltagirone, Modelling of thermal diffusion in multicomponent hydrocarbon mixtures by molecular dynamics, DSC mid-term report, ESA internal report, 2001.
5
D. Reith et F. Müller-Plathe, On the nature of thermal diffusion in binary Lennard-Jones liquids, J. Chem. Phys. 112 2436, (2000).
6
W.A. Steele, The interaction of gases with solid surfaces, Pergammon Press, Oxford, 1974.
Index of talks

Simulation and Theory of Liquid Crystal Interfaces

MP Allen
HH Wills Physics Laboratory, Royal Fort, Tyndall Avenue, Bristol BS8 1TL

Studies of the isotropic-nematic interface by Monte Carlo and molecular dynamics simulations have been carried out, and compared with the predictions of Onsager theory and capillary wave theory. The results give new insights into the structure of the interface, the dependence of surface tension on director orientation, and the nature of fluctuations in the interfacial region.

Index of talks

Searching for the nano-structures of thermotropic cubic liquid crystal

Makoto Yoneya 1 and Hiroshi Yokoyama 2

  1. ERATO Yokoyama Nano-structured Liquid Crystal Project, c/o Tsukuba Research Consortium, 5-9-9, Tokodai, Tsukuba, Ibaraki, 300-2635 JAPAN
  2. National Institute of Advanced Industrial Science and Technology (AIST), 1-1-4 Umezono, Tsukuba, 305-8568, JAPAN

Nano-structures of a thermotropic liquid crystal, 1,2-bis-[4-n-octyloxy-benzoyl]-hydrazine (BABH8) were investigated by molecular dynamics simulations. Spontaneous formation of layered domains and hydrogen bond networks were observed in the simulations. Based on the results, we propose the model nano-structures of the cubic liquid crystal phase of this BABH8 molecules.

Index of talks

Atomistic Simulations of Liquid Crystals at Interfaces

Mark Shield, Andrew McDonald, Duncan Binger and Simon Hanna
H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, U.K.

Results are presented from atomistic computer simulations of molecules of the liquid crystal 8CB in contact with corrugated substrates and free surfaces. The corrugated substrates are modelled using a modulated and integrated Lennard-Jones potential, which has been parameterised to represent the crystal faces of polyethylene. A united atom representation is used to eliminate the hydrogen atoms from the 8CB molecules. Electrostatic interactions have not been included. Simulations involving up to 768 8CB molecules in a 2-D periodic box have been performed over timescales of up to 10 ns. It is found that different types of ordering occur at the corrugated and free surfaces. At the corrugated surface, planar ordering is observed, which becomes less regular, as the distance from the substrate increases. At the free surface, the 8CB molecules are observed to form a homeotropic type of alignment, with the molecular long-axes perpendicular to the substrate. At lower temperatures 300 - 325 K), there is a sharp transition between the two ordered domains, with the free-surface alignment being somewhat irregular. At higher temperatures (375 - 400 K), the homeotropic alignment forms more readily, and a disordered, quasi-isotropic region is observed between the planar substrate molecules and the free-surface molecules. Additional simulations have been performed of free standing liquid crystal films, which display homeotropic alignment at both interfaces. The phase behaviour of these complex systems will be discussed, together with implications for furthering our understanding of the alignment mechanisms in liquid crystal displays.

Index of talks

Molecular simulation of a liquid crystal chevron

Doug Cleaver and Richard Webster
Materials Research Institute, Sheffield Hallam University

A chevron is a metastable structure formed by a confined smectic liquid crystal. The chevron 'tip' is an interface between two domains of smectic with different alignments, but it is argued that the smectic layers may maintain some level of integrity across this interface. In practice, chevrons have proved sufficiently stable to be the basis for a family of fast switching display devices.

Theoretical models indicate that positional surface anchoring is essential for chevron formation and that the transition to the (thermodynamically stable) tilted layer structure can involve either layer slip at the surfaces or layer hopping at the chevron tip.

Here we present molecular simulations, performed using parallel replicated-data molecular dynamics of the Gay-Berne liquid crystal model, showing the formation of a chevron and its relaxation into a tilted layer structure. We particularly investigate the effect of the surface boundary conditions on this relaxation: the role of surface slip is investigated by comparing the behaviour of cells with both smooth and structured surfaces. The simulations provide both a detailed picture of the structure of the chevron tip and unambiguous evidence of the mechanisms involved in the relaxation from a chevron to a tilted layer structure.

Index of talks

Resonance-Free Methods for Multiple Time Scale Dynamics

Ben Leimkuhler
Dept. of Maths. and Computer Science, University of Leicester, Leicester, LE17RH UK

Molecular models necessarily include dynamical contributions on several time-scales. Special methods (e.g multiple timestepping) have been proposed to exploit partial separation of the fast and slow forces or variables in a model, but these typically encounter instabilities due to resonances. In this talk, I will discuss some new types of methods which offer intriguing prospects for resonance-free integration with time-steps appropriate to the slower phenomena.

Index of talks

Grain boundary diffusion in ceramics: simulation by kinetic Monte Carlo

J. H. Harding 1, and D.J. Harris 2

  1. Dept. Physics & Astronomy, University College London, Gower St. LONDON WC1E 6BT
  2. Dept. Geological Sciences, University College London, Gower St. LONDON WC1E 6BT

It is well known that diffusion in polycrystalline ceramics is often dominated by diffusion along the grain boundaries at low and intermediate temperatures. Grain boundary diffusion therefore controls many solid-state processes such as sintering, creep and the growth of oxide films on metals. Although one can often find the low-temperature end of a diffusion experiment ascribed to `grain boundary diffusion', detailed, accurate measurements of grain boundary diffusion constants in ceramics are rare. We show how methods based on an encounter model for diffusion can be used to simulate the grain boundary diffusion coefficients in ceramics. Boundaries in oxides of the rock-salt and corundum structures are used as examples of the method. The anisotropy of diffusion in boundaries (expected from the picture of a grain boundary as a dislocation array and seen in experiment) is well reproduced. The calculated activation energies for grain boundary diffusion are in reasonable agreement with experiment. Problems in comparing the simulations with experiments on polycrystals are discussed.

Index of talks

Hard-spheres and the crystal-melt interfacial free energy of close-packed crystals

Brian B. Laird1 and Ruslan Davidchack2

  1. Department of Chemistry, University of Kansas, Lawrence, KS 66045 USA
  2. Department of Mathematics and Computer Science University of Leicester Leicester, UK LE1 7RH UK

We present a direct calculation by molecular-dynamics computer simulation of the crystal/melt interfacial free energy for a system of hard spheres. The calculation is performed by thermodynamic integration along a reversible path defined by cleaving, using specially constructed movable hard-sphere walls, separate bulk crystal and fluid systems, which are then merged to form an interface. We find the interfacial free energy to be slightly anisotropic with a value equal to 0.62, 0.64 and 0.58 kT/σ2 for the (100), (110) and (111) fcc crystal/fluid interfaces, respectively. These values are consistent with earlier density functional calculations and recent experiments measuring the crystal nucleation rates from colloidal fluids of silica spheres that have been interpreted to give an estimate of the crystal/melt interfacial free energy for the hard-sphere system of 0.55kT/σ2 , slightly lower than the directly determined value reported here. In addition, we show that the crystal-melt interfacial free energy for close-packed materials, such as metals, can be determined with quantitative accuracy using only a hard-sphere model.

Index of talks

Transport Coefficients and Dynamical Properties of Near-hard Sphere Fluids

David M. Heyes 1, Jack G. Powles and Gerald Rickayzen 2

  1. Department of Chemistry, School of Physics and Chemistry, University of Surrey, Guildford GU2 7XH, UK
  2. The Physics Laboratory, University of Kent, Canterbury, CT2 7NZ, UK

The hard-sphere system is widely used in statistical mechanics as a reference state in theories of liquids and solids. Its uses have traditionally been quite broad, extending from equations of state, the structure of molecular liquids and dynamical properties. It has also found a new lease of life as a model system for the ever increasing range of complex materials (e.g., colloids and powders). For these systems the hard-sphere can be an even more realistic representation of the effective pair potential, which can be steeply repulsive and have a negligible attractive component. It must be borne in mind, however, that the hard-sphere particle potential is fundamentally unrealistic in that the pair potential is discontinuous and non-differentiable unlike those for all real systems. Considerable care is required in extrapolating from the steeply repulsive potential to the hard-sphere potential as many quantities diverge either to zero or infinity and the order in which the limit is made, of n, N etc. see below), may be significant. Non-physical results such as purely exponential and delta function time correlation functions may be generated.

In a series of papers [1 - 4] we have explored, by statistical mechanics and molecular dynamics simulations, the dynamical properties of steeply repulsive 'near-hard-sphere' (SRP) fluids, mainly using the potential φ(r)=ε(σ/r)n where ε and σ set the interaction energy and lengthscales, respectively, and n is an adjustable exponent. We have been particularly interested in the behaviour of these systems as they become more like hard-spheres [1 - 2] . In addition to being of intrinsic interest, these fluids furnish new perspectives on the behaviour of the hard-sphere system itself. We show, for example, that at short times the time correlation functions (those relevant to the collective property transport coefficients) obey simple scaling behaviour in terms of a renormalised 'time' involving the parameter characterising the steepness of the potential (i.e. t replaced by nt). We also consider the factors in the pair potential that give rise to infinitely rapidly decaying short time relaxation in the hard-sphere limit.

Although the hard-sphere fluid has been very successful as a reference fluid for example, in developing analytical equations of state it has serious deficiencies in accounting for the dynamical relaxation processes in real systems and the hard-sphere fluid, in fact, is not a good reference fluid for the viscoelastic aspects of rheology [1 - 2] .

References

1
J.G. Powles and D.M. Heyes, Viscoelastic Behaviour of Fluids with Steeply Repulsive Potentials, Mol. Phys. , 98 917-927 (2000).
2
J.G. Powles, G. Rickayzen and D.M. Heyes, Purely Viscous Fluids, Proc. Roy. Soc.: Series A, 455 3725-3742 (1999).
3
D.M. Heyes and J.G. Powles, Thermodynamic, mechanical and transport properties of fluids with steeply repulsive potentials, Molec. Phys. , 95 259-267 (1998).
4
D.M. Heyes and J.G. Powles, Thermal Conductivity of Fluids with Steeply Repulsive Potentials, Molec. Phys. 99 1077-1089 (2001).
Index of talks

Phase diagrams of polydisperse van der Waals fluids and interfacial properties

L. Bellier-Castella 1, H. Xu 1, M. Baus 2

  1. Département de Physique des Matériaux (UMR 5586 du CNRS), Université Claude Bernard-Lyon1, 69622 Villeurbanne Cedex, France
  2. Physique des Polymères, Université Libre de Bruxelles, Campus Plaine, CP 223, B-1050 Brussels, Belgium

The phase behavior of a system composed of spherical particles with a monomodal size distribution is investigated theoretically within the context of the van der Waals approximation for polydisperse fluids [1] It is shown how the binodals, spinodals, cloud- and shadow- curves as well as all the (polydispersity induced) critical points can be obtained for a variety of interaction potentials. The polydispersity induced modifications of the phase diagram (even for a polydispersity index I as small as I ∼ 1.01) should be observable in some colloidal dispersions. The theory also predicts that for certain thermodynamic states (e.g. low temperatures and large polydispersities) the ordinary two-phase coexistences become metastable relative to a fractionation of the system into three phases [2] , reducing hereby the polydispersity of each of the coexisting phases. Finally, the same vdW description is also used to study the combined effect of both the polydispersity and the spatial non-uniformity induced by a planar interface between a low-density fluid phase (enriched in small particles) and a high-density fluid phase (enriched in large particles). We shall describe the adsorption properties and the surface tension as a function of the polydispersity and the temperature.

References

1
L. Bellier-Castella, H. Xu and M. Baus J. Chem. Phys. 113 , 8337(2000).
2
L. Bellier-Castella, H. Xu and M. Baus J. Chem. Phys. 115 , (2001).
Index of talks

Polarizability anisotropy relaxation in liquid ethanol

Marco Paolantoni 1 , 2, Branka M. Ladanyi 1, and Rosario Sergio Cataliotti 2

  1. Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 USA
  2. Dipartimento di Chimica, Universita' di Perugia, Via Elce di Sotto 8, 06100, Perugia, Italy

Despite the important role played by ethanol as hydrogen bonding solvent, only very recently computer simulation studies have been performed in the pure liquid in order to clarify the molecular basis of the structural and dynamical properties of this compound [1 - 6] . Some of these studies have been focused on the analysis of the dielectric relaxation spectrum as a function of the temperature [5] , or on the evaluation of the dynamic wave vector dependent dielectric properties at room temperature [6] . By contrast, our analysis is devoted to the study of the relaxation of the polarizability anisotropy directly involved in several spectroscopic techniques such as depolarized Rayleigh scattering and optical Kerr effect. In this case the interpretation of experimental data requires many assumptions mainly due to the strong influence of the interaction-induced polarizability that contributes to the overall relaxation on all time scales.

A molecular dynamics simulation study is performed for ethanol at two different temperatures using the optimized potentials for liquid simulations (OPLS) [7] and including one internal degree of freedom corresponding to the torsional motion about the C-O bond. The molecular contribution to the total polarizability is calculated using a four site version of the Thole model [8] . We include the interaction-induced contribution to the polarizability using both a center-center and a site-site dipole-induced-dipole (DID) interaction models. The relaxation of the sum of molecular polarizability anisotropies is due to orientational and torsional mechanisms that partially contribute also to the relaxation of the interaction-induced polarizability. So by projecting this component of the interaction-induced polarizability along the sum of molecular polarizability anisotropies we can separate a collision induced (CI) contribution, dependent mainly on the translational degrees of freedom [9] .

All the relevant time correlation functions are analyzed in terms of different contributions to the total relaxation and compared with previous simulations and with experimental data where possible.

References

1
Saiz L.; Padró J.A.; Guàrdia E. J.Phys. Chem. B 101 , 78-86, (1997).
2
Padró J.A.; Saiz L.; Guàrdia E. J. Mol. Struct. 416 , 243-248, (1997).
3
Saiz L.; Padró J.A.; Guàrdia E. Mol. Phys. 97 , 897-905, (1999).
4
González M.A.; Enciso E.;Bermejo F.J.; Bée M. Phys. Rew. B 61, 6654-6666, (2000).
5
González M.A.; Enciso E.;Bermejo F.J.; Jiménez-Ruiz M.; Bée M. Phys. Rew. E 61, 3884-3895, (2000).
6
Saiz L.; Guàrdia E.; Padró J.A. J.Chem. Phys. 113 , 2814-2822, (2000).
7
Jorgensen J. J. Phys. Chem. 90, 1276-1284 (1986).
8
van Duijnen P. Th.; Swart M. J.Phys. Chem. A 102, 2399-2407, (1998).
9
Ladanyi B. M.; Liang Y. Q. J. Chem. Phys. 103, 6325-6332, (1995).
Index of talks

Development of a new all-atom polarisable, flexible interaction potential for water:
Results for clusters, liquid water and various ice polymorphs

Christian J. Burnham and Sotiris S. Xantheas
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 906 Battelle Boulevard, PO Box 999, MS K8-91, Richland, WA 99352, USA

We present the development of a new flexible, all-atom polarizable interaction potential for water that is parametrized using high quality electronic structure calculations of water clusters. The new model is an extension of the previously developed [1] model and it is based on smeared Coulombic and dipole dipole interactions according to Thole [2]. Prominent features of the water dimer potential energy surface and their relevance in the accurate description of properties such as the second virial coefficient are outlined and used in the parameterization of the two-body interaction. Many-body effects are included via atomic-site dipoles and polarizabilities. The effect of intramolecular flexibility is described by an ab-initio derived monomer potential energy and dipole surface following a scheme that allows for intramolecular charge transfer that is necessary to reproduce the experimentally deduced features of the dipole moment surface. The model reproduces the total binding energies of the first few (n = 2-8 ) clusters to within < 0.5 kcal/mol (< 1%) when compared to the MP2 complete basis set limit results, and the temperature dependence of the second virial coefficient, the liquid radial distribution functions (RDFs) and diffusion coefficient quite accurately. It furthermore yields accurate lattice parameters and energetics for various ice polymorphs such as ice Ih, II and XI. In addition, it reproduces the increase in the H-O-H angle from the gas phase value of 104.52° to the experimentally observed tetrahedral value in ice Ih in contrast to existing flexible models, which show a decrease. We will further discuss the origin of this effect and its connection to the use of a "non-linear", with respect to the nuclear displacements, monomer dipole moment surface.

References

1
Burnham C.J., Li J.-C., Xantheas S.S., Leslie M. J Chem. Phys. 110 , 4566 (1999).
2
Thole B.T. Chem. Phys. 59 , 341 (1981).
Index of talks

A Collapsing Bubble in a Liquid - a Model for Sonoluminescence.

C. Xiao 1, D.M.Heyes 1 and J.G.Powles 2

  1. Department of Chemistry, School of Physics and Chemistry, University of Surrey, Guildford GU2 7XH, UK
  2. The Physics Laboratory, The University of Kent at Canterbury

We have carried out the first reported Molecular Dynamics simulation of a collapsing cavity in a liquid [1]. The simulation shows a series of distinct stages. At one stage copious very hot molecules evaporate into the cavity. This corresponds to what would be temperatures as high as 6,000K for water, sufficient to produce sonoluminescence. A statistical mechanical theory (in collaboration with G. Rickayzen) for the observed behaviour will be described if time permits.

References

1
Submitted to Phys. Rev. Letters.
Index of talks

Hydrolysis Reactions in Supercritical Water: A Computer Simulation Study.

Robin E. Westacott 1, 2, 3, Peter J. Rossky 1, and Keith P. Johnston 2

  1. Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
  2. Department of Chemical Engineering University of Texas at Austin, Austin, TX 78712
  3. Current Address: Department of Mechanical and Chemical Engineering, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS

Hydrolysis reactions are an important class of laboratory chemical reaction that are, at the same time, ubiquitous in such industrial processes as the production of alcohols and ethers, and the destruction of waste organic materials. In ambient water, the first stage of these SN1 reactions corresponds to the formation of ions from a covalent molecular reactant, followed by the subsequent reaction of the organic ion to form products. The ionic intermediates are stabilised under these conditions by the strong hydration afforded by the dense solvent water. At the other extreme, in the gas phase, no such solvent stabilisation is available, and radicals are the stable dissociated intermediates formed. In supercritical water, the solvent density, and the corresponding solvating capacity, can be tuned by changing the pressure at constant temperature above the critical temperature. In this paper, we will present the results of molecular dynamics simulations which explore how electrostriction, i.e. the effects of density augmentation around a solute, influence stabilisation of ionic products in the dissociation of t-butyl chloride in supercritical water at low solvent density. As the solvent density is decreased, the adiabatic reaction free energy surface approaches the shape observed for the gas phase. These results differ dramatically from those obtained using a simple Born model approach, which would predict covalent products at much higher solvent densities.

Index of talks

Solvation in room temperature ionic liquids

C. Hanke, N. Atamas and R. M. Lynden-Bell
Atomistic Simulation Group, School of Mathematics and Physics, The Queen's University, Belfast BT7 1NN, UK

Simulations have been performed on dilute solutions of water, methanol, dimethyl ether and propane in liquid dimethylimidizolium chloride. The solvation properties change as the solute properties vary from hydrogen bonding through polar to non-polar. The local structure around a non-polar solute is determined by the packing of the ions whcih try to maintain an optimum ion-ion interaction. At the other extreme, water and methanol form strongly hydgrogen-bonded complexes with the chloride ions. These properties are demonstrated by examining energetics, radial distribution functions including the the ranked neighbour distribution functions of Keyes [1] and the three dimensional local distributions of Svishchev and Kusalik [2] .

This work has now been extended to mixtures of water and dimethylimidizolium chloride of varying compositions.

References

1
Keyes T. J. Chem. Phys. 110 , 1097 (1999)
2
Svishchev I.M., Kusalik P.G. J. Chem. Phys. 99 , 3049 (1993)
Index of talks

Surface Tension of the Liquid-Vapour Interface of KI.

Andrés Aguado, Mark Wilson, and Paul A. Madden.
Physical and Theoretical Chemistry Laboratory, University of Oxford. South Parks Road, Oxford OX1 3QZ, UK.

Molecular dynamics simulations in the NVT ensemble are used to calculate the surface tension γ and study the structural properties of the liquid-vapour interface of a simple molten salt like KI. The focus of the present study is put in the effect that several terms in the interionic potential and simulation models have on the calculated surface tension. Specifically, we analyse the dependence of γ on: (a) boundary conditions employed in the Ewald summations of Coulomb interactions; (b) truncation of dispersion interactions; (c) inclusion of polarization effects; (d) lateral and perpendicular sizes of the slab employed in the simulations (finite size effects). Our results show unambiguously that (a) the employment of vacuum boundary conditions in the direction perpendicular to the interface helps to maintain the mechanical equilibrium of the interface; (b) an Ewald summation of dispersion interactions is necessary to avoid substantial truncation effects; (c) polarization tends to decrease γ by significant amounts, and improves the agreement with experiment; (d) Varying the width of the simulation slab in the interval [ 5/3L,3L], with L the lateral length of the simulation cell, has not any effect on the calculated surface tensions. On the contrary, sizeable finite size corrections emerge upon increasing the lateral dimensions, which is equivalent to explicitly include capillary waves of increasingly longer wave lengths. In all cases, a reduction of γ comes with a corresponding increase of the interfacial width. Several structural indicators like tangential pair distribution functions or structure factors at the interface are compared with those corresponding to the bulk liquid. The analysis of these indicators points to the presence of interesting clustering phenomena at the interface, which are the direct consequence of the existence of capillary waves.

Index of talks

Molecular dynamics studies of the self-assembly of lipids and surfactants

Siewert-Jan Marrink and A. Mark
Dept of Biophysical Chemistry, University of Groningen, Nijenborgh 4, Groningen, 9712 XJ The Netherlands

The self-assembly of surfactants and lipids into a variety of of possible aggregation states is a complex process of which the details are poorly understood. Here we report a series of molecular dynamics simulations in which we observe the spontaneous self-assembly of a variety of lipids and surfactants into simple micelles, mixed micelles, worm-like micelles or bilayers. The final aggregate type depends on the chemical structure of the aggregating molecules, which we model in atomic detail. Because we use detailed models we obtain realistic insights into the time scales of the aggregation processes, and of the intermediate structures involved.

Index of talks

The Effect of Corrosion Inhibitor Films on Deposition and Adhesion of Paraffin Wax to Metal Surfaces

M. San-Miguel and P.M. Rodger
Department of Chemistry, University of Warwick, Coventry CV4 7AL UK

Molecular dynamics simulations have been used to study the deposition of alkane waxes onto representative oil pipeline surfaces, and to determine how the deposition process is modified in the presence of a corrosion inhibitor coating. It is shown that the oxide films found on pipeline surfaces do not act as nucleation sites for wax growth. On the other hand, the additives often used to form a protective film against corrosion of the pipeline were shown to promote deposition of long-chain alkanes in a manner likely to seed wax formation. The use of molecular simulation has been shown to be a viable and powerful tool for gathering mechanistic information about the interplay between corrosion prevention and wax formation. Such mechanistic information is vital for developing multipurpose additive blends to control the plethora of undesirable deposition processes that can occur from oil.

Index of talks

Molecular dynamics study of bending processes on DNA-chain in water solution initiated by Pt-complexes.

Alexander Issanin and Walter Langel
Institut fuer Chemie und Biochemie, Universität Greifswald, Soldmannstrasse 23, 17489 Greifswald, Germany
langel@mail.uni-greifswald.de

CisPlatin (PtCl2(NH3)2) is a widely used anticancer drug. Its mechanism of interaction with cells has been studied on a molecular level and it is well established, that death of the cell is induced by complexes of the platinum compound to two adjacent guanine bases. These biadducts are bent and may react with some cell proteins, which are not affected by normal DNA. Structures of these bent biadducts have been studied by NMR in solution and by X-ray diffraction at crystals, both results are being significantly different.

We studied the bending mechanism of the DNA duplex during the formation of the biadduct in solution. The oligonucleotide with 10 basepairs in form of canonical B-DNA surrounded with ~3500 TIP3P water molecules and counterions was subjected to molecular dynamics simulation using the AMBER forcefield. During trajectories of up to 2000 ps a stable bent structure was attained, which resembles to experimental data from the solution rather than from the crystal.

The local deformation of the two basepairs occurs on a very short timescale, whereas the global bending of the DNA molecule is slowed down by the solution and takes several hundred ps. The rapid local deformation induces stress on the hydrogen bonds between the two DNA strands, and the force field used earlier for the bent structure only had to be adjusted to avoid breaking of these bonds during the bending process.

There are several classes of anticancer medicine which contain different Pt-core. CisPlatin is a prototype for complexes with one Pt atom bound covalently to two neighboring bases. Further work includes the study of complexes with two Pt atoms, connected to DNA in different ways and phenanthrolyne-Pt complexes working as intercalators without chemical binding to the DNA which also seem to show anticancer activity.

Index of talks

DNA Dynamics and Information Transfer

S.A. Harris
Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK.

The biological importance of DNA stems from the ability of this molecule to store information within its base sequence. This information is then expressed through interactions between the helix and the numerous DNA binding proteins which are able the read the DNA sequence by displaying a high affinity for certain sites but not for others. The question then arises as to how such proteins are able to recognise their binding sites with such high specificity. The DNA helix is almost uniform along its length, both in terms of shape and chemical composition. Any local sequence dependant structural variation in the DNA that may distinguish one site from another must therefore be small. Furthermore, the dynamic nature of the molecule at physiological temperatures ensures that the helix is continuously changing shape due to thermal agitation. If very small changes in shape are significant in the recognition process, then the dynamic behaviour of the molecule must also be considered.

Possibly the simplest example of DNA sequence selective recognition is provided by compounds which bind in the minor groove of AT rich DNA. The present study focuses on the complexation of the small drug molecule Hoechst 33258 with the DNA sequence d(CTTTTGCAAAAG)2. This sequence contains two identical binding sites separated by an intervening GC pair which isolates the two bound drugs. Remarkably, binding to the TTTT sites has been found to be highly co-operative, so that that the association of a single drug molecule at one site ensures that a second drug molecule is of order 2000 times more likely to be accommodated at the second site [1] . When bound, the two drugs are separated by around 15Å with the intervening cavity filled with water molecules. Therefore, a direct contact mechanism cannot explain the co-operative nature of the drug/DNA interaction, as there are no close molecular contacts between the two drugs. Consequently, co operative binding requires a mechanism by which information concerning the occupancy of this first site is transferred by the DNA helix to the second site.

We have undertaken a detailed structural and thermodynamic analysis of the free DNA, the 1:1 drug/DNA complex and the 2:1 drug/DNA complex using molecular dynamics (MD) simulation. Our results show that drug induced changes in DNA structure are small, indicating that co-operativity in this interaction cannot be explained in terms of long range conformational changes. Rather, information transfer between the two binding sites is the result of changes in the dynamic behaviour of the molecule. The change in configurational entropy of the DNA for successive binding events has been calculated from the three MD trajectories using a novel methodology based on the Schlitter algorithm [2] . The results show that the entropy cost involved in attaching the second drug molecule is much less than is incurred by the attachment of the first. Therefore, communication between distant sites is predominately an entropic effect in this system. The interaction is co-operative simply because most of the restriction in flexibility of the helix is caused by the binding of the first drug.

The molecular origins of co-operativity in the absence of conformational change clearly cannot be understood unless the dynamic properties of the system are taken into account. The results presented in this study serve to illustrate the importance of flexibility in determining the properties of biomolecules such as DNA in general.

References

1
Gavathiotis E., Sharman G. J. and Searle M. S. Nucleic Acids Res. 28(3) , 728-735 (2000).
2
Schlitter J. Chem. Phys. Letts. 215 , 617-621 (1993).
Index of talks

Simulation of Glass and Gel transitions in Colloidal Systems

A.M. Puertas 1,2, M. Fuchs 1 and M. Cates 1

  1. Department of Physics & Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ, UK
  2. Departament of Applied Physics, University of Almeria, 04120 Almeria, SPAIN

Colloidal systems with a short range attraction have been observed to undergo non-ergodicity transitions even at low packing fractions. This transition is usually called gel transition , and takes place at high interaction strength. The aim of this work is to reproduce by simulations such transitions, and to study them with the formalism of mode coupling theory (MCT). We have considered a system of particles with short range attraction, mimicking the depletion interaction in a colloid-polymer mixture. Two different non-ergodicity transitions have been observed, approached from the fluid phase. As the density is increased, the usual glass transition takes place, driven by excluded volume effects. In contrast, at moderate densities, another non-ergodicity transition is approached as the strength of the interaction increases. Both transitions can be rationalized within MCT formalism, which also predicts a glass-gel transition at high density and high interaction strength, ending in a singularity. Close to this singularity, a logarithmic decay in the correlation function is expected. This feature is also found in the simulations.

Index of talks

Simultaneous calculation of the helical pitch and the twist elastic constant in chiral liquid crystals by molecular simulation

Michael P. Allen 1 Guido Germano 2

  1. H. H. Wills Physics Laboratory, University of Bristol, Royal Fort, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
  2. Theoretische Physik, Universität Bielefeld, 33501 Bielefeld, Germany

We present a molecular simulation method that yields simultaneously the equilibrium pitch wavenumber and the twist elastic constant of a chiral nematic liquid crystal by sampling the torque density. A simulation of an untwisted system in periodic boundary conditions gives the product of these two quantities; a further simulation with a uniform twist applied provides enough information to separately determine them. We test our new method for a model potential, comparing the results with those obtained from a thermodynamic integration route, from an order fluctuation analysis, and from a thermodynamic perturbation theory analysis valid in the limit of weak chirality.

Index of talks

Calculating forces and torques in rigid-molecule liquid crystal simulations

Michael P. Allen 1 Guido Germano 2

  1. H. H. Wills Physics Laboratory, University of Bristol, Royal Fort, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
  2. Theoretische Physik, Universität Bielefeld, 33501 Bielefeld, Germany

We apply a direct method for deriving compact expressions for forces and torques to a family of rigid-molecule models which are extensions of the well-known Gay-Berne and Perram-Wertheim classes of pair potentials. We examine the use of these potentials to model biaxial molecules, and their possible extension to weakly chiral, banana-shaped, and pear-shaped, molecules.

Index of talks

Simulation of rod-sphere mixtures.

Dmytro Antypov and Doug Cleaver
MRI SHU, Howard Street, Sheffield S1 1WB

The behaviour of binary mixtures of prolate and spherical particles has been studied via molecular dynamics simulation. The use of soft interactions such as the Lennard-Jones and the Generalised Gay-Berne potentials brings a variety of new phenomena that cannot be observed in a "fully entropy driven" system of hard particles.

The subject of interest of this work is the internal structure of the mixture and its dependence on density, temperature and various parameters characterising the intermolecular interactions. Here we present results for four rod-sphere systems which differ from each other only in the interaction between unlike particles. Both the mixing-demixing behaviours and the transitions between the isotropic and any liquid crystalline phases have been studied for each system. A range of contrasting structures have been observed for the four mixtures, particularly at low temperatures.

Index of talks

Molecular Dynamics Simulations of Biomembranes and Small Molecule Permeation

D. Bemporad and J.W. Essex
Chemistry Department, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK

In order to reach their biological target, drugs have to cross cell membranes, and understanding passive membrane permeation is therefore crucial for rational drug design. Molecular dynamics simulations offer a powerful way of studying permeation at the single molecule level, yielding detailed dynamic and thermodynamic data. Biological membranes have a very inhomogeneous character and a highly anisotropic behaviour. A computer model of such a complex system is proposed. Static and dynamic properties have been calculated and compared with available experimental data, suggesting that the model is able to reproduce membrane physical properties. A method to study the permeation of small organic molecules across the above membrane model is also proposed. Free energy profiles and diffusion coefficients along the bilayer normal have been calculated for small organic molecules, and both properties are shown to depend strongly on the chemical nature of the permeant, the position in the membrane interior and the size, shape and conformational flexibility of the permeant. These data also allow for the calculation of permeability coefficients, the results for which are compared with the available experimental data.

Index of talks

Calculation of the rotational viscosity of a nematic liquid crystal

D. L. Cheung 1, S. J. Clark 2 and M. R. Wilson 1

  1. Department of Chemistry, University of Durham, South Road, Durham, DH1 3LE UK
  2. Department of Physics, University of Durham, South Road, Durham

Equilibrium molecular dynamics calculations have been performed for the liquid crystal molecule PCH5 using a fully atomistic model. Simulation data has been obtained for a series of temperatures in the nematic phase and has been used to calculate the rotational viscosity co-efficient through the angular velocity correlation function. We find good agreement between simulation and experimental results.

Index of talks

Modelling the effect of inhibitors on the growth of wax crystals

D. M. Duffy and P. M. Rodger
Department of Chemistry, University of Warwick, Coventry, UK, CV4 7AL
d.m.duffy@warwick.ac.uk, p.m.rodger@warwick.ac.uk

The precipitation of high molecular weight hydrocarbons from crude oil causes waxy deposits to build up on pipeline walls and leads to a reduction in flow of the oil. Certain chemicals are known to be beneficial in reducing the wax deposition rate but the inhibitor mechanism is poorly understood. Many of the effective inhibitors have a comb-shaped polymer structure and experiments have demonstrated that such polymers increase the meta-stable zone width (MSZW) of wax in a model oil [1] and decrease the size of wax crystals grown from solution [2].

In order to elucidate the inhibitor mechanism on a molecular scale we have used molecular dynamics (MD) to study the interaction of a typical inhibitor (poly(octadecyl acrylate)) with the surfaces of paraffin crystal surface. Small polymer units (dimers) were found to interact strongly with the crystal surfaces and introduce local distortion to the growing crystal [3]. Larger units (octamers) were found to stabilise a configuration in which the growing crystal was centred on the inhibitor and incommensurate with the underlying crystal [4]. The inhibitor disrupted the lamellar structure typical of paraffin crystals.

The incommensurate growth established by the MD calculations was strongly indicative of a model in which growth is blocked by immobile impurities. Such growth has been modelled, using a Monte Carlo (MC) procedure originally due to van Enckevort and van den Berg [5]. We have developed an extension to this model that introduces anisotropy into the defect and crystal structure. We used bond energy parameters obtained from the MD simulations in the MC model and demonstrated that the adsorbed inhibitor could block the crystal growth up to reasonable values of the supersaturation.

References

1
A.J. Hennessy, A. Neville and K.J. Roberts J. Cryst. Growth 198-199 , 830, (1999).
2
R. Kern and R. Dassonville J. Cryst. Growth 116 , 191 (1992).
3
D.M. Duffy and P.M. Rodger PCCP 2 , 4804 (2000).
4
D.M. Duffy and P.M. Rodger in preparation
5
W.J.P. van Enckevort and A.C.J.F. van den Berg J. Cryst. Growth 183 , 441 (1998).
Index of talks

Computer simulations of soft repulsive spherocylinders and the prediction of helical twisting powers for chiral dopants

David J. Earl and Mark R. Wilson
Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, U. K.

In the computer simulation of liquid crystal phases it is desirable to use a model molecule that emulates accurately the essential physics of real mesogenic molecules and in addition is efficient with respect to computational cost. The most commonly used and studied systems are the Gay-Berne mesogen and the hard spherocylinder model. In this study, the phase diagram for a ``hybrid'' system of soft repulsive spherocylinders (SRS) of aspect ratio (L/D) equal to 4 has been mapped out using the parallel molecular dynamics program GBMOLDD in the NVE and NpT ensembles. Our results show that soft repulsive spherocylinders can form stable nematic and smectic liquid crystalline phases. The relative cheapness of the computational model ( ∼ 3-4 times faster to simulate than a Gay-Berne potential) makes this an ideal reference system for future work.

We have used the spherocylinder model to calculate helical twisting powers, βM , for five chiral dopant molecules immersed in a liquid crystalline solvent. To do this we use free energy perturbation Monte Carlo simulations to grow an atomistic model of a chiral dopant into a twisted nematic phase represented by SRS molecules. βM can be calculated from the free energy difference for the growth of an enantiomer and its mirror image. rmail

Index of talks

Hydrostatic compression of carbon nanotube bundles modelled using constant stress molecular dynamics

J.A. Elliott, J. Sandler, M.S.P. Shaffer and A.H. Windle
Department of Materials Science and Metallurgy, University of Cambridge,UK.

We present evidence for a reversible collapse transition of hollow single-walled carbon nanotubes (SWNT) under hydrostatic pressure, based on constant stress (NST) molecular dynamics simulations carried out using DL_POLY [1]. A macromolecular force field for carbon nanotubes was parameterised by reproducing the experimental high pressure equation of state for graphite [2], and then applied to 2D hexagonal bundles of SWNTs under an isotropic stress field. The results indicate an abrupt change in cell volume for 10,10 tubes at around 2.5 GPa, which corresponds to the pressure at which Raman peak shifts in the E2g(2) in-plane vibrational modes of graphitic materials have been observed in a diamond anvil pressure cell. The NST simulations add weight to the hypothesis that these peaks shifts are due to collapse of the SWNTs to form flattened agglomerates of graphene sheets. We have studied the collapse point and compressibilities of the high pressure structures which are formed as a function of tube diameter, and compare the predictions with those of continuum theory for deformation of a uniform cylinder as a function of hydrostatic pressure.

References

1
T.R. Forrester and W. Smith, DL_POLY molecular dynamics code, CCP5 of the EPSRC.
2
M. Hanfland, H. Beister and K. Syassen Phys. Rev. B 39 , 12598 (1989).
Index of talks

Cluster free energies for cosmic dust nucleation

Jayesh Bhatt and Ian Ford
Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK.

Dust in the cosmos forms in the same way that clouds form in our atmosphere. When vapour is cooled below the dew point, the condensed phase becomes thermodynamically more stable. In the atmosphere, the condensing material is water, and the cooling takes place through the adiabatic expansion of rising plumes of air, for example. In the cosmos, the materials are more varied, including metals and oxide minerals, and are ejected in cooling flows from particular stars. There is much uncertainty as to the identity of the primary nucleating material in these flows. This would not necessarily be the material with the highest dew point, since vapours can often be supercooled below this temperature through the existence of a nucleation barrier. We are attempting to calculate this barrier, and the critical supercooling, for a number of possible condensing materials, including MgO and TiO2. The clusters are likely to be solid, but liquids are not entirely ruled out. We use Monte Carlo simulation of clusters, incorporating some novel methods to calculate the free energy of the critical cluster, and hence the nucleation barrier.

Index of talks

Brownian translational motion on mainfolds with application to cubic phase model surfaces and NMR.

P. Håkansson, L. Persson and P.-O Westlund

In this work a general method to simulate Brownian translational diffusion on manifolds is presented. This method can take any implicit defined surface into the diffusion equation. We calculate the time correlation functions that determine contribution from surface diffusion to the observable spin relaxation rates. We apply this to bicontinuous Cubic liquid crystals that can be described by triply periodic minimal surfaces. We present the curvature dependence of relaxation on Schwarz-P minimal surface and compare it to different offsets. These are introduced by First breaking the symmetric periodicity and secondly on a parallel displacement of the surface as compared to the minimal surface. These relaxation effects are presented as spectral densities, directly related to relaxation rates detected by NMR measurement.

Index of talks

Simulation of mixtures of water and room-temperature ionic liquids

C.G.Hanke and R.M.Lynden-Bell
Atomistic Simulation Group, Dept. of Physics, Queen's University Belfast, Belfast, UK

The molecular dynamics program DL_POLY was used to simulate mixtures of the room temperature ionic liquids mmim/Cl and mmim/Pf6 with water in different ratios have been investigated. For all this systems, the local structure, the interaction energies and dynamical properties were evaluated.

Index of talks

Estimates of the Thermodynamics Properties of Liquid-Like Clusters

S.A. Harris and I. J. Ford
Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK.

The theory of aerosol nucleation requires detailed information about the properties of small molecular clusters. This is because the formation of a macroscopic particle can be viewed as the consequence of the formation of a critical cluster, which often contains only a few tens of molecules. Clusters smaller than the critical size tend to evaporate while the critical cluster has equal probabilities for subsequent growth or decay; once a critical cluster is formed, therefore, growth to macroscopic sizes is very likely.

It is the uncertainty in our knowledge of the thermodynamic properties of small clusters that leads to the great disparity between experimental and theoretical nucleation rates. In particular, for the formations of liquid droplets, it is necessary to know the free energy of formation of liquid-like clusters of just a few molecules. In order to calculate both the internal energy and entropy of such systems, we have performed molecular dynamics (MD) simulations of individual clusters of various sizes. Calculating the mean energy is relatively easy and probably accurate, however we have estimated the cluster entropy using an approximate relationship between the configurational entropy of the system and the range of cluster shapes sampled in the MD trajectory as suggested by Schlitter [1] . Schäfer et al [2] have studied trajectories of ideal gas and bulk Lennard-Jones fluids, and using the Schlitter algorithm, have shown that the entropies of these fluids are predicted correctly within 20% for the ideal gas and within about 5% for the Lennard Jones case. However, since the entropy depends upon the range of molecular shapes observed in the MD trajectory, the results may be sensitive to the precise way in which such clusters are defined. Therefore, we are also investigating the role of the cluster definition in determining the thermodynamics properties of such systems.

References

1
J. Schlitter Chem. Phys. Letts. 215 , 617-621 (1993)
2
H. Schäfer, A. E. Mark and W. F. van Gunsteren J. Chem. Phys. 113 , 7809 (2000)
Index of talks

The simulation of biomembranes using a Gay-Berne model

David Haubertin, J.W. Essex, T. Howes
Chemistry Department, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK

In recent years the number of simulations of hydrated, fluid phase, lipid bilayers has grown rapidly. All the simulations generally employ molecular dynamics and/or Monte Carlo methods to study a system usually consisting of ∼100 lipids and a few thousand water molecules. The study of biological membranes has also been extended to include small molecule diffusion within the membrane.

However, the simulations are time-consuming and require powerful computational resources due to the size of the system. The development of membrane models that are less computationally demanding and still allow to access membrane behaviour, therefore appear highly desirable.

With this in mind, we are applying the concepts used to model liquid crystalline mesophases to the modelling of a lipid membrane. The most popular model for the simulation of the liquid crystals is that developed by Gay and Berne [1] , in which molecules are modelled by ellipsoids of various length and breath ratios. In this model the individual atoms of the molecule are subsumed into a single ellipsoid that interacts with its neighbours through an anisotropic intermolecular potential.

This model has already been applied to model the hydrocarbon region of a lipid bilayer [2] and has proved to give A good fit with experiments. We are extending this model to reproduce an entire phospholipid membrane (tail, glycerol and head-group) including the presence of solvent. Our final goal is the study of small drugs diffusion within this environment in order to establish a predictive model for drug bioavailability.

This poster will present the current state of this model.

References

1
J.G. Gay, B.J. Berne J. Chem. Phys. 74 , 3316-3319 (1981)
2
L.Whitehead, C.M. Edge, J.W. Essex J. Comp. Chem. Submitted for publishing.
Index of talks

Simulation of the Interface between Titanium and Biomolecules in Solution by First Principles MD

Walter Langel and Lars Menken,
Institut für Chemie und Biochemie der Universität Greifswald, Soldmannstrasse 23, 17489 Greifswald, Germany,
langel@mail.uni-greifswald.de, www.chemie.uni-greifswald.de/~plasma

Favourable mechanic properties make titanium a widely used material for medical implants. It is one of the least toxic metals, but cell growth on its surfaces suffers from their inertness. Outside a vacuum chamber titanium is passivated by a thin oxide layer, whose structure depends on the oxidization process. Most often rutile is formed, which typically has (110) and (100) surfaces. They are hydroxylated by exposition to water vapour in air or to solutions. Biological cells are immobilised on by attaching to peptides such as the sequence RGDS, which are chemically bound to the oxide. In practice connecting peptides to the hydroxylated surface is not straightforward, and an intermediate SiO2 layer may be provided, to which siloxanes are linked.

This study aims at modelling the reactions of amino acids with hydroxylated rutile and to find more direct pathways for binding peptides to practical implants. We use the Car-Parrinello method with Trouillier-Martins pseudopotentials for cells with up to 110 atoms and present the following results of our simulations:

Relaxation of the clean surface is in agreement with similar calculations, and it is shown that apparent differences with experimental results are due to different data treatment. For the physisorption of water on perfect rutile (110) and (100) hydrogen bonded configurations were found, which agree with experimental findings. A typical reactive surface defect is generated by omitting a single bridging atom, and dissociation of a water molecule in such a vacancy is found. Eventually configurations with an OH-density corresponding to room temperature TiO2 were stable.

Detailed experimental studies on the adsorption of larger molecules on rutile in general carried out in the ultra high vacuum chamber on dehydrated surfaces. Organic acids such as formic acid form two chemical bonds between the two carboxyl oxygens and two adjacent Ti atoms in the surface, since the acid proton can dissociate off and bind to a bridging O of the rutile. This very stable configuration was reproduced in a simulation of methionin on (110).

Dehydrated surfaces are irrelevant for applications, and we mimic more realistic systems by placing one amino acid on top of three layers of TiO2 in a 10 Å vacuum which is filled by water molecules up to the standard density. The water configuration is first optimized by forcefield molecular mechanics. During the first principles molecular dynamics runs the system is slowly heated up from 40 to 310 K, where the molecules have a significant mobility.

According to earlier experiments hydroxyl groups on the surface play a major role in the adsorption process of amino acids on TiO2. In our calculation a configuration with the two carboxyl O hydrogen bonded to surface hydroxyls is stable in vacuum. In solution the doubly bonded O only formed a hydrogen bond to one surface hydroxyl group. It was further reported that esther condensation of the amino acid and a surface hydroxyl group leads to a stable chemically bound configuration. Indeed the energy of such a configuration is lower by about 100 kJ/mol in vacuum than of the only hydrogen bonded one. The esther condensation would, however, imply the insertion of the carboxyl group into an oxygen vacancy in the surface, but this group does not appear to be very reactive in our calculations. We, therefore, look for reactions of other parts of the amino acids with the titanium dioxide surface. First results seem to suggest that the -S-H group of cystein is reactive, and that the substitution of its H by a surface Ti is a straightforward process in solution.

Index of talks

Chiral Recognition in Complex Systems

R. Lukac, A.J. Clark, M.A. san Miguel, A. Rodger, P.M. Rodger
Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK

Computer Simulations are of great importance for prediction of the results for the chiral high performance liquid chromatography (HPLC). On the hand of the results of simulations it is possible to drop expenses and improve efficiency in production of drugs.

A large set of molecular dynamics simulations has been done on a linked dimeric carbohydrate (LDC) / benzoin dimers, solvated in THF. Selectivities have been calculated from free energies for the left and for the right handed benzoin with many dockings for various LDC conformations in order to cover the phase space as much as possible and to take into account the dominant contributions to free energy. The explanations are supported by pair-correlation functions.

Index of talks

Atomistic Simulations of 8CB

Andrew McDonald and Simon Hanna
H H Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK

The molecular fluid 4-n-octyl-4'-cyanobiphenyl (8CB) is observed experimentally to exhibit liquid crystalline ordering. We have performed molecular dynamics simulations of 8CB in the bulk using an atomically detailed united-atom force field. The model does not explicitly include hydrogen atoms, instead 'uniting' them into the adjacent carbon atoms. This permits detailed analysis of intramolecular degrees of freedom in the fluid while remaining computationally tractable. We also neglect electrostatics, choosing to focus on the effects of short range forces in the system. Such a model is not intended, therefore, to reproduce experimental results exactly.

For our largest system of 595 molecules we observe a thermotropically driven isotropic - smecticA transition at around 400K. Characteristic changes in molecular shape and intra-molecular conformation with temperature are analysed. As the liquid is cooled through the transition the molecular cores are found both to elongate and to become less uniaxial. In addition, the distribution of angles between the molecular core and the flexible tails becomes more sharply peaked as the temperature decreases.

We also investigate the effects of system size on the bulk properties of the system observing significant effects up to the largest system size used. Simulations of the related molecule 4-n-hexyl-4'-cyanobiphenyl (6CB) show a decrease in the transition temperature with tail length, as expected from experiment.

Finally, we compare the bulk behaviour of 8CB with that of an isolated droplet of 8CB molecules for a number of key state points.

Index of talks

The LDA structure simulation and thermodynamic discontinuity between LDA and Supercooled water

V.P.Shpakov 1,2,3, P.M.Rodger 1, J.S.Tse 2, D.D.Klug 2, V.R.Belosludov 3

  1. Warwick University, Coventry CV4 7AL, UK
  2. Steacie Institute for Molecular Sciences, NRC, Ottawa, Ontario, Canada K1A OR6
  3. Institute of Inorganic Chemistry, SB of RAS, Novosibirsk 630090, Russia

The relationship between the structure of amorphous ices with the different forms of liquid water is of current interest since it has been postulated that below the second critical point (∼ T=220K, P=1 kbar) the liquid phase separates into two distinct liquid phases: a low-density liquid (LDL) a high-density liquid (HDL) [1] . The pressure amorphized amorphous phase of ice (HDA) and the phase prepared by annealing HDA at 120 K are considered in this hypothesis as the corresponding glassy states of LDL and HDL. However, there are significant differences between LDA and hyperquenched glassy water(HGW) in their kinetic and thermodynamic behaviour [2] . Recent Raman spectroscopic studies and an incoherent inelastic neutron scattering study [3] call into question the validity of a thermodynamic connection between amorphous ices and liquid phases of water. The present investigation serves to clarify this issue via simulations. First, the experimental LDA-RMC structure [4] with 1536 water molecules in the cell , has been optimized by the conjugate-gradient method using a slightly modified TIP4P potential for water. The final structure (Structure I) has a calculated potential energy of -51.3 kJ/mol which differs by 4 kJ/mol from the potential energy of Ic ice structure (-55.3 kJ/mol). Significantly, the obtained structure is in reasonable agreement with available structural data for LDA at 77K. The calculated energy difference between supercooled water and Ic ice at 150 K of 4 kJ/mol is too large in comparison with the experimental enthalpy difference of 1.3-1.4 kJ/mol. This discrepancy may be connected with the structural differences between LDA and supercooled water. It is significant to emphasize that the water-water potential used here successfully reproduced the experimental enthalpy difference between Ic ice and ices II and IX at 150 K. Structure I was then used as the starting structure for long NPT MD simulations at zero pressure and a number of temperatures (77,95,110,130,150 K). At T=77 K, the optimized structure has an energy of -52.6 kJ/mol (Structure II). However at T=110 K and higher, a further drift of energy was calculated which gave an energy of ∼ -53.4 kJ/mol for a quenched structure at T=150 K (Structure III). The analysis of structure III shows that it is similar to that of supercooled liquid at ambient pressure and T=193 K as calculated by Tanaka [5] . In contrast, the structure II has a lower (∼90 %) percent of four coordinated water molecules in comparison with structure III (∼97%) and the density agreed with experimental density of LDA at ambient pressure. The calculations of correlation functions for structure II and structure III (recovered to T=77 K) are in good agreement with experimental data for both structures. The difference is similar to the observed experimental difference between the HQW and LDA. In conclusion, we suggest: 1) structure II can be a model LDA structure; 2) structure III as the supercooled water structure at T=150 K; 3) the observed drift is the fast part of LDA melting. The results suggest a lack of thermodynamic continuity between LDA and supercooled water.

References

1
O. Mishima, H. E. Stanley Nature 396 , 329 (1998)
2
G. P. Johari J. Chem. Phys. 112 , 8573 (2000)
3
J. S. Tse, D. D. Klug, C. A. Tulk, I. Swainson, E. C. Svensson, C. -K. Loong, V. Shpakov, V. R. Belosludov, R. V. Belosludov and Y. Kawazoe Nature 400 , 647 (1999)
4
D. D. Klug, J. S. Tse, C. A. Tulk, E. C. Svensson, I. Swainson, V. P. Shpakov, V. R. Belosludov Phys. Rev. Lett. 85 , 3185 (2000)
5
H. Tanaka Phys. Rev. Lett. 80 , 113 (1998)
Index of talks

Aqueous solvation, an ab initio / classical free energy perturbation

Stuart Murdock and Prof. Ruth Lynden-Bell 1, Dr. Graham Sexton 2

  1. Atomistic Simulation Group, Physics Department, Queen's University Belfast, Belfast, Northern Ireland, BT7 1NN United Kingdom
  2. Syngenta Jealot's Hill Research Center Bracknell Berkshire U.K.

Solvation studies of three relatively interesting conformations of N-methyl-4-piperidinol show differences which relate to the conformational geometry. Calculations were initially performed classically using the spc/e water model and empirical parameters for the solute. These classical simulations were then 'corrected' to simulations where the solute is represented by Density Functional Theory. It is important to note that the solute polarisation and solute - solvent interaction is perturbed whenever statistics are accumulated, but phase space is sampled using completely empirical potentials. This gives an interesting comparison between a fixed point charge description of the solute and a continuous electronic distribution which changes with respect to solvent configuration.

Index of talks

Minimum perimeter partitions of the plane into equal numbers of regions of two different areas

M. A. Fortes and P. I. C. Teixeira
Departamento de Engenharia de Materiais e ICEMS, Instituto Superior Tecnico, Avenida Rovisco Pais, P-1049-001 Lisbon, Portugal

We identify the minimum-perimeter periodic tilings of the plane into regions of areas 1 and λ in a one-to-one proportion (minimal tilings). For λ close to 1, the minimal tiling is hexagonal. For smaller values of λ the minimal tilings contain pairs of regions with 5 and 7, 4 and 8, and 3 and 9 sides, the regions with fewer sides having smaller area. The correlation between area fraction and number of sides in the minimal tilings is approximately linear and consistent with Lewis' law.

Index of talks

Chirality induction from chiral mesogens to adsorbed monolayers

Makoto Yoneya and Hiroshi Yokoyama
ERATO Yokoyama Nano-structured Liquid Crystal Project, c/o Tsukuba Research Consortium, 5-9-9, Tokodai, Tsukuba, Ibaraki, 300-2635 JAPAN

Monolayer structures of a chiral mesogen, (R)- or (S)-[4'-(1-methylheptyloxy) -3'-nitrobiphenyl-4yl] 4-(trans-5-decenyloxy) benzoate, adsorbed on graphite were investigated by molecular dynamics simulations to clarify the mechanism of chirality inductions from chiral mesogens to chiral monolayers. We propose a molecular model that is based on coupling between the up-down symmetry breaking and the molecular tilt direction symmetry breaking of the monolayer. From the proposed model, we further predict alternative reversal of the 2-D chirality of the monolayer when the chiral carbon is shifted along alkyl chain. This is a two-dimensional analogue of the "odd-even" effect on twist sense reversal in bulk chiral nematic systems.

Index of talks

Thermodynamical properties of sodium microclusters

Feng-Shou Zhang
Atomistic Simulation Group, School of Mathematics and Physics, The Queen's University, Belfast BT7 1NN, United Kingdom
and
Institute of Modern Physics, The Chinese Academy of Sciences, P.O. Box 31, Lanzhou 730000, China

Structural properties of clusters at finite temperatures are not only of scientific interest, but also have some technological implications. There have been several theoretical and experimental studies during last decade. In the present work, we will discuss a novel theoretical approach which provides not only isomerisation and solid-to-liquid phase transition, but also pseudorotation.

Index of talks

Last modified 28 October 2002 		 
 
   
 
 
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