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For: Sychrovský V, Vokácová Z, Sponer J, Spacková N, Schneider B. Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids. J Phys Chem B 2007;110:22894-902. [PMID: 17092041 DOI: 10.1021/jp065000l] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Szántó JK, Dietschreit JCB, Shein M, Schütz AK, Ochsenfeld C. Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment. J Chem Theory Comput 2024;20:2433-2444. [PMID: 38497488 DOI: 10.1021/acs.jctc.3c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
2
Taghavi A, Riveros I, Wales DJ, Yildirim I. Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations. J Chem Theory Comput 2022;18:3637-3653. [PMID: 35652685 DOI: 10.1021/acs.jctc.2c00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
3
Fukal J, Buděšínský M, Páv O, Jurečka P, Zgarbová M, Šebera J, Sychrovský V. The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31 P NMR shift in DNA. J Comput Chem 2022;43:132-143. [PMID: 34729803 DOI: 10.1002/jcc.26778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/11/2022]
4
Krivdin LB. Recent advances in computational 31 P NMR: Part 2. Spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020;58:500-511. [PMID: 31808570 DOI: 10.1002/mrc.4973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
5
Fukal J, Páv O, Buděšínský M, Rosenberg I, Šebera J, Sychrovský V. Structural interpretation of the 31P NMR chemical shifts in thiophosphate and phosphate: key effects due to spin–orbit and explicit solvent. Phys Chem Chem Phys 2019;21:9924-9934. [DOI: 10.1039/c9cp01460h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
6
Fukal J, Páv O, Buděšínský M, Šebera J, Sychrovský V. The benchmark of 31P NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate. Phys Chem Chem Phys 2017;19:31830-31841. [DOI: 10.1039/c7cp06969c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
7
Gil-Ley A, Bottaro S, Bussi G. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics. J Chem Theory Comput 2016;12:2790-8. [PMID: 27153317 PMCID: PMC4910146 DOI: 10.1021/acs.jctc.6b00299] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/30/2022]
8
Čech P, Kukal J, Černý J, Schneider B, Svozil D. Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics 2013;14:205. [PMID: 23800225 PMCID: PMC3694522 DOI: 10.1186/1471-2105-14-205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/28/2013] [Indexed: 12/03/2022]  Open
9
Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013;42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
10
Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012;14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
11
Benda L, Sochorová Vokáčová Z, Straka M, Sychrovský V. Correlating the 31P NMR chemical shielding tensor and the 2J(P,C) spin-spin coupling constants with torsion angles ζ and α in the backbone of nucleic acids. J Phys Chem B 2012;116:3823-33. [PMID: 22380464 DOI: 10.1021/jp2099043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
12
Dračínský M, Pohl R, Slavětínská L, Hřebabecký H, Buděšínský M. The determination of sulfoxide configuration in five-membered rings using NMR spectroscopy and DFT calculations. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.tetasy.2011.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
13
Benda L, Schneider B, Sychrovský V. Calculating the Response of NMR Shielding Tensor σ(31P) and 2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+ Cation. J Phys Chem A 2011;115:2385-95. [DOI: 10.1021/jp1114114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
14
Dračínský M, Pohl R, Slavětínská L, Janků J, Buděšínský M. The determination of sulfoxide configuration in six-membered rings using NMR spectroscopy and DFT calculations. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.tetasy.2011.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
15
Ebrahimi A, Habibi-khorassani M, Haghani A. Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR, NBO and AIM analyses. Mol Phys 2011. [DOI: 10.1080/00268976.2010.521781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
16
Šponer J, Šponer JE, Petrov AI, Leontis NB. Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B 2010;114:15723-41. [PMID: 21049899 PMCID: PMC4868365 DOI: 10.1021/jp104361m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
17
Přecechtělová J, Novák P, Munzarová ML, Kaupp M, Sklenář V. Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations. J Am Chem Soc 2010;132:17139-48. [DOI: 10.1021/ja104564g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
18
Dracínský M, Pohl R, Slavetínská L, Budesínský M. Observed and calculated 1H and 13C chemical shifts induced by the in situ oxidation of model sulfides to sulfoxides and sulfones. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010;48:718-726. [PMID: 20661941 DOI: 10.1002/mrc.2658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
19
Gilg K, Mayer T, Ghaschghaie N, Klüfers P. The metal-binding sites of glycose phosphates. Dalton Trans 2009:7934-45. [PMID: 19771356 DOI: 10.1039/b909431h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
20
Vokáčová Z, Bickelhaupt FM, Šponer J, Sychrovský V. Structural Interpretation of J Coupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Pairing. J Phys Chem A 2009;113:8379-86. [DOI: 10.1021/jp902473v] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
21
Vokácová Z, Budĕsínský M, Rosenberg I, Schneider B, Sponer J, Sychrovský V. Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings. J Phys Chem B 2009;113:1182-91. [PMID: 19128019 DOI: 10.1021/jp809762b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
22
Pedersoli S, Tormena CF, dos Santos FP, Contreras RH, Rittner R. Stereochemical behavior of 1JCH and 2JCH NMR coupling constants in α-substituted acetamides. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
23
Svozil D, Sponer JE, Marchan I, Pérez A, Cheatham TE, Forti F, Luque FJ, Orozco M, Sponer J. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B 2008;112:8188-97. [PMID: 18558755 DOI: 10.1021/jp801245h] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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