Areas of Support

Consulting on all aspects of molecular modeling using computational chemistry methods for chemistry, biology, and materials science based applications including proteins, nucleic acids, zeolites, molecular clusters, etc. Calculating molecular properties such as molecular geometry, conformational analysis, chemical reaction profiles, vibrational and electronic spectra, electron density, electrostatic potential, molecular orbitals, etc. Methods employed include quantum mechanical based calculations (using Q-Chem, GAMESS, NWChem, etc), molecular dynamics simulations (using AMBER, CHARMM, etc), and hybrid quantum mechanical - molecular mechanical (QM/MM) calculations, which combine approaches of different levels of theory. Financial support provided by NIH grants.

Research Interests

I am interested in development of computational methods in theoretical chemistry and their applications for real molecular systems, using massive parallel computing. Although different topics in the field of quantum chemistry are the area under my research, aspects of combined quantum mechanical - molecular mechanical calculations (QM/MM) are the main subject of my current interest. The QM/MM method has been used in my research in study challenging and important biochemical systems such as cytochrome P450, myoglobin, soluable guanylate cylase, thrombin, antifolates, integrins, monophosphate decarboxylase, yellow proteins, vitamin B12, bacteriorhodopsin and DNA methylation. My work is carried out in collaboration with scientists from the Chemistry Department of the University at Buffalo, the Hauptman-Woodward Medical Research Institute, and from Q-Chem Inc.

Teaching

Graduate level : Computer Modeling of Biological Systems

Selected Presentations at International Conferences

• The 7th International Conference on Bioinformatics and Bioengineering, Harvard Medical School, Boston, MA, USA, 2007, lecturer.

• 1st Georgian Bay International Conference on Bioinorganic Chemistry, Ontario, Canada, 2007, lecturer.

• The 2006 International Accelrys Conference, Baltimore, MD, USA, 2006, invited lecturer.

• The 2006 International Conference on Bioinformatics and Computational Biology, Las Vegas, NV, USA, 2006, discussion presenter.

• 230th meeting of the American Chemical Society, Washington DC, USA, 2005, lecturer.

List of Selected Publications

• M. Freindorf, Y. Shao, J. Kong, T.R. Furlani, Combined QM/MM Calculations of Active-Site Vibrations in Binding Process of P450cam to Putidaredoxin.  J. Inorg. Biochem. 102, 427 (2008), PDF.

• M. Freindorf, M.D. Jones,  Y. Shao, J. Kong, T.R. Furlani, Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein, Toward Petascale Level of Protein Calculations. Proceedings of the 7th International Conference on Bioinformatics and Bioengineering, Harvard Medical School, Boston, MA, USA, 614 (2007), PDF.

• C.-T. Chiang, M. Freindorf, T.F. Furlani, R.L. DeLeon, J.P. Richard, J.F. Garvey, Enhancement of a Lewis Acid-Base Interaction via Solvation: Ammonia Molecules and the Benzene Radical Cation. J. Phys. Chem. A. 111, 6068 (2007), PDF.

• M. Freindorf, Y. Shao, J. Kong, T.R. Furlani, Combined QM/MM Studies of Binding Effect of Cytochrome p450cam to Putidaredoxin. Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology, Las Vegas, NV, USA, 391 (2006), PDF.

• M. Freindorf, Y. Shao, J. Kong, T.F. Furlani, A Combined Density Functional Theory and Molecular Mechanics (QM/MM) Study of FeCO Vibrations in Carbonmonoxy Myoglobin. Chem. Phys. Letters. 419, 563 (2006), PDF.

• D.N. Shin, M. Freindorf, T.R. Furlani, R.L. DeLeon, J.F. Garvey Nitrosamide, (H2NNO), Formation within [(NO)m(NH3)n]+ Clusters: Theory & Experiment. I. J. Mass Spectrom. 255-256, 28 (2006), PDF.

• M. Freindorf, Y. Shao, T.F. Furlani, J. Kong, Lennard-Jones parameters for combined QM/MM method using B3LYP/6-31+G*/AMBER potential J. Comput. Chem. 26, 1270 (2005), PDF.

• M. Freindorf, P.M. Kozlowski, A combined density functional theory and molecular mechcanics study of the relationship between the structure of coenzyme B12 and its binding to methylmalonyl-CoA mutase. J. Am. Chem. Soc. (communication), 126, 1928 (2004), PDF.

• M. Freindorf, P.M. Kozlowski, DFT study of the metal coordination center domain of Fe(II)-bleomycin. J. Phys. Chem. A, 105, 7267 (2001), PDF.