List of Publications

57. Local Conformational Variations Observed in B-DNA Crystals Do Not Improve Base Stacking. Computational Analysis of Base Stacking in d(CATGGGCCCATG)2 B<->A Intermediate Crystal Structure, J. Sponer, J. Florián, H.-L. Ng, J. E. Sponer and N. Spacková, Nucleic Acid Res. 28, 4893-4902 (2000).

56. Ab initio Evaluation of the Potential Surface for General Base/Acid Catalyzed Thiolysis of Formamide and Hydrolysis of Methyl Thiolformate: A Reference Solution Reaction for Studies of Cysteine Proteases, M. Strajbl, J. Florián and A. Warshel, J. Phys. Chem. , submitted.

55. Circe Effect versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme, A. Warshel, J. Florián, M. Strajbl, J. Villa, ChemBioChem 2 109-111 (2001)

54. Remarkable Catalytic Enhancement of Orotidine 5'monophosphate Decarboxylase Is Due To Transition State Stabilization Rather Than To Ground State Destabilization, A. Warshel, M. Strajbl, J. Villa, J.Florián, Biochemistry 39, 14728 - 14738 (2000).

53. Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine-Thymine, Adenine-Cytosine and Adenine-Difluorotoluene Mismatches, J. Florián, M. F. Goodman and A. Warshel, J. Phys. Chem. B 104, 10092 - 10099 (2000).

52. Q-Chem 2.0: A High-performance Ab Initio Electronic Structure Program Package, J. Kong, C. A. White, A. I. Krylov, D. Sherrill, R. D. Adamson, T. R. Furlani, M. S. Lee, A. M. Lee, S. R. Gwaltney, T. R. Adams, C. Ochsenfeld, A. T. B. Gilbert, G. S. Kedziora, V. A. Rassolov, D. R. Maurice, N. Nair, Y. Shao, N. A. Besley, P. E. Maslen, J. P. Dombroski, H. Daschel, W. Zhang, P. P. Korambath, J. Baker, E. F. C. Byrd, T. V. Voorhis, M. Oumi, S. Hirata, C.-P. Hsu, N. Ishikawa, J. Florián, A. Warshel, B. G. Johnson, P. M. W. Gill, M. Head-Gordon, J. A. Pople, J. Comput. Chem. 21, 1532 - 1548 (2000).

51. Ab initio Evaluation of the Potential Surface for General Base Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases, M. Strajbl, J. Florián and A. Warshel, J. Am. Chem. Soc. 122, 5354 - 5366 (2000).

50. Ab initio/LD Studies of Chemical Reactions in Aqueous Solution: The Reference Free-Energy Surfaces for the Acylation Reactions Occuring in Serine and Cysteine Proteases, M. Strajbl, J. Florián and A. Warshel, Int. J. Quantum. Chem. 77, 44 (2000).

49. Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model, J. Florián and A. Warshel, J. Phys. Chem. B 103, 10282 (1999).

48. Catalytic Hydrolysis of Adenosine 2',3'-Cyclic Monophosphate by Cu(II)terpyridine, L. A. Jenkins, J. K. Bashkin, J. D. Pennock, J. Florián and A. Warshel, Inorg. Chem. 38, 3215 - 3222 (1999).

47. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution. Ab Initio/Langevin Dipoles Study, J. Florián, J. Sponer and A. Warshel, J. Phys. Chem.B 103, 884 - 892 (1999).

46. Mechanistic Alternatives in Phosphate Monoester Hydrolysis: What Conclusions Can Be Drawn From Available Experimental Data? J. Åqvist, K. Kolmodin, J. Florián and A. Warshel, Chemistry&Biology 6, R71 - R80 (1999).

45. Quantum-Chemical Insights into Mechanisms of the Nonenzymatic Hydrolysis of Phosphate Monoesters, J. Florián, and A. Warshel, Phosphorus, Sulfur and Silicon and Related Elements 144-146, 525-528 (1999).

44. On the Reactivity of Phosphate Monoester Dianions In Aqueous Solution: Brønsted Linear Free-Energy Relationships Do Not Have an Unique Mechanistic Interpretation, J. Florián, J. Åqvist and A. Warshel, J. Am. Chem. Soc. 120, 11524 - 11525 (1998).

43. Hybrid ab initio Quantum Mechanics/Molecular Mechanics (QM(ai)MM) Calculations of Free Energy Surfaces For Enzymatic Reactions: The Nucleophilic Attack in Subtilisin, J. Bentzien, R. P. Muller, J. Florián and A. Warshel, J. Phys. Chem. B 102, 2293 - 2301 (1998).

42. Computer Simulations of Enzyme Catalysis. Finding Out What Has Been Optimized By Evolution, A. Warshel and J. Florián, Proc. Natl. Acad. Sci. USA. 95, 5950 - 5955 (1998).

41. Conformational Flexibility of Phosphate, Phosphonate and Phosphorothioate Methyl Esters in Aqueous Solution, J. Florián and M. Strajbl and A. Warshel, J. Am. Chem. Soc. 120, 7959 - 7966 (1998).

40. Phosphate Ester Hydrolysis in Aqueous Solution: Associative Versus Dissociative Mechanisms, J. Florián and A. Warshel, J. Phys. Chem. B 102, 719 - 734 (1998).

39. Quantum Mechanical - Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution, J. Bentzien, J. Florián, T. M. Glennon and A. Warshel, in: Combined Quantum Mechanical & Molecular Mechanical Methods, ACS Symposium Series 712, J. Gao and M. A. Thompson, Eds., pp. 16 - 34 (1998).

38. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Nucleic Acid Constituents: 9: Tetrahydrofuran, M. Strajbl, V. Baumruk and J. Florián, J. Phys. Chem. B 102, 1314 - 1319 (1998).

37. Density Functional Calculations of the Pseudorotational Flexibility of Tetrahydrofuran, M. Strajbl and J. Florián, Theor. Chem. Accounts 99, 166 - 170 (1998).

36. Langevin Dipoles Model for Ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes, and Conformational Analysis in Aqueous Solution, J. Florián and A. Warshel, J. Phys. Chem. B 101, 5583 - 5595 (1997).

35. A Fundamental Assumption about OH- Attack in Phosphate Hydrolysis Is Not Fully Justified, J. Florián and A. Warshel, J. Am. Chem. Soc. 119, 5473 - 5474 (1997).

34. Semiempirical and Ab Initio Modeling of Chemical Processes: From Aqueous Solution to Enzymes, R. P. Muller, J. Florián, A. Warshel, in: Biomolecular Structure and Dynamics, G. Vergoten and T. Theophanides, Eds., Kluwer, Dordrecht, 1997, pp. 47 - 77.

33. Coupled-Cluster and Density Functional Calculations of the Molecular Structure, Infrared Spectra, Raman Spectra, and Harmonic Force Constants for Methanol, J. Florián, J. Leszczynski, B. G. Johnson and L. Goodman, Mol. Phys. 91, 439 - 447 (1997).

32. Molecular Structure, Vibrational Spectra and Quantum Mechanical Force Fields of Modified Oligonucleotide Linkages: 1. Methyl Methoxymethyl Phosphonate, M. Strajbl, V. Baumruk, J. Florián, L. Bednárová, I. Rosenberg and J. Stepánek, J. Mol. Struct. 415, 161 - 177 (1997)

31. Activation of Alcohols and Ketones by Surface Hydroxyls of Strong Solid Acids, L. Kubelková, J. Kotrla, J. Florián, T. Bolom, J. Fraissard, L. Heeribout, C. Doremieuxmorin, Studies in Surface Science and Catalysis 101, 761 - 770 (1996).

30. Nonplanar DNA Base Pairs, J. Sponer, J. Florián, P. Hobza and J. Leszczynski, J. Biomol. Struct. Dyn. 13, 827 - 833 (1996).

29. Ab Initio Investigation of Molecular Structure of Methyl Methoxymethyl Phosphonate, a Promising Nuclease-Resistant Alternative of Phosphodiester Linkage, M. Strajbl and J. Florián, J. Biomol. Struct. Dyn. 13, 687 - 694 (1996).

28. IR and Raman Spectra, Tautomerism, and Scaled Quantum Mechanical Force Fields of Protonated Cytosine, J.Florián, V. Baumruk, and J. Leszczynski, J. Phys. Chem., 100, 5578 - 5589 (1996) .

27. Scaled Quantum Mechanical Force Fields, Vibrational Spectra, and Conformational Flexibility of Sodium Dimethyl Phosphate and Dimethyl Phosphate Anion, J. Florián,, V. Baumruk, M. Strajbl, L. Bednárová and J. Stepánek, J. Phys. Chem. 100, 1559-1568 (1996).

26. Spontaneous DNA Mutations Induced by Proton Transfer in the Guanine-Cytosine Base Pair: An Energetic Perspective, J. Florián, and J. Leszczynski, J. Am. Chem. Soc., 118, 3010 - 3017 (1996).

25. The Prediction of Raman Spectra by Density Functional Theory: Preliminary Findings, B. G. Johnson and J. Florián, Chem. Phys. Lett. 247, 120 - 125 (1995).

24. What Changes Occur in Vibrational Spectra of Guanine and Cytosine When They Form the Watson-Crick Base Pair? A Quantum-Chemical SCRF HF.6-31G* Study, J. Florián and J. Leszczynski, Int. J. Quantum Chem.: Quantum. Biol. Symp. 22, 207 - 225 (1995),

23. On the Intermolecular Vibrational Modes of the Guanine... Cytosine, Adenine...Thymine and Formamide...Formamide H-bonded Dimers, J. Florián, J. Leszczynski and B. G. Johnson, J. Mol. Struct. 349, 421 - 426 (1995).

22. Structure, Energetics, and Force Fields of the Cyclic Formamide Dimer: MP2, Hartree-Fock and Density Functional Study, J. Florián and B. G. Johnson, J. Phys. Chem. 99, 5899 - 5908 (1995).

21. Pyridinium Ions - New Probe for Basic Sites of Solid Acids, J. Kotrla, J. Florián, L. Kubelková and J. Fraissard, Coll. Czech. Chem. Commun. 60, 393 - 402 (1995).

20. Vibrational Spectra of Hydrogen-Bonded Complexes on Zeolite Surfaces as a Benchmark for Evaluating Performance of Ab Initio Methods, J. Florián, L. Kubelková and J. Kotrla, J. Mol. Struct. 349, 435 - 438 (1995)

19. H-Bonding and Interaction Energy of Acetonitrile Neutral and Pyridine Ion-Pair Complexes in Zeolites of Various Acidity: FTIR and Ab Initio Study, L. Kubelková, J. Kotrla and J. Florián, J.Phys.Chem., 99, 10285-10293 (1995).

18. Ab Initio Study of the Structure of Guanine - Cytosine Base Pair Conformers in Gase Phase and Polar Solvent , J. Florián, J. Leszczynski and S. Scheiner, Mol. Phys. 84, 469 - 480 (1995).

17. Theoretical Investigation of the Molecular Structure of the pk Base Pair, J. Florián and J. Leszczynski, J. Biomol. Struct. Dyn., 12, 1055 - 1062 (1995).

16. Proton Transfer between H-Zeolite and Adsorbed Acetone or Acetonitrile: Quantum Chemical and FTIR Study, J. Florián and L. Kubelková, J. Phys. Chem. 98, 8734 - 8741 (1994).

15. Variation of Atomic Charges During Proton Transfer in Hydrogen Bonds, J. Florián and S. Scheiner, J. Comput. Chem. 15, 553 - 560 (1994).

14. Comparison and Scaling of Hartree-Fock and Density Functional Harmonic Force Fields: 1. Formamide-Monomer, J. Florián and B. G. Johnson, J. Phys. Chem. 98 , 3681 - 3687 (1994).

13. The Double Proton Transfer: From the Formamide Dimer to the Adenine - Thymine Base Pair, V. Hrouda, J. Florián, M. Polásek and P. Hobza, J.Phys.Chem. 98 , 4742 - 4747 (1994).

12. Proton Transfer in the Adenine-Thymine Base Pair, J. Florián, V. Hrouda and P. Hobza, J. Am. Chem. Soc. 116, 1457-1460 (1994).

11. Structure, Energetics and Harmonic Vibrational Spectra of the Adenine-Thymine and Adenine*-Thymine* Base Pairs: Gradient Nonempirical and Semiempirical Study, V.Hrouda, J.Florián and P.Hobza, J. Phys. Chem. 97, 1542 - 1557 (1993).

10. Comment on 'Vibrational Motions of Bases of Nucleic Acids as Revealed by Neutron Inelastic Scattering and Resonance Raman Spectroscopy: 1. Adenine and its Deuterated Species', J. Florián, J. Phys. Chem. 97, 10889 (1993).

9. Evaluation of Scaled Quantum Mechanical Methods of Interpretation of Solid State Nucleic Acid Bases Vibrational Spectra, J. Florián, J. Mol. Struct. 294, 25 - 28 (1993).

8. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Solid State Nucleic Acid Constituents: 6. Guanine and Guanine-Residue, J. Florián, J. Phys. Chem. 97, 10649 - 10658 (1993).

7. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Solid State Nucleic Acid Constituents: 5. Thymine and Uracil, J. Florián and V. Hrouda, Spectrochim. Acta 49A, 921 -938 (1993).

6. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Solid State Nucleic Acid Constituents: 4. N7Protonated Guanine, J. Florián and V. Baumruk, J. Phys. Chem. 96, 9283 - 9287 (1992).

5. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Solid State Nucleic Acid Constituents: 3. 2-Aminoadenine, J. Florián, P. Mojzes and J. Stepánek, J. Phys. Chem. 96, 9278 - 9282 (1992).

4. Ab Initio Calculations of the Effect of Protonation on Vibrational Spectra of Adenine, J. Florián, in: Proton Transfer in Hydrogen Bonded Systems, T.Bountis (Editor), NATO ASI 291B, pp. 233 - 238, Plenum, New York 1992.

3. UV Resonance Raman Spectra and Vibrational Assignment of In-plane Normal Vibrational Modes of 2-Aminoadenine and its Deuterium-Substituted Species, P. Mojzes, J. Florián, L. Chinsky, P. Y. Turpin, and J. Stepánek, in: Proceedings of XIIIth. International Conference on Raman Spectroscopy, W. Kiefer, M. Cardone, G. Schaack, F. W. Schneider, M. W. Schrotter (Eds), pp. 340-341, Wiley, New York 1992.

2. Crystal of Adenine and Dissociated and Nondissociated Chloroacetic Acid - A Promissing Model System for the Study of Proton Transfer Phenomena, J. Florián, V. Baumruk, J. Maixner and J. Zachová, in: Proton Transfer in Hydrogen Bonded Systems, T.Bountis (Ed.), NATO ASI 291B, pp. 229 -232 Plenum, New York 1992.

1. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Differently Protonated Adenine, J. Florián, J. Mol. Struct. (Theochem) 253, 83 - 99 (1992).