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  • 1990-1994  (149)
  • 1985-1989
  • 1992  (149)
  • Biochemistry  (149)
  • 1
    ISSN: 1432-0533
    Keywords: Adult canine lysosomal storage disease ; Morphology ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary We describe a novel late-onset lysosomal lipid storage disease affecting a Tibetan terrier. The principal clinical manifestations include visual loss, progressive cerebellar ataxia and dementia. A necropsy of an affected 10-year-old dog demonstrated cerebellar atrophy. Histological analysis revealed extensive loss of retinal ganglion cells and cerebellar Purkinje cells, and mild to moderate loss of neurons in the cerebrum, basal ganglia and spinal cord. There were generalized neuronal hypertrophy and multifocal neuronal necrosis associated with the presence of enlarged macrophages. Neurons and perineuronal macrophages contained cytoplasmic granules that stained with PAS, luxol fast blue and several lectins. The granules were sudanophilic and autofluorescent. Electron microscopic analysis revealed lysosomes laden with lamellated membrane structures in neurons, pancreatic ductal and centroacinar cells and in cultured fibroblasts. These findings indicate lysosomal storage of both lipid and carbohydrate. Biochemical analysis of brain lipids and numerous lysosomal enzyme assays of leukocytes and cultured fibroblasts were unsuccessful in elucidating the underlying enzyme defect, although a generalized increase of brain gangliosides was noted.
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  • 2
    ISSN: 1432-0738
    Keywords: Bis(tributyltin) oxide ; Liver ; Electron microscopy ; X-ray microanalysis ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The toxic effects of bis (tributyltin) oxide (TBTO) on the rat liver were studied with an electron microscope and the accumulation sites of tin were determined with an X-ray microanalyzer. The activities of serum enzymes and the concentration of serum bilirubin were also analyzed. Male Wistar rats received an intramuscular injection of 0.5 ml/kg of TBTO. Marked swelling of the mitochondria appeared in the hepatocytes 4 h after injection of TBTO. Cytoplasmic vacuoles, which contained degenerated mitochondria, gradually increased in number in these hepatocytes. This in turn may have caused a decrease in the volume of hepatic cell cords and an enlargement of sinusoids in the entire hepatic lobule. However, fine structures of intrahepatic bile ducts were not altered. By X-ray microanalysis, tin peaks were preferentially obtained from swollen mitochondria of the hepatocytes. By polarographic analysis of the respiratory responses of mitochondria, it was demonstrated that rates of state 4 respiration and respiratory control ratio were significantly disturbed in TBTO-treated rats in comparison with those of controls. The activities of AST (aspartate aminotransferase) and ALT (alanine aminotransferase) were significantly increased after TBTO treatment, but those of ALP (alkaline phosphatase), LAP (leucine aminopeptidase) and total bilirubin were not changed. These results indicated that parenterally administered TBTO accumulated in the liver cell mitochondria and disturbed oxidative phosphorylation. Mitochondrial dysfunction might induce severe damage of the hepatocytes. Four days after injection of TBTO, hepatic structures and chemical indices were almost restored by the regeneration of hepatocytes.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    European journal of epidemiology 8 (1992), S. 340-345 
    ISSN: 1573-7284
    Keywords: Dermatomycosis ; Biochemistry ; Microsporum canis ; Morphology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Seventy-two strains of Microsporum canis, of different origins, were examined from a morphological point of view and tested in relation to their hydrolytic activity on tyrosine, xanthine, casein, gelatin, their ureasic activity and their capacity to assimilate different nitrogenous substances. The morhological aspects, that vary within the M. canis isolates, were constant in the strains isolated from rabbits. A strain with particular features was isolated many times from the dogs and cats coming from the same breeder. In one case of pseudomycetoma, different isolates suggested the co-existence in animals of two different strains, one present on fur, the other responsible for deep lesions.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1433-0350
    Keywords: Skeletal muscle ; Phosphofructokinase deficiency ; Biochemistry ; Morphology ; Enzyme histochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Muscle phosphofructokinase (PFK) deficiency in man is responsible for at least two forms of myopathy; one is characterized by painful contractures of muscles and typically occurs in adults, whereas the other is often disabling and typically occurs in childhood, with psychomotor and growth retardation. In this investigation, a young myopathic patient with severe mental retardation and aplasia of the cerebellar vermis presented with muscular hypotrophy of the limbs, generalized hypotonia, convergent strabismus and marked pain during passive movement. Biopsy of quadriceps femoris muscle showed variation in the fiber size with sarcoplasmic areas positive for periodic acid-Schiff stain. Histochemical qualitative reaction for PFK showed no staining of muscle fibers; ultrastructural studies showed abnormal accumulation of glycogen granules in both intermyofibrillar and subsarcolemmal areas. While some enzyme activities in the muscular crude extract were significantly lower than in controls, direct assay of PFK revealed no activity, thus demonstrating that the child's myopathy was due to the lack of PFK activity.
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  • 5
    ISSN: 1432-1106
    Keywords: MPTP ; Dopamine ; Degeneration ; Mouse ; Protection ; Uptake ; Immunocytochemistry ; Image analysis ; Biochemistry ; Substantia nigra ; Neostriatum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Based on the observations that the psychostimulant drug amphetamine in combination with physiotherapy can promote recovery of brain function after brain injury, we have studied the ability of the vigilance promoting drug Modafinil to counteract 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-(MPTP)-induced degeneration of the nigrostriatal dopamine (DA) neurons of the black mouse. MPTP was given s.c. in a dose of 40 mg/kg and the mice were sacrificed 2 weeks later. The effects of acute and chronic treatment with Modafinil were studied on MPTP-induced DA neurotoxicity. The substantia nigra and neostriatum were taken to both biochemical and histochemical analysis of presynaptic parameters of the nigrostriatal DA neurons, the latter in combination with image analysis. In separate experiments in rats in vivo tests for DA uptake blocking activity were made using intrastriatal microdialysis to study superfusate levels of DA and its metabolites and the 4-α-dimethylmetatyramine (H77/77) model to test for a possible ability of Modafinil to protect against H77/77-induced depletion of forebrain DA stores. Chronic treatment with Modafinil in doses of 10 to 100 mg/kg counteracted the MPTP-induced disappearance of nigral TH IR nerve cell body profiles and neostriatal TH IR nerve terminal profiles as evaluated after 2 weeks with image analysis. Chronic treatment with Modafinil (10–100 mg/kg) also dose-dependently counteracted the MPTP-induced disappearance of striatal DA uptake binding sites as evaluated at the same time interval. Also in the dose range 10–100 mg/kg Modafinil counteracts the MPTP-induced depletion of DA stores both in the neostriatum and the substantia nigra. In the acute experiments Modafinil (30 mg/kg) protected against the MPTP-induced depletion of striatal DA, dihydrophenylacetic acid (DOPAC) and homovanillic acid (HVA) levels both when given 15 min before, at the same time and 3 h following the MPTP injection. In the substantia nigra, however, these protective actions of Modafinil were only observed when the drug was coadministered with MPTP. Experiments with microdialysis in intact rats failed to demonstrate any increases of superfusate DA levels in neostriatum with 30 mg/kg of Modafinil. Modafinil in high doses of 2 × 50 mg/kg, however, significantly counteracted the H77/77 induced DA depletion of striatal DA stores. Thus, morphological and biochemical evidence has been obtained that Modafinil in the dose range 10–100 mg/kg protects against MPTP-induced degeneration of the nigrostriatal DA neurons of the black mouse. The results also indicate that the protective action of Modafinil is not caused by monoamine oxidase inhibition or by DA uptake inhibition, although the latter action may contribute in the highest dose used (100 mg/kg). Instead, it is hypothesized that its protective action may be related to actions on GABAergic mechanisms as evidenced by reduced cortical GABA outflow in doses of 3–30 mg/kg (Tanganelli et al. 1991) and/or to other unknown mechanisms.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Pharmacy world & science 14 (1992), S. 297-304 
    ISSN: 1573-739X
    Keywords: Biochemistry ; Didanosine ; Drug evaluation ; Pharmacokinetics ; Pharmacology ; Side effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract In this article the literature about didanosine, an antiretroviral drug, is reviewed. The mechanism of action, biochemical pharmacology, pharmacokinetics, and clinical results of phase-I trials are discussed. Serious adverse effects such as pancreatitis and peripheral neuropathy have occurred in these trials. An antiretroviral effect was observed in terms of an increase in CD4+ lymphocytes and a decrease in p24 antigen levels in HIV-infected individuals. Didanosine seems to be a promising drug against HIV infection, but knowledge about its clinical efficacy is scanty.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-0878
    Keywords: Intestine ; Sodium transport ; Enterocyte ; Plasma membranes ; Stereology ; Biochemistry ; Cytochemistry ; Domestic fowl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The coprodaeum of the domestic hen maintained on a low-NaCl diet adapts by enhanced sodium transport. This study examines the adaptive response at the single cell and whole organ levels. Surface areas of apical (microvillous) and basolateral plasma membranes of columnar absorptive epithelial cells were estimated by use of ultrastructural stereology. The activities of succinic dehydrogenase (a mitochondrial enzyme) and ouabain-sensitive, potassium-dependent paranitrophenyl phosphatase (a sodium pump enzyme) were determined in tissue homogenates. Sodium, potassium-ATPase (pump enzyme) activity in cell membranes was localized by ultrastructural cytochemistry. Apical and basolateral membranes responded differently. In high-NaCl hens, the membrane signature of the average cell was 32 μm2 (apical), 932 μm2 (lateral) and 17 μm2 (basal). Cells from low-NaCl hens had more apical membrane (49 μm2 per cell) but essentially the same area of basolateral membrane. However, total surfaces per organ were greater for all membranes. Sodium pump enzymes were localized in basolateral membranes. Enzyme activities per unit mitochondrial volume and per unit basolateral membrane surface were higher in low-NaCl birds. These findings are discussed in the context of known mechanisms of transcellular sodium transport via apical ion channels and basolateral pumps.
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  • 8
    ISSN: 1432-0878
    Keywords: Histamine ; Biochemistry ; Immunocytochemistry ; Retina ; Photoreceptors ; Paraboloid ; Turtle, Pseudemys scripta (Chelonia)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary A combination of immunocytochemical and biochemical methods was used to study histamine in the turtle retina. Histamine-like immunoreactivity was localized within paraboloids of certain cone photoreceptors by use of two different antisera directed against histamine. Preincubation of eyecups in Ringer's containing 10 μM histamine selectively increased the immunoreactivity of these photoreceptor paraboloids. The present localization of histamine in paraboloids indicated that, although histamine is in photoreceptors of the turtle retina, it may play some metabolic or neuromodulatory role, and not function as a neurotransmitter.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 17-32 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An overall adsorption quantity for a heterogeneous solid is usually expressed by an integral equation, which contains a distribution function that describes heterogeneous properties of this solid. The calculation of this distribution function is an ill-posed problem. The current article shows that the difficulties arising from the ill-posed nature of an adsorption equation can be overcome with the regularization method. This work presents general principles of regularization for solving the ill-posed problems without detailed mathematical considerations. The application of the regularization method to calculate a distribution function from any overall adsorption functions is illustrated with both simulated and experimental adsorption isotherms.
    Additional Material: 9 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 57-65 
    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 application of molecular mechanics methods for the study of structures has become a standard approach to conformational analysis. The MM2 force field has been extended to include imines. In general, a diverse group of aliphatic and aromatic imine structures can now be treated. The rotational energy profiles and barriers to N-substituted imines about the Csp2—Csp2 single bonds adjacent to C=N functional group were calculated via ab initio MO theory. Information obtained from the quantum mechanical calculations at the 3-21G, 6-31G*, and MP4/6-31G* //6-31G* levels was used both to study the phenomena involved and to parameterize MM2. The syn-anti isomerization was also studied, and the mechanistic pathways have been evaluated. In cases where the comparison with experimental data can be made, the agreements are good.
    Additional Material: 5 Ill.
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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 85-92 
    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 semiempirical MO method SINDO1, originally suitable for first- and second-row atoms, is extended to transition metals from scandium to zinc. The core Hamiltonian elements in a symmetrically orthogonalized atomic orbital (OAO) basis set are modified and the parameters are optimized to reproduce the experimental geometries, heats of formation, and ionization potentials. An application of the method to a selected number of molecules, as well as a comparison between calculated and experimental data is reported.
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 76-84 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for the calculation of local and global curvatures of molecular surfaces is presented. The analysis is based on a surface representation as a set of points in 3-D space (“dotted surface” representation). The surface data are used to subdivide the surfac into domains with different curvatures. All domains are characterized by a reference point with a corresponding curvature profile specifiying the topological properties in its neighborhood. The curvature profiles provide a method for a systematic comparison of the shapes of different molecules. Such a strategy is important for the treatment of molecular recognition problems. The enzyme-inhibitor complex trypsin/BPTI was chosen to demonstrate the scopes of the method.
    Additional Material: 10 Ill.
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
    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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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 187-198 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article we report a newly developed direct CI program and its preliminary applications. This program is based mainly on the relationship between direct and exchange type loops and the rederivation of the external loop shapes.
    Additional Material: 1 Ill.
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 229-239 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An optimized ellipsoidal cavity has been defined for use in self-consistent reaction field (SCRF) calculations for the incorporation of aqueous medium effects. The location, size, and orientation of the cavity is obtained by minimizing the average interaction between the solute and a simplified water molecule over the surface of the cavity. The calculated hydration energies of organic cations and neutral molecules using this cavity and the SCRF method of Rinaldi and Rivail with the AM1 wave function led to surprisingly good agreement with the experimental data. The optimized cavities are discussed in relation to those based on van der Waals' volumes and on polarizability criteria.
    Additional Material: 8 Ill.
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 214-228 
    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 space available to four inhibitors of the bacterial enzyme thermolysin has been searched in the enzyme binding site using a method that combines Monte Carlo type techniques with energy minimization for exploration of the conformational potential energy hypersurface. Molecular mechanics methodology using the AMBER force field was employed for computation of the molecular energetics. Solvation energies were also included in the calculations by employing a technique that estimates hydration energies based on the exposed solvent accessible surface area for each atom of the inhibitor and active site. It was found that in each case, the crystallographically observed conformation was among the low energy conformers discovered. In fact, in three of the calculations it was the lowest energy conformation. The methodology described in this article is expected to be quite useful for studies involving computer aided design and evaluation of enzyme inhibitors.
    Additional Material: 6 Ill.
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  • 17
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 492-504 
    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 previously published empirical charge scheme has been adapted for use in studies of quantitative structure-property relationships. New parameters have been developed to allow the inclusion of nitrates, nitriles, sulfides, thiols, thiophenes, and sulfoxides. No changes have been made to the original scheme, thus preserving all previous results. A few simple additions to the program have made it possible to calculate atomic charges in a variety of ionic structures containing a formally positive nitrogen or a formally negative oxygen. The results obtained for ions are consistent with a number of concepts surrounding the familiar inductive and resonance effects.
    Additional Material: 7 Ill.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
    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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  • 19
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 541-550 
    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 variable force field model for radical dimerization was developed. It uses MM2 force constants for most atoms and new parameters only for the core atoms involved in bonding changes. The change in hybridization from sp2 to sp3 is modeled using distance-dependent switch functions. The validity of the model has been tested by calculating the minimum energy path of the dimerization of di-tert-butylmethyl radicals. The calculated and experimental values for the enthalpy of activation of both dimerization of the radicals and dissociation of the dimer are in excellent agreement. The model has also been successfully applied to the stereoselective dimerization of 1-phenylneopentyl radicals: The form of the potential energy surface yields an explanation for the observed stereoselectivity. Another common feature in radical dimerization seems to be the formation of adsorption complexes prior to dimerization that can lead to increased reactivity. The results suggest that it is important to analyze the whole reaction path and not only the transition state alone.
    Additional Material: 12 Ill.
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  • 20
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 414-422 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In ab initio Hartree - Fock crystal orbital calculations of chemical and physical properties of polymers, the huge number of two-electron integrals restricts the size of the elementary cell. Therefore, the question arises how the storage and computation resources of modern parallel supercomputers can be exploited. In this work, we report the parallelization of the one- and two-electron integral programs, respectively, for the parallel computer SUPRENUM. A short description of the hardware and software environment of this supercomputer is given. The results are discussed with respect to speed-up and efficiency.
    Additional Material: 8 Ill.
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  • 21
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
    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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  • 22
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 901-911 
    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 quantum mechanical energy is examined in which groups of one, two, three, and four localized electron pairs found within a molecule are separately computed. From these results, the interaction energies of the electron pairs taken one, two, three, and four at a time form the terms of a convergent molecular mechanics like expansion of the molecular ground state energy. This procedure can be used with any size consistent quantum mechanical method. The computational time for large molecules depends chiefly upon the order needed in the energy expansion to obtain sufficient convergence and not on the particular quantum mechanical method used. Preliminary results within the framework of a semiempirical CNDO/2 model Hamiltonian show at the Hartree-Fock and Møller-Plesset perturbation levels that relative energies converge to within a few tenths of a kcal/mol of the exact values at the four body level for molecules that have little delocalization. In strained ring and aromatic systems, convergence is however not nearly as rapid. Results can be improved somewhat by using larger interacting fragments containing two or more electron pairs over three or more atomic centers. © 1992 by John Wiley & Sons, Inc.
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  • 23
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Correlated molecular mulitpole moments and compact correlated cumulative atomic multipole moment (CCAMM) representation of molecular charge distribution in ground as well as in excited states have been derived directly from multiple reference double-excitation configuration interaction (MRD-CI) wave functions for BH and H2CO molecules using several extended basis sets with multiple polarization functions. This approach extends previously introduced uncorrelated and correlated CAMMs, and allows obtaining inexpensive modeling of electrostatic effects involving molecules in excited electronic states. © 1992 by John Wiley & Sons, Inc.
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  • 24
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 275-313 
    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 performance of a Runge-Kutta method of fourth order in dynamic simulations within Davydov's so-called |D2〉 state ansatz is studied by comparison with analytical solutions available for two special cases. Further, the Runge-Kutta method is compared with the one-step procedure used by Su and Schrieffer. A detailed analysis of the structure and energetics of Davydov solitons is given. The differences in the dynamics between open chain ends and periodic boundary conditions are also discussed. The properties of the soliton detector plot introduced by Lomdahl and Kerr are studied. Finally, three widely used initial states for Davydov soliton dynamics are compared.
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  • 25
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 314-317 
    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-PM3 calculations, carried out on an experimentally determined structure of an intermediate in the cycloaddition of an electrophilic azide and a nucleophilic 1,3-dipolarophile, show that the semiempirical MO scheme models this structure closely. Transition structures for formation of the intermediate and ring closure of the latter are described.
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  • 26
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 268-274 
    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 the natural bond orbital method, one may associate the valence bond configuration and Lewis structure concepts to wave functions consisting of molecular orbitals and thus gain intuitive insight into the molecular potential energy curves. Natural bond orbital analysis of the restricted open shell Hartree-Fock and unrestricted Hartree-Fock wave functions for the BeH ground state provides an intuitive model to help understand the nature of the bonding in this open shell species. The contrasting behavior of the bonding orbitals for different spins can be attributed to differences in the Pauli repulsive interactions with the lonepair orbitals. Such behavior occurs in BeH(2Σ) but does not in CO+(2Π) because the Pauli repulsion depends on the orbital overlap.
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  • 27
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
    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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  • 28
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 399-407 
    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 are reported for dimerization-induced changes, Δk, in the harmonic force constant k of the H-bonded OH in water dimer. Two dimer geometries are considered. Δk is obtained by considering the perturbation of a given monomer OH potential by the interaction energy in the dimer in question. The interaction energy is partitioned to identify the role of the various contributions to Δk. The sensitivity of Δk to the choice of the one-electron basis set is studied by using five different basis sets, some of which have a set of bond functions in the H—O bond. At the correlated level, correction for basis set superposition error is found to be essential. A comparison is made of the correlation contribution to Δk as given by the CEPA1, MP2, MP3, and MP4 methods. Of these, MP2 gives exaggerated results. Nevertheless, for economical and reasonably accurate calculations on large systems the MP2 approach in the ESPB basis set is advocated. The most accurate calculations yield a shift Δv0-;1 of - 121 cm-1 for the uncoupled donor O-H vibrational frequency in water dimer.
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  • 29
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    Journal of Computational Chemistry 13 (1992), S. 730-748 
    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 computational method for exploring the orientational and conformational space of a flexible ligand within a macromolecular receptor site is presented. The approach uses a variant of the DOCK algorithm [Kuntz et al., J. Mol. Biol., 161, 288 (1982)] to determine orientations of a fragment of the ligand within the site. These positions then form the basis for exploring the conformational space of the rest of the ligand, using a systematic search algorithm. The search incorporates a method by which the ligand conformation can be modified in response to interactions with the receptor. The approach is applied to two test cases, in both of which the crystallographically determined structures are obtained. However, alternative models can also be obtained that differ significantly from those observed experimentally. The ability of a variety of measures of the intermolecular interaction to discriminate among these structures is discussed.
    Additional Material: 10 Ill.
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  • 30
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    Journal of Computational Chemistry 13 (1992), S. 468-477 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Relative log P values of dimethylether to methanol and dimethylamine to methylamine were calculated in the chloroform/water system using Monte Carlo simulations and statistical perturbation theory. Correct ordering of the calculated relative log Ps was obtained for the two pairs although the method leads to an overestimation of these values. In aqueous solution, both dimethyl ether and dimethylamine solutes are proton acceptors forming a single hydrogen bond to water. Dimethylamine forms a stable N—H-Ow hydrogen bond while the water hydrogen is poorly localized in the O—H-Ow bond to the ether. In chloroform, the solvent molecules are less ordered around the solutes than was found around methanol and methylamine.
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  • 31
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    Journal of Computational Chemistry 13 (1992), S. 792-792 
    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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  • 32
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    Journal of Computational Chemistry 13 (1992), S. 793-798 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simulation data from an off-lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local confomational changes in a window of three consecutive monomer units. The time autocorrelation functions of end-to-end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms. © 1992 by John Wiley & Sons, Inc.
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  • 33
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    Journal of Computational Chemistry 13 (1992), 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: Among some 2-substituted 4H-1,3,2-benzodioxaphosphorin 2-sulfides, the 2-OMe derivative has the sulfur atom mainly in the quasiequatorial position. On the other hand, the conformation in which the sulfur is quasiaxial is favored in the 2-NHMe and 2-Et derivatives. We have done ab initio molecular orbital calculations for the model compounds, and such a substituent effect was reproduced. Moreover, the effect was discussed in terms of the intramolecular electrostatic interactions and the degree of charge distribution.
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  • 34
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    Journal of Computational Chemistry 13 (1992), S. 551-559 
    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 direct method for the ab initio calculation of the magnetic susceptibility and chemical shielding tensors based on the individual gauge for localized molecular orbitals (IGLO) formalism is introduced. “Direct” in this context means we avoid storing the two-electron repulsion integrals in favor of recalculating them whenever necessary. In conjunction with the Direct-SCF package TURBOMOLE Direct IGLO (DIGLO) permits calculation of magnetic second-order properties for large molecules by minimizing peripheral disc storage requirements. The size of the molecules to be treated is limited only by the amount of CPU time available. The performance of DIGLO is demonstrated for some selected examples.
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  • 35
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    Journal of Computational Chemistry 13 (1992), S. 579-584 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Protein-folding potentials, designed with the explicit goal that the global energy minimum correspond to crystallographically observed conformations of protein molecules, may offer great promise toward calculating native protein structures. Achieving this promise, however, depends on finding an effective means of dealing with the multiple-minimum problem inherent in such potentials. In this study, a protein-folding-potential test system has been developed that exhibits the properties of general protein-folding potentials yet has a unique well-defined global energy minimum corresponding to the crystallographically determined conformation of the test molecule. A simulated-annealing algorithm is developed that locates the global minimum of this potential in four of eight test runs from random starting conformations. Exploration of the energy-conformation surface of the potential indicates that it contains the numerous local minima typical of protein-folding potentials and that the global minimum is not easily located by conventional minimization procedures. When the annealing algorithm is applied to a previously developed actual folding potential to analyze the conformation of avian pancreatic polypeptide, a new conformer is located that is lower in energy than any conformer located in previous studies using a variety of minimization techniques.
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  • 36
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    Journal of Computational Chemistry 13 (1992), S. 614-621 
    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 computational chemistry study of the artificial redox enzyme synthesized by covalently attaching flavin to cyclodextrins explains some of its properties. Calculations indicate that the flavin moiety covalently attached to cyclodextrin is not within the cavity of cyclodextrin. This result is consistent with the UV-vis spectrum of the artificial enzyme. The calculations also indicate hydrogen bonds formed between the carbonyl groups of the catalytic functionality and the hydroxyl groups of cyclodextrin play a role in their most stable conformation. This explains the observed overall stability of these artificial enzymes compared to riboflavin. Electrostatic energies and solvation energies play a major role in the stability of the hosts and the orientation of guests included within the artificial enzymes. The rates of oxidation of various thiols catalyzed by the artificial enzyme can be explained by the relative distances between the sulfur atom of the substrates and C(4a) of the flavin moiety.
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  • 37
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An evaluation of the CHARMm force field for small molecules is described. Using different force field conditions and computational techniques, a wide variety of compounds are analyzed. rms deviations of Cartesian coordinates for 49 diverse organic molecules taken from the Cambridge Crystallographic Data Base and internal coordinate geometries for 28 other molecules are reported. Results are described with different dielectrics, dihedral constraints, and crystal packing to allow analysis of deviations from experimental data and give precise statements of the reliability of the parameters used in the force field. Torsional barriers (rms = 0.4) and conformational energy differences (rms = 0.4) are examined and comparisons made to other force fields such as MM2, Tripos, and DREIDING. The results confirm that CHARMm is an internally consistent all purpose force field with energy terms for bonds, angles, dihedrals, and out-of-plane motions, as well as nonbonded electrostatic and van der Waals interactions. Reported CHARMm results (rms = 0.006 Å for bonds, rms = 1.37° for angles, and rms = 3.2° for dihedrals) are in excellent agreement with high quality electron diffraction data. © 1992 by John Wiley & Sons, Inc.
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  • 38
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    Journal of Computational Chemistry 13 (1992), S. 952-962 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
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  • 39
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    Journal of Computational Chemistry 13 (1992), S. 963-970 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simulations of periodic boxes of tetrafluoromethane and trifluoromethane were run to determine van der Waals parameters for fluorine and for hydrogen attached to a fluorine-bearing carbon. The simulations of CF4 were performed first to determine the optimal van der Waals radius R* and well depth ε for fluorine by adjusting these parameters to reproduce the experimental molar volume and enthalpy of vaporization of CF4. The best values of R* and ε were determined to be 1.75 Å and 0.061 kcal/mol. Using these fluorine parameters, the simulations of CHF3 were then performed to determine if the hydrogen of this molecule required a smaller R* than that used for the “normal” hydrocarbon hydrogen determined by Spellmeyer and Kollman (results in preparation). That R* was determined by running Monte Carlo simulations on methane, ethane, propane, and butane and adjusting R* and ε for carbon and hydrogen to reproduce the experimental molar volume and enthalpy of vaporization. It was found that an Rε of 1.21 Å was optimal, significantly smaller than the R* = 1.49 Å found by Spellmeyer for “normal” hydrocarbon hydrogens. This value of R* is in good agreement with the R* for the hydrogen in CHF3 derived independently using ab initio calculations and molecular mechanics on F3C—H… OH2 by Veenstra et al. © 1992 by John Wiley & Sons, Inc.
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  • 40
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    Journal of Computational Chemistry 13 (1992), S. 1022-1035 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.
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  • 41
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    Journal of Computational Chemistry 13 (1992) 
    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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  • 42
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    Journal of Computational Chemistry 13 (1992), S. 1011-1021 
    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 Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is presented here as an extension of the Umbrella Sampling method for free-energy and Potential of Mean Force calculations. This algorithm possesses the following advantages over methods that are currently employed: (1) It provides a built-in estimate of sampling errors thereby yielding objective estimates of the optimal location and length of additional simulations needed to achieve a desired level of precision; (2) it yields the “best” value of free energies by taking into account all the simulations so as to minimize the statistical errors; (3) in addition to optimizing the links between simulations, it also allows multiple overlaps of probability distributions for obtaining better estimates of the free-energy differences. By recasting the Ferrenberg-Swendsen Multiple Histogram equations in a form suitable for molecular mechanics type Hamiltonians, we have demonstrated the feasibility and robustness of this method by applying it to a test problem of the generation of the Potential of Mean Force profile of the pseudorotation phase angle of the sugar ring in deoxyadenosine. © 1992 by John Wiley & Sons, Inc.
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  • 43
    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 of the potential energy surfaces of CH2N2, CHFN2, and CF2N2 at MP4SDTQ/6-31G*//MP2(full)/6-31G* reveal several surprising features. While diazomethane is more stable than diazirine, only the three-membered ring forms of the fluorine-substituted isomers are known experimentally. We find fluorodiazomethane and difluorodiazomethane not to be viable species: They have no barriers toward exothermic dissociation into N2 and CHF or CF2, respectively. In contrast, the three-membered ring isomers, fluorodiazirine and difluorodiazirine, have high barriers toward dissociation despite being high in energy. Diazomethane bends easily; a nonplanar Cs minimum is found at MP2(full)/6-31G* but C2v symmetry is preferred at QCISD/6-31G*. © 1992 by John Wiley & Sons, Inc.
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  • 44
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    Journal of Computational Chemistry 13 (1992), S. 1089-1097 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.
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  • 45
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    Journal of Computational Chemistry 13 (1992), S. 41-56 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Distance geometry and molecular dynamics simulation techniques were compared in their ability to search the conformational potential energy surface of β-cyclodextrin. Structures generated by the DISGEO program were minimized using three different atomic point charge sets. Some of these structures were used as starting points for molecular dynamics simulation in vacuo at 298K. The distance geometry results showed that the global features of the conformational potential energy surface were generally independent of the point charge set. The distance geometry technique was able to find structures of lower energy than those obtained by direct minimization of the X-ray or neutron diffraction structures. However, the molecular dynamics simulation technique was consistently able to find structures of lower energy than those generated by distance geometry. Root mean square fit of the trajectory structures to the starting structure showed that the simulation allowed the molecule to explore regions of the potential energy surface in the neighborhood of the starting structure. Both the distance geometry and molecular dynamics simulation techniques showed that β-cyclodextrin can adopt a wide range of conformations in the gas phase and that these conformations are much less symmetrical than the crystalline structure.
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  • 46
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    Journal of Computational Chemistry 13 (1992), S. 254-255 
    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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  • 47
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    Journal of Computational Chemistry 13 (1992), S. 570-578 
    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 Tyson-Fife reaction-diffusion equations are solved numerically using a locally implicit approach. Since the variables evolve at very different time scales, the resulting system of equations is stiff. The reaction term is responsible for the stiffness and the time step is increased by using an implicit method. The diffusion operator is evaluated explicitly and the system of implicit nonlinear equations is decoupled. The method is particularly useful for parameter values in which the equations are very stiff, such as the values obtained directly from the experimental reaction rate constants. Previous efforts modified the parameters on the equations to avoid stiffness. The equations then become a simplified model of excitable media and, for those cases, the locally implicit method gives a faster although less accurate solution. Nevertheless, since the modified equations no longer represent a particular chemical system an accurate solution is not as important. The algorithm is applied to observe the transition from simple motion to compound motion of a spiral tip.
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  • 48
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    Journal of Computational Chemistry 13 (1992), S. 585-594 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial \cos \phi }}\frac{{\partial \cos \phi }}{{\partial x}} $$\end{document} where φ is a bond or torsion angle, E(φ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, -1/sin φ, when φ is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, φ°, other than 0 or π, such as in E(φ) = κ[1 + cos(nφ - phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial x}} $$\end{document} This form still possesses singularities for the bond angle forces since the last factor is undefined when φ is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.
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  • 49
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    Journal of Computational Chemistry 13 (1992), S. 371-379 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: For the calculation of atomic charges in molecules, a new fast procedure based on extended Mulliken population analysis is presented. The reliability of the new population analysis is tested within the AM1 approximation and the results are compared in detail with those obtained by different methods reported in the literature.
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  • 50
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    Journal of Computational Chemistry 13 (1992), S. 457-467 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic calculation for molecules using approximated variational wave functions leads to well known difficulties connected with the application of the Hellmann-Feynman (H—F) theorem. This is due to the basis set inadequacies in the underlying calculations. This defect can easily be remedied by floating functions, whose centers are optimized in space. We can keep almost everything of the traditional wave function with a nuclear-fixed basis set, but we apply single floating to ensure the H—F theorem. Then, one can obtain a wave function obeying the H—F theorem. This provides a great conceptual simplification and may lead to practical advantages. The single floating scheme, which retains one expansion center per nucleus, is successfully applied to a series of small molecules using SCF and CASSCF wave functions with sufficiently polarized basis sets.
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  • 51
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    Journal of Computational Chemistry 13 (1992), S. 429-442 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Errors in free energies for molecular replacement and for conformation change of a small model peptide have been determined empirically by repeated simulations from different starting points. All calculations have been done using thermodynamic integration, in which the system's potential energy is coupled to a parameter λ, that is increased or decreased by a small amount at each step of the simulation. The effects of several factors that may alter the precision are evaluated. These factors include: the length of the simulation, the dependence of the potential energy on λ, the use of conformational restraints, and their magnitude and form. The methods used for restraint and conformational forcing are described in detail. The free energy change, calculated as the mean from several successive simulations with alternately increasing and decreasing λ, is found to be independent of the length of the simulations. As expected, longer simulations produce more precise results. The variation of the calculated free energies is found to consist of two parts, a random error and a systematic hysteresis, i.e., a dependence on the direction in which λ changes. The hysteresis varies as the inverse of the length of the simulation and the random error as the inverse square root The advantage of the use of a different (nonlinear) dependence of the attractive and repulsive parts of the nonbonded potential energy on the coupling parameter when “creating” particles in solution is found to be very large. This nonlinear coupling was found to be superior to the use of linear coupling and a nonlinear change of the coupling parameter with the simulation time. The hysteresis in conformational free energy calculations is found to increase markedly if too weak a forcing restraint is chosen. It is shown how to deconvolute the contribution of a torsional restraint from the dependence of the free energy on a torsion angle.
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  • 52
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    Journal of Computational Chemistry 13 (1992), S. 505-524 
    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 ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor-dependent terms in the potential function at points on a three-dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.
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  • 53
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    Journal of Computational Chemistry 13 (1992), S. 135-141 
    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 preliminary study of the capability of the finite difference and finite element methods (FDM, FEM) to evaluate eigenvalues of one-, two-, and three-dimensional self-adjoint operators is reported with reference to applications dealing with the description of vibrational levels. Results of harmonic oscillator model potentials and ab initio PES for the water molecule are obtained by using the FDM. In spite of the large matrices used, low accuracy, nonvariational results are found. A different method, based on FEM and normal coordinates, is therefore proposed. Two nearly harmonic cases are studied and it is shown that variational results with higher accuracy can be obtained with a moderate cost. The vibrational levels of the water molecule are also calculated in order to compare the results with those of the FDM treatment.
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  • 54
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    Journal of Computational Chemistry 13 (1992), S. 148-154 
    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 performance of Atomic Natural Orbital (ANO) basis sets for calculations involving nonempirical core pseudopotentials has been studied by comparing the results for atomic and molecular nitrogen obtained using contracted ANO basis sets with those obtained using both the primitive set and a segmented one. The primitive set has been optimized at the SCF level for atomic N treated as a five-electron pseudo-atom, and consists of 7s and 7p primitive GTOs supplemented by 2d and 1f GTOs optimized at the CI level. From this primitive set three contracted [3s 3p 2d 1f] sets have been obtained. The first one has been derived from the ANOs of the neutral atom, the second has been obtained from an averaged density matrix and the third one is a segmented set. For the atom, the segmented set gives a zero contraction error at the SCF level as it must be in valence-only calculations. The ANO basis sets show some small contraction error at the SCF level but perform better in CI calculations. However, for the diatomic N2 molecule the ANO basis sets exhibit a rather large contraction error in the calculated SCF energy. A detailed analysis of the origin of this error is reported, which shows that the conventional strategy used to derive ANO basis sets does not work very well when pseudopotentials are involved.
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  • 55
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    Journal of Computational Chemistry 13 (1992), S. 160-164 
    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 coarse-grain, parallel approach to direct Hartree-Fock calculations is presented and discussed. The suggested scheme allows for a near asymptotic speedup involving a very low parallelization overhead without compromising the vector performance of vector-parallel architectures. A shared-memory MIMD implementation, for which very high speeds of computation have been achieved, is discussed in detail.
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  • 56
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    Journal of Computational Chemistry 13 (1992), S. 240-253 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient algorithm for constrained geometry optimization in Cartesian coordinates is presented. It incorporates mode-following techniques within both the classical method of Lagrange multipliers and the penalty function method. Both constrained minima and transition states can be located and, unlike the standard Z-matrix using internal coordinates, the desired constraints do not have to be satisfied in the initial structure. The algorithm is as efficient as a Z-matrix optimization while presenting several additional advantages.
    Additional Material: 2 Ill.
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  • 57
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    Journal of Computational Chemistry 13 (1992), S. 199-213 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute-solvent coupling in a self-consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field-dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.
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  • 58
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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: Procedures have been developed to generate molecular electrostatic potentials based on correlated wave function from ab initio or semiempirical electronic structure programs. A new algorithm for point-wise sampling of the potential is described and used to obtain partial atomic charges via a linear, least squares fit between classical and quantum mechanical electrostatic potentials. The proposed sampling algorithm is efficient and promises to introduce less rotational variance in the potential derived partial charges than algorithms applied previously. Electrostatic potentials and fitted atomic charges from ab initio (HF/6-31G* and MP2/6-31G*) and semiempirical (INDO/S; HF, SECI, and SDCI) wave functions are presented for the electronic ground (S0) and excited (1Lb, 1La) states of 3-methylindole. © 1992 by John Wiley & Sons, Inc.
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  • 59
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    Journal of Computational Chemistry 13 (1992), S. 997-1003 
    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 closely related Cs (1) and C2v (3) structures of CH5+ have been reinvestigated at many ab initio levels using MP2/6-31G** and MP2/6-311 + + G(2df, 2pd) geometries. The largest basis sets employed were 6-311G(3df, 2p), 6-311 + + G(3df, 3pd), and the Dunning “correlation consistent” polarized triple-split valence basis set (cc-pVTZ). Electron correlation was probed at the MP4 level, but the QCISD method was also used with the largest basis sets. While electron correlation favors 3 over 1 by about 2 kcal/mol, the correlated relative energies with all basis sets employed range from 0.36-1.03 kcal/mol in favor of 1. The best estimate of this difference, 0.86 kcal/mol, is essentially identical with the (scaled) zero-point energy difference, 0.84 kcal/mol, favoring 3 over 1. These results indicate that 1 and 3 have almost exactly the same energy at 0 K. Our best value for the dissociation energy of CH5+ is 42.0 kcal/mol [QCISD(T)/6-311 + + G(3df, 3pd)//MP2(fu)/6-311 + + G(2df, 2pd), corrected to 298 K], which agrees very well with the experimental value. © 1992 by John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 13 (1992), S. 1037-1046 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical AM1, MNDO-PM3, and MNDO/M, as well as ab initio Hartree-Fock and Möller-Plesset calculations using the 4-31G, 6-31G(d,p), and 6-31 +G(d,p) basis sets have been done on the water-assisted addition of water to formaldehyde. ab initio methods predict a reduction of 30% of the bimolecular ΔG0,
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    Journal of Computational Chemistry 13 (1992), S. 1079-1088 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is introduced that can generate reaction-pathway hypotheses for computer-assisted elucidation. A key aspect of the algorithm is its ability to conjecture reaction intermediates and products that are not input to the algorithm. The formal basis for the conjecture is stoichiometry, i.e., species variables are used in the construction of a pathway, and their molecular formulas are inferred when sufficient stoichiometric constraint is placed on the variables. These conjectured species have a degree of plausibility when the algorithm is used systematically to search for the simplest pathways consistent with given experimental evidence. The MECHEM system for computer-assisted elucidation under development by the author adapts this algorithm to generate initial pathway hypotheses from experimental data. © 1992 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 13 (1992), S. 1109-1113 
    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 protein-dipole Langevin-dipole (PDLD) model developed by Warshel and co-workers is an approach to evaluate electrostatic interactions in protein systems from microscopic sights. This model grasped the main physical factors and required little computations. But it might need the tests from every aspect. In the present work, we have chosen the solvation energies of Asp3, Glu7, Glu49, and Asp50 in bovine pancreatic trypsin inhibitor (BPTI) as a calibration to discuss the influences of parameters and conditions on the simulation results in the PDLD model. Some improvements have been proposed. The calculated solvation energies associated with ionizing the four acidic groups in BPTI and aspartic acid in solution are found in good agreement with the corresponding observed results if the improved PDLD approach and computational methods are used. © 1992 by John Wiley & Sons, Inc.
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  • 63
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    Journal of Computational Chemistry 13 (1992), S. 1119-1124 
    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 particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two- and three-dimensional system. © 1992 by John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 13 (1992), S. 478-491 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An extensive conformational analysis of 3′-azido-3′-deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine - furan, furan - azide, furan - methylene, and methylene - hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2—;HO), which until recently has not been mentioned in the literature, is observed in a few low-energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6—;OH and H6—Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OH—Ofur, which also has not been mentioned for AZT in the literature until recently). The AM1-optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
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  • 65
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    Journal of Computational Chemistry 13 (1992), S. 539-540 
    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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  • 66
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    Journal of Computational Chemistry 13 (1992), S. 810-820 
    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 systematic derivation procedure that greatly facilitates the application of the Taylor method to the integration of kinetic models is developed. In addition, an algorithm that gives the integration step as a function of the required level of accuracy is proposed. Using the Taylor method, application of this algorithm is immediate and largely reduces the integration time. In addition, a new method of integration of kinetic models, whose most important feature is the self-adaptability to the stiffness of the system along the integration process, is developed. This “stiffness-adaptive” Taylor method (SAT method) makes use of several algorithms, combining them to meet the particular requirements of the integration of each species along the integration process. In comparison with the Runge-Kutta-Felhberg, Runge-Kutta-Calahan, Taylor, and Gear methods, the SAT method is the best to integrate non-stiff and stiff kinetic systems, giving the best accuracy and the smallest computing time. © 1992 by John Wiley & Sons, Inc.
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  • 67
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    Journal of Computational Chemistry 13 (1992), S. 842-850 
    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 molecular electrostatic potential (MEP) distribution of anisole, chlorobenzene, and fluorobenzene obtained from STO-3G, 3-21G, and 6-31G* basis set ab initio and MNDO and AM1 semiempirical wave functions is investigated to explain the differences among the MEP features obtained for polychlorodibenzo-p-dioxins. The main topological features as well as the absoltue and relative minima location obtained from ab initio calculations are independent from the choice of the basis set. MNDO calculations are in good agreement with the ab initio ones in the case of anisole and fluorobenzene, while they incorrectly describe the MEP of chlorobenzene. The AM1 fails to localize the absolute minimum of fluorobenzene and does not find the minimum above the chlorobenzene chlorine atom. The poor agreement of both semiempirical methods with ab initio for any kind of chlorinated compounds is confirmed by results obtained for chloreothylene and chloroethane. We hypothesize that the main problem concerning these methods is that they freeze a too large amount of electrons in the atomic core of elements belonging to the second row, which makes for a wrong description of the core-valence electron interactions. Results obtained by modifying the AM1 parameters related to these interactions confirm our hypothesis. © 1992 by John Wiley & Sons, Inc.
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  • 68
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    Journal of Computational Chemistry 13 (1992), S. 874-882 
    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 solving the approximate Schrödinger equation (SE) for a single internal motion is presented. In the SE the reduced moment of inertia I(φ) and potential energy V(φ) are expressed as functions of the torsional angle φ. Molecular examples include ethane, chloroethane, and 1,2-dichloroethane for which I(φ) and V(φ) have been derived from the HF/6-31G* optimized geometries and energies at φ increments of 30°. The resulting potential energy curves, energy levels, and wave functions are shown graphically. The calculated fundamental torsional frequencies are found to fall within 10 cm-1 of the experimental values. Approximations for the off-diagonal energy matrix elements, and numerical accuracy of torsional energy levels, are shown to be satisfactory. Attention is called to the computer programs developed for this work and their applications to torsional studies in relevant areas of spectroscopy, thermodynamics, and reaction rates. © 1992 by John Wiley & Sons, Inc.
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  • 69
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    Journal of Computational Chemistry 13 (1992), S. 912-918 
    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 electronegativities () of some 36 atoms/groups (including some 6 ionic ones) X are calculated from the atomic charges in the corresponding methyl species CH3X that were obtained by applying Bader's theory of atoms in molecules. The numerical values of the for the various groups studied are reasonable and correlate linearly with the two existing experimental scales for group electronegativity, Inamoto's i scale and the 1JCC (ortho-ipso) coupling constants in the monosubstituted benzenes, to satisfactory extents. The relations between the values and some “critical properties” of the various CH3X molecules considered are also studied. It is suggested that in a molecule PX, rP/R where rP is the distance of Bader's critical point on the bond PX of length R from the atom P or the binding atom of the group P can be a very good measure of the electronegativity of the atom/group X. © 1992 by John Wiley & Sons, Inc.
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  • 70
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    Journal of Computational Chemistry 13 (1992), S. 622-632 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.
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  • 71
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    Journal of Computational Chemistry 13 (1992), S. 657-666 
    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 theory with the 6-31G* basis set has been used to investigate the geometries and preferred conformations for urea, derivatives of urea, and a few complicated amide derivatives. The results from the ab initio calculations provide insight into the gas-phase rotational barrier about the C—N bond and have been used to generate parameters for the MM2(87) molecular mechanics program. When applicable, theoretical structures are compared with corresponding previously reported experimental geometries. Urea is predicted to be nonplanar with pyramidal amino groups.
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  • 72
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    Journal of Computational Chemistry 13 (1992), S. 681-692 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical AM1, MINDO/3, and MNDO methods have been used in the study of the alkaline hydrolysis of β-lactam antibiotics through a base-catalyzed, acyl-cleavage, bimolecular mechanism. In this work, the hydroxyl ion has been chosen as nucleophilic agent and the azetidin-2-one ring like a model of β-lactam antibiotic. The MINDO/3 method does not predict correctly the energies of small rings. This, together with the fact that, like MNDO, it cannot detect the occurrence of hydrogen bonds, gives rise to uncertain estimates of energy barriers. The AM1 method can be considered the most suitable for studying the hydrolysis of β-lactam compounds.
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  • 73
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    Journal of Computational Chemistry 13 (1992), S. 718-721 
    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 geometry of acryloyl fluoride was optimized completely at the RHF/6-31G* level of theory at 10 points on the theoretical potential energy curve for internal rotation. The energies obtained were used to determine a six term cosine expansion of the torsional potential energy function. This function was then refined using the experimental torsional transition frequencies in the s-trans and s-cis wells in conjunction with the geometrical parameters optimized at the RHF/6-31G* level. The effective potential function obtained is compared with previous results. The necessity of accounting for relaxation of the geometry upon internal rotation is stressed. © 1992 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 13 (1992), S. 772-791 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 838-841 
    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 bond and group equivalent scheme that allows the calculation of heats of formation for carboxylic acids and esters from ab initio 6-31G* energies has been developed. For a group of 16 compounds, the rms error for the calculated heats of formation was 0.64 kcal/mol. Heats of formation have been predicted for an additional seven compounds for which the experimental values are either unknown or suspect. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 830-837 
    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 semi-empirical NDDO method, generalized from a similar scheme at the CNDO/2 level developed previously, is presented to treat very large molecules. The extended molecular system is divided into a relatively small subsystem where substantial chemical changes take place and an environment remaining more-or-less unperturbed during the process. Expanding the wave function on an atomic hybrid basis an SCF procedure is performed for the subsystem in the field of the iteratively determined electronic distribution of the environment. A computer program has been written for the IBM RISC System/6000 530 computer and several test calculations were done for a variety of large classical molecules, like substituted aliphatic hydrocarbons, water oligomers, and a heptapeptide. Protonation energies, proton transfer potential curves, rotational barriers, atomic net charges, and HOMO and LUMO energies, as computed by the exact version of the NDDO method, are fairly well reproduced by our approximation if the subsystem is appropriately defined. © 1992 by John Wiley & Sons, Inc.
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  • 77
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    Journal of Computational Chemistry 13 (1992), S. 860-866 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Application of MNDO, AM1, PM3, MNDO/H, and MNDO/M methods to a set of compounds with intramolecular hydrogen bonds suggested that none of these methods accurately modeled the characteristics of the hydrogen bonds. Since the MNDO/H and MNDO/M methods work well for intermolecular hydrogen bonds, we followed their example and modified MNDO for intramolecular hydrogen bonds by altering the empirical core-core repulsion energy function for all pairs of atoms involved in intramolecular O-H—O bonds. The resulting modified method models the behavior of these bonds quite well, especially as regards their geometry and the barrier to proton transfer. © 1992 by John Wiley & Sons, Inc.
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  • 78
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    Journal of Computational Chemistry 13 (1992), S. 883-887 
    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 quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic-charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to the R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties. © 1992 by John Wiley & Sons, Inc.
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  • 79
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    Journal of Computational Chemistry 13 (1992), S. 1125-1137 
    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 MM2 and MM3 force fields have now been parameterized for ketene and its various derivatives. With the addition of the Csp = O bond stretching and Csp2=Csp=O bond bending parameters, calculations were performed on ketene and six substituted ketene compounds. The MM2 results are quite good with only minimal errors in the calculation of Csp2—H bond lengths and H-Csp2-H bond angles. Additionally, Csp2—F bond parameters in MM2 have been re-adjusted to give better results in monofluorinated species, but, unfortunately, resulting in greater error in the polyfluorinated compounds. The results of geometry calculations by MM3 are similar to those obtained by MM2 with the exception of a significant improvement in the geometry of dimethylketene. The MM3 vibrational frequencies calculated in this study are also in good agreement with available experimental and ab initio results with the exception of a few low frequency in-and out-of-plane bending modes. © 1992 by John Wiley & Sons, Inc.
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  • 80
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    Journal of Computational Chemistry 13 (1992) 
    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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  • 81
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    Journal of Computational Chemistry 13 (1992), S. 1184-1198 
    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 geometries and dissociation energies for the Fe—C and C—H bonds of FeCHn and FeCHn+ (n = 1, 2, 3) have been calculated by ab initio quantum mechanical methods using different effective core potential models and Møller-Plesset perturbation theory. The HW3 ECP model, which has a configuration [core] (n-1)s2, (n-1)p6, (n-1)d1, (n)sm for the transition metals, is clearly superior to the larger core LANL1DZ ECP model with the configuration [core] (n-1)d1, (n)sm. The Fe—C bond energies calculated at correlated levels using the HW3 ECP are in much better agreement with experiment than the LANL1DZ results. This effect is mainly due to the higher number of correlated electrons rather than the inclusion of the outermost core electrons in the Hartree-Fock calculation. At the PMP4/HW3TZ/6-31G(d)//MP2/HW3TZ/6-31G(d) level, the theoretically predicted Fe—C bond energies for FeCHn+ are in the range of 80% of the experimental values and have nearly the same accuracy as all-electron calculations using large valence basis sets and the MCPF method for the correlation energy. © 1992 by John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 13 (1992), S. 1171-1183 
    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 performance of a new crystal packing procedure for the ab initio prediction of possible molecular crystal structures is presented. The method is based upon only molecular information, i.e., no unit cell parameters are assumed to be known. The search for the global crystal energy minimum and all local minima inside an energy window is derived from Monte Carlo simulated annealing methods and has been applied to various organic molecules containing heteroatoms and polar groups. A systematic evaluation of the search method and of the quality of the potential energy function has been established. It is demonstrated that the packing of general organic molecules is possible even with standard force fields like CHARMM provided that the charges defining the electrostatic interactions are based upon physical models rather than transferable empirical parameters. Concepts of crystal packing that were based till now upon assumptions and speculations could be proved or disproved by solving directly the extended global optimization problem related to crystal packing. Crystal structures of molecules as complex as those treated in this article have not been, till now, predicted by a computational approach. In one case, a disagreement between the predicted and experimental structure was evident and, based upon the computations, we suspect that the published structure is the wrong one. © 1992 by John Wiley & Sons, Inc.
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  • 83
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    Journal of Computational Chemistry 13 (1992), S. 1004-1010 
    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 extended Koopmans' theorem has been implemented using multiconfigurational self-consistent field wave functions calculated with the GAMESS, HONDO, and SIRIUS programs. The results of illustrative calculations are presented for the molecules HF, H2O, NH3, CH4, N2, CO, HNC, HCN, C2H2, H2CO, and B2H6. The lowest extended Koopmans' theorem ionization potentials agree well within the experimental values and the ionization potentials representing excited states of the ions show some improvements over the Koopmans' theorem values in most cases. The extended Koopmans' theorem is easily implemented and the time required to calculate the ionization energies is insignificant compared to the time required to calculate the wave function of the un-ionized molecule. © 1992 by John Wiley & Sons, Inc.
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  • 84
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    Journal of Computational Chemistry 13 (1992), S. 1057-1065 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In the present work we have carried out a Monte Carlo simulation of a dissociative electron transfer reaction in a polar solvent. In particular, we have chosen as a very simple model the electrochemical reduction of hydrogen fluoride to give a hydrogen atom and a fluoride anion in a dipolar solvent. From a classical point of view, the electron transfer occurs at the intersection region S* of the diabatic potential hypersurfaces Hpp and Hss, corresponding to the precursor and successor complexes, respectively. We have evaluated both diabatic surfaces using potential functions that have been built up with ab initio methods by us. For each of the obtained configurations the parameter ΔE = Hss - Hpp has been calculated. This parameter is then used as the reaction coordinate for obtaining the diabatic free energy curves of the reaction. Because the activation energy is high, a suitable mapping potential along with the statistical perturbation theory is employed to force the system to evolve toward the intersection region S*. A total of 68,340,000 configurations have been generated. The main conclusion of this article is that Marcus' relationship seems to fail for this kind of inner-sphere processes. © 1992 by John Wiley & Sons, Inc.
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  • 85
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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: Four semiempirical methods (AM1, MNDO, PM3, and MINDO/3) are used to calculate the deformation angles of [n]paracyclophanes and their Dewar benzene isomers for n = 3… 10. The results obtained by all these methods are in good agreement with data from X-ray studies. We have determined the strain energies that, in both series of compounds, are due to two components: (1) the strain energy of deformation of the cycle (aromatic or Dewar Benzene skeletons) and (2) the strain energy of the oligomethylene chain. In [6]paracyclophane, the strain energy [SEring(MNDO) ≍ 32.9 kcal/mol] almost compensates the resonance energy (Eresonance ≈ 36 kcal/mol) so that its chemical properties are closer to alkenes than to benzenic compounds. To better reproduce the enthalpy of the valence isomerization [n]Dewar bezene → [n]paracyclophane, which is poorly calculated with these methods, a correction is proposed and the reaction enthalpy of [6]paracyclophane is estimated to be about ΔHr ≈ 15 ± 15 kcal/mol. It is found that MNDO and MINDO/3 need the smallest corrections, but MNDO leads to better geometries than MINDO/3. In conclusion, MNDO seems to be the best technique for further studies of these compounds. © 1992 by John Wiley & Sons, Inc.
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  • 86
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    Journal of Computational Chemistry 13 (1992), S. 1098-1102 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe two algorithms for the parallel calculation of a CHARMm-like force field in macromolecules. For a molecule with a given number of atoms, we show that there is an optimal number of processors leading to a minimum computation time. At the optimum, both the number of processors and the computation time are proportional to the number of atoms. © 1992 by John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 13 (1992), S. 1103-1108 
    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 problem of the computation of the Centrifugal Distortion Constants (CDC) related to a diatomic potential is considered. The analytical expressions obtained from a reformulation of the Rayleigh-Schrödinger perturbation theory are used [Kobeissi et al., J. Mol. Spectrosc., 138, 1 (1989)]; these are en+1 = 〈Φ0RΦn〉 - Σm=1n em〈Φ0Φn-m〉 where R = 1/r2, Φ0 = ψv is the vibrational wave function (corresponding to the given energy Ev = e0) and Φ1, Φ2,…, are the “rotational corrections” to Φ0, solutions of the rotational (nonhomogeneous) Schrödinger equations. These equations are integrated by using a recent integrator using a powerful local control allowing (for Φ0) a high accuracy. The integrals are computed by using another powerful technique tailored for matrix elements between numerical wave functions [Kobeissi et al., J. Comp. Chem., 10, 358 (1989)]. This numerical treatment is applied to the model Lennard-Jones potential and to the RKR potential of the I2 ground state. In both applications the CDC are computed up to e6 = Nv and e7 = Ov (these two are published for the first time), and up to the dissociation [up to v = 23 for the Lennard-Jones potential, and to v = 108 for the XΣ - I2 (RKR) potential]. © 1992 by John Wiley & Sons, Inc.
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  • 88
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    Journal of Computational Chemistry 13 (1992), S. 1138-1141 
    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 MM3 molecular mechanics program calculates a fair representation of vibrational frequencies for molecules. To make this information more useful, a qualitative intensity calculation has been added, as is described herein. Because each bond in the molecule is assigned a dipole moment, and the vibrational amplitudes are known from the frequency calculation, the change in dipole moment corresponding to each normal mode is readily calculated. In some cases a charge flux has to be added empirically for bond stretchings. This relatively simple calculation has been applied to a number of different functional groups, and gives band intensities adequate for dividing the bands into very strong, strong, medium, weak, or very weak (forbidden) categories. © 1992 by John Wiley & Sons, Inc.
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  • 89
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    Journal of Computational Chemistry 13 (1992), S. 1170-1170 
    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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  • 90
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    Journal of Computational Chemistry 13 (1992), S. 1199-1209 
    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 new formalism is presented, based upon the finite element method, that permits a dual representation of orbitals in terms of exponential or Gaussian functions as both an integral over the space of exponential parameters and as a linear combination of basis functions. The method has been implemented for the atomic Hartree-Fock problem using exponential functions and test calculations made for atoms ranging from B to Cl. Accurate and consistent results can be obtained for a variety of atoms in a simple way using computational schemes that are systematic and hierarchic in nature. The new formalism is promising for any method where the calculation of integrals is not a major problem, such as some approaches of the density functional method and the pseudospectral formulation of ab initio methods. © 1992 by John Wiley & Sons, Inc.
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  • 91
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    Journal of Computational Chemistry 13 (1992), S. 1216-1233 
    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 distribution of conformations of heptaalanine is obtained using a new Monte Carlo (MC) method that grows the chain atom by atom. Resulting configurations are energy minimized and a detailed analysis is performed of the minimum-energy conformers using a method of classification that partitions φψ space. The MC-generated configurations are compared with those generated from high-temperature molecular dynamics (MD) simulations. It is found that the new method generates a wide distribution of low-energy conformers at least 10 times more quickly than the MD. An analysis of the generated energy minima demonstrates that they can be divided into clusters in the space defined by the five pairs of φ - ψ angles of the inner residues. The space occupied by the minima populating each cluster is restricted. © 1992 by John Wiley & Sons, Inc.
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  • 92
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    Journal of Computational Chemistry 13 (1992), S. 1246-1254 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient vector processing algorithm generating PK supermatrices has been developed, in particular aiming at calculations on large molecules. The algorithm utilizes the recurrence relations for electron repulsion integrals. The PK supermatrices are listed in a nearly canonical order so that the Fock matrix generation is efficiently vectorized, no temporary ERI and PK files being used. This is effected by partition of the basis set (atomic orbitals) into subsets of certain appropriate sizes, and the partition approach is named as the three-dimensional partial space method. A high-speed Hartree-Fock calculation including integrals and SCF procedures is achieved. © 1992 by John Wiley & Sons, Inc.
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  • 93
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    Journal of Computational Chemistry 13 (1992), S. 142-147 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimum geometries and harmonic frequencies calculated at the Hartree-Fock and the MP2 level are reported for the fluorohydrocarbon CHF2CH3; basis sets employed range from STO-3G to 6-311G**. The significantly shortened C—C distance of 1.50 Å is reproduced already with the simplest split-valence basis set; the C—F distance of 1.36 Å on the other hand needs MP2 correction at least at the double-ζ or 6-311G* level. Symmetry coordinates defined in terms of internal coordinates are in qualitative agreement with available experimental evidence. Even the best basis set yields frequencies that differ from experimental (anharmonic) values by up to 200 cm-1 indicating the well-known necessity of including higher-order force constants if quantitative agreement with experiment is to be achieved.
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  • 94
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    Journal of Computational Chemistry 13 (1992), S. 183-186 
    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 mechanism of the McLafferty rearrangement of the butanal radical cation to ethylene and vinyl alcohol cation is found, by ab initio calculations, to be stepwise. The results of a previous ab initio study are inconclusive because of symmetry restriction in their geometry optimization.
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  • 95
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    Journal of Computational Chemistry 13 (1992), S. 70-75 
    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 ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH3, NH2, OH, and HC2 as well as the multibonded species CN, BO, N3, OCN, and NO2. The simple Hartree-Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EAad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EAad by 0.2 eV. It is concluded that the LDA/NL method affords EAad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.
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  • 96
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    Journal of Computational Chemistry 13 (1992), S. 93-101 
    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 recently extended SINDO1 method is used to study geometries, electronic structures, and chemical bonding of transition metal organometallic compounds. The optimized distances and angles between metal atoms and organic ligands are in fair agreement with experimental data and are comparable to ab initio results. The comparison of orbital energies between the current method and ab initio methods shows that the method can give a correct description of electronic structure and bonding patterns of organometallic compounds. The method is also used to calculate atomic and bond valence, which are defined in terms of appropriate combinations of first-order density matrix elements for molecules. The valence indices provide a straightforward and easy-to-interpret way to analyze the magnitude of metal-carbon and metal-metal bonds.
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  • 97
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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: From the standpoint of models that use a polarizable continuum to represent the solvent in studying the phenomenon of solvation, a systematic and detailed analysis is made of the influence of the cavity size and shape on calculated energies. The solute is represented by its ab initio wavefunction, and the electronic part of the solvation energy is calculated including terms that take into account electron correlation up to third order. The analysis shows the convenience of modeling the cavity according to considerations of homogeneity, which are based fundamentally on how the solute wavefunction is constructed, i.e., the basis set used.
    Additional Material: 10 Ill.
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  • 98
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    Journal of Computational Chemistry 13 (1992), S. 155-159 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Elementary Jacobi Rotations are used as the basic tools to obtain eigenvalues and eigenvectors of arbitrary real symmetric matrices. The proposed algorithm has a complete concurrent structure, that is: every eigenvalue-eigenvector pair can be obtained in any order and in an independent way from the rest. Examples based on diagonally dominant real symmetric matrices are given.
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  • 99
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    Journal of Computational Chemistry 13 (1992), S. 165-176 
    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 using effective core potentials and polarized split-valence basis sets are reported for the title compounds. The calculated geometries, vibrational frequencies, infrared intensities, harmonic force fields, dipole moments, relative energies, and barriers to pseudorotation are compared with the available experimental data for the known molecules. Predictions are made for those pentahalides that are still unknown. Trends in the calculated properties are identified and discussed.
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  • 100
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    Journal of Computational Chemistry 13 (1992), S. 380-397 
    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 docking explores the binding modes of two interacting molecules. The technique is increasingly popular for studying protein-ligand interactions and for drug design. A fundamental problem problem with molecular docking is that orientation space is very large and grows combinatorially with the number of degrees of freedom of the interacting molecules. Here, we describe and evaluate algorithms that improve the efficiency and accuracy of a shape-based docking method. We use molecular organization and sampling techniques to remove the exponential time dependence on molecular size in docking calculations. The new techniques allow us to study systems that were prohibitively large for the original method. The new algorithms are tested in 10 different protein-ligand systems, including 7 systems where the ligand is itself a protein. In all cases, the new algorithms successfully reproduce the experimentally determined configurations of the ligand in the protein.
    Additional Material: 12 Ill.
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