A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs

Journal of Chemical Theory and Computation ◽

10.1021/ct050102l ◽

2005 ◽

Vol 1 (6) ◽

pp. 1275-1285 ◽

Author(s):

Timothy J. Giese ◽

Edward C. Sherer ◽

Christopher J. Cramer ◽

Darrin M. York

Keyword(s):

Nucleic Acid ◽

Quantum Model ◽

Acid Base ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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Hydrogen-Bonded Nucleic Acid Base Pairs Containing Unusual Base Tautomers: Complete Basis Set Calculations at the MP2 and CCSD(T) Levels

The Journal of Physical Chemistry B ◽

10.1021/jp0661692 ◽

2007 ◽

Vol 111 (3) ◽

pp. 641-645 ◽

Author(s):

Jaroslav Rejnek ◽

Pavel Hobza

Keyword(s):

Nucleic Acid ◽

Basis Set ◽

Acid Base ◽

Complete Basis ◽

Nucleic Acid Base ◽

Complete Basis Set ◽

Hydrogen Bonded

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Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions

Nucleic Acids Research ◽

10.1093/nar/gkj491 ◽

2006 ◽

Vol 34 (3) ◽

pp. 865-879 ◽

Author(s):

R. Oliva

Keyword(s):

Nucleic Acid ◽

Acid Base ◽

Nucleic Acid Base ◽

Tertiary Interactions ◽

Hydrogen Bonded

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At Nonzero Temperatures, Stacked Structures of Methylated Nucleic Acid Base Pairs and Microhydrated Nonmethylated Nucleic Acid Base Pairs are Favored over Planar Hydrogen-Bonded Structures: A Molecular Dynamics Simulations Study

Chemistry - A European Journal ◽

10.1002/1521-3765(20010518)7:10<2067::aid-chem2067>3.0.co;2-s ◽

2001 ◽

Vol 7 (10) ◽

pp. 2067-2074 ◽

Author(s):

Martin Kabeláč ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Nucleic Acid ◽

Molecular Dynamics Simulations ◽

Acid Base ◽

Nucleic Acid Base ◽

Dynamics Simulations ◽

Hydrogen Bonded

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Stabilization Energies of the Hydrogen-Bonded and Stacked Structures of Nucleic Acid Base Pairs in the Crystal Geometries of CG, AT, and AC DNA Steps and in the NMR Geometry of the 5‘-d(GCGAAGC)-3‘ Hairpin: Complete Basis Set Calculations at the MP2 and CCSD(T) Levels

The Journal of Physical Chemistry A ◽

10.1021/jp046738a ◽

2005 ◽

Vol 109 (6) ◽

pp. 1131-1136 ◽

Author(s):

Iwona Da̧bkowska ◽

Haydee Valdes Gonzalez ◽

Petr Jurečka ◽

Pavel Hobza

Keyword(s):

Nucleic Acid ◽

Basis Set ◽

Acid Base ◽

Complete Basis ◽

Nucleic Acid Base ◽

Complete Basis Set ◽

Stabilization Energies ◽

Hydrogen Bonded

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Hartree-fock Study of Hydrogen-bonded Systems in the Absence of Basis-set Superposition Error the Nucleic-acid Base Pairs

New Trends in Quantum Systems in Chemistry and Physics - Progress in Theoretical Chemistry and Physics ◽

10.1007/0-306-46951-0_16 ◽

2005 ◽

pp. 313-333

Author(s):

A. Famulari ◽

M. Sironi ◽

E. Gianinetti ◽

M. Raimondi

Keyword(s):

Nucleic Acid ◽

Basis Set ◽

Acid Base ◽

Basis Set Superposition Error ◽

Hartree Fock ◽

Nucleic Acid Base ◽

Hydrogen Bonded Systems ◽

Hydrogen Bonded

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ChemInform Abstract: Hydrogen-Bonded and Stacked Homo- and Heterodimers of Systems Modeling Nucleic Acid Base Pairs

10.1002/chin.200012283 ◽

2010 ◽

Vol 31 (12) ◽

pp. no-no

Author(s):

A. M. Plokhotnichenko ◽

E. D. Radchenko ◽

S. G. Stepanian ◽

L. Adamowicz

Keyword(s):

Nucleic Acid ◽

Systems Modeling ◽

Acid Base ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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ChemInform Abstract: At Nonzero Temperatures, Stacked Structures of Methylated Nucleic Acid/Base Pairs and Mircrohydrated Nonmethylated Nucleic Acid Base Pairs are Favored over Planar Hydrogen-Bonded Structures: A Molecular Dynamics Simulations Study.

10.1002/chin.200205215 ◽

2010 ◽

Vol 33 (5) ◽

pp. no-no

Author(s):

Martin Kabelac ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Nucleic Acid ◽

Molecular Dynamics Simulations ◽

Acid Base ◽

Nucleic Acid Base ◽

Dynamics Simulations ◽

Hydrogen Bonded

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Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

Journal of the American Chemical Society ◽

10.1021/ja048436s ◽

2004 ◽

Vol 126 (32) ◽

pp. 10142-10151 ◽

Author(s):

Jiří Šponer ◽

Petr Jurečka ◽

Pavel Hobza

Keyword(s):

Nucleic Acid ◽

Interaction Energies ◽

Acid Base ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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The Study of the Stability of Watson-Crick Nucleic Acid Base Pairs in Water and Dimethyl Sulfoxide: Computer Simulation by the Monte Carlo Method

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.1997.10508947 ◽

1997 ◽

Vol 15 (1) ◽

pp. 69-80 ◽

Author(s):

Victor I. Danilov ◽

Nikolay V. Zheltovsky ◽

Oleg N. Slyusarchuk ◽

Valery I. Poltev ◽

James L. Alderfer

Keyword(s):

Computer Simulation ◽

Monte Carlo ◽

Nucleic Acid ◽

Monte Carlo Method ◽

Dimethyl Sulfoxide ◽

Acid Base ◽

The Monte Carlo Method ◽

Nucleic Acid Base ◽

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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 ◽

10.1021/jp953306e ◽

1996 ◽

Vol 100 (13) ◽

pp. 5590-5596 ◽

Author(s):

Jiří Šponer ◽

Jerzy Leszczyński ◽

Pavel Hobza

Keyword(s):

Nucleic Acid ◽

Ab Initio ◽

Base Stacking ◽

Acid Base ◽

Empirical Potential ◽

Nucleic Acid Base

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