Publications:

1. M.Freindorf, D.Cremer, E.Kraka, Gold(I) Assisted Catalysis - A Comprehensive View on the [3,3]-Sigmatropic Rearrangement of Allyl Acetate, Mol. Phys., 116, 611 (2018)

2. T.Sexton, M.Freindorf, E.Kraka, D.Cremer, A Reaction Valley Investigation of the Cycloaddition of 1,3-Dipoles with the Dipolarophiles Ethene and Acetylene: Solution of a Mechanistic Puzzle, J. Phys. Chem. A., 120, 8400 (2016)

3. C.S.Lopez, O.N.Faza, M.Freindorf, E.Kraka, D.Cremer, Solving the pericyclic - pseudopericyclic puzzle in the ringclosure reactions of 1,2,4,6-heptatetraene derivatives, J. Org. Chem. 81, 404, (2016)

4. W. Zou, T.Sexton, E.Kraka, M.Freindorf, D.Cremer, A New Method for Describing the Mechanism of a Chemical Reaction Based on the Unified Reaction Valley Approach, J. Chem. Theory Comput. 12, 650, (2016)

5. M.Freindorf, T.Sexton, E.Kraka, D.Cremer, The Mechanism of the Cycloaddition Reaction of 1,3-Dipole Molecules with Acetylene - An Investigation with the Unified Reaction Valley Approach, Theor. Chem. Acc. 133, 1423, (2014)

6. E.Kraka, M.Freindorf, and D.Cremer, Chiral Discrimination by Vibrational Spectroscopy utilizing Local Modes, Chirality, 25, 185 (2013)

7. E.Kraka, W.Zou, M.Freindorf, D.Cremer, Energetics and Mechanism of the Hydrogenation of XHn for Group IV to Group VII Elements X, J. Chem. Theory and Comput. 8, 4931 (2012)

8. M.Freindorf, E.Kraka, D.Cremer, A Comprehensive Analysis of Hydrogen Bond Interactions Based on Local Vibrational Modes, Int. J. Quantum Chem., 112, 3174 (2012)

9. M.Freindorf, T.R.Furlani, J.Kong, V.Cody, F.B.Davis, P.Davis, Combined QM/MM Study of Thyroid and Steroid Hormone Analogue Interactions with Alphavbeta3 Integrin, J. Biomed. Biotech., 2012, 959057, (2012)

10. C.-T.Chiang, M.Freindorf, T.R.Furlani, R.L.DeLeon, J.F. Garvey, Structure, bonding and reactions within protonated acetone - methanol cluster ions, Chem. Phys. Letters, 509, 102 (2011)

11. L.Muley, B. Baum, M. Smolinski, M. Freindorf, A. Heine, G. Klebe, D.G. Hangauer, Enhancement of Hydrophobic Interactions and Hydrogen Bond Strength by Cooperativity: Synthesis, Modeling, and Molecular Dynamics Simulations of a Congeneric Series of Thrombin Inhibitors, J. Med. Chem., 53, 2126 (2010)

12. J.Kong, Z.Gan, E.Proynov, M.Freindorf, T.R.Furlani, Efficient computation of the dispersion interaction with density functional theory, Phys. Rev. A, 79, 042510 (2009)

13. K.S. Shores, J.P. Charlebois, C.-T. Chiang, R.L. DeLeon, M. Freindorf, T.R. Furlani, J.F. Garvey, Reactions within p-Difluorobenzene/Methanol Heterocluster Ions: A Detailed Experimental and Theoretical Investigation. J. Phys. Chem. A, 113, 2268 (2009)

14. C.-T.Chiang, K.S.Shores, M.Freindorf, T.Furlani, R.L.DeLeon, J.F.Garvey Size-Restricted Proton Transfer within Toluene-Methanol Cluster Ions, J. Phys. Chem. A, 112, 11559 (2008)

15. 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)

16. M.Freindorf, 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)

17. 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)

18. 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)

19. 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)

20. 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, Int. J. Mass Spectrom., 255-256, 28 (2006)

21. 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)

22. 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)

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

24. J.Gao, M.Freindorf, Hybryd ab Initio QM/MM simulation of the N-methylacetamide in aqueous solution, J. Phys. Chem. A, 101, 3182 (1997)

25. J.Gao, N.Li, M.Freindorf, Hybrid QM/MM simulations yield the ground and excited state pKa difference: phenol in aqueous solution, J. Am. Chem. Soc., (communication), 118, 4912 (1996)

26. M.Freindorf, J.Gao, Optimization of the Leonard-Jones parameters for a combined ab initio QM/MM potential using the 3-21G basis set, J. Comput. Chem., 17, 386 (1996)

27. M.Freindorf , C.Marian, B.A.Hess, Theoretical study of the electronic spectrum of the CoH molecule, J. Chem. Phys., 99, 1215 (1993)

28. M.Freindorf, Vibronic couplings in excited state of hydrogen bond dimeric systems, Acta Phys. Polonica, A78, 825 (1990)

29. M.Freindorf, Herzberg-Teller interaction in benzene trimeric system, Acta Phys. Polonica, A76, 547 (1989)

30. M.Freindorf, Herzberg-Teller interaction in benzene dimeric systems. II. Aplication, Acta Phys. Polonica, A73, 649 (1988)

31. M.Freindorf, Herzberg-Teller interaction in benzene dimeric systems. I. Model, Acta Phys. Polonica, A73, 635 (1988)

32. M.Freindorf, Vibronic coupling in benzene derivatives. Trimeric systems, Acta Phys. Polonica, A71, 985 (1987)

33. M.Freindorf, Vibronic coupling in benzene derivatives. Dimeric systems, Acta Phys. Polonica, A70, 461 (1986)

34. M.Freindorf, Effect of frequency change on absorption spectra of molecular trimers, Acta Phys. Polonica, A69, 679 (1986)