Petr Bour, RNDr., CSc.
Welcome to my page
hanicka.uochb.cas.cz
web.quick.cz/bour
Research, teaching:
Institute of Organic Chemistry and Biochemistry
Institute of Chemical Technology, Faculty of Analytical Chemistry (Lecture notes - skripta, in Czech)
Joint projects with:
Charles University, Faculty of Mathematics and Physics
University of Illinois at Chicago, Department of Chemistry
University of Calgary, Department of Chemistry
Contacts:
Address UOCHB AVCR, Flemingovo nam. 2, 16610, Praha 6, Czech Republic
E-Mail bour#uochb.cas.cz
Office phone (420)-220-183-348
FAX (420)-224-310-503
Curriculum Vitae: click here.
Contents
Research projects
- Vibrational optical activity, theory and interpretation of spectra, vibrational circular dichroism, Raman optical activity (see the apparatus), Nuclear magnetic resonance.
- Quantum chemistry, applied calculations, density functional theory, algorithms for large molecules.
- Molecular recognition, rational drug design, covalent DNA-drug complexes, computer modeling in analytical chemistry.
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Scientific Publications
(Almost complete, chronologically, last update December 2004)
[50] Dolensky, B.; Kroulik, V.; Kral, V., Sessler, J. L.; Dvorakova, H.; Bour, P.; Bernatkova, M.; Bucher, C.; Lynch, V. J. Am. Chem. Soc. 2004, 126, 13714-13722. "Calix[4]phyrins. Effect of Peripheral Substituents on Conformational Mobility and Structure within a Series of Related Systems." pdf
[49] Bour, P. J. Chem. Phys. 2004, 121, 7545-7548. "On the influence of the water electrostatic field on the amide group vibrational frequencies." pdf
[48] Bour, P.; Raich, I.; Kaminsky, J.; Hrabal, R.; Cejka, J.; Sychrovsky, V. J. Phys. Chem. A 2004, 108, 6365-6372. "Restricted Conformational Flexibility of Furanose Derivatives: Ab Initio Interpretation of their Nuclear Spin-Spin Coupling Constants." pdf
[47] Bour, P.; Keiderling, T. A. J. Mol. Struct. (Theochem) 2004, 675, 95-105. "Structure, spectra and the effets of twisting of beta-sheet peptides. A density functional theory study." pdf
[46] Andrushchenko, V.; Wieser, H.; Bour, P. J. Phys. Chem. B 2004, 108, 3899-3911. "RNA Structural Forms Studied by Vibrational Circular Dichroism: Ab Initio Interpretation of the Spectra." pdf
[45] Tomankova, Z.; Setnicka, V.; Urbanova, M.; Matejka, P.; Kral, V.; Volka, K.; Bour, P. J. Org. Chem. 2004, 69, 26-32. "Conformational Flexibility of Corey Lactone Derivatives Indicated by Absorption and Vibrational Circular Dichroism Spectra." pdf
[44] Bour, P.; Keiderling, T. A. J.Chem.Phys. 2003, 119, 11253-11262. "Empirical modeling of the peptide amide I band IR intensity in water solution. " pdf
[43] Bour, P. Int. J. Quantum Chem. 2003, 91, 277-283. "Calculation of the NMR Chemical Shifts for Taxol and alpha-Pinene within the Generalized Gradient Approximation." pdf
[42] Andrushchenko, V.; Wieser, H.; Bour, P. J. Phys. Chem. B 2002, 106, 12623-12634. "B-Z Conformational Transition of Nucleic Acids Monitored by VIbrational Circular Dichroism. Ab Initio Interpretation of the Experiment." pdf
[41] Bour, P. Chem. Phys. Lett. 2002, 365, 82-88. "A cluster model of liquid water and its IR spectroscopic response."pdf
[40] Bour, P.; Kubelka, J.; Keiderling, T. A. Biopolymers 2002, 65, 45-69. "Ab Initio Quantum Mechanical Models of Peptide Helices and Their Vibrational Spectra"pdf
[39] Bour, P.; Keiderling, T. A. J. Chem. Phys. 2002, 117, 4126-4132. "Partial optimization of molecular geometry in normal coordinates and use as a tool for simulation of vibrational spectra"pdf
[38] Ruud, K.; Helgaker, T.; Bour, P. J. Phys. Chem. A 2002, 106, 7448-7455. "Gauge-origin independent density-functional theory calculations of vibrational Raman optical activity"pdf
[37] Bour, P.; Sychrovsky, V.; Malon, P.; Hanzlikova, J.; Baumruk, V.; Pospisek, J; Budesinsky, M. J. Phys. Chem. A 2002, 106, 7321-7327. "Conformation of the Dipeptide Cyclo(L-Pro-L-Pro) Monitored by the Nuclear Magnetic Resonance and Raman Optical Activity Spectra. Experimental and Ab Initio Computational Study."pdf
[36] Urbanová, M.; Setnicka, V.; Bour, P.; Navratilova, H.; Volka, K. Biopolymers (Biospectroscopy) 2002, 67, 298-301 "Vibrational Circular Dichroism Spectroscopy STudy of Paroxetine and Femozetine Precursors"pdf
[35] Butkus, E.; Zilinskas, A; Stoncius, S.; Rozenbergas, R.; Urbanova, M.; Setnicka, V.; Bour, P.; Volka, K. Tetrahedron: Asymmetry 2002, 13, 633-638. "Synthesis and chirooptical properties of enantiopure tricyclo[4.3.0.03,8]nonane-4,5,-dione (twistbrendanedione)"pdf
[34] Bour,P.; Navratilova, H.; Setnicka,V.; Urbanova, M.; Volka, K. J. Org. Chem. 2002, 67, 161-168. "(3R, 4S)-4-(4-fluorophenyl)-3-hydroxymethyl-1-methylpiperidine: Conformation and Structure Monitoring by the Vibrational Circular Dichroism."pdf
[33] Setnicka, V.; Urbanova, M.; Bour, P.; Kral, V.; Volka; J. Phys. Chem. A 2001, 105, 8931-8938. "Vibrational Circular Dichroism of 1,1?-Binaphthyl Derivatives: Experimental and Theoretical Study" pdf
[32] P. Bour, Chem. Phys. Lett. 2001, 345, 331-337. "Configuration interaction with Kohn-Sham orbitals and their relation to excited electronic states." pdf
[31] Petr Bour, Josef Kapitan and Vladimir Baumruk, J. Phys. Chem. A 2001, 105, 6362-6368 " Simulation of the Raman Optical Activity of L-Alanyl-L-Alanine" pdf
[30] Kamil Zaruba, Zuzana Tomankova, Jana Charvatova, Ivana Kavenova, Petr Bour, Pavel Matejka, Karel Volka and Vladimˇr Kral Analytica Chimica Acta 2001, 437(1), 39-53."Porphyrin and sapphyrin interactions with nucleobases and nucleosides in HPLC columns. Spectroscopical, quantum chemical and chromatographic investigation" pdf
[29] P. Bour, J. Comp. Chem. 2001, 22, 426-435. "Computations of the Raman Optical Activity via the Sum-Over-States Expansions" pdf
[28] R. A. G. D. Silva, Jan Kubelka, Petr Bour, Sean M. Decatur, and Timothy A. Keiderling, Proc. Natl. Acad. Sci. USA 2000, 97(15), 8318-8323. "Site-Specific Conformational Determination in Thermal Unfolding Studies of Helical Peptides using Vibrational Circular Dichroism with Isotopic Substitution." pdf
[27] Petr Bour, Kamil Záruba, Marie Urbanová, Vladimír Setnicka, Pavel Matejka, Zdenek Fiedler, Vladimír Král, Karel Volka, Chirality 2000, 12 (4), 191-198. "Vibrational circular dichroism of tetraphenylporphyrin in peptide complexes? A computational study" pdf
[26] Bour, P., Kral, V. Coll. Czech. Chem. Comm. 2000, 65(5), 631-643. "Interaction of Distamycin Analogues with DNA Base Pairs: A Computational Study." pdf
[25] Petr Bour, Jan Kubelka, and Timothy A. Keiderling, Biopolymers 2000, 53, 380-395. "Simulations of Oligopeptide Vibrational CD: Effects of Isotopic Labeling."(abstract, text)
[24] Bour, P. J. Comp. Chem.2000, 21,8-16. "Comparison of the Hartree-Fock and Kohn-Sham Determinants as Wave Functions" pdf
[23] Bour, P. J. Phys. Chem. A 1999, 103,5099-5104. "Simulation of the Electronic Circular Dichroism with Rigid Kohn-Sham Orbitals: A Computational Experiment." pdf
[22] Bour, P., Budesinsky, M. J. Chem. Phys. 1999,
[21] Rauk, A.; McCann, J.L.; Wieser, H.; Bour, P.; El’natanov, Y.I.; Kostyanovsky, R.G. Can. J. Chem. 1998, 76, 717-725. "Skeletal Vibrational Circular Dichroism of a Series of Bicyclic Dilactones: The Fingerprint Region?"
[20] Bour, P; McCann, J.; Wieser, H. J. Chem. Phys. 1998, 108, 8782-8789. "The Excitation Scheme. A New ab initio method for calculation of vibrational circular dichroism spectra." jcp02e.doc.
[19] Bour, P. Chem. Phys. Lett. 1998, 288, 363-370. "Calculation of the Raman optical activity via the sum over states expansion".(pdf)
[18] Bour, P; McCann, J.; Wieser, H. J. Phys. Chem. A, 1998, 102, 102-110. "Measurement and Calculation of Absolute Rotational Strengths for Camphor, (-Pinene and Borneol". camphrevised.doc
[17] Bour, P.; Tam, C.N.; Sopkova, J.; Trouw, F.R. J. Chem. Phys. 1998, 108, 351-358. "Measurement and ab initio modelling of the inelastic neutron scattering of solid N-methylformamide." nmf_pap3.doc
[16] Petr Bou(, Jennifer McCann and Hal Wieser, J. Phys. Chem. A 1997, 101, 9783-9790. "Vibrational Circular Dichroism Study of (-)-Sparteine". spart.doc
[15] Tam, C.N.; Bour, P.; Eckert, J.; Trouw, F.R. J. Phys. Chem. 1997, 101, 5877-5884. "Inelastic Neutron Scattering Study of Hydrogen Bonded Solid Formamide at 15 K"
[14] Bour, P.; Baumruk, V.; Hanzlikova, J. Coll. Czech. Chem. Commun. 1997, 9, 1384-1395. "Measurement and Calculation of the Raman Optical Activity of "-pinene and trans-pinane"( pdf)
[13] C.N. Tam, P. Bour and T.A. Keiderling, J. Am. Chem. Soc. 1997, 119, 7061. "An Experimental Comparison of Vibrational Circular Dichroism and Raman Optical Activity width 1-amino-2-propanol and 2-amino-1-propanol as Model Compounds"
[12] Bou(, P.; Sopkov , J.; Bedn rov , L.; Malo(, P.; Keiderling, T.A. J. Comput. Chem. 1997, 18, 646-659. "Transfer of Molecular Property Tensors in Cartesian Coordinates: A New Algorithm for Simulation of Vibrational Spectra."
[11] Bour, P. Chem. Phys. Lett. 1997, 265, 65. "Approximate Ab Initio Calculation of Polarizabilities via the Excitation Scheme"
[10] Tam, C.N.; Bour, P.; Keiderling, T.A. J. Am. Chem. Soc. 1996, 118, 10285-10293. "Vibrational Optical Activity of (3S, 6S)-3,6-Dimethyl-1,4-dioxane-2,5-dione"
[9] Bour, P.; Tam, C.N.; Shaharuzzaman, M; Chickos, J.S. and Keiderling, T.A. J. Phys. Chem. 1996, 100, 15041-15048, "Vibrational Optical Activity Study of trans-d2-Succinic Anhydride"
[8] Bour, P.; Tam, C.N.; Wang, B. and Keiderling, T.A. Molecular Physics 1996, 87(2), 299-318, "Computer Simulations of the Rotationally Resolved Magnetic Vibrational Circular Dichroism of Diamagnetic Molecules".
[7] Tam, C.N.; Bour, P.; and Keiderling, T.A. J Chem. Phys. 1996, 104, 1813, "Observations of Rotational Magnetic Moments in the Ground and Some Excited Vibrational G States of C2H2, C2HD and C2D2 by Magnetic Vibrational Circular Dichroism"
[6] Bour, P.; Tam, C.N.; Keiderling, T.A. J. Phys. Chem. 1996, 100, 2062-2065. "Vibrational Magnetic Dipole Moment of Acetylene in the <5 Mode"
[5] Bour, P.;Tam, C.N.; Keiderling, T.A. J. Phys. Chem. 1995, 99,17810-17813. "Ab Initio Calculation of the Vibrational Magnetic Dipole Moment"
[4] P. Bour and L. Bednarova J.Phys.Chem. 1995, 99, 5961-5966. "Anharmonic Force Field of Formamide. A Computational Study."
[3] Bour, P. J.Phys.Chem. 1994, 98, 8862-8865. "Anharmonic Corrections to Vibrational Energies of Molecules: Water and Dideuteriooxirane."
[2] Bour, P.; Keiderling, T. A. J. A. Chem. Soc., 1993, 15, 9602-9607. "Ab initio Simulations of the Vibrational Circular Dichroism of Coupled Peptides".
[1] Bour, P.; Keiderling, T.A. J.Am.Chem.Soc. 1992, 114, 9100, "Computational Evaluation of the Coupled Oscillator Model in the Vibrational Circular Dichroism of Selected Small Molecules"
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Download
MCM 95 windows
MCM 95 linux
Features: Molecular graphics for PC, input and output in Cartesian or internal coordinates, .PDB files, X-ray fractional coordinates. Output for Gaussian 94, 98, Turbomole, Dalton and Cadpac ab initio programs, output to printer, bitmaps of current screen may be saved. Simple molecular mechanics implemented.
Requirements: Windows 95 and above or Linux RH >7.2, PC from about Intel 486 above
Installation: Windows: unzip mcm95.zip, you can use install.exe to create the directory structure, e.g.
\mcm95\xyz
\mcm95\fragment
\mcm95\peptide
Copy mcm95.exe to the main program directory (\mcm95.exe) and write correct directory names in the configuration file config.mcm in the same directory. Unzip the *.zip files in corresponding directories. Run mcm95.exe as a Windows application. If this sound too difficult, just run mcm95.exe.
Installation: Linux: unzip mcm.zip (tar -xvzf mcm.zip), change mcm.launch and config.mcm according to your directory structure.
Good bye
