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  • Atomic, Molecular and Optical Physics  (13)
  • Theoretical, Physical and Computational Chemistry  (2)
  • 1
    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: Variable electronegativity Pariser-Parr-Pople (VE-PPP) calculations have been carried out on the bases of nucleic acids and 5-fluorouracil. Directions of polarization for the various electronic transitions in these molecules have been calculated using the wave functions obtained by this and the CNDO/S-CI methods. The calculated excitation energies, oscillator strengths, and directions of polarization have been compared with the PPP results due to Pullman and co-workers and Bailey as well as the experimental ones. It has been found that a comparative study of this type is much more useful for understanding the transitions in the molecules than the individual calculations. The VE-PPP method is found to generally give the best results. The directions of polarization have been used to identify the transitions in the molecules and to compare the excitation energies obtained by different methods. It is shown that the transitions in these molecules do not have the characteristics of those of benzene derivatives. All the observed peaks in the molecules have been explained as π*→π.
    Additional Material: 1 Ill.
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  • 2
    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: Electrostatic potential maps of benz(a)anthracene diol epoxide, benzphenanthrene diol epoxide, chrysene diol epoxide, and tryphenylene diol epoxide, which are ultimate carcinogens derived from the corresponding polycyclic aromatic hydrocarbons, have been studied using a dipole of length 1 Å and strength 1 Debye. The net charge distributions in the molecules were obtained using the MNDO molecular orbital method. The maps were drawn for two closest distances of approach between the charged ends of the dipole and atoms of the molecules. Using the electric field directions and values of electrostatic potentials, reactive sites and relative reactivities of these molecules have been examined. Existence of a bay region appears to be important for the carcinogenic activity of a diol epoxide in this class of carcinogens.
    Additional Material: 6 Ill.
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  • 3
    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: Electric-field maps of certain anions and cations of adenine and guanine have been studied. The results are compared with those of neutral adenine and guanine. In all cases, the geometries were fully optimized using the MNDO molecular orbital method and the fields were computed using Mulliken charges. Reactivities and hydrogen-bonding pattern predicted by electric fields, including those of cations, are in satisfactory agreement with experiment. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 4
    ISSN: 0020-7608
    Keywords: hydrogen bonding ; DNA ; base analogs ; stacking interaction ; reaction field ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In a recent experimental study, it was reported that replacement of thymine in the adenine-thymine base pair of DNA by its molecular analogs which cannot form proper hydrogen bonds with adenine (A) does not cause disruption of DNA structure and synthesis. AM1 and ab initio molecular orbital calculations and electric field mapping were carried out in order to examine the possibility of pairing of A with each one of two analogs of thymine in the gas phase. Self-consistent reaction field calculations were also carried out on the individual molecules and their pairs using the polarized continuum model in order to examine their stability in aqueous media. Our results are broadly in agreement with the conclusions drawn in the above-mentioned experimental work.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 351-355, 1998
    Additional Material: 3 Ill.
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  • 5
    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: π-electron SCF-MO theory in its variable electronegativity formalism has been applied to some monosubstituted benzenes. Calculated charge densities and bond orders for the ground and the first excited electronic states are correlated with chemical reactivity and the changes in molecular geometry on electronic excitation. The calculated results for spectra are compared with those obtained using the PPP method and also with the available experimental data.
    Additional Material: 1 Ill.
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  • 6
    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: Various electronic indices calculated by the CNDO/s-CI method for uracil, 5-fluorouracil, thymine, and cytosine and the Woodward-Hoffmann rule applied to the photodimerization of these molecules lead us to the following conclusions: (i) decrease of the C5—C6 bond order consequent to excitation is generally correlated with the photodimerization reaction for all the biological pyrimidines; (ii) excited pyrimidine molecules may be nonplanar and the excitation would be delocalized over both the molecules which photodimerize; (iii) electrostatic interactions may play a significant role in the initial stages of the photodimerization reaction; (iv) singlet precursors to the stable triplet photodimers may exist; and (v) electron density does not, in general, increase in the C5—C6 bond in the excited state as compared to the ground state, contradicting the proposals of some earlier workers. Hybrid population densities and σ-bond orders have been calculated for the first time for the molecules. Fluorine in 5-fluorouracil perturbs the hybrid populations as compared to those of uracil mainly in its vicinity.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    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: The carbene reaction 1CH2 + C2H6 was studied with the semiempirical method SINDO 1. The pertinent transition states and products were obtained by geometry optimization on a CI surface. We find the insertion reaction forming C3H8 greatly favored compared to the double insertion leading to CH4 + C2H4. The result is qualitatively the same for the reaction of the two possible intermediate radicals CH3 and C2H5. The geometries and energies of all transition states are presented.
    Additional Material: 2 Ill.
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  • 8
    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: It has been shown that an easier procedure to the study of molecular electrostatic potentials than the prevalent monopole isopotential approach is to use a dipole as the mapping device: allow the dipole to move on a geometrical surface enclosing the molecule such that the distance between the surface and the nearest atoms of the molecule (closest distance of approach) is fixed, say at 2 Å, calculate the electrostatic interaction energy between the molecule and the dipole at different points of the surface, and let the dipole orient itself along the minimum energy direction and treat these minimum energies as the desired electrostatic potentials. Thus the favorable binding sites of a given molecule for other species along with their relative orientations can be obtained. This procedure has been applied to the nucleic acid bases using the necessary input data from two independent sources. Thus success of the procedure in predicting important features of molecular electrostatic potentials has been demonstrated.
    Additional Material: 4 Ill.
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  • 9
    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: A molecular orbital geometry optimization study of the potential surface of guanine, guanine—O2, and guanine—O2—water reaction products in the ground state has been carried out. The origin of the asymmetric double-well potential surface of guanine suggested earlier on the basis of experimental observations has been explained. The most stable binding of O2 with guanine (G) is found to occur at the C4C5 double bond of the latter molecule. In the case of G—O2—water reaction product (HOO—G—OH), the groups —OOH and —OH bind at C4 and C8, respectively. The possiblity of a polymeric reaction product of the type R1—(G—O—O—G)n—R2 (R1, R2 = H, OH) has also been suggested. These results are broadly supported by experimental observations. The mechanism of spectral oscillations observed in UV-irradiated guanine solutions has been discussed.
    Additional Material: 3 Ill.
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  • 10
    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: Four esters of 5-cyano-1,6-dihydro-6-oxo-3-pyridinecarboxylic acid involving substitutions of methyl, isopropyl, tert-butyl, and phenyl groups at the 2-position, which exhibit varying degrees of cardiotonic activities, have been studied using the electric-field and electrostatic potential mapping techniques. The net charge distributions in the molecules were obtained using the MNDO method. Electric-field mapping has been performed in three-dimension in order to obtain information about the possible structure-activity relationships of these compounds. The results show a prominent electric-field region in the methyl-substituted compound extending from near the oxygen atom O6 to near the methyl group. This fact and orientation of the electric field in this region, in view of the Erhardt model, may be related to the greater cardiotonic activity of the methyl-substituted molecule in comparison to those of the other molecules of this class. © 1992 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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