Petr Bour, Prof., RNDr., DSc.

 Welcome to my page

hanicka.uochb.cas.cz

Leading research scientist at The Institute of Organic Chemistry and Biochemistry

Professor of chemistry at The Institute of Chemical Technology, Department of Analytical Chemistry

Teaching also at The Charles University, Faculty of Mathematics and Physics

Lecture notes, skripta (in Czech)

Themes for PhD. students

International collaboration

University of Illinois at Chicago, Department of Chemistry

University of Calgary, Department of Chemistry

University of Szeged

University of Tromso

University of Wyoming


Contact

Mail/physical UOCHB AVCR, Flemingovo nam. 2, 16610, Praha 6, Czech Republic
E-Mail bour#uochb.cas.cz
Telephone (420)-220-183-348

Curriculum Vitae


Research Interest

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Scientific Publications

EndNote list

[158] Andrushchenko, V.; Padula, D.; Zhivotova, E.; Yamamoto, S., Bour, P. Chirality 2014, 26, 665-662. "Magnetic Circular Dichroism of Porphyrin Lanthanide M3+ Complexes." pdf

[157] Kessler, J.; Bour, P. J. Comput. Chem. 2014, 35, 1552-1559. "Molecular Dynamics with Helical Periodic Boundary Conditions." pdf

[156] Kessler, J.; Keiderling, T. A.; Bour, P. J. Phys. Chem. B 2014, 118, 6937-6945. "Arrangement of Fibril Side Chains Studied by Molecular Dynamics and Simulated Infrared and Vibrational Circular Dichroism Spectra." pdf

[155] Stepanek, P.; Bour, P. Phys. Chem. Chem. Phys. 2014, 16, 20639-20649. "Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions." pdf

[154] Sebestik, J.; Bour, P. Angew. Chem. Int. Ed. 2014, 53 (35), 9236-9239. "Observation of Paramagnetic Raman Optical Activity of Nitrogen Dioxide." pdf

[153] Yamamoto, S.; Furukawa, T.; Bour, P.; Ozaki, Y. J. Phys. Chem. A 2014, 118, 3655-3662. "Solvated States of Poly-l-alanine alpha-Helix Explored by Raman Optical Activity." pdf

[152] Wu, T.; Zhang, X. P.; You, X. Z., Li, Y. Z., Bour, P. ChemPlusChem 2014, 79, 698-707. "Chirality Transfer in Magnetic Coordination Complexes Monitored by Vibrational and Electronic Circular Dichroism." pdf

[151] Makrlik, E.; Novak, V.; Vanura, P.; Bour; P. J. Radioanal. Nucl. Chem. 2013, 298, 2065-2068. "Complexation of the cesium cation with lithium ionophore VIII: extraction and DFT study." pdf

[150] Makrlik, E.; Novak, V.; Vanura, P.; Bour; P. Monatsh. Chem. 2013, 144, 1607-1611. "Experimental and theoretical study on complexation of Li+ with lithium ionophore VIII." pdf

[149] Li, X.; Hopmann, K. H.; Hudecova, J.; Isaksson, J.; Novotna, J.; Stensen, W.; Andrushchenko, V.; Urbanova, M.; Svendsen, J. S.; Bour, P.; Ruud, K. J. Phys. Chem. A 2013, 117, 1721-1736. "Determination of Absolute Configuration and Conformation of a Cyclic Dipeptide by NMR and Chiral Spectroscopic Methods." pdf

[148] Dracinsky, M.; Prochazkova, E.; Kessler, J.; Sebestik, J.; Matejka; P.; Bour, P. J. Phys. Chem. B 2013, 117, 7297-7307. "Resolution of Organic Polymorphic Crystals by Raman Spectroscopy." pdf

[147] Parchansky, V.; Kapitan, J.; Kaminsky, J.; Sebestik, J.; Bour, P. J. Phys. Chem. Lett. 2013, 4, 2763-2768. "Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity." pdf

[146] Yamamoto, S.; Bour, P. J. Comput. Chem. 2013, 34, 2152-2158. "Transition Polarizability Model of Induced Resonance Raman Optical Activity." pdf

[145] Hudecova, J.; Profant, V.; Novotna, P.; Baumruk, V.; Urbanova, M.; Bour, P. J. Chem. Theory Comput. 2013, 9, 3096-3108. "CH Stretching Region: Computational Modeling of Vibrational Optical Activity." pdf

[144] Kaminsky, J.; Budesinsky, M.; Taubert, S.; Bour, P.; Straka, M. Phys. Chem. Chem. Phys. 2013, 15, 9223-9230. "Fullerene C70 characterization by 13C NMR and the importance of the solvent and dynamics in spectral simulations." pdf

[143] Stepanek, P.; Straka, M.; Andrushchenko, V.; Bour, P. J. Chem. Phys. 2013, 138, 151103. "Fullerene resolution by the magnetic circular dichroism." pdf

[142] Zawada, Z.; Safarik, M.; Dvorakova, E; Janouskova, O.; Brezinova, A.; Stibor, I.; Holada, K.; Bour, P.; Hlavacek, J.; Sebestik, J. Amino Acids 2013, 44, 1279-1292. "Quinacrine reactivity with prion proteins and prion-derived peptides." pdf

[141] Stepanek, P.; Bour, P. J. Comput. Chem. 2013, 34, 1531-1539. "Computation of Magnetic Circular Dichroism by Sum Over States Summations." pdf

[140] Kessler, J.; Dracinsky, M.; Bour, P. J. Comput. Chem. 2013, 34, 366-371. "Parallel Variable Selection of Molecular Dynamics Clusters as a Tool for Calculation of Spectroscopic Properties." pdf

[139] Sebestik, J.; Safarik, M.; Bour, P. Inorg. Chem. 2012, 51 (8), 4473-4481. "Ferric Complexes of 3-Hydroxy-4-pyridinones Characterized by Density Functional Theory and Raman and UV.vis Spectroscopies." pdf

[138] Yamamoto, S.; Bour, P. Angew. Chem. Int. Ed. 2012, 51(44), 11058-11061. "Detection of Molecular Chirality by Induced Resonance Raman Optical Activity in Europium Complexes." pdf

[137] Benda, L.; Straka, M.; Sychrovsky, V.; Bour, P.; Tanaka, Y. J. Phys. Chem. A. 2012, 116, 8313-8320. "Detection of Mercury.TpT Dinucleotide Binding by Raman Spectra: A Computational Study." pdf

[136] Hudecova, J.; Hornicek, J.; Budesinsky, M.; Sebestik,J.; Safarik,M.; Zhang, G.; Keiderling, T. A.; Bour, P. ChemPhysChem 2012, 13(11), 2748-2760. "Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment." pdf

[135] Wu, T.; Zhang, X. P.; Li, C. H.; Bour, P.; Li, Y. Z.; You, X. Z. Chirality 2012, 24, 451-458. "Vibrational and Electronic Circular Dichroism Monitoring of Copper(II) Coordination with a Chiral Ligand." pdf

[134] Wang, B.; Bour, P.; Keiderling, T. A. Phys. Chem. Chem. Phys. 2012, 14, 9586-9593. "Rotationally Resolved Magnetic Vibrational Circular Dichroism of the Paramagnetic Molecule NO." pdf

[133] Kessler, J.; Jakubek, M.; Dolensky, B.; Bour, P. J. Comput. Chem. 2012, 33, 2310-2317. "Binding Energies of Five Molecular Pincers Calculated by Explicit and Implicit Solvent Models." pdf

[132] Dracinsky, M.; Jansa, P.; Bour., P. Chem. Eur. J. 2012, 18, 981-986. "Computational and Experimental Evidence of Through-Space NMR Spectroscopic J-Coupling of Hydrogen Atoms." pdf

[131] Novak, V.; Sebestik, J.; Bour., P. J. Chem. Theory Comput. 2012, 8, 1714-1720. "Theoretical Modeling of the Surface-Enhanced Raman Optical Activity." pdf

[130] Li, X.; Hopmann, K. H.; Hudecova., J.; Stensen, W.; Novotna., J.; Urbanova., M.; Svendsen, J. S.; Bour., P.; Ruud. K. J. Phys. Chem. A 2012, 116, 2554-2563. "Absolute Configuration of a Cyclic Dipeptide Reflected in Vibrational Optical Activity: Ab Initio and Experimental Investigation." pdf

[129] Uchiyama, T.; Miura, T.; Takeuchi, H.; Dairaku, T.; Komuro, T.; Kawamura, T.; Kondo, Y.; Benda, L.; Sychrovsky, V.; Bour, P.; Okamoto, I.; Ono, A.; Tanaka, Y. Nucleic Acids Res. 2012, 40(12), 5766-5744. "Raman spectroscopic detection of the T-HgII-T base pair and the ionic characteristics of mercury." pdf

[128] Yamamoto, S.; Kaminsky, J.; Bour, P. Anal. Chem. 2012, 84, 2440-2451. "Structure and Vibrational Motion of Insulin from Raman Optical Activity Spectra." pdf

[127] Dracinsky, M.; Bour, P. J. Comput. Chem. 2012, 33, 1080-1089. "Vibrational Averaging of the Chemical Shift in Crystalline a-Glycine." pdf

[126] Yamamoto, S.; Li, X.; Ruud, K.; Bour, P. J. Chem. Theory Comput. 2012, 8(3), 977-985. "Transferability of Various Molecular Property Tensors in Vibrational Spectroscopy." pdf

[125] Hopmann, K. H.; Sebestik,J.; Novotna, J.; Stensen, W.; Urbanova, M.; Svenson, J.; Svendsen, J. S.; Bour, P.; Ruud, K. J. Org. Chem. 2012, 77 (2), 858-869. "Determining the Absolute Configuration of Two Marine Compounds Using Vibrational Chiroptical Spectroscopy." pdf

[124] Stepanek, P.; Andrushchenko, V.; Ruud, K.; Bour, P. J. Phys. Chem. A 2012, 116 (1), 778-783. "MCD Porphyrin Protonation Studied by Magnetic Circular Dichroism." pdf

[123] Hudecova, J; Hopmann, K. H.; Bour, P. J. Phys. Chem. B 2012, 116, 336-342. "Correction of Vibrational Broadening in Molecular Dynamics Clusters with the Normal Mode Optimization Method." pdf

[122] Profant, V.; Baumruk, V.; Li, X.; Safarik, M.; Bour, P. J. Phys. Chem. B 2011, 115, 15079-15089. "Tracking of the Polyproline Folding by Density Functional Computations and Raman Optical Activity Spectra." pdf

[121] Zawada, Z.; Sebestik, J.; Safarik, M.; Bour, P. Eur. J. Org. Chem. 2011, 6989-6997. "Dependence of the Reactivity of Acridine on Its Substituents: A Computational and Kinetic Study." pdf

[120] Andrushchenko, V.; Tsankov, D.; Krasteva, M.; Wieser, H.; Bour, P. J. Am. Chem. Soc. 2011, 133, 15055-15064."Spectroscopic Detection of DNA Quadruplexes by Vibrational Circular Dichroism." pdf

[119] Dracinsky, M.; Benda, L.; Bour, P. Chem. Phys. Lett. 2011, 512, 54-59. "Ab initio modeling of fused silica, crystal quartz, and water Raman spectra." pdf

[118] Bour, P. Angew. Chem. Int. Ed. 2011, 50, 5611-5612. "Computational Spectroscopy" (book review) pdf

[117] Dolensky, B.; Parchansky, V.; Matejka, P.; Havlik,M.; Bour, P.; Kral,V. J. Mol. Struct. 2011, 996, 69-74. "Determination of relative configuration of symmetrical bis-Troegers base derivatives." pdf

[116] Hopmann, K.; Ruud, K.; Pecul, M.; Kudelski, A.; Dracinsky, M. ; Bour, P. J. Phys. Chem. B 2011, 115, 4128-4137. "Explicit versus Implicit Solvent Modeling of Raman Optical Activity Spectra." pdf

[115] Yamamoto, S.; Watarai, H.; Bour, P. ChemPhysChem 2011, 12, 1509-1518. "Monitoring the Backbone Conformation of Valinomycin by Raman Optical Activity" pdf

[114] Standara, S.; Kulhanek, P.; Marek, R.; Hornicek, J.; Bour, P.; Straka, M. Theor. Chem. Acc. 2011, 129, 677-684. "Simulations of 129Xe NMR chemical shift of atomic xenon dissolved in liquid benzene" pdf

[113] Kaminsky, J.; Bour, P.; Kubelka, J. J. Phys. Chem. A 2011, 115, 30-34. "Simulations of the Temperature Dependence of Amide I Vibration." pdf

[112] Yamamoto, S.; Bour, P. Collect. Czech. Chem. Commun. 2011, 76, 567-583. "On the Limited Precision of Transfer of Molecular Optical Activity Tensors." pdf

[111] Kaminsky, J.; Kubelka, J.; Bour, P. J. Phys. Chem. A 2011, 115, 1734-1742. "Theoretical Modeling of Peptide a-Helical Circular Dichroism in Aqueous Solution." pdf

[110] Sebestik, J.; Bour, P. J. Phys. Chem. Lett. 2011, 2, 498-502. "Raman Optical Activity of Methyloxirane Gas and Liquid." pdf

[109] Andrushchenko, V. V.; Bour, P. Chirality 2010, 22, E96-E114. "Applications of the Cartesian Coordinate Tensor Transfer Technique in the Simulations of Vibrational Circular Dichroism Spectra of Oligonucleotides." pdf

[108] Stepanek, P.; Bour, P.; Straka, M. Chem. Phys. Lett. 2010, 500, 54-58. "Assignment of the He@C84 isomers in experimental NMR spectra using density functional calculations." pdf

[107] Gauger, D. R.; Andrushchenko, V. V.; Bour, P.; Pohle, W. Anal. Bioanal. Chem. 2010, 398, 1109-1123." A spectroscopic method to estimate the binding potency of amphiphile assemblies." pdf

[106] Kumprecht, L.; Budesinsky, M.;Bour, P.; Kraus, T. New J. Chem.2010, 34,2254-2260. "alpha-Cyclodextrins reversibly capped with disulfide bonds." pdf

[105] Yamamoto, S.; Straka, M.; Watarai, H.; Bour, P. Phys. Chem. Chem. Phys. 2010, 12, 11021-11032. "Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy." pdf

[104] Profant, V.; Safarik, M.; Bour, P.; Baumruk, V. Spectroscopy 2010, 24, 213-217. "Raman optical activity study of poly-L-proline chains of various lengths." pdf

[103] Hudecova, J.; Kapitan, J.; Baumruk, V.; Hammer, R. P.; Keiderling, T. A.; Bour, P. J. Phys. Chem. A 2010, 114, 7642-7651. "Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide" pdf

[102] Parchansky, V.; Bour, P. J. Chem. Phys. 2010, 133, 044117. "Transferability of anharmonic force fields in simulations of molecular vibrations." pdf

[101] Ivani, I,; Baumruk, V.; Bour, P. J. Chem. Theory Comput. 2010, 6, 2095-2102. "A Fourier Transform Method for Generation of Anharmonic Vibrational Molecular Spectra." pdf

[100] Kaminsky, J.; Raich, I.; Tomcakova, K.; Bour, P. J. Comput. Chem. 2010, 31, 2213-2224. "Conformational Behavior of Simple Furanosides Studied by Optical Rotation" pdf

[99] Paulson, L. O.; Kaminsky, J.; Anderson, D. T.; Bour, P.; Kubelka, J. J. Chem. Theory Comput. 2010, 6, 817-827. "Theoretical Study of Vibrationally Averaged Dipole Moments for the Ground and Excited C=O Stretching States of trans-Formic Acid." pdf

[98] Kapitan, J.; Dracinsky, M.; Kaminsky, J.; Benda, L.; Bour, P. J. Phys. Chem. B 2010, 114, 3574-3582. "Theoretical Modeling of Magnesium Ion Imprints in the Raman Scattering of Water." pdf

[97] Hornicek, J.; Dvorakova, H.; Bour, P. J. Phys. Chem. A 2010,, 114, 3649-3654. "Intramolecular Proton Transfer in Calixphyrin Derivatives." pdf

[96] Dracinsky, M.; Castano, O.; Kotora, M.; Bour, P. J. Org. Chem. 2010, 75, 576-581."Rearrangement of Dewar Benzene Derivatives Studied by DFT." pdf

[95] Dracinsky, M.; Bour, P. J. Chem. Theory Comput. 2010, 6, 288-299."Computational Analysis of Solvent Effects in NMR Spectroscopy." pdf

[94] Benda, L.; Bour, P.; Muller, N.; Sychrovsky, V. J. Phys. Chem. B 2009, 113, 5273-5281."Theoretical Study of the Effective Chemical Shielding Anisotropy (CSA) in Peptide Backbone, Rating the Impact of CSAs on the Cross-Correlated Relaxations in L-Alanyl-L-alanine" pdf

[93] Roy, A.; Bour, P.; Keiderling, T. A. Chirality 2009, 21, S163-S171."TD-DFT Modeling of the Circular Dichroism for a Tryptophan Zipper Peptide with Coupled Aromatic Residues." pdf

[92] Kapitan, J.; Johannessen, C.; Bour, P.; Hecht, L.; Barron, L. D. Chirality 2009, 21, S4-S12."Vibrational Raman Optical Activity of 1-Phenylethanol and 1-Phenylethylamine: Revisiting Old Friends." pdf

[91] Andrushchenko, V.; Matejka, P.; Anderson, D. T.; Kaminsky, J.; Hornicek, J.; Paulson, L. O.; Bour, P. J. Phys. Chem. A 2009, 113, 9727-9736."Solvent Dependence of the N-Methylacetamide Structure and Force Field." pdf

[90] Bour, P. ChemPhysChem 2009, 10, 1983-1985."Cross-Polarization Detection Enables Fast Measurement of Vibrational Circular Dichroism." pdf

[89] Parchansky, V.; Matejka, P.; Dolensky, B.; Havlik, M; Bour, P. J. Mol. Struct. 2009, 934, 117-122."Modeling of a Troger's tweezer and its complexation properties." pdf

[88] Havlik, M; Parchansky, V.; Bour, P.; Kral, V.; Dolensky, B. Collect. Czech. Chem. Commun. 2009, 74(7-8), 1091-1099."Bridged bis-Troger' base molecular tweezers as new cavitand family." pdf

[87]Dracinsky, M.; Kaminsky, J.; Bour, P. J. Phys. Chem. B 2009, 113, 14698-14707. "Structure of the Alanine Hydration Shell as Probed by NMR Chemical Shifts and Indirect Spin-Spin Coupling." pdf

[86] Sebek, J.; Kapitan, J.; Sebestik, J.; Baumruk, V.; Bour, P. J. Phys. Chem. A 2009, 113, 7760-7768."L-Alanyl-L-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra." pdf

[85] Huang, R.; Wu, L.; McElheny, D.; Bour, P.; Roy, A.; Keiderling, T. A. J. Phys. Chem. B 2009, 113, 5661-5674."Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip beta-Hairpin Peptide Using 13C Isotopic Labeling and IR Spectroscopy." pdf

[84] Kaminsky, J.; Kapitan, J.; Baumruk, V.; Bednarova, L.; Bour, P. J. Phys. Chem. A 2009, 113, 3594-3601."Interpretation of Raman and Raman Optical Activity Spectra of a Flexible Sugar Derivative, the Gluconic Acid Anion" pdf

[83] Kaminsky, J.; Sebek, J.; Bour, P. J. Comp. Chem. 2009, 30, 983-991."Molecular Dynamics with Restrictions Derived from Optical Spectra." pdf

[82] Dracinsky, M.; Kaminsky, J.; Bour, P. J. Chem. Phys. 2009, 130, 094106."Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging." pdf

[81] Andrushchenko, V.; Bour, P. J. Phys. Chem. B 2009, 1, 283-291."Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study." pdf

[80] Kubelka, J.; Bour, P. J. Chem. Theory Comput. 2009, 5, 200-207."Simulation of Vibrational Spectra of Large Molecules by Arbitrary Time Propagation" pdf

[79] Andrushchenko, V.; Bour, P. J. Comput. Chem. 2008, 29, 2693-2703."Circular Dichroism Enhancement in Large DNA Aggregates Simulated by a Generalized Oscillator Model." pdf

[78] Bour, P.; Kim, J.; Kapitan, J.; Hammer, R. P.; Huang, R.; Wu, L.; Keiderling, T. A. Chirality 2008, 20, 1104-1119."Vibrational Circular Dichroism and IR Spectral Analysis as a Test of Theoretical Conformational Modeling for a Cyclic Hexapeptide" pdf

[77] Budesinsky, M.; Danecek, P.; Bednarova, L.; Kapitan, J.; Baumruk, V.; Bour, P.. J. Phys. Chem. A 2008, 112, 8633-8640."Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides." pdf

[76] Sebek, J.; Bour, P.. J. Phys. Chem. A 2008, 112, 2920-2929. "Ab Initio Modeling of the Electronic Circular Dichroism Induced in Porphyrin Chromophores" pdf

[75] Budesinsky, M.; Sebestik, J.; Bednarova, L.; Baumruk, V.; Safarik, M.; Bour, P.. J. Org. Chem. 2008, 73, 1481-1489. "Conformational Properties of the Pro-Gly Motif in the D-Ala-L-Pro-Gly-D-Ala Model Peptide Explored by a Statistical Analysis of the NMR, Raman, and Raman Optical Activity Spectra." pdf

[74] Kapitan, J.; Hecht, L.; Bour, P.. Phys. Chem. Chem. Phys. 2008, 10, 1003-1008. "Raman spectral evidence of methyl rotation in liquid toluene." pdf

[73] Sychrovsky, V; Budesinsky, M.; Benda, L.; Spirko, V.; Vokacova, Z.; Sebestik, J.; Bour, P. J. Phys. Chem. B 2008, 112, 1796-1805. "Dependence of the L-Alanyl-L-Alanine Conformation on Molecular Charge Determined from Ab Initio Computations and NMR Spectra." pdf

[72] Sebestik, J.; Bour, P. Chem. Phys. Lett. 2008, 451, 233-236. "Molecular dynamics simulation of chiral chromatography." pdf

[71] Kim, J.; Kapitan, J.; Lakhani, A.; Bour, P.; Keiderling, T. A. Theor. Chem. Acc. 2008, 119, 81-97. "Tight .-turns in peptides. DFT-based study of infrared absorption and vibrational circular dichroism for various conformers including solvent effects" pdf

[70] Andrushchenko, V.; Wieser, H.; Bour, P. J. Phys. Chem. A 2007, 111, 9714-9723. "DNA Oligonucleotide-cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra." pdf

[69] Hornicek, J.; Kapralova, P.; Bour, P. J. Chem. Phys. 2007, 127, 084502. "Simulations of vibrational spectra from classical trajectories: Calibration with ab initio force fields." pdf

[68] Danecek, P.; Kapitan, J.; Baumruk, V.; Bednarova, L.; Kopecky, V.; Bour, P. J. Chem. Phys. 2007, 126, 224513. "Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions." pdf

[67] Danecek, P.; Bour, P. J. Comp. Chem. 2007, 28, 1617-1624. "Comparison of the Numerical Stability of Methods for Anharmonic Calculations of Vibrational Molecular Energies." pdf

[66] Sebek, J.; Gyurcsik, B.; Sebestik, J.; Kejik, Z.; Bednarova, L.; Bour, P. J. Phys. Chem. A 2007, 111, 2750-2760. "Interpretation of Synchrotron Radiation Circular Dichroism Spectra of Anionic, Cationic, and Zwitterionic Dialanine Forms." pdf

[65] Bour, P. J. Chem. Phys. 2007, 126, 136101, "Matrix formulation of the surface-enhanced Raman optical activity theory." pdf

[64] Bednarova, L.; Malon, P.; Bour, P. Chirality 2007, 19(10), 775-786. "Spectroscopic properties of the nonplanar amide group: A computational study." pdf

[63] J. Kim; Huang, R.; Kubelka, J.; Bour, P.; Keiderling, T. A. J. Phys. Chem. B 2006, 110, 23590-23602. "Simulation of Infrared Spectra for beta-hairpin Peptides Stabilized by an Aib-Gly Turn Sequence: Correlation between Conformational Fluctuation and Vibrational Coupling" pdf

[62] Kapitan J.; Baumruk, V.; Kopecky Jr.; Pohl, R.; Bour, P. J. Am. Chem. Soc. 2006, 128(41), 13451-13462. "Proline Zwitterion Dynamics in Solution, Glass, and Crystalline State" pdf

[61] Kubelka, J.; Kim, J.; Bour, P.; Keiderling, T. A. Vib. Spectrosc. 2006, 42, 63-73. "Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures." pdf

[60] Sebek, J.; Bour, P. J. Phys. Chem. A 2006, 110, 4702-4711. "Geometry and Solvent Dependence of the Electronic Spectra of the Amide Group and Consequences for Peptide Circular Dichroism." pdf

[59] Kapitan, J.; Baumruk, V.; Kopecky, V.; Bour, P. J. Phys. Chem. A 2006, 110, 4689-4696. "Conformational Flexibility of L-Alanine Zwitterion Determines Shapes of Raman and Raman Optical Activity Spectral Bands". pdf

[58] Kapitan,J.; Baumruk, V.; Kopecky,.; Bour, P. J. Am. Chem. Soc. 2006, 128, 2438-2443. "Demonstration of the Ring Conformation in Polyproline by the Raman Optical Activity" pdf

[57] Bour, P.; Keiderling, T. A. J. Phys. Chem. B 2005, 109, 23687-23697. " Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure: Method Comparisons with the Trpzip Model Hairpin" pdf

[56] Bour, P.; Budesinsky, M.; Spirko, V.; Kapitan, J; Sebestik, J.; Sychrovsky, V. J. Am. Chem. Soc. 2005, 127, 17079-17089. "A Complete Set of NMR Chemical Shifts and Spin-Spin Coupling Constants for L-Alanyl-L-alanine Zwitterion and Analysis of Its Conformational Behavior." pdf

[55] Bour, P. Collect. Czech. Chem. Commun. 2005, 70, 1315-1340. "Convergence properties of the normal mode optimization and its combination with molecular geometry constraints". pdf

[54] Bour, P.; Andrushchenko, V.; Kabelac, M.; Maharaj, V.; Wieser, H. J. Phys. Chem. B 2005, 109, 20579-20587. "Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides". pdf

[53] Bernatkova, M.; Dvorakova, H.; Adrioletti, B.; Kral, V.; Bour, P. J. Phys. Chem. A 2005, 109, 5518-5526. "Conformational Transitions of Calixphyrin Derivatives Monitored by Temperature-Dependent NMR Spectroscopy. Ab Initi Interpretation of the Spectra." pdf

[52] Bour, P.; Michalik, D.; Kapitan, J. J. Chem. Phys. 2005, 122, 144501. "Empirical solvent correction for multiple amide group vibrational modes" pdf

[51] Bour, P.; Keiderling, T. A. J. Phys. Chem. B 2005, 109, 5348-5357. "Ab Initio Modeling of Amide I Coupling in Antiparallel beta-sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra."" pdf

[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] Urbanova, 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 Vladim°r 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] Bour, P.; Zaruba, K.; Urbanova, M.; Setnicka, V.; Matejka, P.; Fiedler, P.; Kral, V.; Volka, K. 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." pdf

[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. 1999,110, 2836-2843. "Sum-Over-States calculation of the nuclear spin-spin coupling constants." pdf

[21] Rauk, A.; McCann, J.L.; Wieser, H.; Bour, P.; Elínatanov, 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." pdf

[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" pdf

[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." pdf

[16] Bour,P.; McCann, J; Wieser, H. J. Phys. Chem. A 1997, 101, 9783-9790. "Vibrational Circular Dichroism Study of (-)-Sparteine" pdf

[15] Tam, C.N.; Bour, P.; Eckert, J.; Trouw, F.R. J. Phys. Chem. A 1997, 101, 5877-5884. "Inelastic Neutron Scattering Study of Hydrogen Bonded Solid Formamide at 15 K" pdf

[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" pdf

[12] Bour, P.; Sopkova;, J.; Bednarova;, L.; Malon, 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." pdf

[11] Bour, P. Chem. Phys. Lett. 1997, 265, 65. "Approximate Ab Initio Calculation of Polarizabilities via the Excitation Scheme" pdf

[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" pdf

[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" pdf

[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". pdf

[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" pdf

[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" pdf

[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." pdf

[4] P. Bour and L. Bednarova J.Phys.Chem. 1995, 99, 5961-5966. "Anharmonic Force Field of Formamide. A Computational Study." pdf

[3] Bour, P. J.Phys.Chem. 1994, 98, 8862-8865. "Anharmonic Corrections to Vibrational Energies of Molecules: Water and Dideuteriooxirane." pdf

[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" pdf

[1] Bour, P.; Keiderling, T.A. J.Am.Chem.Soc. 1992, 114, 9100-9105."Computational Evaluation of the Coupled Oscillator Model in the Vibrational Circular Dichroism of Selected Small Molecules." pdf

Book Chapters

EndNote list
Keiderling, T. A., Silva, R. A. G. D., Decatur, S. M. & Bour, P. (1999)."Thermal unfolding of helical alanine containing peptides. Isotopic labeling yields site-secific conformations with VCD. In Spectrocopy of Biological Molecules: New Directions (Greve, J., Puppels, G. J. & Otto, C., eds.), pp. 63-64. Kluwer AP, Dortrecht.

Kubelka, J., Silva, R. A. G. D., Bour, P., Decatur, S. M. & Keiderling, T. A. (2002). Chirality in peptide vibrations. Ab Initio computational studies of length, solvation, hydrogen bond, dipole coupling and isotope effects on vibrational CD. In Chirality: Physical Chemistry. ACS Symposium Series (Hicks, J. M., ed.), Vol. 810, pp. 50-64. American Chemical Society, Washington DC.

Kubelka, J., Bour, P. & Keiderling, T. A. (2009). Quantum Mechanical Calculations of Peptide Vibrational Force Fields and Spectral Intensities. In Advances in Biomedical Spectroscopy, Biological and Biomedical Infrared Spectroscopy (Barth, A. & Haris, P. I., eds.), Vol. 2, pp. 178-223. IOS Press Amsterdam.

Polyanichko, A. M., Andrushchenko, V., Bour, P. & Wieser, H. (2011). Vibrational Circular Dichroism Studies of Biological Macromolecules and their Complexes In Circular Dichroism: Theory and Spectroscopy (Rodgers, D. S., ed.). Nova, Hauppauge, NY.

Benda, L., Stepanek, P., Kaminsky, J.; Bour, P. (2012). Spectroscopic Analysis: Ab initio Calculation of Chiroptical Spectra. In Comprehensive Chirality (Tranter, G. E., ed.), pp. 8.27. Elsevier Ltd., Oxford.

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Download
MCM 95 windows
MCM 95 linux
Other Programs

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.

 

 

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