Citations (47)
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Read on this site (7)
Svatava Neugebauerová & Jaroslav Kypr. (2000) Invariant and Variable Base Stacking Geometries in B-DNA and A-DNA. Journal of Biomolecular Structure and Dynamics 18:1, pages 73-81.
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J. Šponer, J.V. Burda, P. Mejzlík, J. Leszczynski & P. Hobza. (1997) Hydrogen-bonded Trimers of DNA Bases and their Interaction with Metal Cations: Ab initio Quantum-chemical and Empirical Potential Study. Journal of Biomolecular Structure and Dynamics 14:5, pages 613-628.
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Jiří Šponer, Jerzy Leszczynski, Vladimír Vetterl & Pavel Hobza. (1996) Base Stacking and Hydrogen Bonding in Protonated Cytosine Dimer: The Role of Molecular ion-dipole and Induction Interactions. Journal of Biomolecular Structure and Dynamics 13:4, pages 695-706.
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Jiří Šponer & Pavel Hobza. (1994) G.C. Base Pair in Parallel-Stranded DNA—A Novel Type of Base Pairing: An ab initio Quantum Chemical Study. Journal of Biomolecular Structure and Dynamics 12:3, pages 671-680.
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P. Martel, B. Hennion, D. Durand & P. Calmettes. (1994) Low-Frequency Vibrations of a Nucleoside Analog. Journal of Biomolecular Structure and Dynamics 12:2, pages 401-411.
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J. Šponer, J. Jursa & J. Kypr. (1994) Interaction Between the Guanine Amino Group and the Adenine Six Membered Ring Stabilizes the Unusual Conformation of the CpA Step in B-DNA. Nucleosides and Nucleotides 13:8, pages 1669-1677.
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J. Sponer, R. Burcl & P. Hobza. (1994) Interactions Between Amino Groups in DNA. An Ab Initio Study and a Comparison with Empirical Potentials. Journal of Biomolecular Structure and Dynamics 11:6, pages 1357-1376.
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Articles from other publishers (40)
Manuel Rieger & Martin Zacharias. (2022) Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations. The Journal of Physical Chemistry B 126:20, pages 3640-3647.
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Martin Zacharias. (2020) Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. The Journal of Physical Chemistry B 124:46, pages 10345-10352.
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Holger Kruse & Jiří Šponer. (2019) Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. The Journal of Physical Chemistry A 123:42, pages 9209-9222.
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Jiří Šponer, Manoj K. Shukla, Jing Wang & Jerzy Leszczynski. 2017. Handbook of Computational Chemistry. Handbook of Computational Chemistry
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Jiří Šponer, Manoj K. Shukla, Jing Wang & Jerzy Leszczynski. 2016. Handbook of Computational Chemistry. Handbook of Computational Chemistry
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Holger Kruse, Marek Havrila & Jiřı́ Šponer. (2014) QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. Journal of Chemical Theory and Computation 10:6, pages 2615-2629.
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E.L. Albuquerque, U.L. Fulco, V.N. Freire, E.W.S. Caetano, M.L. Lyra & F.A.B.F. de Moura. (2014) DNA-based nanobiostructured devices: The role of quasiperiodicity and correlation effects. Physics Reports 535:4, pages 139-209.
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Miroslav Krepl, Marie Zgarbová, Petr Stadlbauer, Michal Otyepka, Pavel Banáš, Jaroslav Koča, Thomas E. CheathamIIIIII, Petr Jurečka & Jiří Šponer. (2012) Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. Journal of Chemical Theory and Computation 8:7, pages 2506-2520.
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Pavel Banáš, Arnošt Mládek, Michal Otyepka, Marie Zgarbová, Petr Jurečka, Daniel Svozil, Filip Lankaš & Jiří Šponer. (2012) Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. Journal of Chemical Theory and Computation 8:7, pages 2448-2460.
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Jiřı́ Šponer, Manoj K. Shukla & Jerzy Leszczynski. 2012. Handbook of Computational Chemistry. Handbook of Computational Chemistry
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F. F. MaiaJr.Jr., V. N. Freire, E. W. S. Caetano, D. L. Azevedo, F. A. M. Sales & E. L. Albuquerque. (2011) Anhydrous crystals of DNA bases are wide gap semiconductors. The Journal of Chemical Physics 134:17.
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Jiří Šponer, Judit E. Šponer, Anton I. Petrov & Neocles B. Leontis. (2010) Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?. The Journal of Physical Chemistry B 114:48, pages 15723-15741.
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Daniel SvozilPavel HobzaJiří Šponer. (2009) 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?. The Journal of Physical Chemistry B 114:2, pages 1191-1203.
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Claudio A. Morgado, Petr Jurečka, Daniel Svozil, Pavel Hobza & Jiří Šponer. (2009) Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description. Journal of Chemical Theory and Computation 5:6, pages 1524-1544.
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Ivana Beššeová, Michal Otyepka, Kamila Réblová & Jiří Šponer. (2009) Dependence of A-RNA simulations on the choice of the force field and salt strength. Physical Chemistry Chemical Physics 11:45, pages 10701.
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Piotr Cysewski. (2008) The post-SCF quantum chemistry characteristics of the energetic heterogeneity of stacked guanine–guanine pairs found in B-DNA and A-DNA crystals. Journal of Molecular Structure: THEOCHEM 865:1-3, pages 36-43.
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Jiří Šponer, Petr Jurečka, Ivan Marchan, F. Javier Luque, Modesto Orozco & Pavel Hobza. (2006) Nature of Base Stacking: Reference Quantum‐Chemical Stacking Energies in Ten Unique B‐DNA Base‐Pair Steps. Chemistry – A European Journal 12:10, pages 2854-2865.
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John A. Rose & Akira Suyama. (2004) Physical modeling of biomolecular computers: Models, limitations, and experimental validation. Natural Computing 3:4, pages 411-426.
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Petr Jurečka, Jiří Šponer & Pavel Hobza. (2004) Potential Energy Surface of the Cytosine Dimer: MP2 Complete Basis Set Limit Interaction Energies, CCSD(T) Correction Term, and Comparison with the AMBER Force Field. The Journal of Physical Chemistry B 108:17, pages 5466-5471.
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P.S Kushwaha, Anil Kumar & P.C Mishra. (2004) Electronic transitions of guanine tautomers, their stacked dimers, trimers and sodium complexes. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 60:3, pages 719-728.
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Sebastian Wärmländer, Judit E. Sponer, Jiři Sponer & Mikael Leijon. (2002) The Influence of the Thymine C5 Methyl Group on Spontaneous Base Pair Breathing in DNA. Journal of Biological Chemistry 277:32, pages 28491-28497.
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Lihua Wang, Brian E. Hingerty, A.R. Srinivasan, Wilma K. Olson & Suse Broyde. (2002) Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions. Biophysical Journal 83:1, pages 382-406.
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Filip Lankaš, Thomas E. CheathamIIIIII, Nad’a Špačáková, Pavel Hobza, Jörg Langowski & Jiří Šponer. (2002) Critical Effect of the N2 Amino Group on Structure, Dynamics, and Elasticity of DNA Polypurine Tracts. Biophysical Journal 82:5, pages 2592-2609.
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Piotr Cieplak. 2002. Encyclopedia of Computational Chemistry. Encyclopedia of Computational Chemistry.
Patrick Gendron, Sébastien Lemieux & François Major. (2001) Quantitative analysis of nucleic acid three-dimensional structures. Journal of Molecular Biology 308:5, pages 919-936.
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Ji?� ?poner, Jerzy Leszczynski & Pavel Hobza. (2001) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 61:1, pages 3-31.
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Filip Lankaš, Jiřı́ Šponer, Pavel Hobza & Jörg Langowski. (2000) Sequence-dependent elastic properties of DNA 1 1Edited by I. Tinoco. Journal of Molecular Biology 299:3, pages 695-709.
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E. B. Starikov. (2000) Nucleic acids as objects of material science: Importance of quantum chemical and quantum mechanical studies. International Journal of Quantum Chemistry 77:5, pages 859-870.
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Jiande Gu, Jerzy Leszczynski & Manju Bansal. (1999) A new insight into the structure and stability of Hoogsteen hydrogen-bonded G-tetrad: an ab initio SCF study. Chemical Physics Letters 311:3-4, pages 209-214.
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Pavel Hobza, Martin Kabel�?Ji?� ?poner, Petr Mejzl�k & Ji?� Vondr�?ek. (1997) Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results. Journal of Computational Chemistry 18:9, pages 1136-1150.
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J. Šponer & P. Hobza. (1997) MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 267:3-4, pages 263-270.
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Vladimı́r Špirko, Jiřı́ Šponer & Pavel Hobza. (1997) Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs. The Journal of Chemical Physics 106:4, pages 1472-1479.
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Christopher A. Hunter & Xiang-Jun Lu. (1997) DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. Journal of Molecular Biology 265:5, pages 603-619.
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Jire� Seponer, Jerzy Leszczynski & Pavel Hobza. (1996) Base stacking in cytosine dimer. A comparison of correlatedab initio calculations with three empirical potential models and density functional theory calculations. Journal of Computational Chemistry 17:7, pages 841-850.
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Ji?� ?poner & Pavel Hobza. (1996) DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations. International Journal of Quantum Chemistry 57:5, pages 959-970.
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H.A. Gabb, S.R. Sanghani, C.H. Robert & C. Prévost. (1996) Finding and visualizing nucleic acid base stacking. Journal of Molecular Graphics 14:1, pages 6-11.
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Jiří Šponer, Jerzy Leszczyński & Pavel Hobza. (1996) Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs. The Journal of Physical Chemistry 100:13, pages 5590-5596.
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