J
Jiří Šponer
Researcher at Academy of Sciences of the Czech Republic
Publications - 351
Citations - 21710
Jiří Šponer is an academic researcher from Academy of Sciences of the Czech Republic. The author has contributed to research in topics: Ab initio & Molecular dynamics. The author has an hindex of 73, co-authored 329 publications receiving 19600 citations. Previous affiliations of Jiří Šponer include National University of Mongolia & University of Utah.
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Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.
TL;DR: MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together.
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Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations.
Pavel Hobza,Jiří Šponer +1 more
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Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
Marie Zgarbová,Michal Otyepka,Michal Otyepka,Jiří Šponer,Jiří Šponer,Arnošt Mládek,Pavel Banáš,Pavel Banáš,Thomas E. Cheatham,Petr Jurečka +9 more
TL;DR: The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations, and improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures.
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Density functional theory and molecular clusters
TL;DR: DFT interaction energy exhibits the same basis set extension dependence as the Hartree‐Fock (HF) interaction energy, so the Boys‐Bernardi function counterpoise procedure should be employed for elimination of the DFT basis set superposition error.
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Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.
TL;DR: This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years and provides an overview of key electronic properties of standard and selected modified nucleobases.