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• Biochemistry  (3)
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• 1
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 16 (1995), S. 777-789
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: We compare the electrostatic potential surrounding several natural and synthetic nucleic acid bases calculated using an atom-centered multiple expansion (ACME) derived from integration of the charge distribution with that from potential-derived charges (PDCs) obtained using the CHELPG procedure. When the multipole expansions are carried out to octapoles, the root mean square (rms) error in the potential is always less than that from PDCs. Electrostatic interactions in pairs of these nucleic acid bases were also evaluated using ACMEs up to octapoles and PDCs. The electrostatic interaction energies from ACMEs were found always to be larger than those from PDCs or the total self-consistent field (SCF) interaction energy. The value of the electrostatic energy differs by as much as approximately 19 or as little as approximately 8 kJ/mol between the ACME and PDC methods. The rank ordering provided by the electrostatic models is grossly similar but differs in the ranking of systems with two and three hydrogen bonds. A rigid twist about the N—H ⃛ N axis of the pairs was examined using SCF calculations and the electrostatic models. It was found that with ACMEs the energy required for a 90-degree rotation was always higher than that found from SCF calculations. With PDCs, similar results are obtained, except with the adenine/thymine and 9-methyl-adenine/1-methyl-thymine pairs. In these instances, the barrier is about 4 kJ/mol lower than that found with SCF calculations. These results demonstrate that integration of the charge density can provide convergent multipole expansions that provide a more accurate description of the electrostatic potential than the commonly used PDC model. In addition, the description of electrostatic interactions during twisting of AT and mAmT given by this model is shown to be somewhat anomalous. © 1995 by John Wiley & Sons, Inc.
Type of Medium: Electronic Resource
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• 2
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Molecular orbital calculations using the 3-21G basis set have been performed for iso-butylene (IB; 2-methyl-1-propene), difluoro-iso-butylene (DFIB; 1,1-difluoro-2-methyl-1-propene), hexafluoro-iso-butylene (HFIB; 3,3,3-trifluoro-2-(trifluoromethyl)-1-propene), and perfluoro-iso-butylene (PFIB; 1,1,3,3,3-pentafluoro-2-(trifluoromethyl)-1-propene). The effects of fluorine substitution were studied by comparison of several calculated quantities of the fluorinated compounds with those of IB. Through an analysis of the computed electron density distributions, it is suggested that a vinylic fluorine acts as a π acceptor, by electron transfer into the C—F bond, and a π repeller, by polarization of the adjacent π electrons. An allylic fluorine acts as a π attractor through electrostatic effects, although in HFIB a minor contribution from hyperconjugation was evident. Finally, electrostatic potentials for the molecules were calculated. These show that fluorine substitution has large effects on the electrostatic potential associated with the π electrons. These effects change the sign of the calculated electrostatic potential in the plane containing the π bond to such an extent that PFIB is quite susceptible to nucleophilic attack.
Type of Medium: Electronic Resource
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• 3
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 8 (1987), S. 499-509
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Accurate and efficient integration of the electron density function over arbitrary regions has been previously achieved by exploiting a separation of variables. Recently, a computer program has been written that calculates ρ, \documentclass{article}\pagestyle{empty}\begin{document}$\buildrel{\rightharpoonup}\over{\nabla}$\end{document}ρ, and ∇2ρ in an expeditious fashion, taking advantage of the separation of variables in the electron density function. Accurate integrations of ∇2ρ over arbitrary regions can also be accomplished. The structure of the program is suited especially to vector processors. As a result of the efficiencies of these programs, functions of the electron density, such as the density itself, the surrounding electrostatic potential, ∇ρ, and ∇2ρ have been calculated in three dimensions. Results of calculations for nitrated cubanes are presented illustrating how the effects of the nitro groups are manifested in the electron density and associated properties.