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  • 1
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic potential V(r) that the nuclei and electrons of a molecule create in the surrounding space is well established as a guide in the study of molecular reactivity, and particularly, of biological recognition processes. Its rigorous computation is, however, very demanding of computer time for large molecules, such as those of interest in recognition interactions. We have accordingly investigated the use of an approximate finite multicenter multipole expansion technique to determine its applicability for producing reliable electrostatic potentials of dibenzo-p-dioxins and related molecules, with significantly reduced amounts of computer time, at distances of interest in recognition studies. A comparative analysis of the potentials of three dibenzo-p-dioxins and a substituted naphthalene molecule computed using both the multipole expansion technique and Gaussian 82 at the STO-5G level has been carried out. Overall we find that regions of negative and positive V(r) at 1.75 Å above the molecular plane are very well reproduced by the multipole expansion technique, with up to a 20-fold improvement in computer time.
    Additional Material: 4 Ill.
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  • 2
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general procedure is presented for computing the gas phase heats of formation of a wide variety of organic compounds. ΔE for the formation of the molecule from its elements at 0 K is obtained from density functional calculations (Gaussian 92/DFT) for optimized geometries. This result is converted to ΔH at 298 K by assuming ideal behavior and adding the translational, rotational, and vibrational energies. Additive correction terms corresponding to the various coordination states of the carbons, nitrogens, and oxygens were developed using a database of 54 compounds. The experimental ΔHƒo values of these compounds are then reproduced with an average absolute error of 3 kcal/mol and a standard deviation of 4 kcal/mol. For a group of 10 test cases that were not part of the database, the average absolute error is 3.5 kcal/mol and the standard deviation is 4.1 kcal/mol. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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  • 3
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures and relative stabilities of furoxan and some of its isomers, e.g., the 1,2-dinitrosoethylenes, have been determined by means of ab initio Hartee-Fock and Møller-Plesset calculations. Geometries were optimized at the HF/3-21G, HF/6-31G* and MP2/6-31G* levels, and subsequently used for computing MP2/6-31G*, MP3/6-31G*, and MP4/6-31G* energies. The results are markedly affected by the inclusion of electronic correlation, which renders three of the isomers unstable. It also emphasizes the importance of a zwitterionic contribution to the structure of furoxan, which promotes ring-opening through a cis 1,2-dinitrosoethylene intermediate/transition state that has an MP4/6-31G*//MP2/6-31G* energy that is 31.6 kcal/mol above furoxan.
    Additional Material: 1 Ill.
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  • 4
    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: Our objective in this work is to gain insight into the contrasting carcinogenic activities of vinyl chloride (definitely carcinogenic) and trans-dichloroethylene (apparently inactive). The initial metabolic step for each molecule is believed to be epoxidation of the double bond, and there is evidence indicating that for vinyl chloride, this epoxide (chlorooxirane) is its ultimate (direct-acting) carcinogenic form. This article presents the findings of a computational study of the reactive properties of trans-dichlorooxirane (the epoxide of trans-dichloroethylene). An ab initio SCF-MO procedure was used to determine the energy requirements for stretching the C—O and C—Cl bonds (SN1 reactivity) and to study the epoxide's SN2 interactions with ammonia, taken as a model nucleophile. The starting points were the oxygen- and chlorine-protonated forms of the epoxide. The structure of the system was reoptimized at each step along the various reaction pathways. The results of this work are compared to an analogous earlier study of the reactive properties of chlorooxirane. The chlorineprotonated C—Cl bonds are found to have much lower energy barriers to stretching than do the oxygen-protonated C—O bonds. In the SN2 processes, intermediate complexes are formed with ammonia by both the oxygen- and the chlorine-protonated epoxides; the latter complexes are the more stable. Based on our results, we propose two mechanisms (one SN1 and the other SN2) whereby trans-dichlorooxirane can interact with N7 of guanine to produce an adduct analogous to one formed by chlorooxirane, which has been found to be the primary in vivo DNA alkylation product of vinyl chloride and to which has been attributed the carcinogenicity of the latter. Overall, trans-dichlorooxirane is found to be chemically more reactive than chlorooxirane; this may help to account for the much lesser carcinogenic and mutagenic activities of trans-dichloroethylene, since the epoxide may be reacting with other cellular nucleophiles before it reaches the key site(s) at which the carcinogenic or mutagenic interaction would occur. We also offer some speculations concerning other possible factors related to the differing carcinogenicities of vinyl chloride and trans-dichloroethylene, such as ease of epoxide formation and the likelihood of oxygen protonation.
    Additional Material: 3 Tab.
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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: The aim of this study has been to determine how the hydrogen bond between formaldehyde and ammonia is affected by the ring-opening interaction of protonated ethylene oxide with the ammonia nitrogen. Our purpose is to gain insight into the possible effect of carcinogenic epoxides upon the hydrogen bonding within DNA base pairs; it is known that such epoxides react with nucleophilic sites in DNA, including amine nitrogens that are involved in hydrogen bonds to carbonyl groups. We have used an ab initio self-consistent-field molecular orbital procedure to compute optimized structures, interaction energies, and other properties of interest. The H2CO·HNH2 system and the protonated epoxide were found to form two stable complexes, with syn and anti orientations. Their formation is accompanied by a significant overall strengthening of the H2CO·HNH2 hydrogen bond, as indicated by both calculated force constants and bond lengths. An analysis of these and other properties, such as atomic charges, suggests that the interaction is leading to the formation of N-protonated ethanolamine, which is linked to the formaldehyde through the proton on the nitrogen. If carcinogenic epoxides have a similar strengthening effect upon some of the hydrogen bonds in DNA, it could interfere in the replication and transcription processes.
    Additional Material: 4 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: An ab initio self-consistent-field molecular orbital (SCF-MO) procedure has been used to compute the average local ionization energies [Ī(r)] of some strained molecules on three-dimensional surfaces defined by the contour of electronic density equal to 0.002 electrons/bohr3. Ī(r) is rigorously defined within the framework of SCF-MO theory and can be interpreted as the average energy needed to ionize an electron at any point in the space of a molecule. Thus, the positions of the smallest Ī(r) values (ĪSmin) on the surfaces of molecules are the sites expected to be the most reactive to electrophiles. We find ĪSmin, near the C—C bond midpoints of saturated three-membered, but not foru-membered, hydrocarbon rings. These ĪS,min are interpreted as reflecting the “σ-aromatic” character of the former. Our Ī(r) data effectively provide a “fingerprint” characterizing saturated three-membered rings, which is useful, for example, in analyzing molecules such as [1.1.1] propellane. Our results for the latter are consistent with the interpretation of it having a biradical character, as has been suggested earlier.
    Additional Material: 1 Ill.
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  • 7
    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: Local density functional theory (DFT-LDA) has been explored as a tool for obtaining the molecular electrostatic potential V(r), using the code DMol. We have presented and discussed DFT-LDA electrostatic potentials for a representative series of molecules: ethylene, benzene, formamide, cytosine, and 2,3,7,8-tetrachlorodibenzo-p-dioxin. V(r) results obtained with a double numerical plus polarization (DNP) basis set show the key features that are characteristic of the ab initio potentials of these compounds and suggest that this is a useful approach, especially for large molecules that are difficult to study by ab initio methods.
    Additional Material: 5 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: The X-NO2 rotational energy barriers of nitromethane, nitroethylene, nitrobenzene, and a group of nitramines have been computed using a local density functional (LDF) procedure, using ab initio Hartree-Fock (HF)-optimized structures of the ground and rotational transition states. The results have been discussed in relation to HF and some correlated ab initio values and the available experimental data. Our LDF barriers are overall quite reasonable, in generally satisfactory agreement with the experimental and correlated ab initio results. © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Tab.
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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: Several computational approaches, including Gaussian-2 (G2) and nonlocal density functional theory (DFT-GGA ), have been used to calculate the energy requirements for (a) H2N—NO2 dissociation (through N—N bond scission), (b) inversion of the amine group, and (c) isomerization through the nitro-nitrite rearrangement. Taking zero-point energies into account, the G2 predictions are 53.6 kcal/mole for the dissociation energy and 1.5 kcal/mole for the inversion barrier. The corresponding DFT-QGA values are 48.4 and 0.9 kcal/mole, and an activation energy of 48.7 kcal/mole for the nitro-nitrite rearrangement. The DFF-OGA results indicate that dissociation and rearrangement should be competitive for H2N-NO2. The same conclusion was reached earlier by Saxon and Yoshimine on the basis of MRCISD/6-3lG* calculations, although their computed energy requirements differ from the present ones by approximately 8 kcal/mole. © 1992 John Wiley & Sons, Inc.
    Additional Material: 7 Tab.
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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: An isodesmic energy analysis has been carried out at the MP2/6-31G*//HF/3-21G level for the nonplanar ground state (1) of 1,3,5,7-cyclooctateraene and for two planar forms, one having complete π delocalization (2) and the other having alternating single and double bonds (3). 1 is found to have a considerable degree of stabilization, which is attributed to limited π delocalization. The polyene 3 is the more stable of the two planar forms; it is a transition state in the inversion between two possible nonplanar structures. 2 is found to be a triplet at the Hartree-Fock level and is a critical point on an alternate pathway between the two possible arrangements of alternating single and double bonds in 3. Both 2 and 3 have negative isodesmic energies, indicating the presence of stabilizing factors. Our results for 3 show that an “antiaromatic” system need not necessarily show a net destabilization. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
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