Ilya Yanov

Simple STM Tip Functionalization for Rapid DNA Sequencing : An Ab Initio Green's Function Study

An ab initio nonequilibrium Greens function study of the electron-transport properties of the adenine, thymine, cytosine, and guanine DNA bases located between gold electrodes has been performed. One-electron transmission spectra were calculated for both gold and sulfur-modified gold electrodes, which are model conditions of scanning tunneling microscopy (STM) experiments with the different tips. It is shown that the nature of chemical bonding between molecules and metal electrodes plays the most significant role in the overall conductance of the systems. The distance between electrodes and the size of molecules are less important, at least when both sides of the molecule form chemical contact with the electrodes. On the basis of the obtained results, a simple two-pass DNA sequencing scheme is suggested.

An active site model and the catalytic activity mechanism of the new fullerene-based catalyst : (η2-C60)Pd(PPh3)2

Abstract A theoretical description of the adsorption of acetylene molecules on palladium-phosphine fullerene complexes has been developed based on the results of ab initio quantum chemical calculations. This process can be considered as a model of the preliminary stage of C[dbnd]C triple bond scission in acetylene compounds. the HF, LSDA, BPW91, B3LYP, and MP2 levels of theory with different basis sets were employed in the theoretical predictions. the calculations were performed for the cluster model of the active site. Based on the performed calculations and experimental data one can conclude that the preliminary interactions of the catalyst with the substrate facilitates the interaction of the complex substrate-catalyst with H2 by decreasing the energy barrier. the theoretical results indicate that it is possible to explain this effect without including solvent interactions into the model system.

The molecular structure and electronic spectrum of the C@C60 endohedral complex: An ab initio study

We performed ab initio quantum-chemical studies at the HF and B3LYP levels of theory to determine the geometry and electronic spectra of the C@C60 complex. The STO-3G and 6-31G(d) basis sets were employed. Two different types of stable conformations for the endohedral atom related to the centers of five- and six-member rings were found. The estimated potential barrier between those conformations is small; under certain conditions, the endohedral atom can transfer from one location in the molecular cage to another. The influence of the location of endohedral carbon atom on the electronic spectrum of C60 is discussed.

Chapter 4 – Computer simulation of fullerenes and fullerites

This chapter is devoted to non-carbon and fullerene-like clusters. It describes the role of the fullerene molecule in cluster research. It addresses one of the most controversial questions concerning the mechanism of formation of the fullerene molecule and reveals the role of the defects of the fullerene molecule and their possible applications. The results of molecular dynamic simulations show the possibility for the production of selected types of defects in the process of atomic implantation. Solid state properties of the fullerene molecule are also discussed. Superconductivity in doped fullerites is one of their most intriguing properties from a theoretical point of view. Herein, lies the greatest prospects concerning the practical application of fullerene compounds. The history of this phenomenon and the ways of enhancing of the superconductive properties of fullerene molecules are discussed in the chapter. The chapter also describes the application of the non-equilibrium Greens function formalism to the investigation of the current-voltage dependence of the fullerene molecule. This method can be also applied to a wide range of nanomolecular devices.

High performance computing on the Cray T3E and IBM SP2 systems with the parallel version of GAUSSIAN 94

Abstract Benchmark tests were performed to study the efficiency of parallel computations on a Cray T3E 1200 and IBM SP2 systems with the parallel version of commercial quantum chemistry set of programs GAUSSIAN 94. Representative molecular systems (a complex between nitrobenzene and the hydrated surface of clay minerals, a complex of guanosine phosphate with a hydrated magnesium cation, and a fullerene molecule) have been investigated. These species represent the systems of current interest in the fields of environmental, biological, and material science as well as general chemistry. Our benchmark tests were designed to investigate a performance of a popular Hartree–Fock (HF) and DFT/B3LYP levels of theory with the STO-2G, STO-3G, 3-21G*, 4-31G, 6-31G, and 6-31G(d) basis sets. The wallclock time and efficiency of parallelization for links 502 and 703 were studied.

Network visualization system for computational chemistry

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built‐in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.