Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculationsHOBZA, Pavel; SPONER, Jiri.Journal of the American Chemical Society. 2002, Vol 124, Num 39, pp 11802-11808, issn 0002-7863, 7 p.Article

Indirect NMR spin-spin coupling constants ³J(P,C) and ²J(P,H) across the P-O-H-C link can be used for structure determination of nucleic acidsSYCHROVSKY, Vladimfr; SPONER, Jiri; TRANTIREK, Lukas et al.Journal of the American Chemical Society. 2006, Vol 128, Num 21, pp 6823-6828, issn 0002-7863, 6 p.Article

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairsJURECKA, Petr; SPONER, Jiri; CERNY, Jiri et al.PCCP. Physical chemistry chemical physics (Print). 2006, Vol 8, Num 17, pp 1985-1993, issn 1463-9076, 9 p.Article

Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanineSYCHROVSKY, Vladimir; SPONER, Jiri; HOBZA, Pavel et al.Journal of the American Chemical Society. 2004, Vol 126, Num 2, pp 663-672, issn 0002-7863, 10 p.Article

The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT studyBURDA, Jaroslav V; SPONER, Jiri; LESZCZYNSKI, Jerzy et al.PCCP. Physical chemistry chemical physics (Print). 2001, Vol 3, Num 19, pp 4404-4411, issn 1463-9076Article

Accurate interaction energies of hydrogen-bonded nucleic acid base pairsSPONER, Jiri; JURECKA, Petr; HOBZA, Pavel et al.Journal of the American Chemical Society. 2004, Vol 126, Num 32, pp 10142-10151, issn 0002-7863, 10 p.Article

Theoretical study of the guanine → 6-thioguanine substitution in duplexes, triplexes, and tetraplexesSPACKOVA, Nad'A; CUBERO, Elena; SPONER, Jiri et al.Journal of the American Chemical Society. 2004, Vol 126, Num 44, pp 14642-14650, issn 0002-7863, 9 p.Article

Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and TetraloopsKREPL, Miroslav; REBLOVA, Kamila; KOCA, Jaroslav et al.The Journal of physical chemistry. B. 2013, Vol 117, Num 18, pp 5540-5555, issn 1520-6106, 16 p.Article

Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditionsSPONER, Judit E; MLADEK, Arnost; SPONER, Jiří et al.PCCP. Physical chemistry chemical physics (Print). 2013, Vol 15, Num 17, pp 6235-6242, issn 1463-9076, 8 p.Article

Nature and magnitude of aromatic stacking of nucleic acid basesSPONER, Jiri; RILEY, Kevin E; HOBZA, Pavel et al.PCCP. Physical chemistry chemical physics (Print). 2008, Vol 10, Num 19, pp 2595-2610, issn 1463-9076, 16 p.Article

DNA deformability at the base pair levelLANKAS, Filip; SPONER, Jiri; LANGOWSKI, Jörg et al.Journal of the American Chemical Society. 2004, Vol 126, Num 13, pp 4124-4125, issn 0002-7863, 2 p.Article

Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acidsSPONER, Judit E; SYCHROVSKY, Vladimir; HOBZA, Pavel et al.PCCP. Physical chemistry chemical physics (Print). 2004, Vol 6, Num 10, pp 2772-2780, issn 1463-9076, 9 p.Article

Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditionsSZABLA, Rafat; SPONER, Judit E; SPONER, Jiří et al.PCCP. Physical chemistry chemical physics (Print). 2013, Vol 15, Num 20, pp 7812-7818, issn 1463-9076, 7 p.Article

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexesMORGADO, Claudio A; SVOZIL, Daniel; TURNER, Douglas H et al.PCCP. Physical chemistry chemical physics (Print). 2012, Vol 14, Num 36, pp 12580-12591, issn 1463-9076, 12 p.Article

Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNASYCHROVSKY, Vladimir; MÜLLER, Norbert; SCHNEIDER, Bohdan et al.Journal of the American Chemical Society. 2005, Vol 127, Num 42, pp 14663-14667, issn 0002-7863, 5 p.Article

Dependence of A-RNA simulations on the choice of the force field and salt strengthBESSEOVA, Ivana; OTYEPKA, Michal; REBLOVA, Kamila et al.PCCP. Physical chemistry chemical physics (Print). 2009, Vol 11, Num 45, pp 10701-10711, issn 1463-9076, 11 p.Article

Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNAMLADEK, Arnost; SPONER, Jiří; SUMPTER, Bobby G et al.PCCP. Physical chemistry chemical physics (Print). 2011, Vol 13, Num 23, pp 10869-10871, issn 1463-9076, 3 p.Article

Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin―Ricin Internal LoopHAVRILA, Marek; REBLOVA, Kamila; ZIRBEL, Craig L et al.The Journal of physical chemistry. B. 2013, Vol 117, Num 46, pp 14302-14319, issn 1520-6106, 18 p.Article

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4', 6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential studvREHA, David; KABELAC, Martin; RYJACEK, Filip et al.Journal of the American Chemical Society. 2002, Vol 124, Num 13, pp 3366-3376, issn 0002-7863Article

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptionsMORGADO, Claudio A; JURECKA, Petr; SVOZIL, Daniel et al.PCCP. Physical chemistry chemical physics (Print). 2010, Vol 12, Num 14, pp 3522-3534, issn 1463-9076, 13 p.Article

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studiesSPONER, Jiří; MLADEK, Arnost; SPONER, Judit E et al.PCCP. Physical chemistry chemical physics (Print). 2012, Vol 14, Num 44, pp 15257-15277, issn 1463-9076, 21 p.Article

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar―phosphate backbone and their comparison with modern density functional theoryMLADEK, Arnost; KREPL, Miroslav; SVOZIL, Daniel et al.PCCP. Physical chemistry chemical physics (Print). 2013, Vol 15, Num 19, pp 7295-7310, issn 1463-9076, 16 p.Article