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  • 1
    Electronic Resource
    Electronic Resource
    Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study (1994)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 116 (1994), S. 709-714 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00081a036
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  • 2
    Electronic Resource
    Electronic Resource
    H-Bonded and Stacked DNA Base Pairs: Cytosine Dimer. An Ab Initio Second-Order Moeller-Plesset Study (1995)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 792-798 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00107a023
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  • 3
    Electronic Resource
    Electronic Resource
    Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study (1994)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 3161-3164 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100063a019
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  • 4
    Electronic Resource
    Electronic Resource
    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 (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 11042-11050 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The amino group nonplanarity in nucleic acid bases, aniline, aminopyridines, and aminotriazine was investigated by ab initio methods with and without inclusion of correlation energy utilizing medium and extended basis sets. For all the systems studied, the amino group was found to be nonplanar and the coupled cluster method [CCSD(T)] "nonplanarities'' and inversion barriers slightly higher than their second-order many-body perturbation-theory (MP2) counterparts. To assess the reliability of the calculations, inversion splittings for aniline and aniline-ND2 were evaluated by solving a two-dimensional vibrational Schrödinger equation for the large-amplitude inversion and torsion motions, while respecting the role of small-amplitude C–N stretching and H–N–H bending motions. Because a large number of points is required for the description of the aniline potential energy surface, the Hartree–Fock (HF) method with 6-31G* basis set was utilized. The vibrational calculations were performed within the framework of the semirigid bender Hamiltonian of Landsberg and Bunker. Excellent agreement between experimental and theoretical inversion-torsion frequencies for fundamental, overtone, and combination modes was found, which gives strong evidence for the adequacy of the theoretical model used in general, and potential energy surface in particular. Similarity between the HF, MP2, and CCSD(T) aniline inversion barriers and amino group nonplanarities gives us confidence that the MP2 and CCSD(T) inversion barriers and amino group nonplanarities of the DNA bases, aminopyridine, and aminotriazine, are close to the actual values which are still experimentally unknown. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472904
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  • 5
    Electronic Resource
    Electronic Resource
    Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 1472-1479 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Intermolecular vibrational modes of the H-bonded adenine...thymine Watson–Crick (AT) base pair were studied for the first time using multidimensional nonharmonic treatment. Relying on a Born–Oppenheimer–like separation of the fast and slow vibrational motions, the complete multidimensional vibrational problem is reduced to a six-dimensional subproblem in which all rearrangements between the pair fragments (i.e., adenine and thymine) can be described. Following the Hougen–Bunker–Johns approach and using appropriate vibrational coordinates, a nonrigid reference is defined which covers all motions on the low-lying part of the intermolecular potential surface and which facilitates the derivation of a suitable model Hamiltonian. The potential energy surface is determined at the ab initio Hartree–Fock level with minimal basis set (HF/MINI-1) and an analytic potential energy function is obtained by fitting to the ab initio data. This function is used to calculate vibrational energy levels and effective geometries within the framework of the model Hamiltonian, disregarding the role of the kinematic and potential (in-plane)–(out-of-plane) interactions. The calculations are in reasonable agreement with the normal coordinate analysis (harmonic treatment) thus indicating physical correctness of this standard approach for an approximate description of the lowest vibrational states of the AT base pair. In addition, to get a deeper insight, harmonic vibrational frequencies of the AT pair and 28 other base pairs are evaluated at the same and higher levels of theory [ab initio Hartree–Fock level with split-valence basis set (HF/6-31G**)]. The HF/MINI-1 and HF/6-31G** intermolecular harmonic vibrational frequencies differ by less than 30%. For all the base pairs, the buckle and propeller vibrational modes [for definition and nomenclature see R. E. Dickerson et al., EMBO J. 8, 1 (1989)] are the lowest ones, all being in the narrow interval (from 4 to 30 cm−1 in the harmonic approximation). Although most of the evaluated harmonic frequencies are qualitatively correct approximations to the genuine vibrational frequencies, in some cases due to a strong nonharmonic behavior of the buckle motion, they become physically meaningless. To get physically correct results in such cases, apparently, the standard harmonic oscillator approach should be replaced by a more adequate approach, for instance, by the approach we used in the case of the adenine...thymine pair. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473296
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  • 6
    Electronic Resource
    Electronic Resource
    Metal ions in non-complementary DNA base pairs: an ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair (1999)
    Springer
    JBIC 4 (1999), S. 537-545 
    Details
    ISSN: 1432-1327
    Keywords: Key words Ab initio ; Silver ; Nucleobase ; Cytosine ; Adenine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Ab initio calculations have been carried out to characterize the structure and energetics of a silver(I) complex with the cytosine-adenine DNA base pair and an aqua ligand in the coordination sphere of Ag. In addition, we have also studied analogous complexes with Cu(I) and Au(I), and structures in which adenine has been replaced by purine in order to investigate the structural role of the adenine amino group. The calculations revealed that all metal-modified structures are dominated by the metal-base interactions, while the water-metal ion interaction and many-body interligand repulsion are less important contributions. Nevertheless, the structural role of the water molecule in the complex is quite apparent and in agreement with an earlier crystallographic study. The metal-modified base pairs exhibit large conformational flexibility toward out-of-plane motions (propeller twist and buckle), comparable or, in some cases, even larger than that observed in the base pairs without metal ions. All structures have been optimized within the Hartree-Fock approximation, while interaction energies were evaluated with the inclusion of electron correlation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050376
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  • 7
    Electronic Resource
    Electronic Resource
    Tautomerism of xanthine: The second-order MØller-Plesset study (1995)
    Springer
    Structural chemistry 6 (1995), S. 281-286 
    Details
    ISSN: 1572-9001
    Keywords: Tautomeric equilibria ; xanthine ; DNA ; ab initio
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Four 9H and four 7H tautomers of DNA base xanthine were studied by the ab initio LCAO-MO method at the MP2/6-311G**//HF/6-31G** and MP2/6-31G**//HF/6-31G** approximations. All calculated structures are minima at the HF/6-31G** potential energy surface with the dioxo 7H tautomer (A1) being the global minimum. The second most stable tautomer, dioxo-9H (B1) is by 9 kcal/mol less stable. For the A1 → B1 transition the calculated MP2 energy gap corresponds to the equilibrium constant of 2 × 10−7. Therefore, only the major tautomeric form A1 is predicted to be detectable in the gas phase. The 7H and 9H groups of tautomers are discussed separately. Within both groups, the dioxo form (A1-7H, B1-9H) is the most stable one and is succeeded by the 2-dihydroxy (A2, B2) form. However, while the energy difference between A1 and A2 is 10 kcal/mol, the energy difference between B1 a B2 is only 2 kcal/mol. The effect of polar environment was estimated by the SCRF method, using a spherical cavity, at the HF/6-31G** level. These calculations did not change the gas phase stability order of the tautomers. However, the energy difference between A1 and B1 decreased from 9 kcal/mol at the HF/6-31G** level to 4 kcal/mol at the SCRF HF/6-31G** level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02293121
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  • 8
    Electronic Resource
    Electronic Resource
    Density functional theory and molecular clusters (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1315-1325 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Density functional theory (DFT) methods, including nonlocal density gradient terms in the exchange and correlation energy functionals, were applied to various types of molecular clusters: H-bonded, ionic, electrostatic, and London. Reliable results on the structure and stabilization energy were obtained for the first two types of cluster as long as Becke3LYP and Becke3P86 functionals and basis sets of at least DZ + P quality were used. DFT methods with currently available functionals failed completely, however, for London-type clusters, for which no minimum was found on the potential energy surfaces. DFT interaction energy exhibits the same basis set extension dependence as the Hartree-Fock (HF) interaction energy. Therefore, the Boys-Bernardi function counterpoise procedure should be employed for elimination of the DFT basis set superposition error. © 1995 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540161102
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  • 9
    Electronic Resource
    Electronic Resource
    Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1136-1150 
    Details
    ISSN: 0192-8651
    Keywords: empirical force fields ; semiempirical quantum chemical methods ; ab initio SCF with dispersion energy ; H-bonded and stacked DNA base pairs ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical energy functions (AMBER 4.1, CFF95, CHARMM23, OPLS, Poltev), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and the nonempirical ab initio self-consistent field (SCF) method utilizing a minimal basis set combined with the London dispersion energy (SCFD method) were used for calculation of stabilization energies of 26 H-bonded DNA base pairs, 10 stacked DNA base pairs (thymine was replaced by uracil), and the B-DNA decamer (only DNA bases were considered). These energies were compared with nonempirical ab initio beyond Hartree-Fock values [second-order Møller-Plesset (MP2)/6-31G*(0.25)]. The best performance was exhibited by AMBER 4.1 with the force field of Cornell et al. The SCFD method, tested for H-bonded pairs only, exhibited stabilization energies that were too large. Semiempirical quantum chemical methods gave poor agreement with MP2 values in the H-bonded systems and failed completely for stacked pairs. A similar failure was recently reported for density functional theory calculations on base stacking. It may be concluded that currently available force fields provide much better descriptions of interactions of nucleic acid bases than the semiempirical methods and low-level ab initio treatment. © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1136-1150
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations (1996)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 57 (1996), S. 959-970 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Interactions of DNA bases frequently involve the DNA base amino groups. In contrast to the empirical force fields, the ab initio calculations predict nonplanar DNA base amino groups. The same conclusion also follows from the density functional theory (DFT) calculations. Both local and nonlocal density approximations were used. Optimized geometries of two other molecules with nonplanar amino groups (aniline, formamidine) are presented for comparison. The influence of nonplanar DNA base amino groups on the conformational variability of DNA is discussed. © 1996 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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