Collection of Czechoslovak Chemical Communications - digital archive 

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• Moe May Myat, Benny Jonathan, Liu Jianbo: Collision-induced dissociation of homodimeric and heterodimeric radical cations of 9-methylguanine and 9-methyl-8-oxoguanine: correlation between intra-base pair proton transfer originating from the N1–H at a Watson–Crick edge and non-statistical dissociation. Phys. Chem. Chem. Phys. 2022, 24, 9263. <https://doi.org/10.1039/D2CP00312K>
• Parkan Ali, Mirzaei Mahmoud, Tavakoli Naser, Homayouni Alireza: Molecular interactions of indomethacin and amino acids: Computational approach. MGC 2022, 21, 611. <https://doi.org/10.3233/MGC-210157>
• Liu Yue, Ma Congcong, Leonen Calvin J. A., Chatterjee Champak, Nováková Gabriela, Marek Aleš, Tureček František: Tackling a Curious Case: Generation of Charge-Tagged Guanosine Radicals by Gas-Phase Electron Transfer and Their Characterization by UV–vis Photodissociation Action Spectroscopy and Theory. J. Am. Soc. Mass Spectrom. 2021, 32, 772. <https://doi.org/10.1021/jasms.0c00459>
• Park Gyuri, Kang Byunghwa, Park Soyeon V, Lee Donghwa, Oh Seung Soo: A unified computational view of DNA duplex, triplex, quadruplex and their donor–acceptor interactions. Nucleic Acids Research 2021, 49, 4919. <https://doi.org/10.1093/nar/gkab285>
• Kaur Sarabjeet, Sharma Purshotam, Wetmore Stacey D.: Can Cyanuric Acid and 2,4,6‐Triaminopyrimidine Containing Ribonucleosides be Components of Prebiotic RNA? Insights from QM Calculations and MD Simulations. ChemPhysChem 2019, 20, 1425. <https://doi.org/10.1002/cphc.201900237>
• Kaur Sarabjeet, Sharma Purshotam, Wetmore Stacey D.: Structural and electronic properties of barbituric acid and melamine-containing ribonucleosides as plausible components of prebiotic RNA: implications for prebiotic self-assembly. Phys. Chem. Chem. Phys. 2017, 19, 30762. <https://doi.org/10.1039/C7CP06123D>
• Masoodi Hamid Reza, Bagheri Sotoodeh, Abareghi Mahsa: The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study. Journal of Biomolecular Structure and Dynamics 2016, 34, 1143. <https://doi.org/10.1080/07391102.2015.1072734>
• Hudecová Jana, Profant Václav, Novotná Pavlína, Baumruk Vladimír, Urbanová Marie, Bouř Petr: CH Stretching Region: Computational Modeling of Vibrational Optical Activity. J. Chem. Theory Comput. 2013, 9, 3096. <https://doi.org/10.1021/ct400285n>
• Dračínský Martin, Jansa Petr, Bouř Petr: Computational and Experimental Evidence of Through‐Space NMR Spectroscopic J Coupling of Hydrogen Atoms. Chemistry A European J 2012, 18, 981. <https://doi.org/10.1002/chem.201102272>
• Kessler Jiří, Jakubek Milan, Dolenský Bohumil, Bouř Petr: Binding energies of five molecular pincers calculated by explicit and implicit solvent models. J Comput Chem 2012, 33, 2310. <https://doi.org/10.1002/jcc.23063>
• Banáš Pavel, Mládek Arnošt, Otyepka Michal, Zgarbová Marie, Jurečka Petr, Svozil Daniel, Lankaš Filip, Šponer Jiří: Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J. Chem. Theory Comput. 2012, 8, 2448. <https://doi.org/10.1021/ct3001238>
• Benda Ladislav, Straka Michal, Sychrovský Vladimír, Bouř Petr, Tanaka Yoshiyuki: Detection of Mercury–TpT Dinucleotide Binding by Raman Spectra: A Computational Study. J. Phys. Chem. A 2012, 116, 8313. <https://doi.org/10.1021/jp3045077>
• Lim Siew Choo, Bowler Matthew W., Lai Ting Feng, Song Haiwei: The Ighmbp2 helicase structure reveals the molecular basis for disease-causing mutations in DMSA1. Nucleic Acids Research 2012, 40, 11009. <https://doi.org/10.1093/nar/gks792>
• Chawla Mohit, Sharma Purshotam, Halder Sukanya, Bhattacharyya Dhananjay, Mitra Abhijit: Protonation of Base Pairs in RNA: Context Analysis and Quantum Chemical Investigations of Their Geometries and Stabilities. J. Phys. Chem. B 2011, 115, 1469. <https://doi.org/10.1021/jp106848h>
• Panigrahi Swati, Pal Rahul, Bhattacharyya Dhananjay: Structure and Energy of Non-Canonical Basepairs: Comparison of Various Computational Chemistry Methods with Crystallographic Ensembles. Journal of Biomolecular Structure and Dynamics 2011, 29, 541. <https://doi.org/10.1080/07391102.2011.10507404>
• Klusák Vojtěch, Dobeš Petr, Černý Jiří, Vondrášek Jiří: How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins. Collect. Czech. Chem. Commun. 2011, 76, 605. <https://doi.org/10.1135/cccc2011033>
• Sharma Purshotam, Šponer Judit E., Šponer Jiří, Sharma Sitansh, Bhattacharyya Dhananjay, Mitra Abhijit: On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets—Quantum Chemical Insights into RNA Structural Biology. J. Phys. Chem. B 2010, 114, 3307. <https://doi.org/10.1021/jp910226e>
• Svozil Daniel, Hobza Pavel, Šponer Jiří: Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?. J. Phys. Chem. B 2010, 114, 1191. <https://doi.org/10.1021/jp910788e>
• Sharma Purshotam, Sharma Sitansh, Chawla Mohit, Mitra Abhijit: Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches. J Mol Model 2009, 15, 633. <https://doi.org/10.1007/s00894-008-0384-y>
• Wu Yan, Sa Rongjian, Li Qiaohong, Wei Yongqin, Wu Kechen: Theoretical studies on the bonding of Cd2+ to adenine and thymine: Tautomeric equilibrium and metalation in base pairing. Chemical Physics Letters 2009, 467, 387. <https://doi.org/10.1016/j.cplett.2008.11.073>
• Parchaňský Václav, Matějka Pavel, Dolenský Bohumil, Havlík Martin, Bouř Petr: Modeling of a Tröger’s tweezer and its complexation properties. Journal of Molecular Structure 2009, 934, 117. <https://doi.org/10.1016/j.molstruc.2009.06.030>
• Ran Jiong, Hobza Pavel: Nature of Bonding in Nine Planar Hydrogen-Bonded Adenine···Thymine Base Pairs. J. Phys. Chem. B 2009, 113, 2933. <https://doi.org/10.1021/jp810001v>
• Lippert Bernhard, Gupta Deepali: Promotion of rare nucleobase tautomers by metal binding. Dalton Trans. 2009, 4619. <https://doi.org/10.1039/b823087k>
• Saha Saumitra, Wang Feng: N-K spectra of adenine amino tautomers. J Phys Conf Ser 2009, 185, 012040. <https://doi.org/10.1088/1742-6596/185/1/012040>
• Neihsial Siamkhanthang, Lyngdoh Richard H. Duncan: Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search. J Comput Chem 2008, 29, 1788. <https://doi.org/10.1002/jcc.20942>
• Dkhissi Ahmed, Blossey Ralf: Metahybrid Density Functional Theory and Correlated ab Initio Studies on Microhydrated Adenine−Thymine Base Pairs. J. Phys. Chem. B 2008, 112, 9182. <https://doi.org/10.1021/jp803110n>
• Kapitán Josef, Hecht Lutz, Bouř Petr: Raman spectral evidence of methyl rotation in liquid toluene. Phys. Chem. Chem. Phys. 2008, 10, 1003. <https://doi.org/10.1039/B713965A>
• Sharma Purshotam, Mitra Abhijit, Sharma Sitansh, Singh Harjinder, Bhattacharyya Dhananjay: Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base pairs: The Trans Watson-Crick:Watson-Crick Family. Journal of Biomolecular Structure and Dynamics 2008, 25, 709. <https://doi.org/10.1080/07391102.2008.10507216>
• Kabeláč Martin, Sherer Edward C., Cramer Christopher J., Hobza Pavel: DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations versus Experiment in Vacuo. Chemistry A European J 2007, 13, 2067. <https://doi.org/10.1002/chem.200601007>
• Schreiber Marko, González Leticia: Structure and bonding of Ag(I)–DNA base complexes and Ag(I)–adenine–cytosine mispairs: An ab Initio study. J Comput Chem 2007, 28, 2299. <https://doi.org/10.1002/jcc.20743>
• Bhattacharyya Dhananjay, Koripella Siv Chand, Mitra Abhijit, Rajendran Vijay Babu, Sinha Bhabdyuti: Theoretical analysis of noncanonical base pairing interactions in RNA molecules. J Biosci 2007, 32, 809. <https://doi.org/10.1007/s12038-007-0082-4>
• Sharma Purshotam, Mitra Abhijit, Sharma Sitansh, Singh Harjinder: Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies. J Chem Sci 2007, 119, 525. <https://doi.org/10.1007/s12039-007-0066-9>
• Krishnan G.M., Kühn O.: Identifying adenine–thymine base pairing by anharmonic analysis of the hydrogen-bonded NH stretching vibrations. Chemical Physics Letters 2007, 435, 132. <https://doi.org/10.1016/j.cplett.2006.12.072>
• Harries William E.C., Khademi Shahram, Stroud Robert M.: The role of tryptophan cation���pi interactions on ammonia transport through the AmtB ammonia channel. International Congress Series 2007, 1304, 15. <https://doi.org/10.1016/j.ics.2007.07.054>
• Yao Chunxiang, Tureček František, Polce Michael J., Wesdemiotis Chrys: Proton and hydrogen atom adducts to cytosine. An experimental and computational study. Int J Mass Spectrosc 2007, 265, 106. <https://doi.org/10.1016/j.ijms.2007.01.013>
• Wolken Jill K., Yao Chunxiang, Tureček František, Polce Michael J., Wesdemiotis Chrys: Cytosine neutral molecules and cation–radicals in the gas-phase. Int J Mass Spectrosc 2007, 267, 30. <https://doi.org/10.1016/j.ijms.2007.02.016>
• Schreiber Marko, González Leticia: The role of Ag(I) ions in the electronic spectroscopy of adenine–cytosine mispairs. J Photochem Photobiol A Chem 2007, 190, 301. <https://doi.org/10.1016/j.jphotochem.2007.01.035>
• Sundaresan Neethu, Suresh Cherumuttathu H.: A Base-Sugar−Phosphate Three-Layer ONIOM Model for Cation Binding:  Relative Binding Affinities of Alkali Metal Ions for Phosphate Anion in DNA. J. Chem. Theory Comput. 2007, 3, 1172. <https://doi.org/10.1021/ct600245w>
• Černý Jiří, Jurečka Petr, Hobza Pavel, Valdés Haydée: Resolution of Identity Density Functional Theory Augmented with an Empirical Dispersion Term (RI-DFT-D):  A Promising Tool for Studying Isolated Small Peptides. J. Phys. Chem. A 2007, 111, 1146. <https://doi.org/10.1021/jp066504m>
• Andrushchenko Valery, Wieser Hal, Bouř Petr: DNA Oligonucleotide−cis-Platin Binding:  Ab Initio Interpretation of the Vibrational Spectra. J. Phys. Chem. A 2007, 111, 9714. <https://doi.org/10.1021/jp074572i>
• Kabeláč Martin, Hobza Pavel: Hydration and stability of nucleic acid bases and base pairs. Phys. Chem. Chem. Phys. 2007, 9, 903. <https://doi.org/10.1039/B614420A>
• Pluháčková Kristýna, Jurečka Petr, Hobza Pavel: Stabilisation energy of C6H6⋯C6X6 (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels. Phys. Chem. Chem. Phys. 2007, 9, 755. <https://doi.org/10.1039/B615318F>
• Tureček František: Modeling Deoxyribonucleic Acid and Ribonucleic Acid Damage in the Gas Phase. Eur J Mass Spectrom (Chichester) 2007, 13, 89. <https://doi.org/10.1255/ejms.848>
• Kubař Tomáš, Hanus Michal, Ryjáček Filip, Hobza Pavel: Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations. Chemistry A European J 2006, 12, 280. <https://doi.org/10.1002/chem.200500725>
• Zendlová Lucie, Hobza Pavel, Kabeláč Martin: Potential Energy Surfaces of the Microhydrated Guanine⋅⋅⋅Cytosine Base Pair and its Methylated Analogue. ChemPhysChem 2006, 7, 439. <https://doi.org/10.1002/cphc.200500311>
• Sen Kakali, Basu Samita, Bhattacharyya Dhananjay: Ab initio studies on excited state intramolecular electron transfer in 4‐amino‐N‐methylphthalimide and 3‐amino‐N‐methylphthalimide. Int J of Quantum Chemistry 2006, 106, 913. <https://doi.org/10.1002/qua.20866>
• Kourafalos Vassilios N., Marakos Panagiotis, Mikros Emmanuel, Pouli Nicole, Marek Jaromír, Marek Radek: Synthesis and tautomerism study of 7-substituted pyrazolo[3,4-c]pyridines. Tetrahedron 2006, 62, 11987. <https://doi.org/10.1016/j.tet.2006.09.081>
• Liu Yuemin, Hu Xiche: Molecular Determinants for Binding of Ammonium Ion in the Ammonia Transporter AmtBA Quantum Chemical Analysis. J. Phys. Chem. A 2006, 110, 1375. <https://doi.org/10.1021/jp054261c>
• Herbert Holly Elizabeth, Halls Mathew D., Hratchian Hrant P., Raghavachari Krishnan: Hydrogen-Bonding Interactions in Peptide Nucleic Acid and Deoxyribonucleic Acid:  A Comparative Study. J. Phys. Chem. B 2006, 110, 3336. <https://doi.org/10.1021/jp055865j>
• Otyepka Michal, Sklenovský Petr, Horinek Dominik, Kubař Tomáš, Hobza Pavel: How the Stabilization of INK4 Tumor Suppressor 3D Structure Evaluated by Quantum Chemical and Molecular Mechanics Calculations Corresponds Well with Experimental Results:  Interplay of Association Enthalpy, Entropy, and Solvation Effects. J. Phys. Chem. B 2006, 110, 4423. <https://doi.org/10.1021/jp056890s>
• Sundaresan Neethu, Pillai C. K. S., Suresh Cherumuttathu H.: Role of Mg2+ and Ca2+ in DNA Bending:  Evidence from an ONIOM-Based QM-MM Study of a DNA Fragment. J. Phys. Chem. A 2006, 110, 8826. <https://doi.org/10.1021/jp061774q>
• Haley Terence P., Graybill Eric R., Cybulski Slawomir M.: Ab initio calculations of dispersion coefficients for nucleic acid base pairs. The Journal of Chemical Physics 2006, 124. <https://doi.org/10.1063/1.2197832>
• Downton M. T., Wang F.: Differentiation of adenine non-planarity in valence molecular orbitals. Molec Sim 2006, 32, 667. <https://doi.org/10.1080/08927020600860911>
• Auweter Sigrid D., Oberstrass Florian C., Allain Frédéric H.-T.: Sequence-specific binding of single-stranded RNA: is there a code for recognition?. Nucleic Acids Research 2006, 34, 4943. <https://doi.org/10.1093/nar/gkl620>
• Harris Sarah Anne: Modelling the biomechanical properties of DNA using computer simulation. Phil. Trans. R. Soc. A. 2006, 364, 3319. <https://doi.org/10.1098/rsta.2006.1906>
• Hobza Pavel, Zahradník Rudolf, Müller-Dethlefs Klaus: The World of Non-Covalent Interactions: 2006. Collect. Czech. Chem. Commun. 2006, 71, 443. <https://doi.org/10.1135/cccc20060443>
• Vondrášek Jiří, Bendová Lada, Klusák Vojtěch, Hobza Pavel: Unexpectedly Strong Energy Stabilization Inside the Hydrophobic Core of Small Protein Rubredoxin Mediated by Aromatic Residues:  Correlated Ab Initio Quantum Chemical Calculations. J. Am. Chem. Soc. 2005, 127, 2615. <https://doi.org/10.1021/ja044607h>
• Kabeláč Martin, Zendlová Lucie, Řeha David, Hobza Pavel: Potential Energy Surfaces of an Adenine−Thymine Base Pair and Its Methylated Analogue in the Presence of One and Two Water Molecules:  Molecular Mechanics and Correlated Ab Initio Study. J. Phys. Chem. B 2005, 109, 12206. <https://doi.org/10.1021/jp045970d>
• Bouř Petr, Andrushchenko Valery, Kabeláč Martin, Maharaj Vanitha, Wieser Hal: Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides. J. Phys. Chem. B 2005, 109, 20579. <https://doi.org/10.1021/jp051218g>
• Brauer Brina, Gerber R. Benny, Kabeláč Martin, Hobza Pavel, Bakker Joost M., Abo Riziq Ali G., de Vries Mattanjah S.: Vibrational Spectroscopy of the G· · ·C Base Pair:  Experiment, Harmonic and Anharmonic Calculations, and the Nature of the Anharmonic Couplings. J. Phys. Chem. A 2005, 109, 6974. <https://doi.org/10.1021/jp051767m>
• Černý Jiří, Hobza Pavel: The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking. Phys. Chem. Chem. Phys. 2005, 7, 1624. <https://doi.org/10.1039/B502769C>
• Dąbkowska Iwona, Jurečka Petr, Hobza Pavel: On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level. The Journal of Chemical Physics 2005, 122. <https://doi.org/10.1063/1.1906205>
• Bera Partha Pratim, Schaefer Henry F.: (G–H) • –C and G–(C–H) • radicals derived from the guanine·cytosine base pair cause DNA subunit lesions. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6698. <https://doi.org/10.1073/pnas.0408644102>
• Guallar Victor, Borrelli Kenneth W.: A binding mechanism in protein–nucleotide interactions: Implication for U1A RNA binding. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 3954. <https://doi.org/10.1073/pnas.0500888102>
• Fanfrlík Jindřich, Rejnek Jaroslav, Hanus Michal, Hobza Pavel: Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches. Collect. Czech. Chem. Commun. 2005, 70, 1756. <https://doi.org/10.1135/cccc20051756>
• Sečkářová Pavlı́na, Marek Radek, Maliňáková Kateřina, Kolehmainen Erkki, Hocková Dana, Hocek Michal, Sklenář Vladimír: Direct determination of tautomerism in purine derivatives by low-temperature NMR spectroscopy. Tetrahedron Letters 2004, 45, 6259. <https://doi.org/10.1016/j.tetlet.2004.06.088>