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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 36-45 
    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 variable-size simplex optimization method is used to reparametrize the I + A and β parameters of an INDO approximation to the perturbed Hartree-Fock calculation of 13C chemical shifts in hydrocarbons. The absolute shifts for 39 nuclei in a set of molecules containing up to four carbons are reproduced within a standard error of 9.9 ppm for an unconstrained optimization and to a standard error of 10.0 ppm for an optimization constrained to yield gross atomic charges in agreement with double-zeta ab initio calculations.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 64-68 
    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 recently developed ab initio pseudopotential molecular orbital approach was applied to the Te42+ ion, a system outside the practical reach of conventional all-electron treatments. Computations were carried out with a minimal STO-4G basis set. Results account reasonably well for the observed optical absorption spectrum and suggest the origin of a hitherto unassigned weak band. Ground-state properties, which included the structure, force field, and vibrational frequencies, were also investigated. Treated as a free, gas-phase ion, tetratellurium (II) yielded a bond length 0.05 Å shorter than the experimental value for the ion in a crystal lattice. Placement of static, point-charge counterions in the Te42+ coordination sphere increased the bond length to a value 0.005 Å longer than derived by experiment. Calculations on neutral, cyclic Te4 provided a theoretical single-bond reference length 0.09 Å longer than that obtained for the ion in a counterion environment. Comparisons between observed and calculated frequencies suggest an assignment of the vibrational spectrum different from the provisional assignment in the literature.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 111-117 
    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 molecular mechanical force field for fluorinated ethylenes and propylenes is described. The field computes geometries, dipole moments, and energy differences between isomers and rotamers. Component analysis indicates that “classical” strains alone (skeletal, nonbonded, electrostatic) cannot account for energy relationships. The discussion is supplemented by a semiempirical quantum chemical comparison of cis- and trans-FCH=CHF and of gauche- and anti-FCH2CH2F.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 99-109 
    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 study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C—O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C—C—O—H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C—C and C—O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 281-284 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations at the STO-3G and 4-31G levels have been carried out on propylamine and ethylmethylamine, using geometries determined by molecular mechanics by allowing complete molecular relaxation in all degrees of freedom except for torsion about the central bond, and at 30° increments for the latter. It was found that a butanelike potential exists in each case. From 0° (cis) to 360° in order, the 4-31G values for the energy extrema are 5.92, 0.12, 3.88, 0.00, 3.94, and 0.51 kcal/mole for propylamine (with the nitrogen lone pair gauche to carbon), and 7.06, 1.45, 3.44, 0.0, 2.87, and 1.44 kcal/mole for ethylmethylamine.
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  • 6
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 188-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water-uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N1—H and O2, N3—H and O2, and N3—H and O4. Open structures form at O4, N1—H, and N3—H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N1—H and the cyclic one at N1—H and O2. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N3—H and a cyclic structure at N3—H and O4. The third cyclic structure at N3—H and O2 collapses to the “wobble” dimer at N3—H and O4. The two “wobble” dimers are significantly more stable than the open dimer formed at O4, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N1—H than N3—H, owing to a more favorable molecular dipole moment alignment when association occurs through H1. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water-uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.
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  • 7
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 373-385 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations with full geometry optimization have been carried out on the planar cCc, cTc, tTc, tCt, tTt, and cCt conformers of β-hydroxyacrolein using the 4-21G basis set, and on the cCc and cCt conformers using the 4-31G basis set. The hydrogen-bonded cCc conformer is the most stable and the cCt conformer the least stable, with the other conformers following the above sequence. β-Hydroxy substitution has scarcely any influence on the geometry of the trans-acrolein structure, whereas the geometry of the cis-acrolein structure shows significant changes which depend on whether the O—H group is cis or trans with respect to the CHO group about the C=C bond. The ΔET values for cis → trans isomerization about the C—C bond in cCt and cTc support the hypothesis that these changes in geometry are the result of a destabilizing interaction in cCt and a stabilizing interaction in cTc. The geometry of the hydrogen-bonded structure cCc sets it apart from all the other conformers: it has by far the longest C=C, the longest C=O, the longest O—H, the shortest C—C, and the shortest C—O. Its formation from cCt involves a lengthening of C=C, C=O, and O—H and a shortening of C—C and C—O, indicating a delocalization of charge within the ring. 4-21G calculations have also been made for a distorted cCt structure that has the same bond lengths and angles as the equilibrium cCc structure, and the distortion energy, cCt (equm. geom.) → cCt (distorted geom.), is found to be +13.1 kJ mole-1. Taking the energy of this distorted cCt structure as the baseline, the hydrogen-bonding energy in cCc is found to be  - 80.3 kJ mole-1.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 9
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 392-401 
    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 all-valence-electron CNDO/2 calculations were performed for the three isomeric nitrophenols. Using the newly derived σ-core charges and subsequently revising the valence-state ionization potentials and one-center two-electron repulsion integrals, Pariser-Parr-Pople (PPP) CI calculations were performed on the title compounds following the Nishimoto-Forster scheme. A better agreement between theory and experiment has been observed in spectral assignments compared to the conventional PPP approach. Information from the CNDO/2 calculations was used to obtain useful electronic structural parameters and to get a quantitative insight into the chemical reactivity of these molecules. All the results were compared with the basic compounds, phenol and nitrobenzene. The electronic spectra of these isomers were recorded in both polar and nonpolar solvents.
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  • 10
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 416-421 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water-water interactions and nonadditivity effects are also significant.
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  • 11
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 460-469 
    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 conformational behavior of the C-terminal neurotensin pentapeptide, Arg-Pro-Tyr-Ile-Leu OH [NT(9-13)], was investigated using empirical energy calculations. A special aim was to display the specific contribution of each residue to induce conformations able to interact with biological receptors. Restrictions were then introduced in intramolecular interactions involving the Arg side chain and the terminal COOH group. The stablest conformations include in the order of decreasing stability: a distorted helical form for the C-terminal tetrapeptide, a (Pro2-Tyr3) β turn I, an α helix, an extended form, and a (Tyr2-Ile3) β turn III, which are energetically rather close (ΔE 〈 3 kcal/mol). The NT(9-13) peptide appears then as a rather flexible molcule with a noteworthy ability of adaptation to a substrate. Extended forms would be in agreement with a zipper model of interactions with receptors, whereas folded forms involving helices and β, γ turns would support a lock and key model. The specific contribution of side chains, specially those of Tyr and Arg residues as well as the key position of the Pro residue emerge clearly from this study.
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  • 12
    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 triplet-triplet absorption spectrum of naphthalene (3B1g ← 3B2u; 3Ag ← 3B2u) was calculated using an ab initio method with a STO-3G basis set and moderately large configuration interaction. Eight bands were found in the region 18,000-45,000 cm-1 and compared with those of the experimental spectrum. The strongest band observed at about 44,000 cm-1 was assigned to a 3Ag ← 3B2u tansition. The excited triplet and singlet ground-state electronic charge distributions are compared.
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  • 13
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 28-36 
    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 topological resonance energy (TRE) model was introduced independently by the Zagreb Group (in 1975) and by Aihara (in 1976). Several practical obstacles arise in the computation of TRE. Ways to surmount them are pointed out. Descriptions of algorithms, optimizations, and the efficient computer program are presented. Possible numerical instability is discussed.
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 62-68 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF molecular orbital calculations have been performed to ascertain the conformational preferences of protonated, neutral, and deprotonated amidine [HC(=NH)NH2], using the 3-21G split valence basis set. The states of eight stable species, eight transition states, and four higher-order saddle points have been determined by complete geometry optimization utilizing analytic energy gradient techniques. Protonation at the amidine =NH is preferred over the -NH2 site by 37.1 kcal/mol. Neutral amidine has rotational barriers of 9.6 and 11.7 kcal/mol for the HN=CN cis and trans isomers, respectively, while all the stable HC(NH2)2+ and HC(NH)2- species possess torsional barriers larger than 23 kcal/mol. There is, however, essentially free C - N single-bond rotation in HC(=NH)NH3+, the calculated barriers being 0.7 and 1.8 kcal/mol for the cis and trans HN=CN isomers, respectively.
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  • 15
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    Journal of Computational Chemistry 3 (1982), S. 89-94 
    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 conformation of the cyclic pentapeptide malformin A has been deduced by systematically generating possible models for the molecule, and minimizing the conformation energy of each. Only one of the low-energy solutions is fully consistent with the reported CD and NMR spectra, and this is the proposed model. The disulfide ring linking adjacent cystine residues is highly strained, as has been predicted from the S—S vibration frequency. The conformation of the backbone, but not that of the disulfide ring, is similar to a model previously proposed.
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 422-432 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH3, NH2, OH, F, C2H3, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N3, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N3, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N1, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N3 a poorer site for hydrogen bonding than N1, primarily because of a stronger π electron-withdrawing effect at N3. However, the relative stabilities of complexes hydrogen bonded at N1 and N3 are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N3. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.
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  • 17
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 18
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Closed-shell SCF calculations on the ground states and direct SCF calculations on the ionized doublet states were carried out for a series of ten-electron hydrides. The correlation of ionization potentials with the degree of protonation and the nuclear charge has been studied for hole states derived from excitation out of both the core and valence molecular orbitals. Calculated proton affinities of the ground states and hole states derived from a given symmetry orbital show a similar trend to that of the ionization potentials.
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  • 19
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    Journal of Computational Chemistry 3 (1982), S. 40-46 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several deficiencies and potential sources of error in the torsion angle driving method, the approach employed most frequently for the simulation of conformational interconversions, have been studied. A general explanation of the observed effects is given in terms of the energy surface and of the effects brought about by “side valleys.” Several examples of molecular mechanics calculations of conformational interconversions, among them the cyclohexane ring inversion, illustrate the problems.
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  • 20
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    Journal of Computational Chemistry 3 (1982), S. 75-88 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article develops computer programs for computer generation of nuclear spin species and nuclear spin statistical weights of rovibronic levels. The programs developed here generate nuclear spin species and statistical weights from the group structures known as generalized character cycle indices (GCCIs) which are computed easily from the character table of the PI group of the molecule under consideration. Procedures are illustrated with examples.
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  • 21
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    Journal of Computational Chemistry 3 (1982), S. 112-116 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations are reported for the H2SSH· and H2SCl· radicals and for the H2SClH+· radical cation. The two neutral species are found to be very weakly bound van der Waals' complexes, whereas the H2SClH+· radical cation is bound by 11.9 kcal mol-1 at MP2/4-31G. The importance of charge in σ* radicals is discussed.
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  • 22
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    Journal of Computational Chemistry 3 (1982), S. 117-124 
    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 blend of Haselgrove's method and the biased selection method for evaluating multidimensional integrals was tested. The results were mixed. The error estimate varied from being proportional to 1/N when N was less than ca. 60,000 to being proportional to 1/√N when N was greater than 60,000. Also, for N greater than 60,000, the error estimate was one-half the error estimate given by biased selection alone. These numbers should be compared with the 10,000 points used to find an optimum set of Haselgrove's parameters. It is reasonable to expect that if 100,000 points were used in the optimization of Haselgrove's parameters that the above results would be found with 60,000 replaced by 600,000.
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  • 23
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    Journal of Computational Chemistry 3 (1982), S. 135-139 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is well known that if the formation of hydrocarbons during Fischer-Tropsch synthesis occurs via the condensation polymerization mechanism, there is little hope for selectivity enhancement in the desired range of products. Recent data on low surface area model catalysts, where readsorption is unlikely, have shown that at low conversions, the product distribution obeys the condensation polymerization mechanism and the distribution of products is shifted to lower-molecular-weight hydrocarbons. We have used a computer simulation of the growth of hydrocarbon chains to obtain a picture of the catalyst surface under synthesis conditions. Such an approach could prove useful in distinguishing between various theoretical models. We have applied the simulation to compare the changes in selectivity when readsorption occurs and when it does not. The dynamic behavior of the reacting system which is obtained from the computer results has shown that selectivity to lower-molecular-weight hydrocarbons is a stronger function of the extent of reaction than the incorporation of readsorption into the chain growth mechanism.
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  • 24
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO has been extended to sulfur, but without inclusion of 3d AOs. Calculations are reported for heats of formation, geometries, dipole moments, and ionization energies of a variety of sulfur-containing molecules. The average discrepancy between calculated and observed heats of formation is larger than for compounds of other elements, a difference probably due, at least partly, to the lower accuracy of the thermochemical data for sulfur compounds. The calculated dipole moments agree well with experiment as do the calculated ionization energies, except for those corresponding to ionization from sulfur “lone-pair” orbitals which are too high by ca. 1 eV, probably as a result of the neglect in NDDO of interactions between inner and valence shell orbitals. As in the case of other third-period elements, the calculated heats of formation of compounds of sulfur in its higher valence states (SIV, SVI) were too positive by large amounts, due presumably to the neglect of 3d AOs.
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  • 25
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    Journal of Computational Chemistry 4 (1983), S. 127-135 
    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 relativistic effective core potential (REP) has been generated for the uranium atom and used in self-consistent-field calculations of the A states of UH, UF, and their ions. Energy curves were calculated at the base configuration level which ensures the dissociating atoms are described by Hartree-Fock wavefunctions. The electronic bonding of these molecules is found to be similar to that of comparable alkaline-earth hydrides and fluorides. The uranium 6p, 6d, and 5f orbitals retain their atomic character but the orbitals extend into the bonding region and are distorted by overlap repulsion and electrostatic effects. Nonetheless, the atomic energetic coupling determines that low energy states will have the maximum spin multiplicity and maximum orbital angular momentum projection consonant with the charge-transfer bonding.
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  • 26
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    Journal of Computational Chemistry 3 (1982), S. 229-233 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Fifty-one structures have been calculated by the MINDO/3 method to evaluate the errors introduced by branching and by the presence of the heteroatom. The structures are evaluated by comparisons which reveal that the calculated ΔHf values reflect a bias because of the presence of the heteroatom. With two carbons or more in a chain attached to a heteroatom group, a linear relationship exists which makes possible the calculation of reasonably accurate ΔHf values for unbranched alcohols, primary or secondary amines, ethers, thioethers, thiols, and alkyl chlorides. Branching errors do not seem to be linearly related among the systems. Some errors in calculations of geometries are also discussed.
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    Journal of Computational Chemistry 3 (1982), S. 234-250 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical HF/6-31G* (Hartree-Fock, 6-31G* basis set) and MP2/6-31G* (second-order Møller-Plesset, 6-31G* basis set) vibrational frequencies based on complete quadratic force fields have been obtained for a set of 36 one- and two-heavy-atom molecules comprising first-row elements for which experimental spectroscopic data are available. Frequencies calculated at the HF/6-31G* level are an average of 12.6% higher than experimental values. Partial treatment of electron correlation via the perturbation method of Møller and Plesset, terminated at second order, leads to a significant reduction in this error, although theoretical MP2/6-31G* frequencies are still larger than the experimental quantities by 7.3%. Part of the difference may be traced to the restriction of quadratic force fields, as comparison with experimental harmonic frequencies shows deviations of only 9.5% and 4.7% for the two levels, respectively. The calculated frequencies are used in conjunction with the corresponding theoretical equilibrium structures to obtain absolute molecular entropies, which may in turn be used to yield entropies of reaction. These latter quantities are generally in good accord with entropies derived using experimental structures and frequencies.
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  • 28
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    Journal of Computational Chemistry 3 (1982), S. 265-268 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicit functional forms for both the two-electron Coulomb integral, (aa∣bb), and the one-center core-orbital integrals, ZA-1 (aa∣ZA), are derived which permit the penetration integrals to be fully derived and calculated. With these forms the 3Σu+ of the H2 molecule is unstable. These forms are generalized so that they are suitable for optimizing semiempirical predictions of experimental one-electron properties.
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  • 29
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    Journal of Computational Chemistry 3 (1982), S. 277-282 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: A simple but efficient coupled iteration procedure is proposed for searching saddle points and extrema along the line of constrained minimum energy paths by (analytical) calculation of the derivatives, i.e., the reduced forces and reduced force constants. The advantage of the method is shown with analytical potentials as well as a calculation of HCH—HNC rearrangement, as working examples.
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  • 30
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Ab initio calculations using the unscaled 4-31G basis set have been carried out on the cc, tc, and tt conformers of carbonic acid and the bicarbonate ion, with full geometry optimization assuming the structures to be planar. The complete harmonic force field is reported for the (most stable) tt conformer and for the bicarbonate ion, also selected quadratic force constants for the cc and tc conformers. The changes in certain bond lengths and stretching force constants in the cc → tc, tc → tt, and cc → tt conformer conversion reactions are indicative of intramolecular hydrogen bonding, C=O…H—O and H—O…H—O, which is examined in greater detail by partitioning the overall conformer conversion energy into distortion and bonding energy components. The fundamental vibration frequencies for the tt conformer and the bicarbonate ion are calculated from the force constant matrices, and hence, using a scaling factor based on a comparison of calculated and experimental values for the bicarbonate ion and trans-formic acid, a value is predicted for the zero-point energy of the tt conformer. A new estimate of ΔH˚ for the hydration reaction, H2O + CO2 → H2CO3, at 298 K in the gas phase; is made from thermochemical data, +20.2 ± 3.4 kJ mol-1, which, together with estimates of (H298˚ - H0˚) and the zero-point energy for H2CO3, gives +8.1 ± 7.0 kJ mol-1 for ΔET(expt). ΔET calculated from the 4-31G basis set data is -29.1 kJ mol-1. Comparison of the experimental value, the Hartree-Fock limit value, and values calculated with a variety of basis sets for the bond separation reaction, CO2 + CH4 → 2H2CO, suggests that the differences, ΔET(expt) minus ΔET(SCF), are due mainly to basis set limitations and not substantial correlation energy contributions.
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    Journal of Computational Chemistry 3 (1982), S. 344-353 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures of fluorobenzene, 1,3-difluorobenzene, 1,3,5-trifluorobenzene, 1,2,3-trifluorobenzene, pentafluorobenzene, and hexafluorobenzene have been determined by the ab initio gradient method with a 4-21 basis set. Approximate corrections have been developed to yield re and r0 structures so that comparison can be made with the available experimental information. The C—F bond distance decreases in a uniform manner with increasing fluorination of the ring, either on adjacent or on meta sites. The ring structure also shows systematic deformation, with a decrease of about 0.01 Å in the C—C bond length adjacent to the point of substitution and an increase of about 2.5˚ in the ring angle at the substitution site in those cases where the requirement of ring closure permits.
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  • 32
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    Journal of Computational Chemistry 3 (1982), S. 372-380 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Spin-orbit and dispersion energy contributions to the energy curves of XeF are examined. A rapid variation in the spin-orbit coupling with internuclear separation is found for both the ground and excited states. This result can explain the experimentally observed ordering of the ionic excited states when the spin-orbit perturbation couples 2σ and 2π energy curves obtained by both all-electron and effective core potential (ECP) calculations at the first-order configuration interaction (FOCI) level of accuracy. Damped dispersion energy contributions to the ground-state energy curve are shown to be comparable to the charge transfer contribution. The energy curve for XeF is in reasonable agreement with experimental results and a calculation of the analogous XeCl curve confirms the qualitative correctness of the calculation. The energy curves and transition moments were then applied to two problems related to the efficiency of the XeF laser. Photodissociation of the X state provides a means of removing a bottlenecked vibrational level but a calculation of the radiative transition probability between the X and A states finds the cross section is too small to yield rates competitive with collisional deactivation. The bottlenecked state may also be removed by electron dissociative attachment but the calculated energy curves for the X states of XeF and XeF- do not cross at a low energy indicating a small cross section.
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    Journal of Computational Chemistry 4 (1983), S. 58-67 
    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 low-cost microcomputer and package of assembly language routines has been developed to emulate the structure and performance of a large analog computer. The advantages of the analog computer, as implemented in this scheme, include (1) a significant reduction in the programming effort involved in modeling complex dynamic systems and (2) the control of the simulation and model parameters in a completely interactive and flexible manner. The symbolic nomenclature and schematic representations involving devices, such as integrators, comparators, multipliers, and function generators, offers a powerful alternative to the more conventional numerical methods, that is, to provide very simply the solutions to large systems of differential equations. This approach invariably leads the user to a more thorough understanding of the dynamic character of the system. The technique is illustrated using a chemical kinetics example involving the simulation of laser-induced fluorescence. The results of this work have provided an assessment of a systematic error that occurs when using induced resonance fluorescence to measure OH concentrations in the troposphere of the earth.
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    Journal of Computational Chemistry 4 (1983), S. 110-113 
    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 rapid method is described for calculating the number of bonds on the shortest path between each two pairs of atoms of a molecule.
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    Journal of Computational Chemistry 4 (1983), S. 48-52 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of basis functions on molecular one-electron property expectation values calculated by approximate methods is examined using weighted and unweighted least-squares Gaussian-type orbital function expansions of Slater-type orbital functions.
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    Journal of Computational Chemistry 4 (1983), S. 73-83 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Structures XY⋅3XY⋅2XY3 of symmetry C2v (of which propane is an example) are examined and the rearrangement due to the internal rotation of the end groups XY3 studied. The isomerization graph is constructed, various forms of which are displayed and the symmetry of which has been determined. The order of the group is 72. There are nine prime (irreducible) representations (4A + E + 4G) with the following partitioning of the elements into classes: 1, 42, 62, 9, 122, 18. When the mechanism for rearrangement is generalized to include enantiomers, a duplex graph is produced with the order of the group 144 which is isomorphic to the group S2(S3,S2) (generalized wreath product of the symmetric group S2 and S3). The corresponding graph has been constructed and displayed in one of more symmetrical forms. Isomorphism of groups of order 144 is discussed and a procedure is outlined in which correspondence between distinctive combinatorial objects is established by inducing permutations of m elements from available permutations of n elements. The scheme is based on selection of suitable graph invariants in one system and their labeling as m objects which form the basis for representation of the symmetry for the other system.
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    Journal of Computational Chemistry 4 (1983), S. 114-122 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The MM2 molecular mechanics force field, as modified for halogens, is able to predict the structures, dipole moments, and energies of the isomers of benzene hexachloride. For benzene tetrachloride and naphthalene tetrachloride the field exaggerates the stability of conformers with axial chlorine, but gives satisfactory results if the field is modified to allow for interaction between electronegative substituents and the π electrons.
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    Journal of Computational Chemistry 4 (1983), S. 124-124 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 333-336 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The nearest-neighbor exclusion model for intercalation was studied using an energetical approach. It was shown that creation of the intercalation site in the exclusion model corresponds to the same energetical destabilization of the structure as in the standard model of intercalation. The stability of the intercalation complex formed in the case of the exclusion model is lower by 68 kcal/mol as compared with the standard model, but geometrical structures of both complexes are very similar. The electrostatic molecular potential method was also used to further characterize the intercalation site formed within both models of intercalation.
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    Journal of Computational Chemistry 4 (1983), S. 181-186 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Gaussian basis sets, consisting of 15 s-type, 11 p-type, and 6 d-type functions, for the fourth-row main group elements, In-Xe, are presented. In order to compare these basis sets with larger ones, calculations have been performed in I2 and TeO2.
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    Journal of Computational Chemistry 4 (1983), S. 241-251 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: STO-3G minimal basis sets for first- and second-row transition metals have been formulated and applied to the calculation of equilibrium geometries for a variety of inorganic systems, metal carbonyls, and organometallic compounds. While the overall level of agreement with experiment is not as good as that previously noted for main-group compounds, most trends and many subtle features in geometries are reproduced.
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    Journal of Computational Chemistry 4 (1983) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 267-275 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: A procedure has been devised to determine the automorphism partition and the automorphism group for nondirected graphs. The general approach is to reveal the permutational symmetry by means of its systematic destruction. Symmetry decomposition pathways are created by numerically weighting specific series of vertices. Each pathway leads to a discrete ordered vector. Each pair of pathways that match reveals an element of the automorphism group. Results are presented for two molecular graphs. Further potential applications of this approach to problems of isomorphism, canonical labeling, and structural indexing are discussed.
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    Journal of Computational Chemistry 4 (1983), S. 276-282 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A scheme is presented that enables photographic representation of the (two-dimensional) surfaces of (three-dimensional) molecular orbitals and electron density functions. The algorithm has been implemented by a program which is completely general and computationally efficient.
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    Journal of Computational Chemistry 5 (1984), S. 225-229 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Changes of electronic charge distribution following the lowest singlet n-π* transitions of benzaldehyde, benzamide, benzoic acid, the phthalaldehydes, pyridine, and the diazines have been examined using the CNDO-S/CI method. A Singlet n-π* transition is found as a general rule to direct electronic charges to the para position of the atom in the ring that carries the lone pair or to which the substituent carrying the lone pair is attached.
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    Journal of Computational Chemistry 5 (1984), S. 217-224 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The MINDO/3 calculations were performed on the potential energy profile involved in the equilibrium \documentclass{article}\pagestyle{empty}\begin{document}$$ \begin{array}{l} {\rm crotonic acid \rightleftharpoons isocrotonic acid \rightleftharpoons but-3-enoic acid} \\ {\rm (III)\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(II)\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(I)} \\ {\rm } \,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\to {\rm propene + CO}_{\rm 2} \\ \end{array} $$\end{document}Optimized structures of stable molecules and transition states have been determined; thermodynamic stabilities of pure acids and barriers indicated that the equilibrium can be set up from any acids. It was argued that direct decarboxylation is only conceivable from (I), since in this process a 1, 5-hydrogen shift is involved, whereas a higher barrier process of 1, 3-hydrogen shift is required in direct decarboxylations from other acids. Direct interconversion of (I) and (III) was found to be unfavorable due to a high barrier involved.
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    Journal of Computational Chemistry 5 (1984), S. 261-262 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 5 (1984), S. 252-260 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: Formulas are given for convergence-accelerated lattice sums over all intermolecular Coulomb, London, and repulsive interactions. Their implementation in the consistent force field is described. Optimum values of convergence constant and summation limit are found for r-12, r-9, and r-1 interaction terms. Energy minimization in all degrees of freedom, also intramolecular, for crystals of Ar, KCl, and C2H6 is reported.
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    Journal of Computational Chemistry 5 (1984), S. 248-251 
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    Notes: The equilibrium between three pairs of 1,4- and 1,6-dialkylcyclooctatetraenes was investigated with the two quantum mechanical algorithms, IBMOL and PCILO. PCILO computations reproduce the trend of stability within each pair of isomers obtained earlier by Allinger with molecular mechanics calculations, while IBMOL computations do not. These results not only can be explained in the light of, but also are a confirmation of Allinger's conclusions that the conformational stability is governed by the magnitude of the van der Waals' attraction between the two alkyl groups: The dispersion energy, which is essentially an electron correlation effect, is not accounted for by a method like IBMOL that, albeit ab initio, is based on the Hartree-Fock independent particle model, while it is fairly well reproduced by a method like PCILO that, albeit semiempirical, is based on a configuration interaction approach. Simulation of the full configuration interaction (CI) correction through a suitable dispersion term brings IBMOL results to a good agreement with the molecular mechanics ones.
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    Journal of Computational Chemistry 5 (1984), S. 263-271 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The effect of correlation energy on the relative stability of different structures and dissociation products of complex lithium beryllohydrides has been investigated. The adequacy of the method employed (third-order Möller-Plesset perturbation theory) and the basis set dependence have been assessed. Trends of the correlation energy according to the molecular structure have been discussed, and the validity of an additive scheme based on electron pair contributions has been tested.
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    Journal of Computational Chemistry 5 (1984), S. 280-287 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program is described which evaluates the second-order Møller-Plesset energy using the integral list formed by HONDO 5. In this program use may be made of full molecular symmetry for most common point groups, even if they contain two-dimensional representations. The algorithm for the integral transformation may also be applied to other methods beyond Hartree-Fock. Some numerical results and timings are presented.
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    Journal of Computational Chemistry 5 (1984), S. 299-306 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Molecular mechanical calculations for hetero-substituted hydrocarbons present certain difficulties that are not encountered in dealing with hydrocarbons. Ways are proposed to overcome such difficulties, sometimes by two-step or iterative computation. The following topics are considered: fitting the force field by using data from studies in solution; ways to estimate atomic charges or, alternatively, bond moments; ways to account for field effects upon atomic charges and bond moments.
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    Journal of Computational Chemistry 4 (1983), S. 461-469 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy calculations are presented for the head-to-head dimerized β helices for Gramicidin A transmembrane channel structures. The calculations take into account both left- and right-handed β helices, and various side-chain conformations. The energetics of the dimerization is studied by considering various docking geometries. It is concluded from these vacuum-energy calculations that the lowest energy conformation for the channel dimer is that comprised of left-handed β helices.
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    Journal of Computational Chemistry 5 (1984), S. 197-199 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Group equivalents which are useful for converting energies derived from ab initio calculations into enthalpies of formation have been obtained. They allow ΔHf to be estimated from 6-31G* energies with an uncertainty on the order of ±2 kcal/mol.
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    Journal of Computational Chemistry 5 (1984), S. 207-215 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The effect of different exponents, Slater, Burns, Clementi, and Best Limited Molecular Orbital (BLMO) on the approximate one-electron property expectation values from minimum basis-set calculations is reported for Roothaan-Hartree-Fock (RHF), neglect of diatomic differential overlap (NDDO), and maximum overlap method (MOM) calculations on FH, CO, and LiH.
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    Journal of Computational Chemistry 5 (1984), S. 241-247 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous investigators have shown that statistical mechanical averages for configuration-dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche-trans energy difference for rotation about C—C bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2O—CH2—CH2—OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean-square unperturbed end-to-end distance, mean-square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche-trans energy difference for rotation about C—C which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche-trans energy difference for rotation about the C—O bond. This energy difference is overestimated by MM2.
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    Journal of Computational Chemistry 5 (1984), S. 290-290 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 58
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: A modified version (MM2′) of the Allinger's 1977 force field is checked against cycloheptane and cyclooctane. Cycloheptane is characterized by two pseudorotating itineraries, chair/twist-chair and boat/twist-boat, separated by a barrier of 8.5 kcal mol-1. The activation energy in the C/TC pseudorotation is estimated to be 0.96 kcal mol-1, while B and TB transform into each other freely at an energy level 3.8 kcal mol-1 above the global energy minimum (TC). With cyclooctane the lowest energy is calculated for the boat-chair form which participates in a pseudorotational process with TBC through a saddle point lying 3.5 kcal mol-1 above BC. The chair/chair and boat/boat families contain only one local minimum, crown and BB, respectively, on the MM2′ surface. The results are presented as an illustration for quick coverage of torsional energy surface by two-bond driver calculation with the block-diagonal Newton-Raphson minimization, followed by the force search of stationary points by full-matrix Newton-Raphson optimization.
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  • 59
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    Journal of Computational Chemistry 5 (1984), S. 343-348 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical calculations by the combined empirical force-field (EFF)-extended Hückel molecular orbital (EHMO) approach confirm that octalene and benzo-|c|-octalene present π-bond fixation with a common single bond between the cyclooctatetraene and cyclooctatriene fragments, whereas the structure of dibenzo-|c, j|-octalene is characterized by a central double bond. The dynamic behavior of these compounds is discussed and the interconversion energy barriers are calculated; the inversion of the cyclooctatriene ring is faster than that of the cyclooctatetraene ring in octalene, but it is slower in benzo-|c|-octalene.
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  • 60
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    Journal of Computational Chemistry 5 (1984), S. 358-362 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO has been parametrized for iodine. Since d atomic orbitals (AOS) are not included, the calculations are restricted to II. Heats of formation, molecular geometries, ionization energies, and dipole moments are reproduced with useful accuracy.
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  • 61
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    Journal of Computational Chemistry 5 (1984), S. 381-386 
    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 nitrogen protonation energies of the imino bases HN=CHR, where R is H, CH3, NH2, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree-Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree-Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree-Fock nitrogen protonation energies of the imino bases HN=CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O=CHR.
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  • 62
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    Journal of Computational Chemistry 5 (1984), S. 182-185 
    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 principles of a new method, the method of zero determinants, are described which can be used for the determination of the number of exponentials in accurate, multiexponential decay curves, as well as for the smoothing of multiexponential experimental data. It is based on the idea that the determinant of an overdetermined data matrix for accurate data is zero. The method is not limited by mathematical approximations, and thus uncovers the decay curve hidden in the data set.
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  • 63
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    Journal of Computational Chemistry 5 (1984), S. 411-426 
    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 π-bond order-bond length relationship is reintroduced to the literature and extended to heteronuclear bonds by presenting graphs derived solely by theoretical methods. π-bond order and overlap population results for carbon-carbon, carbon-nitrogen, and carbon-oxygen bonds obtained from ab initio STO-3G calculations using theoretically-optimized geometries are reported for a series of pteridines and for a wide range of small organic molecules. The order-length correlation graphs are used in predicting the “intrinsic” single bond lengths for sp2 - sp2 and sp - sp hybridized C—C, C—N, and C—O bonds, and in evaluating the relative importance of hybridization, π-electron delocalization and bond polarization effects in causing bond shortening in conjugated and hyperconjugated molecules. The calculated value of the π-bond order for a given bond in a molecule is shown to be relatively insensitive to moderate geometry changes: Hence, a use for the correlation graphs in geometry prediction is suggested. Some results for the extended 4-21G basis set are also presented.
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    Notes: The structures and conformational energies of several conformations of propanoic acid, 2-methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4-21G level. The O=C—C—C torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2-methylpropanoic acid there are energy minima at H—C—C=O dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the H—C—C=O torsional potential of 2-methylpropanoic acid are found to be predictable from propanoic acid rotational-potential parameters. Some conformationally dependent, local geometry trends are discussed.
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    Journal of Computational Chemistry 5 (1984), S. 457-465 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Fortran-77 computer program has been written which calculates the rotation-torsion profile of a vibronic transition using an asymmetric top/free internal rotor Hamiltonian. The program is applicable to any molecule that is composed of a frame portion of C2v symmetry a free rotor portion of C3v symmetry. Rotation-torsion bands of A-, B-, and C-type contours may be calculated within an assumed Boltzmann distribution of rotation-torsion level populations or within a specified non-Boltzmann distribution of torsional level populations.
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    Journal of Computational Chemistry 5 (1984) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 5 (1984), S. 500-505 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The organization of a computer code to compute transition moments between states described in different orbital basis sets (a nonorthogonal transition moment) is described. The code is organized to minimize redundant work and allow efficient threshold checking. Three sample calculations are presented.
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    Journal of Computational Chemistry 5 (1984), S. 486-499 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A set of procedures and guidelines are presented for the estimation of bond length, bond angle, and torsional potential constants for molecular mechanics force fields. The force field constants are ultimately derived by “subtracting” nonbonded molecular mechanics energies from corresponding molecular orbital energies using a model compound containing the chemical structure to be parameterized. Case study examples of bond length, bond angle, and torsional rotation force field parameterizations are presented. A general discussion of molecular mechanics force field parameterization strategy is included for reference and completeness. Finally, a curve-fitting program to generate force field parameters from raw data is given in Appendix I.
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    Notes: The vertex numbering obtained by application of the HOC algorithm can be converted into two sequences of numbers: If each vertex starting with vertex 1 is only counted once, the sums of numberings of adjacent vertices form sequence Si (i = 1-N), while the sums of Si values form sequence Mi (i = 1-N). These two sequences can be used for (i) two new topological indices, M and N, the latter being of extremely low degeneracy, and the former correlating with boiling points of alkanes; (ii) a criterion based on sequence Si for ordering graphs which possess the same number N of vertices; and (iii) a quantitative measure, also based on sequence Si, for appreciating the similarity or dissimilarity of pairs of graphs. Comparisons with other topological indices, ordering criteria, and similarity measures for graphs show that the newly devised procedures compare favorably with those known previously.
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    Journal of Computational Chemistry 5 (1984), S. 640-649 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The core potentials for atoms of atomic numer 1-18 fitted to ion spectra by Chang, Habitz, Pittel, and Schwarz have been extended to the molecular case in a Gaussian lobe basis by using a six-Gaussian (6G-POT) representation for the exponential factors of the atomic core potentials. In a (9s/5p/1d) basis the 6G-POT one-electron energies, dipole moments, and Mulliken charges are improved over a one-Gaussian potential form for HF, NH3, and H2O; BeO also yields good agreement within 2.6% of the experimental bond length. For HCl, the core potential shows larger errors in the dipole moment (7%) and one-electron eigenvalues (2%), but a 75% saving in computer time is realized for HCl compared with only about 35% for first-row systems using the 6G-POT core potentials. Analytical expressions are given to extend the 6G-POT method up to s, p, d, f, and g valence shells.
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    Journal of Computational Chemistry 11 (1990), S. 291-296 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The adsorption of methane, ethane, propane, n-butane, ethylene, propene, 1-butene, 1,3-butadiene, acetylene, benzene, toluene, naphthalene, anthracene, and pyrene on the basal plane of graphite has been studied by means of a semiempirical method proposed by Fraga based on a 1/R expansion of atom-atom pair potentials. The energies of interaction obtained agree reasonably well with experimental data and statistical calculations. The orientation of the adsorbed molecules relative to the graphite surface rendered by Fraga's method improves the picture provided by other calculations with empirical potentials. These results display Fraga's method as an economical alternative for the study of physisorption of hydrocarbons on the graphite surface.
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    Journal of Computational Chemistry 11 (1990) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 11 (1990), S. 410-410 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 11 (1990), S. 411-415 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics calculations (MM2') are reported on methylenecyclohexane, 1, methylenecyclopentane, 2, and cyclopentane itself, 3. The calculated torsional energy barrier for the chair/chair interconversion of 1 if 8.7 kcal/mol (experimental ΔH ≠ = 8.4 ±0.1 kcal/mol); compounds 2 and 3 have virtually free pseudorotational pathways (calculated ΔH ≠ = 2.33 and 0.008 kcal/mol, respectively).
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    Journal of Computational Chemistry 11 (1990), S. 194-204 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To build a kinetic model of a cell with diffusion one has to solve a coupled nonlinear partial differential equation system consisting of several hundred equations. (Several hundred chemical components undergoing several hundred reactions.) To solve this formidable mathematical problem the division of the model cell into compartments (most biochemical reactions take place in a certain part of the cell) was suggested.1 Solving the differential equation system in one compartment, the results can be used as input at other compartments until mutually consistent solutions are achieved.To test this suggestion 10 coupled chemical reactions with diffusion were investigated in a model that contains three compartments. The results in the case of pure diffusion are in excellent agreement with and without compartmentalization. After this the full problem was treated by compartmentalization using for the solution of the differential equation system a discretization of the concentrations as functions of space and time and the Newton-Raphson iterative procedure. The results obtained give reasonable space and time dependence for the concentrations of all 10 components.
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    Journal of Computational Chemistry 11 (1990) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 77
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted phenolates in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: H, F, Cl (only MNDO and AM1), CN, CH3, OH, NO2, OCH3, COOH, and NH2. The results are compared with experimental values (high-pressure mass spectroscopy) at 600 K. The MINDO/3 method overestimates the experimental PAs with a mean percentual error of ca. 4.3%. The MNDO results agree much better with the experimental values and are only ca. 1.3% too high. However, the best agreement is observed for the AM1 method, where the mean percentual error is only ca. 0.69% (in absolute value). The greatest disagreement is found for 2-hydroxyphenolate (ca. +2.0%) and 2-carboxyphenolate (ca. +2.7%). The PA of 2-nitrophenolate is underestimated by ca. 1.6%. Correlations between the calculated proton affinities on the one hand, charge densities on the acid H atom of the phenols, charges on the O atom in the phenolate ions, and substituent parameters on the other hand are studied. Particularly good linear relationships are found for the 3- and 4-monosubstituted compounds within the AM1 formlism. For the 2-substituted phenolates, only the AM1 method is satifactory. As a general conclusion, the AM1 method appears to be distinctly superior to MNDO for the calculation of PAs, and definitely superior to MINDO/3.
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    Journal of Computational Chemistry 11 (1990), S. 346-350 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic partial charges for three model systems that mimic the metal-ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
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    Journal of Computational Chemistry 11 (1990), S. 382-395 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The coefficients in power series, in the variable time, describing coupled nonlinear chemical reactions are easily obtained from a recursion relation. Since these series have a limited radius of convergence they are not very useful as such. If the series are inverted to give time as a function of the appropriate power of a progress variable, the new series converge over the entire time course of the reaction. If, further, the long-time asymptotic behavior, obtained from the linearized kinetic equations, is used, one can obtain a series expansion for a function that describes the correct short-time behavior. This function can be estimated very well using truncated series. The method works well for consecutive nonlinear reactions where the progress variables are monotonic functions of time; this includes many cases where the concentrations of intermediate species go through a maximum as the reaction progresses.
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    Journal of Computational Chemistry 11 (1990), S. 361-373 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An improved method for computing potential-derived charges is described which is based upon the CHELP program available from QCPE.1 This approach (CHELPG) is shown to be considerably less dependent upon molecular orientation than the original CHELP program. In the second part of this work, the CHELPG point selection algorithm was used to analyze the changes in the potential-derived charges in formamide during rotation about the C—N bond. In order to achieve a level of rotational invariance less than 10% of the magnitude of the electronic effects studied, an equally-spaced array of points 0.3 Å apart was required. Points found to be greater than 2.8 Å from any nucleus were eliminated, along with all points contained within the defined VDW distances from each of the atoms. The results are compared to those obtained by using CHELP. Even when large numbers of points (ca. 3000) were sampled using the CHELP selection routine, the results did not indicate a satisfactory level of rotatational invariance. On the basis of these results, the original CHELP program was found to be inadequate for analyzing internal rotations.
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    Journal of Computational Chemistry 11 (1990), S. 401-409 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center-to-center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.
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    Notes: Different methods such as molecular dynamics, systematic, or stochastic search and a special “generic shape” algorithm have been employed in the conformational analysis of a nine-membered lactam. Furthermore, crystal data were used to generate conformations of the compound under consideration. The various methods are compared in terms of their efficiency and completeness in the search for conformations with an energy content of up to 60 kJ/mol above the global minimum. Additionally, the generated conformations have been optimized by different techniques, molecular mechanics and quantum chemical calculations, to compare the number of existing local minima and their relative energies and geometries.
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    Journal of Computational Chemistry 11 (1990), S. 1169-1180 
    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 dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (α-helical decaglycine) in vacuo, a protein (Pancreatic Trypsin Inhibitor, PTI) in vacuo, and a fully solvated protein (PTI in water). The equations of motion were integrated using Andersen's velocity version of the Verlet algorithm with internal contraints (the RATTLE algorithm). The accuracy with which the equations of motion are integrated has been analyzed for several different simulation conditions. The effects of various nonbonded interaction truncation schemes on the conservation of energy have been examined, including the use of atomic cutoffs, and (neutral group) residue cutoffs. The use of a smoothing function to eliminate the discontinuities in the potential at the cutoff leads to a significant improvement in the accuracy of the integration for each of the systems studied. The accuracy with which the equations of motion are integrated using the RATTLE algorithm for pure water and for the solvated protein are found to be comparable when the nonbonded interactions are tapered with a smoothing function at the cutoff.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Orbital mapping analysis, based on EHT and CNDO/2 semiempirical molecular orbitals, has been used to survey the thermal, disrotatory, ring-opening isomerizations of bicyclo[2.2.0]hexa-2,5-dienes (Dewar benzenes), bicyclo[2.1.0]pent-2-enes, and bicyclo[2.1.0]pent-2-en-5-yl ions to their planar isomers. Results indicate that isoelectronic substitution (CH replaced by C-, O+, N, NH+, etc.) in the molecular framework may favor allowed thermal reactions in some cases, in contrast to the disallowed reaction predicted for the parent hydrocarbons.
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    Journal of Computational Chemistry 1 (1980), S. 59-63 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous attempts to determine the strengths of multiple metal-metal bonds are reviewed. Estimates of 73 and 97 kcal/mole for the Mo—Mo bond energies in Mo2Cl84- and Mo2(O2CH)4, respectively, are obtained by combining the known experimental bond energy in Mo2 (96.5 ± 5 kcal/mole) with the results of SCF-Xα-SW calculations on Mo2, Mo2Cl84-, and Mo2(O2CH)4. Possible errors in the estimates are discussed. It is noted that the quadruple bonds in the complexes are predicted stronger per component than the sextuple bond in the diatomic.
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  • 86
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    Journal of Computational Chemistry 1 (1980), S. 76-80 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical force field calculations were performed on hexamethylbenzene to elucidate the internal motions of the methyl groups. When the benzene ring is constrained to be planar (as in solid-phase studies), the methyl groups undergo a geared, disrotatory motion. When this constraint is relaxed, results are force field dependent. Calculated barriers are in good agreement with experimentally determined values.
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  • 87
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 88
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations have been carried out for the neutrals X—NH2, X—OH, and X—F and the anions X—NH- and X—O- with substituents X = Li, BeH, BH2, CH3, NH2, OH, and F. All structures have been fully optimized with the 4-31G basis set which is found to perform considerably better than the minimal STO-3G basis in predicting the lengths of strongly polar bonds. A quantitative analysis of interactions between the directly bonded groups, utilizing energy changes in hydrogenation reactions, is presented and rationalized with the aid of perturbation molecular orbital theory. Favorable interactions occur when electron-donor groups bond to electron-acceptor groups. This applies to both σ and π interactions, the relative importance of which depends on the particular substituents.
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  • 89
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    Journal of Computational Chemistry 12 (1991), S. 385-390 
    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 method is presented by which ab initio (or empirical) force fields and structures can be converted to molecular mechanics energy parameters. Using Cartesian coordinates, the effect of van der Waals and other nonquadratic interactions is eliminated from the original spectroscopic force field, and molecular mechanics force constants and reference geometry parameters are derived. The computed parameters yield molecular structure and vibrational frequencies that are identical to the original ones. The transformation produces a complete general valence force field, which in most cases is impractical, and a procedure to reduce the number of force constants is therefore described. Different ways of applying the transformation are outlined.
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  • 90
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    Journal of Computational Chemistry 12 (1991), S. 402-409 
    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 numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln(N) seconds of CPU time on a VAX-8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure-volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 105 Pa). R.m.s. gradients of 10-4 kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure-induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X-ray crystallography.
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  • 91
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    Journal of Computational Chemistry 1 (1980), S. 199-203 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Open (1) and cyclic (2) singlet forms of CO3 were investigated by means of ab initio calculations. At the highest level of theory employed, MP2/6-31G* (which includes the effects of electron correlation), 2 was indicated to be much more stable than 1 and thermodynamically stable toward dissociation into CO2 and O(3P). The open form 1 has a long O—O bond and can be regarded as a weak dative complex between CO2 and a singlet oxygen atom.
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  • 92
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    Journal of Computational Chemistry 12 (1991), S. 454-468 
    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 finite difference method for solving the Poisson-Boltzmann equation is used to calculate the reaction field acting on a macromolecular solute due to the surrounding water and ions. Comparisons with analytical test cases indicate that the solvation forces can be calculated rapidly and accurately with this method. These forces act to move charged solute atoms towards the solvent where they are better solvated, and to screen interactions between charges. A way of combining such calculations with conventional molecular dynamics force fields is proposed which requires little modification of existing molecular dynamics programs. Simulations on the alanine dipeptide show that solvent forces affect the conformational dynamics by reducing the preference for internal H-bonding forms, increasing the R-alpha helix preference and reducing transition barriers. These solvent effects are similar to previous explicit solvent simulations, but require little more computation than vacuum simulations. The method should scale up with little increase in computational cost to larger molecules such as proteins and nucleic acids.
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  • 93
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 94
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    Journal of Computational Chemistry 12 (1991), S. 536-545 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation, atomic charges, and geometries of some 110 structures involving substituted singlet and triplet phenyl and 4,4-dimethyl-1,4-dihydronaphthalene carbenes and the corresponding diazomethanes were calculated by MINDO/3, MNDO, AM1, and PM3 semiempirical molecular orbital methods. The singlet-triplet gaps for AM1 and PM3 calculations for the para derivatives in both systems have been successfully correlated with Brown σ+ constants. Good correlations with σ+ were found for the charges on the carbenic centers of the singlets as well as with the energy barrier for rotation of the aryl group about the C-C single bond in substituted singlet phenylcarbenes. Comparisons of these results with experimental data indicate that AM1 and PM3 are much better than MNDO and MINDO/3 in predicting the intrinsic substituent effects in singlet carbenes.
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  • 95
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    Journal of Computational Chemistry 12 (1991), S. 560-564 
    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 general theory of three-electron Hylleraas-Configuration-Interaction method using linear correlation factors of the form rij has been implemented for molecular systems using cartesian Gaussians as basis sets. A brief review of the theory and the form of the three-electron integrals is presented. Additionally, a table of numerical values of some selected three-electron integrals is given. Results from test calculations on H3 using the full form of the theory are presented for some simple basis sets. A discussion of the computational problems that need to be overcome before this approach is competitive with traditional methods is included.
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  • 96
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    Journal of Computational Chemistry 12 (1991), S. 606-610 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Geometry optimization directly in Cartesian coordinates using the EF and GDIIS algorithms with standard Hessian updating techniques is compared and contrasted with optimization in internal coordinates utilizing the well known Z-matrix formalism. Results on a test set of 20 molecules show that, with an appropriate initial Hessian, optimization in Cartesians is just as efficient as optimization in internals, thus rendering it unnecessary to construct a Z-matrix in situations where Cartesians are readily available, for example from structural databases or graphical model builders.
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  • 97
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    Journal of Computational Chemistry 12 (1991), S. 620-626 
    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 protocol to replace “10-12” hydrogen bonding function with the “6-12” form to reproduce hydrogen bond distances, energies, and geometries in molecular mechanics calculations is described. The 6-12 function was least-squares fit to the normally employed 10-12 form of the function for the hydrogen bond types of the Weiner et al. force field by iterating over the A and B coefficients. A weighting function was used to fit the curves in the most critical areas. The 6-12 hydrogen bond model was compared with the Weiner et al. force field, OPLS/AMBER fore field, and quantum mechanical calculations on two simple systems, the water dimer and the chloride-water interaction. The 6-12 model produced structures, energies, and geometries that were consistent with the other molecular mechanics calculations and showed reasonable agreement to the quantum mechanical results for the water dimer. The 6-12 model was also compared with normal calculations using a 10-12 model on several representative systems. The results indicate that the 6-12 function, when substituted by the procedure outlined in this work, yields structures and hydrogen bond properties that are similar to the normal 10-12 model.
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  • 98
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using computer model building, the three-dimensional structure of an enzyme from Streptomyces R61 that is inhibited by ß-lactam antibiotics has been constructed starting from incomplete X-ray crystallographic data for this 37.4 kDa protein. The so-called DD-peptidase catalyzes transpeptidation and hydrolysis of peptides terminating in D-Ala-D-Ala and is a model for bacterial transpeptidases and carboxypeptidases essential in the biosynthesis of the peptidoglycan layer of the cell wall. The structure, which was completed with the SYBYL molecular modeling package, has been refined by energy minimization and molecular dynamics using Quanta/CHARMm software. A simulation of 105 ps was run with waters of solvation in the active site. From these computations, the interatomic distances between the active serine and key residues around the active site were determined. Inadequacies at reproducing geometric details of the ß-lactam ring of a cephalosporin are pointed out which are typical of most commercially available force fields.
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  • 99
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    Journal of Computational Chemistry 12 (1991) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 100
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    Journal of Computational Chemistry 12 (1991), S. 645-663 
    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 stochastic search method was employed to find as many conformers on the MM2 and MM3 energy surfaces as possible for cyclic saturated hydrocarbons with ring sizes from 9 through 12. The number found was 8 MM2 (8 MM3) for 9 rings, 18 MM2 (16 MM3) for 10 rings, 40 MM2 (29 MM3) for 11 rings, and 111 MM2 (90 MM3) for 12 rings. A measure of similarity between pairs of conformers of a compound, called conformational distance, is described. It was used to correlate similar MM2 and MM3 conformers. It was discovered that some conformers on each energy surface are not close to minima on the other surface in rings larger than 9. On refinement with the other optimizer, they changed considerably - going downhill to other previously found minima on the other energy surface or (in a few cases) going to minima which had not been found by direct searches. Conformational distance was also employed as an indication of which pairs of MM2 (or MM3) conformers are likely to interconvert rapidly. A new stochastic procedure of using small kicks was used to search for the most likely interconversion processes among the conformers. There is fairly good agreement between the most facile pathways located by it and unusually short conformational distances. Several additional 12-ring conformers (not found with previous methods) were located through application of this small kick procedure.
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