Louis A. Clark

Object-oriented Programming Paradigms for Molecular Modeling

This paper discusses the application of object-oriented programming (OOP) design concepts to the development of molecular simulation code. A number of new languages such as Fortran 90 (F90) have been developed over the last decade that support the OOP design philosophy. We briefly describe the salient features of F90 and some basic object-oriented design principles. As an illustration of the design concepts we implement a general interface in F90 for calculating pairwise interactions that can be extended easily to any number of different forcefield models. The ideas presented here are used in the development of a mu ltipurpose si mulation c ode, named Music. An example of the use of Music for grand canonical Monte Carlo (GCMC) simulations of flexible sorbate molecules in zeolites is given. The example illustrates how OOP allowed existing code for molecular dynamics and GCMC to be easily combined to perform hybrid GCMC simulations with minimal coding effort.

ADSORPTION ISOTHERM SENSITIVITY TO SMALL CHANGES IN ZEOLITE STRUCTURE

Abstract Grand canonical Monte Carlo (GCMC) simulations of benzene adsorption in different ortho silicalite structures are analyzed to determine the origin of a surprising factor of 3.1 difference in the Henrys law constants. Results indicate that changes of only tenths of angstrom in the lattice oxygen atom positions can reposition the sorbates enough to sizably affect the electrostatics. The small shifts are magnified by the partial cancellation of large electrostatics terms on the hydrogen and carbon atoms. These results underscore the need for potential models that include lattice flexibility and polarizability when the sorbates are tightly fitting, as well as accurate crystallographic structures.

Diffusion mechanisms of normal alkanes in faujasite zeolites

Molecular dynamics simulations of C1 through C14 n-alkanes in a siliceous faujasite zeolite are used to elucidate diffusion mechanisms. Additional simulations of the bulk liquids are conducted to compare the liquid and adsorbed phases. Heats of adsorption, diffusivities, and activation energies are compared with experimental values and agree well. Particularly good agreement is found between predicted self-diffusivities and those measured with pulsed field gradient nuclear magnetic resonance (NMR). Analysis of the chain conformations and motional frequencies indicates that the liquid and adsorbed phases are quite similar, most likely due to the open nature of the faujasite structure. Insights into the influence of local environment on molecular relaxation are also given. Siting results reveal an interesting progression of adsorption sites as the chain length is increased. Shifts of preferred adsorption sites are due to matching between the length scales of sorbate and adsorbent. Alkanes below C6 adsorb pr...

Two general methods for grand canonical ensemble simulation of molecules with internal flexibility

Two simulation methods are presented for generating a grand canonical ensemble of molecules with internal degrees of freedom. Molecular dynamics integration is used as a Monte Carlo perturbation move in these methods. The integration move helps to explore the intramolecular degrees of freedom with high acceptance ratios. The proofs of the acceptance criteria for both methods are presented. Tests are described to show that the simulation produces results matching an analytical solution for a simple test system. The method is further tested by predicting adsorption isotherms of n-butane in the zeolite silicalite. An example using these algorithms to generate adsorption isotherms of more complex chiral molecules in chiral zeolitelike materials is also presented.

A Fukui function overlap method for predicting reactivity in sterically complex systems

A formalism is given for predicting reactivity of complex systems by combining electronic structure calculations with forcefield calculations within a transition state theory framework. The theory is employed in combination with the Fukui function to produce a simulation method capable of the ensemble sampling needed to examine sterically complex systems. An important linkage between reactivity information and energetic quantities is provided by introduction of the Fukui overlap integral. This spatial overlap integral measures the coincidence of electron donating regions on a nucleophile with electron accepting regions on the corresponding electrophilic reactant. We show that configurations with high values of this overlap integral tend to have lower density-functional theory energies. Thus, Fukui functions calculated once on single isolated reactants can be used to quickly estimate the reactivity of configurations generated using conventional forcefield-based simulations. The correlation between energies and high overlap integrals can also be used to identify initial guess configurations for transition state searches. However, in the present implementation, real transition states are not accessible because intramolecular geometry relaxation is not allowed. The proposed method is tested on electrophilic aromatic alkylation reactions. Simulation results successfully reproduce experimental substituent effects in a series of variously substituted aromatics. Especially encouraging is the ability of the simulations to predict steric effects in the reaction of toluene with a series of electrophiles of varying bulkiness. Further applications, previously inaccessible to simulation, are expected in systems where steric effects play a dominant role in determining reaction selectivity.