Crossref Cited-by Linking logo

Collect. Czech. Chem. Commun. 2003, 68, 2231-2282

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

Jiří Šponera,b,* and Pavel Hobzab,*

a Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
b J. Heyrovský Institute of Physical Chemistry and Centre for Complex Molecular Systems and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic

Crossref Cited-by Linking

  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • Dračínský Martin, Jansa Petr, Bouř Petr: Computational and Experimental Evidence of Through-Space NMR Spectroscopic J Coupling of Hydrogen Atoms. Chemistry A European Journal 2012, 18, 981. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • Lippert Bernhard, Gupta Deepali: Promotion of rare nucleobase tautomers by metal binding. Dalton Trans. 2009, 4619. <>
  • Saha Saumitra, Wang Feng: N-K spectra of adenine amino tautomers. J Phys Conf Ser 2009, 185, 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. <>
  • Kapitán Josef, Hecht Lutz, Bouř Petr: Raman spectral evidence of methyl rotation in liquid toluene. Phys. Chem. Chem. Phys. 2008, 10, 1003. <>
  • 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. <>
  • Kabeláč Martin, Sherer Edward C., Cramer Christopher J., Hobza Pavel: DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations versus Experiment in Vacuo. Chem. Eur. J. 2007, 13, 2067. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • 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. <>
  • Kabeláč Martin, Hobza Pavel: Hydration and stability of nucleic acid bases and base pairs. Phys. Chem. Chem. Phys. 2007, 9, 903. <>
  • 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. <>
  • Tureček František: Modeling Deoxyribonucleic Acid and Ribonucleic Acid Damage in the Gas Phase. Eur J Mass Spectrom (Chichester) 2007, 13, 89. <>
  • 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. Chem. Eur. J. 2006, 12, 280. <>
  • Zendlová Lucie, Hobza Pavel, Kabeláč Martin: Potential Energy Surfaces of the Microhydrated Guanine⋅⋅⋅Cytosine Base Pair and its Methylated Analogue. Chem. Eur. J. of Chem. Phys. 2006, 7, 439. <>
  • 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. Quantum Chem. 2006, 106, 913. <>
  • 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. <>
  • 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, 204301. <>
  • Downton M. T., Wang F.: Differentiation of adenine non-planarity in valence molecular orbitals. Molec Sim 2006, 32, 667. <>
  • 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. <>
  • Harris Sarah Anne: Modelling the biomechanical properties of DNA using computer simulation. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2006, 364, 3319. <>
  • Hobza Pavel, Zahradník Rudolf, Müller-Dethlefs Klaus: The World of Non-Covalent Interactions: 2006. Collect. Czech. Chem. Commun. 2006, 71, 443. <>
  • 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. <>
  • 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, 204322. <>
  • Bera P. P., Schaefer H. F.: (G-H) -C and G-(C-H)  radicals derived from the guanine{middle dot}cytosine base pair cause DNA subunit lesions. Proceedings of the National Academy of Sciences 2005, 102, 6698. <>
  • Guallar V., Borrelli K. W.: A binding mechanism in protein-nucleotide interactions: Implication for U1A RNA binding. Proceedings of the National Academy of Sciences 2005, 102, 3954. <>
  • 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. <>
  • 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. Tetrahetron Lett 2004, 45, 6259. <>