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  • Biochemistry  (152)
  • 1990-1994  (152)
  • 1985-1989  (1)
  • 1970-1974  (1)
  • 1992  (152)
  • 1
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    New York, NY : Elsevier
    Keywords: Biochemistry ; Enzymes
    Notes: This is a series title, single volumes see link below.
    ISSN: 1557-7988
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  • 2
    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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  • 3
    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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  • 4
    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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  • 5
    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.
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  • 6
    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.
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  • 7
    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.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 9
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.
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  • 10
    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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  • 11
    Electronic Resource
    Electronic Resource
    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.
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  • 12
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Vinyloxyboranes, CH2=CH—;O—;BR2, are shown by ab initio molecular orbital theory to be more stable than the isomeric β-aldoboranes, R2B—CH2—CH=O, by ca. 19 kcal/mol. The MP2/6-31G*/6-31G* + ZPE barrier for the [1,3] boron shift is only 10.9 kcal/mol (R = Me) relative to the aldoborane. Other C2H5BO isomers (β-ketoboranes, boraepoxides and organoboron oxides), which are related to the proposed stages in the carbonylation reaction of boranes, are shown to be plausible intermediates. However, some of the computed barriers for methyl group migrations are unrealistically large, up to ca. 63 kcal/mol.
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 443-456 
    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 present an analytical method for generating a whole protein backbone structure from the coordinates of the α-carbons. The procedure begins by automatically positioning the β-carbons for every residue, and then the positions of the carbonyl groups and the amide nitrogens are also computed. The method is based upon the simultaneous minimization of a number of geometrical constraints that appear in real proteins and that can be very easily formulated as a set of trigonometric relations between the coordinates of the atoms involved in the backbone reconstruction. The resulting algorithm has been tested for proteins of very different sizes and topologies, and can advantageously compete with other methods proposed for this goal both in accuracy and in computational requirements. Possible ways of further refinement of the resulting structures are discussed.
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  • 14
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 16
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 17
    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 free energy gradient or Hessian of a molecule interacting with a liquid represented by a dielectric continuum is derived in the self-consistent reaction field formalism. An ellipsoidal approximation of the cavity is proposed with an algorithm to automatically define the ellipsoid from the nuclear coordinates of the atoms. With this approximation, geometry optimization of the solvated molecule becomes very fast. This method has been implemented in some standard ab initio or semiempirical computational codes. As a first test of the method, full geometry optimization of formamide in a high dielectric constant medium reveals that the CPU time needed for one optimization cycle is less than 3% longer for a solvated species than for the corresponding free molecule.
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  • 18
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
    Additional Material: 6 Ill.
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  • 19
    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 and semiempiridal (AM1) molecular orbital theory has been used to model the cleavage of formamide at the active site of carboxypeptidase A. The model active site consists of a zinc dication coordinated to two imidazoles, an acetate, a water with a hydrogen-bonded formate, and a formamide molecule as model substrate. AM1 has been compared with ab initio theory for the coordination of water and formamide to Zn++ and found to give excellent energetic results. The course of the amide cleavage was therefore calculated with AM1. The first step of the reaction is the dissociation of the zinc-coordinated water to give an active ZnOH+ species. The remote formate acts as proton acceptor. This process has an activation energy of only 4.6 kcal mol-1. The next and rate-determining step is the concerted addition of the ZnOH+ moiety to the formamide C=O bond. The Zn—O distance in the transition state is more than 3 Å. In four further steps, the amide nitrogen is protonated and the C—N bond cleaved. The net activation energy for the entire process is 15.5 kcal mol-1 relative to the active site model and 19.6 kcal mol-1 relative to the most stable point on the calculated reaction profile.
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  • 20
    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 hybrid conformational search algorithm (DMC) is described that combines a modified form of molecular dynamics with Metropolis Monte Carlo sampling, using the COSMIC(90) force field. Trial configurations are generated by short bursts of high-temperature dynamics in which the initial kinetic energy is focused into single bond rotations or alternatively into “corner-flapping” motions in ring systems. Constant temperature and simulated annealing search protocols have been applied to the conformational analysis of several model hydrocarbons (cyclopentane, cyclohexane, cycloheptane, cyclooctane, cycloheptadecane, decane, and tetradecane), and the performance compared with conventional molecular dynamics and Monte Carlo sampling methods. Optimum Metropolis sampling temperatures have been determined and range from 1000-2000 K for acyclic molecules to 3000 K for cyclic systems. Simulated annealing runs are most successful at locating the global minimum when cooling slowing from these optimum temperatures.
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  • 21
    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 ab initio study of 3-chloro-, 3-hydroxy-, 3-mercapto-, and 3-amino-propanenitrile and 4-chloro-bu- tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.
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  • 22
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 23
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 749-767 
    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 large data base of 6-31G*, MNDO, AM1, and PM3 electrostatic potential (ESP) derived point charges of amino acids and monosaccharides is analyzed. We find that MNDO correlates well with 6-31G* ESP derived point charges, while AM1 and PM3 do so quite poorly. Furthermore, scaling MNDO ESP derived point charges enhances the ability of MNDO to reproduce 6-31G* results. We used our data base to attempt to derive a 6-31G* transferable charge model at an atom-by-atom level. We find that it is simple to derive a transferable model for monosaccharides, but for the amino acids statistical difficulties make this a less attractive approach. The transferable charge model for the monosaccharides is slightly better than MNDO, but scaled MNDO charges perform significantly better than the transferable model. We also carried out a QMD simulation on the alanine dipeptide to assess the fluctuations that would be expected in atomic point charges during the course of an MD simulation. Relatively large charge fluctuations are observed and their impact on molecular simulation is addressed. © 1992 by John Wiley & Sons, Inc.
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  • 24
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Finite-difference Poisson-Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge-solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 103 for small molecules. © 1992 by John Wiley & Sons, Inc.
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  • 25
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 26
    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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  • 27
    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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  • 28
    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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  • 29
    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 present an extension of our modified MM2(80) force field MM2MOD in which a potential function for hydrogen bonding in alcohols and ethers is included. The results of applying MM2(85), MM2(87), and MM2MOD on ethylene glycol, 2-methoxyethanol and 1,3-propanediol are reported and compared with available experimental data and ab initio results. It is concluded that hydrogen bonding plays an important role in determining the molecular conformations of these systems. © 1992 by John Wiley & Sons, Inc.
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  • 30
    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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  • 31
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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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  • 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: The electronic structure of cobalt silicide clusters Co7Si7 and Si7Co7 was studied in comparison to that of Co19 and Si17 clusters under the scope of the MINDO/SR method. Clusters Co7Si7 and Si7Co7 represent the environment of a cobalt atom and that of a silicon atom in the cobalt monosilicide bulk, respectively. It is found that the Co—Si bond is essentially sp in character with an indirect participation (by electrostatic interaction) of the cobalt d orbitals. Our calculations show a charge transfer from silicon to the d orbitals of cobalt via sp-sp interaction with an internal sp-d hybridization. The theoretical density of states for cobalt silicide clusters are reported and compared with experimental results of surface spectroscopies. © 1992 by John Wiley & Sons, Inc.
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  • 33
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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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  • 34
    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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  • 35
    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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  • 36
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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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  • 37
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    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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  • 38
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 39
    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 effective core potentials (ECP) and model potentials (MP) has been studied by calculating the geometries and reaction energies of isodesmic reactions for the molecules Ti(CH3)nCl4 - n (n = 0-4) at the Hartree-Fock level of theory. The results are compared with data from all electron calculations and experimental results as far as available. The all electron calculations were performed with a 3-21G basis set from Hehre and a (53321/521/41) basis set from Huzinaga. For the ECP calculations the potentials developed by Hay and Wadt, and for the MP calculations, the model potentials developed by Sakai and Huzinaga, are employed. © 1992 by John Wiley & Sons, Inc.
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  • 40
    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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  • 41
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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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  • 42
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    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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  • 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: 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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  • 44
    ISSN: 0192-8651
    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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  • 45
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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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  • 46
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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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  • 47
    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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  • 48
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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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  • 49
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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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  • 50
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    Journal of Computational Chemistry 13 (1992), S. 1114-1118 
    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 Poisson-Boltzmann equation can be used to calculate the electrostatic potential field of a molecule surrounded by a solvent containing mobile ions. The Poisson-Boltzmann equation is a non-linear partial differential equation. Finite-difference methods of solving this equation have been restricted to the linearized form of the equation or a finite number of non-linear terms. Here we introduce a method based on a variational formulation of the electrostatic potential and standard multi-dimensional maximization methods that can be used to solve the full non-linear equation. © 1992 by John Wiley & Sons, Inc.
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  • 51
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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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  • 52
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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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  • 53
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 54
    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 six-term auxiliary integral expression for the two-electron Gaussian integral is derived on the basis of the Chebyshev polynomial approximation instead of the seven-term Taylor expansion. This expression and the related recurrence formula enable us to perform a high-speed calculation on a vector processing computer.
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  • 55
    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 rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas of internal atoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET-enkephalin using MSEED to compute the solvent-accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent-accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 potential only.
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  • 56
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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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  • 57
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    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.
    Additional Material: 5 Tab.
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  • 58
    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.
    Type of Medium: Electronic Resource
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  • 59
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
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  • 60
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 102-114 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Energy surfaces for the relative orientations of the pyranosyl rings of α,α-, α,β-, and β,β-trehalose and analogues were generated with MM3. Sixteen starting conformations of the rotatable side groups of α,β-trehalose were considered, while only 10 conformations were needed for α,α- and β,β-trehalose because of molecular symmetry. Energies were calculated at 20° increments of the two torsional angles of the glycosidic linkage, but otherwise the molecules were fully relaxed. The structure at the overall minimum for α,α-trehalose agrees well with that found in crystal structures, and also agrees with interpretations of NMR and optical rotation data. The energy surfaces for the three trehaloses differ greatly from each other, but are each similar to those for the corresponding three 2-(6-methyltetrahydropyran-2-yloxy)6-methyltetrahydropyrans. This suggests that linkage type (axial or equatorial) is more important than exocyclic substituents in determining trehalose conformations. A comparison with surfaces from the corresponding 5a-carba trehalose analogues illustrates that the exo-anomeric effect is important in determining disaccharide conformation.
    Additional Material: 11 Ill.
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  • 61
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 62
    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.
    Additional Material: 9 Tab.
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  • 63
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 64
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 351-361 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Linearized embedding is a variant on the usual distance geometry methods for finding atomic Cartesian coordinates given constraints on interatomic distances. Instead of dealing primarily with the matrix of interatomic distances, linearized embedding concentrates on properties of the metric matrix, the matrix of inner products between pairs of vectors defining local coordinate systems within the molecule. Here, the approach is used to explore the full conformation space allowed to small cyclic alkanes, given the constraint of exact bond lenghts and bond angles. Useful general tools developed along the way are expressions for rotation matrices in any number of dimensions and a generalization of spherical coordinates to any number of dimensions. Analytical results give some novel views of the conformation spaces of cyclopropane, cyclobutane, cyclopentane, and eyclohexane. A combination of numerical and analytical approaches gives the most comprehensive description to date of the cycloheptane conformation space with fixed bond lengths and angles. In this representation, the pseudorotation paths of cyclohexane and cycloheptane are closed curved lines on the surfaces of spheres.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource