COMPUTATIONAL CHEMISTRY GROUP

Nowadays, one can hardly imagine the modern organic and organoelement chemistry and even biochemistry without studying the structure and electron density distribution in the synthesized chemical compounds, analysis of reaction pathways, intermediates and transition state structures in chemical reactions.

Since 2006, such studies in the Department of physico-chemical reasearches of the Institute of Organic Chemistry have been carrying out by Dr. Alexander B. Rozhenko. The main idea of the task formulation for theoretical investigation always was and remains to keep a close connection to the experimental projects developed by the colleagues in the Institute. The equipment for theoretical research laboratory has been recently purchased owing to the financial support of the Alexander von Humboldt foundation (Germany). These are two data stations and the 16-core 64-bit DELL server station that is usually used by students and PhD students for the most simple calculations. More heavy calculation jobs are usually distributed on the computer clusters at the V.M. Glushkov Institute of Cybernetics and other research centers in Ukraine and abroad. The group is the sole in Ukraine possessing the official licenses for using the commercial quantum chemistry program packets TURBOMOLE and CRYSTAL-09.

The TURBOMOLE can rightly be considered as one of the most efficient and powerful quantum chemistry program sets, first of all, owing to its suitability for the theoretical study of very large sized molecules (up to several hundreds atoms at the DFT level of approximation!). This makes it possible to carry out DFT or even MP2 geometry optimization for the structures identical to the experimental species and not only for the small model structures, which usually have little resemblance to their synthetic prototypes. The high performance of calculations is provided by using the modern linear-scaling algorithms, Resolution of the Identity (RI) and MARIJ, implemented into the TURBOMOLE. They are especially efficient by calculations of huge clusters, supramolecular or biochemical structures. The program set includes the HP-MPI platform providing a stable and effective parallel execution mode. Besides the traditional geometry optimization, the TURBOMOLE allows calculations of some spectral properties (for instance IR, Raman, UV/Vis and NMR spectra). The special program interface kindly provided by Prof. Ulf Ryde, Lund University, Lund , Sweden, makes it possible to combine easily quantum chemistry approaches with molecular mechanics and molecular dynamic methods. This approximation, also known as QM/MM, is first of all appropriated for the proper describing solute-solvent interactions and for modeling biochemical processes, such as for example protein-protein or protein-substrate interaction. In more detail, the only fragments participating in the interaction are treated using more sophisticated level of approximation (mostly DFT), whereas the rest of several thousand atoms are optimized using molecular mechanics. Currently this is the most superior approach to the quantitative evaluation of thermodynamic parameters of biochemical reactions and can be efficiently used for the study of mechanisms of existing medicaments and design of new drugs. Additionally, the TURBOMOLE program packets can be used for the large-scale modeling in material and nano-chemistry. A useful addition to the TURBOMOLE is the COSMO-therm.

As a rule, the quantum chemistry methods provide information about the structure in vacuum (the gas phase approximation) or used some empirical schemes for modeling solute-solvent interactions. However, these approaches are not suitable for quantum chemical studying periodic (band) structures in crystal phase. The CRYSTAL-09 program is one of the most popular developments for this purpose. This is especially efficient by using in combination with the X-ray investigations of monocrystals currently performed in the Joint Use Center of X-ray Diffractometry (Institute of Organic Chemistry of National Academy of Sciences of Ukraine) and the solid state (MAS) NMR spectroscopy (in cooperation with Prof. V.V. Trachevsky, Joint Use Center “NMR spectroscopy” at the G.V. Kurdyumov Institute of Methalphysics of NAS of Ukraine). It provides a unique information on the crystal effects and interionic and intermolecular interaction in solid phase.

The ORCA program is one of the most dynamically developed quantum chemistry program products with a conditionally free license. Currently it is a good program packet, allowing fast performing either very exact calculations for small structures, using multiconfigurational or multireference methods, or calculate large supramolecular species, owing to the implemented RI and RIJCOSX algorithms. Therefore, the ORCA program set is often used for performing complex and laborious quantum chemical calculations.

Dr. Rozhenko works in the tight cooperation with Department of chemistry at University of Bielefeld, Germany (Prof. W.W. Schoeller, Prof. U. Manthe, Prof. J. Mattay), with the University of Jackson, MS, USA (Prof. J. Leszczynski) and with Institute “Monocrystal”, NAS of Ukraine, Kharkiv, Ukraine (Prof. O.V. Shishkin). This allows using for a solution of the definite theoretical problems the GAUSSIAN-03, GAUSSIAN-09, MOLPRO, AMBER and other program packets.

The most important recent publications:

1. P. Jutzi, A. Mix, B. Neumann, B. Rummel, W. W. Schoeller, H.-G. Stammler, A.B. Rozhenko. Reversible Transformation of a Stable Monomeric Silicon(II) Compound into a Stable Disilene by Phase Transfer: Experimental and Theoretical Studies of the System {[(Me3Si)2N](Me5C5)Si}n with n = 1,2

2. T. Westermann, R. Brodbeck, A.B. Rozhenko, W.W. Schoeller, U. Manthe. Photodissociation of methyl iodide embedded in host-guest complex: a full dimensional (189D) quantum dynamics study of CH3I@resorc[4]arene. J. Chem. Phys. 2011, vol. 135, 184102.

3. A.B. Rozhenko, W.W. Schoeller, M.C. Letzel, B. Decker, J. Mattay. Anion-π Interactions in Adducts of Anionic Guests with Octahydroxy-pyridine[4]arene: Theoretical and Experimental Study. New J. Chem. 2013, 37, 356–365.

4. O.I. Guzyr, S.V. Zasukha, Yu.G. Vlasenko, A.N. Chernega, A.B. Rozhenko, Yu.G. Shermolovich, Simple Route to Adducts of (Amino)(aryl)carbene with Phosphorus Pentafluoride. Eur. J. Inorg. Chem. 2013, p. 4154–4158.

5. A.B. Rozhenko, S.S. Mykhaylychenko, N.V. Pikun, Yu.G. Shermolovich, J. Leszczynski, Intermediate Carbene Formation in the Reaction of Thioamides with Phosphorus (III) Derivatives: Quantum Chemical Investigation. Int. J. Quantum Chem., 2013, DOI: 10.1002/qua.24546.

6. A.B. Rozhenko. Density functional theory calculations of enzyme-inhibitor interactions in medicinal chemistry and drug design. In: Application of Computational Techniques in Pharmacy and Medicine #3. Springer, will be published soon.