Predicting the Properties of Materials and Biomolecules with Computer Modeling

Abstract: The advance of theoretical chemistry methods and the increase in computing power have resulted in the frequent use of computer in chemistry, material science, and biology. Zeolitic imidazole frameworks (ZIFs) are a subclass of MOFs which are materials that are made by coordinating transition metal ions to organic ligands to form porous network structures. We have performed Gibbs ensemble Monte Carlo simulations to study the equilibrium selectivity for an equimolar mixture of CO2 /CH4 in ZIF-93 at 298K and for pressures up to 80 bar. The results of the simulations revealed the role of pressure in the separation performance of ZIF-93 and the preferential adsorption sites of CO2 and CH4. We also present our initial work for Molecular Dynamics simulations of human Inosine Triphosphatase (ITPA) with a P32T mutation complexed with the ITP substrate in explicit aqueous solution. ITPA is an enzyme that is responsible for maintaining a proper level of nonstandard nucleotides in cells. These studies will improve our understanding of gas separation of porous materials and the mechanism of ITPA substrate Binding

Constant-temperature molecular-dynamics algorithms for mixed hard-core/continuous potentials

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/117/3/10.1063/1.1485072.We present a set of second-order, time-reversible algorithms for the isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed hard-core/continuous potentials. The methods are generated by combining real-time Nosé thermostats with our previously developed Collision Verlet algorithm [Mol. Phys. 98, 309 (1999)] for constant energy MD simulation. In all we present five methods, one based on the Nosé–Hoover [Phys. Rev. A 31, 1695 (1985)] equations of motion and four based on the Nosé–Poincaré [J. Comput. Phys. 151, 114 (1999)] real-time formulation of Nosé dynamics. The methods are tested using a system of hard spheres with attractive tails and all correctly reproduce a canonical distribution of instantaneous temperature. The Nosé–Hoover based method and two of the Nosé–Poincaré methods are shown to have good energy conservation in long simulations

A molecular-dynamics algorithm for mixed hard-core/continuous potentials

We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator splitting techniques similar to those that have been used successfully to generate a variety molecular-dynamics integrators. In numerical experiments, the Impulsive Verlet method is shown to be superior to previous methods with respect to stability and energy conservation in long simulations.Comment: 18 pages, 6 postscript figures, uses rotate.st

Constant-temperature molecular-dynamics algorithms for mixed hard-core/continuous potentials

We present a set of second-order, time-reversible algorithms for the isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed hard-core/continuous potentials. The methods are generated by combining real-time Nose' thermostats with our previously developed Collision Verlet algorithm [Mol. Phys. 98, 309 (1999)] for constant energy MD simulation of such systems. In all we present 5 methods, one based on the Nose'-Hoover [Phys. Rev. A 31, 1695 (1985)] equations of motion and four based on the Nose'-Poincare' [J.Comp.Phys., 151 114 (1999)] real-time formulation of Nose' dynamics. The methods are tested using a system of hard spheres with attractive tails and all correctly reproduce a canonical distribution of instantaneous temperature. The Nose'-Hoover based method and two of the Nose'-Poincare' methods are shown to have good energy conservation in long simulations.Comment: 9 pages, 5 figure

Transport properties of CO2-expanded acetonitrile from molecular dynamics simulations

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/126/7/10.1063/1.2434968.Carbon-dioxide-expanded liquids, which are mixtures of organic liquids and compressed CO2, are novel media used in chemical processing. The authors present a molecular simulation study of the transport properties of liquid mixtures formed by acetonitrile and carbon dioxide, in which the CO2 mole fraction is adjusted by changing the pressure, at a constant temperature of 298K. They report values of translational diffusion coefficients, rotational correlation times, and shear viscosities of the liquids as function of CO2 mole fraction. The simulation results are in good agreement with the available experimental data for the pure components and provide interesting insights into the largely unknown properties of the mixtures, which are being recognized as important novel materials in chemical operations. We find that the calculated quantities exhibit smooth variation with composition that may be represented by simple model equations. The translational and rotational diffusion rates increase with CO2 mole fraction for both the acetonitrile and carbon dioxide components. The shear viscosity decreases with increasing amount of CO2, varying smoothly between the values of pure acetonitrile and pure carbon dioxide. Our results show that adjusting the amount of CO2 in the mixture allows the variation of transport rates by a factor of 3–4 and liquidviscosity by a factor of 8. Thus, the physical properties of the mixture may be tailored to the desired range by changes in the operating conditions of temperature and pressure

Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations

The inosine triphosphate pyrophosphatase (ITPA) protein is responsible for removing noncanonical purine nucleoside triphosphates from intracellular nucleotide pools. Absence of ITPA results in genomic instability and increased levels of inosine in DNA and RNA. The proline to threonine substitution at position 32 (P32T) affects roughly 15% of the global population and can modulate treatment outcomes for cancer, lupus, and hepatitis C patients. The substitution of arginine with cysteine at position 178 (R178C) is extremely uncommon and has only been reported in a small cohort of early infantile encephalopathy patients suggesting that a functional ITPA protein is required for life in humans. Here we present molecular dynamic simulations that describe the structure and dynamics of the wild-type ITPA homodimer and two of its clinically relevant mutants, P32T and R178C. The simulation results indicate that both the P32T and R178C mutations alter the structure and dynamic properties of the protein and provide a possible explanation of the experimentally observed effect of the mutations on ITPA activity. Specifically, the mutations increased the overall flexibility of the protein and changed the dominant collective motions of the top lobe as well as the helix 2 of the lower lobe. Moreover, we have identified key active-site residues that are classified as essential or intermediate for inosine triphosphate (ITP) hydrolyzing activity based on their hydrogen bond occupancy. Here we also present biochemical data indicating that the R178C mutant has very low ITP hydrolyzing activity

Van Der Waals Density Functional Study Of Co2 Binding In Zeolitic Imidazolate Frameworks

The van der Waals density functional (vdW-DF) formalism is employed in a study of the binding energetics for CO2 in a set of five zeolitic imidazolate framework (ZIF) compounds. The ZIF structures investigated share the same RHO-type zeolite topology and metal atoms, but feature imidazolate linkers with different chemical functionalization. Three distinct binding sites are identified, for which the binding energies are found to show different dependencies on the functionalization of the linker molecules. The origin of the variations in the binding energies across the ZIF compounds is discussed through analyses of the binding geometries and charge-density distributions. A comparison of the vdW-DF results with those obtained by generalized-gradient-approximation calculations highlights the important contribution of the nonlocal correlation energy to the CO2 binding energies in these compounds

van der Waals density functional study of CO2 binding in zeolitic imidazolate frameworks

This is the publisher's version, also available electronically from http://journals.aps.org/prb/abstract/10.1103/PhysRevB.85.085410The van der Waals density functional (vdW-DF) formalism is employed in a study of the binding energetics for CO2 in a set of five zeolitic imidazolate framework (ZIF) compounds. The ZIF structures investigated share the same RHO-type zeolite topology and metal atoms, but feature imidazolate linkers with different chemical functionalization. Three distinct binding sites are identified, for which the binding energies are found to show different dependencies on the functionalization of the linker molecules. The origin of the variations in the binding energies across the ZIF compounds is discussed through analyses of the binding geometries and charge-density distributions. A comparison of the vdW-DF results with those obtained by generalized-gradient-approximation calculations highlights the important contribution of the nonlocal correlation energy to the CO2 binding energies in these compounds