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Journal of Biomolecular Structure and Dynamics Volume 11, 1994 - Issue 6
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Original Articles

Interactions Between Amino Groups in DNA. An Ab Initio Study and a Comparison with Empirical Potentials

J. Sponer J. Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic, Dolej škova 3, 18223, Prague, Czech Republic; Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, CS-612 65, Brno, Czech Republic
,
R. Burcl J. Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic, Dolej škova 3, 18223, Prague, Czech Republic; Department of Chemistry, Oakland University, Rochester, Michigan, U.S.A.
&
P. Hobza J. Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic, Dolej škova 3, 18223, Prague, Czech Republic
Pages 1357-1376 | Received 10 Feb 1993, Published online: 21 May 2012

Citations (25)

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Read on this site (3)

Jiří Šponer, JuditE. Šponer & Jerzy Leszczynski. (2000) Cation—π and Amino-Acceptor Interactions Between Hydrated Metal Cations and DNA Bases. A Quantum-Chemical View. Journal of Biomolecular Structure and Dynamics 17:6, pages 1087-1096.
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Jan Florián & Jerzy Leszczyński. (1995) Theoretical Investigation of the Molecular Structure of the πκ DNA Base Pair. Journal of Biomolecular Structure and Dynamics 12:5, pages 1055-1062.
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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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Articles from other publishers (22)

Sanchita Mukherjee, Sangeeta Kundu & Dhananjay Bhattacharyya. (2014) Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs. Journal of Computer-Aided Molecular Design 28:7, pages 735-749.
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P. Deepa, P. Kolandaivel & K. Senthilkumar. (2012) Structural properties and the effect of platinum drugs with DNA base pairs. Structural Chemistry 24:2, pages 583-595.
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Tarek M. El-Gogary. (2010) Interaction of angelicin with DNA-bases (III) DFT and ab initio second-order Moeller-Plesset study. International Journal of Quantum Chemistry 110:8, pages 1445-1454.
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Bipul Bezbaruah, Manash L. Das, Rajib L. Sarma, Murshida Karim & C. Medhi. (2010) Ab initio study on the nature of stacking between azaacridine-4-carboxamides with base pairs of DNA. Journal of Molecular Structure: THEOCHEM 947:1-3, pages 107-114.
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Tarek M. El-Gogary & Gottfried Koehler. (2009) Interaction of psoralens with DNA-bases (II): An ab initio quantum chemical, density functional theory and second-order MØller-Plesset perturbational study. Journal of Molecular Structure: THEOCHEM 895:1-3, pages 57-64.
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D. Bandyopadhyay & D. Bhattacharyya. (2006) Estimation of strength in different extra Watson–Crick hydrogen bonds in DNA double helices through quantum chemical studies. Biopolymers 83:3, pages 313-325.
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Neelaabh Shankar, Scott D. Kennedy, Gang Chen, Thomas R. Krugh & Douglas H. Turner. (2006) The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from Its Structure in Crystals of 50S Ribosomal Subunits , . Biochemistry 45:39, pages 11776-11789.
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Suyun Wang & Henry F. SchaeferIIIIII. (2006) The small planarization barriers for the amino group in the nucleic acid bases. The Journal of Chemical Physics 124:4.
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Piotr Cysewski & Żaneta Czyżnikowska-Balcerak. (2005) The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA. Journal of Molecular Structure: THEOCHEM 757:1-3, pages 29-36.
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Oleg V. Shishkin, Oleg S. Sukhanov & Jerzy Leszczynski. (2002) Interactions of Water with Mono- and Diamino Derivatives of N , N ‘-Dimethyluracil . The Journal of Physical Chemistry A 106:34, pages 7828-7833.
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Richard Štefl & Jaroslav Koča. (2000) Unrestrained Molecular Dynamics Simulations of [d(AT) 5 ] 2 Duplex in Aqueous Solution:  Hydration and Binding of Sodium Ions in the Minor Groove . Journal of the American Chemical Society 122:21, pages 5025-5033.
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Petr Bouř & Vladimír Král. (2000) Modelling of DNA Complexes with Distamycin Analogues Using an ab initio Continuum Solvent Model. Collection of Czechoslovak Chemical Communications 65:5, pages 631-643.
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Pavel Hobza & Jiří Šponer. (1999) Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs:  Nonempirical Ab Initio Calculations . Chemical Reviews 99:11, pages 3247-3276.
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Ben Luisi, Modesto Orozco, Jiri Sponer, Francisco J Luque & Zippora Shakked. (1998) On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules. Journal of Molecular Biology 279:5, pages 1123-1136.
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Ken Brameld, Siddharth Dasgupta & William A. Goddard. (1997) Distance Dependent Hydrogen Bond Potentials for Nucleic Acid Base Pairs from ab Initio Quantum Mechanical Calculations (LMP2/cc-pVTZ) . The Journal of Physical Chemistry B 101:24, pages 4851-4859.
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Viktor Brabec, Vladimír Kleinwächter & Vladimír Vetterl. 1996. Bioelectrochemistry of Biomacromolecules. Bioelectrochemistry of Biomacromolecules 1 104 .
Ota Bludský, Jiří Šponer, Jerzy Leszczynski, Vladimír Špirko & Pavel Hobza. (1996) Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion . The Journal of Chemical Physics 105:24, pages 11042-11050.
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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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Jiří Šponer & Pavel Hobza. (1996) Nonempirical ab initio calculations on DNA base pairs. Chemical Physics 204:2-3, pages 365-372.
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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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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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Jiří Šponer, Jerzy Leszczynski & Pavel Hobza. (1996) Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation. The Journal of Physical Chemistry 100:5, pages 1965-1974.
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