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  • Electronic Resource  (136)
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  • 1990-1994  (136)
  • 1990  (136)
  • Biochemistry  (136)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of comparative physiology 160 (1990), S. 183-186 
    ISSN: 1432-136X
    Keywords: Histology ; Biochemistry ; Muscle physiology ; Hibernations ; Metabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Fiber composition, and glycolytic and oxidative capacities of the pectoralis, gastrocnemius, and cardiac muscles from active and hibernating little brown bats (Myotis lucifugus) was studied. The data were used to test two hypotheses: First, since hibernating bats maintain the capability of flight and make use of leg muscles to maintain a roosting position all winter, the fiber composition of the pectoralis and gastrocnemius muscles should not change with season. Second, we tested the hypothesis of Ianuzzo et al. (in press), who propose that the oxidative potential of mammalian cardiac muscle should increase with increasing heart rate while glycolytic potential should not. Our results indicate that the fiber composition of the pectoralis muscle was uniformly fast-twitch oxidative (FO)_ regardless of the time of year, as predicted. However, the gastrocnemius muscle exhibited a change in FO composition from 83% in active to 61% in hibernating animals. Contrary to the variable change in histochemical properties with metabolic state, a trend of reduced maximal oxidative (CS) and glycolytic (PFK) potential during hibernation in both flight and leg muscles was apparent. The oxidative potential of flight and leg muscles decreased by 15.2% and 56.5%, respectively, while the glycolytic potential of the same muscles decreased by 23.5% and 60.5%, respectively. As predicted, the glycolytic potential of cardiac muscle remained constant between active and hibernating bats, although there was a significant decrease (22.0%) in oxidative potential during hibernation.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 291-296 
    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 adsorption of methane, ethane, propane, n-butane, ethylene, propene, 1-butene, 1,3-butadiene, acetylene, benzene, toluene, naphthalene, anthracene, and pyrene on the basal plane of graphite has been studied by means of a semiempirical method proposed by Fraga based on a 1/R expansion of atom-atom pair potentials. The energies of interaction obtained agree reasonably well with experimental data and statistical calculations. The orientation of the adsorbed molecules relative to the graphite surface rendered by Fraga's method improves the picture provided by other calculations with empirical potentials. These results display Fraga's method as an economical alternative for the study of physisorption of hydrocarbons on the graphite surface.
    Additional Material: 4 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    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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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 410-410 
    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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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 411-415 
    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 mechanics calculations (MM2') are reported on methylenecyclohexane, 1, methylenecyclopentane, 2, and cyclopentane itself, 3. The calculated torsional energy barrier for the chair/chair interconversion of 1 if 8.7 kcal/mol (experimental ΔH ≠ = 8.4 ±0.1 kcal/mol); compounds 2 and 3 have virtually free pseudorotational pathways (calculated ΔH ≠ = 2.33 and 0.008 kcal/mol, respectively).
    Additional Material: 4 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 194-204 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To build a kinetic model of a cell with diffusion one has to solve a coupled nonlinear partial differential equation system consisting of several hundred equations. (Several hundred chemical components undergoing several hundred reactions.) To solve this formidable mathematical problem the division of the model cell into compartments (most biochemical reactions take place in a certain part of the cell) was suggested.1 Solving the differential equation system in one compartment, the results can be used as input at other compartments until mutually consistent solutions are achieved.To test this suggestion 10 coupled chemical reactions with diffusion were investigated in a model that contains three compartments. The results in the case of pure diffusion are in excellent agreement with and without compartmentalization. After this the full problem was treated by compartmentalization using for the solution of the differential equation system a discretization of the concentrations as functions of space and time and the Newton-Raphson iterative procedure. The results obtained give reasonable space and time dependence for the concentrations of all 10 components.
    Additional Material: 10 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    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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  • 8
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted phenolates in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: H, F, Cl (only MNDO and AM1), CN, CH3, OH, NO2, OCH3, COOH, and NH2. The results are compared with experimental values (high-pressure mass spectroscopy) at 600 K. The MINDO/3 method overestimates the experimental PAs with a mean percentual error of ca. 4.3%. The MNDO results agree much better with the experimental values and are only ca. 1.3% too high. However, the best agreement is observed for the AM1 method, where the mean percentual error is only ca. 0.69% (in absolute value). The greatest disagreement is found for 2-hydroxyphenolate (ca. +2.0%) and 2-carboxyphenolate (ca. +2.7%). The PA of 2-nitrophenolate is underestimated by ca. 1.6%. Correlations between the calculated proton affinities on the one hand, charge densities on the acid H atom of the phenols, charges on the O atom in the phenolate ions, and substituent parameters on the other hand are studied. Particularly good linear relationships are found for the 3- and 4-monosubstituted compounds within the AM1 formlism. For the 2-substituted phenolates, only the AM1 method is satifactory. As a general conclusion, the AM1 method appears to be distinctly superior to MNDO for the calculation of PAs, and definitely superior to MINDO/3.
    Additional Material: 12 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 346-350 
    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 partial charges for three model systems that mimic the metal-ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
    Additional Material: 3 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 382-395 
    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 coefficients in power series, in the variable time, describing coupled nonlinear chemical reactions are easily obtained from a recursion relation. Since these series have a limited radius of convergence they are not very useful as such. If the series are inverted to give time as a function of the appropriate power of a progress variable, the new series converge over the entire time course of the reaction. If, further, the long-time asymptotic behavior, obtained from the linearized kinetic equations, is used, one can obtain a series expansion for a function that describes the correct short-time behavior. This function can be estimated very well using truncated series. The method works well for consecutive nonlinear reactions where the progress variables are monotonic functions of time; this includes many cases where the concentrations of intermediate species go through a maximum as the reaction progresses.
    Additional Material: 19 Ill.
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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 361-373 
    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 improved method for computing potential-derived charges is described which is based upon the CHELP program available from QCPE.1 This approach (CHELPG) is shown to be considerably less dependent upon molecular orientation than the original CHELP program. In the second part of this work, the CHELPG point selection algorithm was used to analyze the changes in the potential-derived charges in formamide during rotation about the C—N bond. In order to achieve a level of rotational invariance less than 10% of the magnitude of the electronic effects studied, an equally-spaced array of points 0.3 Å apart was required. Points found to be greater than 2.8 Å from any nucleus were eliminated, along with all points contained within the defined VDW distances from each of the atoms. The results are compared to those obtained by using CHELP. Even when large numbers of points (ca. 3000) were sampled using the CHELP selection routine, the results did not indicate a satisfactory level of rotatational invariance. On the basis of these results, the original CHELP program was found to be inadequate for analyzing internal rotations.
    Additional Material: 5 Ill.
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 401-409 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center-to-center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.
    Additional Material: 8 Ill.
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  • 13
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different methods such as molecular dynamics, systematic, or stochastic search and a special “generic shape” algorithm have been employed in the conformational analysis of a nine-membered lactam. Furthermore, crystal data were used to generate conformations of the compound under consideration. The various methods are compared in terms of their efficiency and completeness in the search for conformations with an energy content of up to 60 kJ/mol above the global minimum. Additionally, the generated conformations have been optimized by different techniques, molecular mechanics and quantum chemical calculations, to compare the number of existing local minima and their relative energies and geometries.
    Additional Material: 8 Tab.
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1169-1180 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (α-helical decaglycine) in vacuo, a protein (Pancreatic Trypsin Inhibitor, PTI) in vacuo, and a fully solvated protein (PTI in water). The equations of motion were integrated using Andersen's velocity version of the Verlet algorithm with internal contraints (the RATTLE algorithm). The accuracy with which the equations of motion are integrated has been analyzed for several different simulation conditions. The effects of various nonbonded interaction truncation schemes on the conservation of energy have been examined, including the use of atomic cutoffs, and (neutral group) residue cutoffs. The use of a smoothing function to eliminate the discontinuities in the potential at the cutoff leads to a significant improvement in the accuracy of the integration for each of the systems studied. The accuracy with which the equations of motion are integrated using the RATTLE algorithm for pure water and for the solvated protein are found to be comparable when the nonbonded interactions are tapered with a smoothing function at the cutoff.
    Additional Material: 6 Tab.
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 19-31 
    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 performed “High Temperature Annealed Molecular Dynamics Simulations” (HTAMDS) on the bicyclic 222 cryptand, and on model M+/222 cryptates with different representations of M+. The analysis of four sets of 500 structures allows assessment of the ability of HTAMDS to: (1) interconvert experimentally known conformers starting from one of them, (2) locate the energy minima, (3) generate new conformers of low energy, and (4) account for the average structure observed on the NMR time scale. In view of the ionophoric behavior of 222, structures are also analyzed in terms of the “in/out” orientation of the binding sites. It is found that simulations on the free molecule, although widely sampling the conformational space, do not give structures adequate for cation inclusion. They generate however the lowest energy structure known experimentally and other new closely related ones. Inclusion of the substrate in the simulation (either as a purely electrostatic “driver,” or as a charged sphere) is required to generate conformations found in several complexes. These results suggest that in the field of drug design, conformation of drugs suitable for binding to a given receptor may not be found when the simulations are performed on the isolated drug or substrate.
    Additional Material: 7 Ill.
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  • 16
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 58-63 
    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 simple extension of the Newton-Raphson method is proposed that approximately accounts for anharmonicity in bond-stretching coordinates. By modeling each bonded distance in a polyatomic molecule as a Morse oscillator with no anharmonic stretch-stretch or stretch-bend coupling, a multiplicative correction factor to the Newton-Raphson step is derived. Representative examples suggest that the rate of convergence of the proposed scheme is typically faster than that of the standard Newton-Raphson method.
    Additional Material: 3 Tab.
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  • 17
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 82-87 
    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 finite-field method for the calculation of polarizabilities and hyperpolarizabilities is developed based on both an energy expansion and a dipole moment expansion. This procedure is implemented in the MOPAC semiempirical program. Values and components of the dipole moment (μ), polarizability (α), first hyperpolarizability (β), and second hyperpolarizability (γ) are calculated as an extension of the usual MOPAC run. Applications to benzene and substituted benzenes are shown as test cases utilizing both MNDO and AM1 Hamiltonians.
    Additional Material: 2 Ill.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    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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  • 19
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 265-266 
    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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  • 20
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 249-264 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structural optimizations of the apically substituted isomer of PH4O- and the diapically substituted isomer of PH3FO- with diffuse-function augmented 3-21G* basis sets and with the 6-31 + G* and 6-31 + + G* basis sets result in P-η4-coordination in these anions. The structures obtained are those of a hydride or fluoride ion “solvated” by or complexed with phosphine oxide, rather than phosphoranes. In contrast, 3-21G* basis sets without diffuse functions on the atom in the trans-apical position with regard to the oxy-substituent yield P-η5-phosphorane structures that appear to be computational artifacts of the small basis set; the formation of the P-η4-geometries is curtailed by the insufficient functional description of the potential trans-apical nucleophilic leaving group. The overall neutral apical isomers of PH4O- · E(E = Li+, NH4+), the diapical isomer of PH3FO-Li+, as well as the model-solvated apical isomer of PH4O- · HF favor P-η5-phosphorane geometries at all of these computational levels. The mechanism by which the E-group alters the electronic structures within PH4Oa- is discussed based on the geometries, the molecular orbitals, and electron density analysis techniques.
    Additional Material: 9 Ill.
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  • 21
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1-18 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Counterpoise corrected ab initio calculations are reported for (H2O)2 and H2O-H2CO. Geometry searches were done in the moment-optimized basis DZP' at the SCF, MP2, and CEPA-1 levels of theory, followed by more accurate single-point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are -4.7 ±0.3 kcal/mol for a near-linear (H2O)2 structure and -4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA-1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
    Additional Material: 7 Ill.
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  • 22
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 45-57 
    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 data compression method is presented that is generally applicable to first-order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
    Additional Material: 5 Ill.
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  • 23
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 518-523 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Extended Slater basis sets were developed for the transition metals yttrium through cadmium. Gaussian expansions of these basis sets are extremely useful for ab initio methods which employ six Cartesian Gaussians for the description of the d orbitals. The s-type function generated from the symmetric combination of the x2, y2, and z2 Cartesian Gaussians is used to describe the 4s region, thereby reducing the overall number of functions for molecular calculations and reducing the redundancy in the basis set.
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  • 24
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 541-542 
    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 reparameterized version (PM3) of AM1 has recently been reported and the results for several hundred molecules compared with those from AM1 itself. The comparison implied that PM3 represents a significant improvement over the earlier treatment. The apparently poor performance of AM1 is, however, due to the inclusion of “AM1 results” for elements (A1,P,S) for which AM1 parameters were unavailable. If these are omitted, PM3 is seen to be only marginally better than AM1. Since this conclusion refers only to a specific set of stable molecules, it is not clear whether even this small improvement will apply to other species or studies of reactions. It is in any case insufficient to justify the confusion caused by the release of the new treatment.
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  • 25
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 159-169 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic potentials calculated from AM1 wave functions have been compared with ab initio STO-3G values and qualitative agreement has been found. Atomic charges derived from AM1 electrostatic potentials for both experimental and AM1 optimized geometries are of comparable quality with STO-3G potential derived charges. These results suggest that the AM1 electrostatic potential may be useful both in its own right and also for deriving atomic charges for use in molecular dynamics studies.
    Additional Material: 5 Ill.
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  • 26
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 524-530 
    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 reaction mechanisms of the alkaline hydrolysis of N-methylcarbamates were studied using the AM1 method by assuming two possible pathways: (1) nucleophilic attack of hydroxide ion on the carbonyl carbon to give a tetrahedral complex followed by its breakdown to carbamic acid (BAC2); and (2) proton abstraction by hydroxide ion at the nitrogen atom followed by elimination of the alkoxide ion to form N-methyl isocyanate (E1cB). Reaction coordinate analysis showed that the reaction mechanism is determined by both the stability of an intermediate and the energy barrier for elimination.
    Additional Material: 6 Ill.
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  • 27
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    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
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 573-575 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Entropy and solvent effects are calculated for some conformations of Ala-Gly. The inclusion of these effects in energy calculations show the βII type structure to be the most stable.
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  • 29
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 603-622 
    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 method is presented for defining a smooth, triangulated analytic surface for biological molecules. The surface produced by the algorithm is well-suited for use with a recently developed polarizationcharge technique1 for the computation of the electrostatic potential of solvated molecules, and may also be used for calculations of molecular surface areas and volumes. The new method employs Connolly's definitions of contact, reentrant and saddle surface,2 but includes modifications that preclude the presence of self-interesting reentrant surface, and also insure a rigorous decomposition of contact regions into curvilinear finite elements. The triangulation algorithm may be used in conjunction with the electrostatic methods described previously to compute the electric potential of molecules of arbitrary shape in solution. Applications include the estimation of hydration enthalpies, computation of the electrostatic forces associated with solvation, estimation of interactions between separate charged species in solution, and computation of the three-dimensional form of the molecular electric potential. Test calculations are presented for a double-stranded dinucleotide, the polypeptide enkephalin, and the protein ferredoxin.
    Additional Material: 16 Ill.
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  • 30
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    Journal of Computational Chemistry 11 (1990), S. 636-643 
    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 imposition of symmetry in electronic structure calculations can be plagued by artifactual symmetry-breaking in orbital or configuration amplitudes. While most ab initio computer code is well-developed to impose symmetry constraints in D2h and its subgroups, the problem is not nearly as tractable in higher-symmetry point groups. This article describes the successful modification of existing D2h ab initio computer code to handle symmetry constraints in higher-symmetry point groups. Prospects for the development of ab initio computer code that runs fully under any point group are also discussed.
    Additional Material: 2 Ill.
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  • 31
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    Journal of Computational Chemistry 11 (1990), S. 654-662 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous 4-21G ab initio geometry optimizations of various conformations of the model dipeptides (N-acetyl N'methyl amides) of glycine (GLY) and the alanine (ALA) have been used to help refine the empirical force constants and equilibrium geometry in the CHARMM force field for peptides. Conformationally dependent geometry trends from ab initio calculations and positions of energy minima on the ab initio energy surfaces have been used as guides in the parameter refinement, leading to modifications in the bond stretch, angle bending, and some torsional parameters. Preliminary results obtained with these refined empirical parameters are presented for the protein Crambin. Results for the cyclic (Ala-Pro-DPhe)2 are compared with those from other calculations. It seems that the dihedral angle fit achieved by the new parameters is significantly improved compared with results from force fields whose derivation does not include ab initio geometry trends.
    Additional Material: 2 Ill.
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  • 32
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    Journal of Computational Chemistry 11 (1990), S. 663-679 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Results are presented of topological analyses of the electron density functions of cyclopropeniumyldiazonium dication, 1, of its 2,3-diamino derivative, 2, and of their products 3 and 4, respectively, formed by dediazoniative ring-opening. The new CN-bonding type in 1 and 2, recently realized synthetically in derivatives of 2, is compared to prototypical aliphatic diazonium ions with regard to electronic structure and thermodynamic stability, factors that both are crucial for the appreciation of the mechanisms of deamination reactions of chemical and biochemical significance. Association of the dication with N2 involves density accumulation in the CN bonding region, occurs without major overall charge transfer, and leads to an electrostatically favorable quadrupolar charge distribution in the diazonium ion. The CN-bonding model recently proposed for aliphatic diazonium ions also applies to these dications. 1 is thermodynamically stable while the dediazoniation of 2 is exothermic but kinetically hindered. Our best estimates for the reaction energies of the dediazoniations 1 → 3 + N2 and 2 → 4 + N2, respectively, are 65.5 and -7.2 kcal/mol, respectively. We have found that, in general, the cation is destabilized and that N2 is stabilized upon CN-bond cleavage. Cations force N2 to form diazonium ions. The remarkable difference between the stabilities of 1 and 2 is primarily due to the larger destabilization of the open dication 3 compared to 4. Push-pull interactions between the diazo- and the overall electron-withdrawing amino-functions characterize the electronic structure of 2. CN-Bonding and the overall electronic structure of 2 are incompatible with the usual Lewis resonance notations. Instead of dismissing the Lewis notations, it is shown that the topological description can be reconciled with the Lewis notations if the resonance forms are interpreted in a way that appropriately reflects the atom populations and first moments. Implications of the model with regard to reactivity are discussed.
    Additional Material: 7 Ill.
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  • 33
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    Journal of Computational Chemistry 11 (1990), S. 943-951 
    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 organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX-2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX-2/400 than on the VAX 8650.
    Additional Material: 4 Tab.
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  • 34
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    Journal of Computational Chemistry 11 (1990) 
    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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  • 35
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    Journal of Computational Chemistry 11 (1990), S. 431-439 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is demonstrated that semiempirical methods give electrostatic potential (ESP) derived atomic point charges that are in reasonable agreement with ab initio ESP charges. Furthermore, we find that MNDO ESP charges are superior to AM1 ESP charges in correlating with ESP charges derived from the 6-31G* basis set. Thus, it is possible to obtain 6-31G* quality point charges by simply scaling MNDO ESP charges. The charges are scaled in a linear (y = Mx) manner to conserve charge. In this way researchers desiring to carry out force field simulations or minimizations can obtain charges by using MNDO, which requires much less computer time than the corresponding 6-31G* calculation.
    Additional Material: 4 Tab.
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  • 36
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    Journal of Computational Chemistry 11 (1990), S. 468-486 
    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 algorithm is presented for performing molecular dynamics simulations of peptides with fixed geometry, with the aim of simulating conformational changes and of exploring conformational space. The principle of the method is to expand the potential energy as a Taylor's series in the coordinates around the current point, retaining the force and its first two derivatives, and obtain a series solution of the resulting differential equations using a method due to Lyapunov. By choosing the time step so that the second term in the series is small compared to the first, the true solution can in principle be approximated to any desired degree of accuracy. The algorithm has been used to solve numerically Lagrange's equations of motion for N-acetyl alanine amide and N-acetyl methionide amide, regarded as fixed at their C-termini, under the influence of the ECEPP/2 potential energy function, and time steps of 15-30 fsec have been achieved with little variation in the total energy. Possible directions for future development are discussed.
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  • 37
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    Journal of Computational Chemistry 11 (1990), S. 511-517 
    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 an adaptive, importance sampling Monte Carlo algorithm, the free energy and equation of state of a soft sphere solid are calculated. The Monte Carlo integration technique to be described is unlike standard methods in that it can evaluate directly the partition function and consequently the free energy of a solid. The results for a soft sphere solid are compared with data obtained from a thermodynamic integration method due to Hoover et al.7 The equation of state obtained from Monte Carlo integration is in agreement with Hoover's method while the free energy calculations compare favorably only at densities greater than that of the freezing transition.
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  • 38
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    Journal of Computational Chemistry 11 (1990), S. 899-908 
    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 expanded form of the Wiener number is suggested for characterization of molecular graphs and structure-property correlations. The simple, computer-oriented method for counting of the novel index is briefly discussed.
    Additional Material: 7 Ill.
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  • 39
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    Journal of Computational Chemistry 11 (1990), S. 952-957 
    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 mechanics provides an excellent means of generating reasonable chemical structures in a short amount of time. Using a classical representation, a molecule can be partitioned into a collection of n-fold atomic interactions, each with an associated force constant. In order for a calculation to proceed, all of the required force constants must be known. This article presents a method of rapidly determining the values for missing parameters using appropriately scaled quantum chemical techniques.
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  • 40
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    Journal of Computational Chemistry 11 (1990), S. 1003-1008 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics was used to study the hydration of superoxide (O2-). The Helmholtz free energy of hydration of O2- was estimated by the thermodynamic integration method. The diffusion of O2- and the water structure around O2- were also studied. Two water models were used in the calculations and the results were compared to experiments.
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  • 41
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    Journal of Computational Chemistry 11 (1990), S. 569-572 
    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 hypolipidemic activities of phthalimide and seven related compounds are subjected to a QSAR analysis based on results from AM1 molecular orbital calculations. Least-squares fits show a correlation of the activities with LUMO energies and carbonyl polarities and predict enhanced activities for two new phthalimide derivatives.
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  • 42
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    Journal of Computational Chemistry 11 (1990), S. 1038-1046 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We studied geometries and energies of complexes between water and neutral or protonated imidazole by ab initio molecular orbital calculations using the 4-31G basis set with and without the counterpoise correction. Positions of hydration sites and relative binding energies could be also estimated by using the electrostatic field map of imidazole as calculated by our bond increment method. The reliability of the calculations is confirmed by comparing the geometries of the imidazole-water complex to the experimental ones from the Cambridge Structural Database. These were obtained by X-ray diffraction studies on crystals with water bound to a molecule containing the imidazole fragment.
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  • 43
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    Journal of Computational Chemistry 11 (1990), S. 1072-1075 
    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 method for calculation on many-electron molecular systems with the approximation of the inactive part of a molecule by frozen molecular fragment is presented. In the following method the SCF calculations are performed in two series. First the molecular orbitals resulting from the first SCF calculation (modest basis set) are localized. In the second SCF run, the basis set is extended for the active part of the molecule, while molecular orbitals of the inactive part, selected from the localized set, are kept frozen. The results are in good agreement with the extended basis set calculation.
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  • 44
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    Journal of Computational Chemistry 11 (1990), S. 1094-1100 
    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 acid-catalyzed hydrolysis mechanisms of maleamic (4-amino-4-oxo-2-butenoic) acids were studied using AM1 method. The reaction proceeded mainly in two steps: (1) nucleophilic attack of the undissociated carboxyl group on the adjacent aminocarbonyl carbon via a zwitterionic intermediate; and (2) the rate-determining proton transfer to form the zwitterionic tetrahedral intermediate. In each step, the hydration of water and hydronium ion molecules was important in stabilizing the polarized intermediates. The substituent effects at the amide moiety and the 2,3-positions of the maleamic acids were qualitatively estimated for each step.
    Additional Material: 4 Ill.
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  • 45
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    Journal of Computational Chemistry 11 (1990), S. 1111-1118 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A conformational study of cocaine and its three diastereomers, pseudococaine, allococaine, and allopseu-dococaine was carried out using molecular mechanics and quantum mechanical semiempirical techniques. Molecular dynamics simulations were performed at high temperature to scan their conformational space. Additional molecular dynamics at 312 K were used to explore the conformational flexibility of the compounds around the minimum energy conformation at physiologically relevant temperatures. The AM1 technique was used to refine the description of the minimum energy structures obtained with the molecular mechanics technique and to compute the electronic properties of cocaine and its diastereoisomers. Comparison of the results obtained with previous NMR and X-ray structural data was carried out. The structural information obtained was then used to discuss some aspects of the pharmacology of cocaine and other compounds that bind at the site recognized by it on the dopamine transporter.
    Additional Material: 5 Ill.
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  • 46
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    Journal of Computational Chemistry 11 (1990) 
    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 11 (1990), S. 1139-1146 
    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 prescription for applying the method of molecular similarity calculations based on electrostatic potentials and fields is developed by consideration of a typical structure-activity series. Firm conclusions are drawn about the nature of the grid of points surrounding the molecules and about the choice of geometry, but options for point charges are less clearcut.
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  • 48
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    Journal of Computational Chemistry 11 (1990), S. 1160-1163 
    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 difference in length between two bond orders was reported by Pauling to be essentially the same, regardless of the atoms that make up the bond. To a first approximation these differences hold not only for bond orders 1, 2 and 3 but also for six membered aromatic rings containing all carbon, carbon-nitrogen, nitrogen-nitrogen, carbon-phosphorous, carbon-arsenic, and carbon-antimony bonds. An equation was developed (based upon these differences) that relates bond order and bond length. The output of this equation was compared with those of Gordy and Pauling. Our equation as well as the Gordy equation (with revised constants) return a bond length of 1.4 Å for bond order 1.67 which is consistent with theory. (This bond order was not used in developing either the equation or the revised Gordy constants.)
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  • 49
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    Journal of Computational Chemistry 11 (1990), S. 1164-1168 
    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 modification of Davidson's eigenvalue algorithm, based on the conjugate gradient method, is described. This method needs storage only for a few vectors (five to seven, depending on the implementation), making it practical for very large problems where disk storage is the limiting factor, without the necessity of restarting or discarding some expansion vectors. The convergence characteristics of the modified method are essentially identical with those of the original Davidson method if all expansion vectors are retained in the latter.
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  • 50
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    Journal of Computational Chemistry 11 (1990), S. 1181-1186 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A protocol is given for the construction of phospholipid surfaces that possess variable head groups and thus variable net charge. Ab initio quantum mechanical calculations are performed to establish the necessary force field (AMBER) parameters. The charge distribution is defined by an electrostatic potential method consistent with the ab initio wave function. As a model calculation, a monolayer surface with head groups of phosphatidylserine and phosphatidylcholine derived from the crystal structure of 1,2-dilauroyl-DL-phosphatidylethanolamine (DLPE) is placed in a water bath with two Ca(II) ions present. The resultant surface is energy-optimized followed by 64 ps of molecular dynamics integration. Evaluation of calcium ion coordination environments, characterization of the P-N dipole inclination with respect ot the plane of the monolayer, and calculation of molecular surface area is performed and compared with experimental data.
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  • 51
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    Journal of Computational Chemistry 11 (1990), S. 1206-1216 
    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 (14s11p5d) primitive basis set of Dunning for the third-row main group atoms Ga-Kr has been contracted [6s4p1d]. The core functions have been relatively highly contracted while those which represent the valence region have been left uncontracted to maintain flexibility. Calculations with the [6s4p1d] contraction are reported for a variety of molecules involving third-row atoms. This basis set is found to satisfactorily reproduce experimental properties such as geometric configurations, dipole moments, and vibrational frequencies for a range of molecules. Comparisons are made with the performance of the uncontracted basis set. Polarization functions for the contracted basis set are reported and performance of the basis set with and without polarization functions is examined. A relaxation of the [6s4p1d] contraction to [9s6p2d] for higher level evergy calculations is also presented.
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  • 52
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    Journal of Computational Chemistry 11 (1990), S. 930-942 
    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 effect of the addition of diffuse functions of sp type on the first row atoms (and/or of d type on phosphorus) to a MINI-1 minimal basis set is evaluated by comparing the SCF description of the interaction energy and its decomposition, counterpoise (CP) corrected and uncorrected for basis set superposition errors (BSSEs), with that produced by extended basis sets (6-31G** and 3-21G+) as well as by basis sets (6-31G** + VPS and (2d)S), previously successfully tested, designed to minimize the BSSE. The systems considered are a few anions (F-, HCOO-, H2PO-4) H-bonded to water; the basis set performance on a different geometry (bifurcated instead of linear) of the phosphate-water adduct was also considered. An additional comparison with the interaction energy in a neutral dimer, (HF)2, was carried out. The addition of diffuse functions to the MINI-1 basis set, instead of resorting to extended basis sets, seems to be a sensible choice for anions. The equilibrium distance is shifted towards the reference basis set value at the CP corrected level as well as at the uncorrected one. The spread of the energy due to the basis set is hardly distinguishable when the CP corrected values are plotted. The description of the interaction energy in dimers involving phosphorus is improved using d type diffuse functions.
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  • 53
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    Journal of Computational Chemistry 11 (1990), S. 972-977 
    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 quadrature-point-driven implementation of the standard Rys polynomial method for computing two-electron repulsion integrals of gaussian basis functions has been found to be both concise and openended with respect to the angular momentum of the gaussian functions (i.e., s,p,d,f,g,…). These are important features in certain applications, such as molecular properties and property gradients.
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  • 54
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    Journal of Computational Chemistry 11 (1990), S. 958-971 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Intermolecular potential functions have been developed for use in computer simulations of alkyl ethers. The simple OPLS model was adopted and parameterized to yield good descriptions of bimolecular and ion-molecule complexes as well as to reproduce experimental thermodynamic properties of liquid ethers. The principal testing featured Monte Carlo statistical mechanics simulations for liquid dimethyl ether (DME), ethyl methyl ether (EME), diethyl ether (DEE), and tetrahydrofuran (THF). Average errors of 1-3% are obtained for the computed densities and heats of vaporization including results for THF at pressures up to 5000 atm. The torsional motion about the central C—O bonds in EME and DEE was included in the simulations using rotational potential functions fit to results of molecular mechanics (MM2) calculations. The liquid-state environment is found to have negligible effect on the conformational equilibria.
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  • 55
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    Journal of Computational Chemistry 11 (1990), S. 978-993 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atom-centered partial charges which exactly reproduce the lowest several multipoles of a molecule's charge distribution can be obtained in a straightforward and convenient manner from the output of existing electronic structure calculations. The multipole constraint method is demonstrated by a computation of partial charges for the twenty common amino acids. The electron density employed here, derived from a semiempirical MNDO calculation, incorporates Slater-type orbitals which imbue it with the exponential fall-off vital to electronic tunneling calculations. In addition, a procedure based on these charges is described which divides the original electron density into two components, a large component with a simple electrostatic potential, and a much smaller residual whose several lowest multipoles vanish.
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  • 56
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    Journal of Computational Chemistry 11 (1990), S. 1009-1016 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation and net atomic charges of some 120 structures involving substituted phenols, anilines, and benzoic acids and the corresponding anions were calculated by MNDO, AM1, and PM3 semiempirical methods. The gas phase acidities of substituted phenols and anilines and the net atomic charges on the anionic heteroatoms of the corresponding anions have been successfully correlated with σ- constants. Moreover, good correlations with σ were found for the charges on the acidic hydrogens of substituted phenols and anilines. In contrast, the gas phase acidities of substituted benzoic acids and the charges on the anionic oxygens of the corresponding anions are better correlated with Taft σ° constants. Comparisons of these results with experimental data and ab initio theoretical calculations indicate that AM1 and PM3 methods are much better than MNDO in predicting the acidity of aromatic compounds.
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  • 57
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    Journal of Computational Chemistry 11 (1990), S. 994-1002 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute -9.8 kcal/mol to the free energy of binding, with a 108-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is -11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO-2 group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.
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  • 58
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    Journal of Computational Chemistry 11 (1990), S. 1029-1037 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Pseudopotentials and valence basis sets to be used in calculations for organometallic compounds of zinc and magnesium have been tested in calculations for the M(CH3)n (M = Zn, Mg; n = 1,2) molecules. Valence correlation effects are treated at the SDCI and CEPA levels. The capability of a polarization potential on zinc to account for the valence shell contracting effect of core valence correlation is studied. Properties considered are geometries, force constants, Mulliken populations, ionization potentials, atomization, and binding energies. Differences in bonding between the two dimethyl compounds are discussed.
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  • 59
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    Journal of Computational Chemistry 11 (1990), S. 1061-1071 
    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 method for the evaluation of metal complexes with molecular mechanics calculations is described. The method has been employed to determine the global minimum energy conformations of three seven-coordinate lanthanide complexes. The method searches the potential energy surface of the metal complexes for the global minimum structure using the recently reported Random Incremental Pulse Search (RIPS). The molecular mechanics calculations were performed using the MM2 metal-extended force field (MM2MX). This force field excludes 1-3 bending terms about the metal center and, instead, explicitly includes 1-3 nonbonded van der Waals interactions. This affords a model based mainly on steric interactions about the ligating atoms, and removes the necessity of specifying ligand-metal-ligand bond angles for seven-coordinate and higher metal complexes in which no preferred bond angle can be proficiently determined. The calculated minimum-energy structures were well known seven-coordinate conformations in all cases, and a comparison with X-ray crystallographic is presented.
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  • 60
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    Journal of Computational Chemistry 11 (1990), S. 1147-1150 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Test calculations have shown that correlation energies calculated using the frozen-core approximation in programs, such as the Gaussian series, that assume the lowest MOs to be the core orbitals may be significantly in error. Some valence orbitals in systems involving the heavier alkali metals and electronegative elements have lower energies than the highest core orbitals of the metal and are therefore erroneously omitted from the correlation energy calculation. Some examples are discussed.
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  • 61
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    Journal of Computational Chemistry 11 (1990), S. 1187-1192 
    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 procedure is delineated for finding the optimal superposition of a series of chemical structures. Quaternions are used to represent the absolute orientation of the structures-rotations of the structures need never be carried out explicitly. The Rational Function Optimization method is used to minimize a simultaneous superposition residual similar to the one given by Gerber and Müller. The robustness of the method is illustrated by comparing a series of conformations of a polyene carotenoid.
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  • 62
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    Journal of Computational Chemistry 11 (1990), S. 1247-1247 
    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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  • 63
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    Journal of Computational Chemistry 11 (1990), S. 1234-1246 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general method of analyzing intramolecular torsional potentials in terms of energy second derivatives that couple the rotating atoms is presented. The method offers a rigorous decomposition of the total torsional potential into pairwise (dihedral) interactions and enables one to derive nonbonded torsional interactions between 1-4 atoms as well as between more distant atoms and sites. The method is demonstrated on ethane, propane and acetaldehyde. It is shown that the 1-4 H…H dihedral potentials in ethane and propane are very similar, thereby supporting the notion of transferable force field potential functions. However, the dihedral potentials that are obtained differ from 1-4 potentials that are used in current force fields. Intramolecular three body effects are clearly seen in this method and are found to be relatively large for the dihedral interactions, although in the one case studied (propane) the overall effect on the methyl-methyl interaction is negligible due to cancellation of terms. The analysis explicitly shows that the barrier in acetaldehyde is due mainly to the dihedral H…H interaction.
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  • 64
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    Journal of Computational Chemistry 11 (1990), S. 32-44 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The individual gauge for localized orbitals (IGLO) and localized orbital/local origin (LORG) methods for the calculation of chemical shieldings are compared from their theoretical and computational viewpoints. A detailed analysis of the fluorine α-substituent effect in a series of fluoromethanes is given in terms of the IGLO and LORG bond contributions. The performance of both methods is discussed for molecular systems of fairly different sizes.
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  • 65
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    Journal of Computational Chemistry 11 (1990), S. 64-66 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Additional Material: 1 Ill.
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  • 66
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    Journal of Computational Chemistry 11 (1990), S. 76-81 
    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 hydration energy difference between the alanine and glycine zwitter ions was calculated by both the free energy perturbation method and the acceptance ratio method. The calculations were carried out by using different increments of the mutation parameter λ, δλ = - 0.05, -0.10, and -0.20. The free energy difference calculated by the acceptance ratio method was found to be approximately the same as an average of the two free energy differences in the forward and the backward directions calculated by the perturbation method. The results by the perturbation method were significantly affected by large δλ as compared with that by the acceptance ratio method. The statistical error caused by decreasing the simulation time for sampling equilibrium configurations is discussed.
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  • 67
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    Journal of Computational Chemistry 11 (1990), S. 94-104 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Acidities of 32 hydrocarbons have been calculated using MINDO/3, MNDO, and AM1. All three semiempirical procedures have systematic errors and reproduce experimental acidities poorly. A linear correlation, however, does exist between the calculated and experimental results. Correction of the AM1 or MNDO acidities leads to good agreement with literature values even for acids, such as methane and ethylene, whose conjugate bases are small localized anions. Predictions for several hydrocarbons are given.
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  • 68
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic potential V(r) that the nuclei and electrons of a molecule create in the surrounding space is well established as a guide in the study of molecular reactivity, and particularly, of biological recognition processes. Its rigorous computation is, however, very demanding of computer time for large molecules, such as those of interest in recognition interactions. We have accordingly investigated the use of an approximate finite multicenter multipole expansion technique to determine its applicability for producing reliable electrostatic potentials of dibenzo-p-dioxins and related molecules, with significantly reduced amounts of computer time, at distances of interest in recognition studies. A comparative analysis of the potentials of three dibenzo-p-dioxins and a substituted naphthalene molecule computed using both the multipole expansion technique and Gaussian 82 at the STO-5G level has been carried out. Overall we find that regions of negative and positive V(r) at 1.75 Å above the molecular plane are very well reproduced by the multipole expansion technique, with up to a 20-fold improvement in computer time.
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  • 69
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    Journal of Computational Chemistry 11 (1990), S. 170-180 
    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 3-21G study of the direct addition of HF to C2HnF(4-n), with n = 0 to 4, has been performed to investigate the effect of the substituent on the reaction. Geometry optimization of all charge-transfer complexes and transition states has been done. Standard analysis of activation energies of addition reactions, vibrational and thermodynamical analysis, as well as Morokuma energy decomposition, BSSE correction, PMO analysis, and Pauling bond orders were used to explain the results. A subset of the reactions, including that of C2H4 as reference one and the two most favorable cases, was also studied at the MP2/6-31G(d,p)//HF/6-31G(d,p) level. The barriers so obtained are in agreement with the indirectly found from experimental data. It was found that the effect of the substituent is not monotonic for the additions. Decomposition of the interaction energy is shown to be adequate to explain this nonmonotonic behavior. The implications for laser chemistry of the addition of hydrogen halides to fluorosubstituted olefins is briefly discussed.
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  • 70
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    Journal of Computational Chemistry 11 (1990), S. 217-222 
    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 evaluation of the characteristic polynomial of a chemical graph is considered. It is shown that the operation count of the Le Verrier-Faddeev-Frame method, which is presently considered to be the most efficient method for the calculation of the characteristic polynomial, is of the order n4. Here n is the order of the adjacency matrix A or equivalently, the number of vertices in the graph G. Two new algorithms are described which both have the operation count of the order n3. These algorithms are stable, fast, and efficient. A related problem of finding a characteristic polynomial from the known eigenvalues λi of the adjacency matrix is also considered. An algorithm is described which requires only n(n - 1)/2 operations for the solution of this problem.
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  • 71
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    Journal of Computational Chemistry 11 (1990), S. 236-241 
    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 structure of the general classical trajectory FORTRAN code is discussed for use in molecular dynamics simulations of polymer processes. Substantial reductions in the number of mathematical operations in the code are achieved by using statement functions, modifying the ususal chain rule derivatives, applying appropriate vector identities, and using closure relationships among the required derivatives of the potential.
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  • 72
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 73
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    Journal of Computational Chemistry 11 (1990), S. 311-313 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A common approximation used in ab initio molecular orbital calculations assumes that the changes in energy due to use of a larger basis set (as in the inclusion of polarization orbitals) and to allowance for electron correlation are additives. Thus, small basis sets may be used for correlated ab initio calculations, resulting in a great savings in time. While this approach has been shown to perform acceptably in some cases, a systematic study has not been published. We examined 35 species and computed the heats of reaction for 15 processes at the 6-31G level of theory using polarization and correlation correction up to the MP4 level. The same items were then treated by an additive procedure to attain the same level of theory. We also examined the conrotrary ring opening of cyclobutene. Our results indicate that the errors do cancel to some extent but that the uncertainty associated with open shell species is significantly larger than closed shell systems. This calls into question the use of the procedure in predicting the properties of transition states.
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  • 74
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    Journal of Computational Chemistry 11 (1990), S. 336-345 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simplified formulas for first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for linear and out-of-plane bending motion. They are expressed in a local coordinate system and then rotated to a space-fixed Cartesian coordinate system. For linear motion the important points are: (1) the invariance of the energy with respect to translational and rotational coordinate transformations and (2) the presentation of derivatives of the energy in terms of (α - π)2 rather than (α - π), where α is the bond angle, to avoid indeterminant forms. By factoring the second derivatives of the energy with respect to (α - π) and sinα, analysis in this local coordinate system avoids division by sinα as α → π. The formulas describe linear systems without the need to project the motion onto two perpendicular planes. When the angle is exactly π two degenerate directions arise, and the coordinate axes perpendicular to the axis of the linear sequence of atoms may be chosen arbitrarily. Further refinements and clarifications of methods reported previously to obtain matrix elements for linear and out-of-plane motion are presented.
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  • 75
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    Journal of Computational Chemistry 11 (1990), S. 374-381 
    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 coordination number model (CNM) has been developed that reproduces coordination numbers generated by rigorous Monte Carlo simulations of dilute aqueous solutions. The molecular coordination number is calculated by using the volume of the Voronoi polyhedron surrounding each solute atom and a set of linear least squares fitted parameters. Agreement with simulation data is good, with average deviation of less than 5%. Although CNM is presently parameterized against a simulation database founded on the potential functions of Clementi and coworkers, the method is perfectly general and can be applied to simulation data derived from any potential function form. Finally, the method is fast and can predict coordination numbers within minutes on a microcomputer.
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  • 76
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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: Dimensionless ratios of various moments of conformation-dependent physical properties play an important role in the evaluation of the behavior of chain molecules. For example, the correlation coefficient, ρxy, between two conformation-dependent physical properties, denoted here as x and y, is determined by the three dimensionless ratios 〈x2〉/〈x〉2, 〈y2〉/〈y〉2, and 〈xy〉/〈x〉〈y〉. Angle brackets denote the statistical mechanical average of the enclosed property. In the rotational isomeric state approximation, generator matrices of modest size can often be used for calculation of 〈x〉 and 〈y〉. The dimensions of the matrices grow rapidly upon going to higher moments or to mixed moments, such as 〈xy〉. Formulation of these large matrices, while straight-forward, has been extremely tedious for chains with independent bonds, arbitrary rotational potentials, and arbitrary bond angles (which need not be fixed). Here we describe an approach that quickly and accurately solves this problem for all cases in which the generator matrices required for 〈x〉 and 〈y〉 are known. The algorithm is validitated by successful use for the computation of ρr2s2 for r2 and s2 for freely jointed chains of various n, a case for which an exact analytical result in closed form is available in the literature. Here r2 and s2 denote the squared end-to-end distance and squared radius of gyration for a specified conformation, and n denotes the number of bonds.
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    Journal of Computational Chemistry 11 (1990), S. 351-360 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: ΔH0, ΔS0, and Kp have been calculated by force field methods for two prototype Diels-Alder reactions, the condensation of 1,3-butadiene and ethylene, and the dimerization of 1,3-butadiene. Three force field programs were employed, Allinger's MMP2, Warshel and Karplus' CFF/PI, and Boyd's MOLBD3 (with Anet and Yavari diene parameters). MMP2 and CFF/PI were combined to calculate reactant and product ΔHf0 (by MMP2) and thermodynamic functions S0, CP0, and (HT0 - HO0) by use of CFF/PI molecular geometry and vibrational frequencies. MOLBD3 was used separately to calculate these properties. The combined MMP2, CFF/PI calculations exhibited excellent agreement with available experimental equilibrium data for both reactions, despite uncertainties in the number and energies of adduct conformers in the dimerization reaction. The MOLBD3 results were less satisfying, particularly for the dimerization reaction, because the entropy of 1,3-butadiene was overestimated by 2.5 cal mol-1 K-1.
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  • 78
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom-based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.
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  • 79
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    Journal of Computational Chemistry 11 (1990), S. 493-510 
    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 approach based on computation of the molecular surface interactions (MSI) to estimate several physical properties of pure organic substances is described. MSI are derived from molecular structural data and consist of total molecular surface area, electrostatic molecular surface interactions, and a hydrogen bonding term. This new approach estimates the critical temperature and the molar critical volume of pure organic substances with molecular weights in the range of 40-500 a.u‥ In addition, the following properties can be calculated: the critical pressure, the boiling temperature, the molar volume in liquid state at normal pressure and temperature. The method can be used to predict physical properties of compounds having flexible or rigid, symmetric or asymmetric, polar or nonpolar molecular structures, and compounds with or without hydrogen bonding groups.
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  • 80
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    Journal of Computational Chemistry 11 (1990), S. 680-693 
    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 predicting the conformations of strained molecules using Artificial Intelligence techniques is described and illustrated with some typical examples.
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  • 81
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    Journal of Computational Chemistry 11 (1990), S. 700-733 
    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 combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of the MNDO and AM1 type are used, while the molecular mechanics part is treated with the CHARMM force field. Specific prescriptions are given for the interactions between the QM and MM portions of the system; cases in which the QM and MM methodology is applied to parts of the same molecule or to different molecules are considered. The details of the method and a range of test calculations, including comparisons with ab initio and experimental results, are given. It is found that in many cases satisfactory results are obtained. However, there are limitations to this type of approach, some of which arise from the AM1 or MNDO methods themselves and others from the present QM/MM implementation. This suggests that it is important to test the applicability of the method to each particular case prior to its use. Possible areas of improvement in the methodology are discussed.
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  • 82
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    Journal of Computational Chemistry 11 (1990), S. 837-847 
    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 van der Waals-type parameter set has been developed for hydrogen bonding in the MM2(85) force field to reproduce the structures and binding energies of complexes (H2O)2, (CH3OH)2, H3N … H2O, H3N … HOCH3, (CH3)3N … H2O, and HCONH2 … H2O reported in the literature. The MM2(85) force field modified in this way was then applied to the title compound to explain its unexpected stability, unusual properties of its hydroxyl group, and solvent effect on the reaction mechanism in the condensation of Kryptofix 22 ® with epichlorohydrine.
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  • 83
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    Journal of Computational Chemistry 11 (1990), S. 848-867 
    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 force field has been extended to include alkenes. Forty-five compounds were examined, and structures, conformational equilibria, heats of formation, and rotational barriers, were calculated. For a smaller representative group, the vibrational spectra and entropies were also calculated. In general, these quantities, except for the vibrational spectra, agree with available data to approximately within experimental error. The vibrational frequencies for a set of eight well-assigned structures were calculated to a root-mean-square error of 47 cm-1.
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    Journal of Computational Chemistry 11 (1990), S. 868-895 
    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 has been extended to conjugated systems. A VESCF method is applied to the pi-system to calculate bond orders, from which various stretching and torsional parameters are obtained. The procedure gives somewhat better results than the analogous MM2 calculations. It has been applied to a study of 81 compounds of aromatic and other conjugated hydrocarbons, as well as 45 alkenes and unconjugated polyenes. The structures calculated are generally in good agreement with experiment, and the heats of formation of these compounds can be calculated with a rms value of 0.62 kcal/mol, which may be compared with the average experimental error of 0.61 kcal/mol. In addition, vibrational frequencies for five representative conjugated model structures are calculated, with an rms value of 46 cm-1, and from these, other properties such as entropy can be calculated.
    Additional Material: 29 Tab.
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  • 85
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1047-1060 
    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 algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.
    Additional Material: 13 Ill.
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  • 86
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    Journal of Computational Chemistry 11 (1990), S. 1076-1079 
    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 method of approximation of the frozen molecular fragment (FMF) we derived has been applied to calculations of proton affinities. Results are in good agreement with experimental data and extended basis set calculations.
    Additional Material: 3 Tab.
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  • 87
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    Journal of Computational Chemistry 11 (1990), S. 1087-1093 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Myelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. It is this protein that is destroyed in such demyelinating diseases as multiple sclerosis. We have examined the predicted structures of one segment of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and co-workers as modified by Chuman, Momany, and Schafer. We have focused upon a segment, 87-118, containing the Pro-Pro-Pro sequence (residues 100-102), which has been predicted from standard algorithms to exist in a hairpin loop connecting anti-parallel beta-strands. Several local energy minima have been found and reported. Tripoline sequences are not rare in proteins, but their structure and function is still uncertain.
    Additional Material: 4 Ill.
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  • 88
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    Journal of Computational Chemistry 11 (1990), S. 1125-1138 
    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 molecular mechanics force field for alkanes is presented. The force field aims to eliminate some identified failures of the well-known MM2 force field. The new energy function gives an improved prediction of the rotational barriers of highly congested molecules, a better calculation of short nonbonded contacts, and the correct reproduction of bond elongation in small torsion angles. The calculation of sublimation enthalpies is also improved. The standard deviation of the formation enthalpies for a set of 54 compounds is 0.63 kcal/mol; this compares with the reported value of 0.42 calculated with MM2 and MM3 for different sets. The force field parameters were obtained using a least squares method.
    Additional Material: 1 Ill.
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  • 89
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    Journal of Computational Chemistry 11 (1990), S. 1151-1159 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Because it has O(N5) operations, a low computation to data transfer ratio, and is a compact piece of code, the four-index transformation is a good test case for parallel algorithm development of electronic structure calculations. We present an algorithm primarily designed for distributed-memory machines. Unlike the previous algorithm of Whiteside et al., ours is not designed with a particular architecture in mind. It is a general algorithm in the sense that not only can it be used on some common architectures but it can utilize some of the advantages inherent in each. In addition, we present formulas predicting that there would be a twofold decrease in communication time if our algorithm was used instead of that of Whiteside et al., on a square array of processors and up to an N-fold decrease if the two algorithms were implemented on a hypercube.
    Additional Material: 2 Ill.
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  • 90
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1193-1205 
    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 common requirement in conformational analysis is the identification of a molecule's lowest energy conformations. The application of the A* algorithm to this problem is examined. The algorithm uses heuristic information about the problem domain to direct the search and has been implemented in a system for performing automated conformational analysis. The method is detailed and sample results presented. Some limitations of the approach are identified.
    Additional Material: 13 Ill.
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  • 91
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    Journal of Computational Chemistry 11 (1990), S. 1217-1233 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have used Hayes-Stone Intermolecular Perturbation Theory (IMPT) to study the variation with distance and orientation of the various components of the interaction energy of the N — H…O = C hydrogen bonded trans- formamide/formaldehyde complex, a model system for hydrogen bonding in proteins. The directionality of the total interaction energy is similar to that of the electrostatic component alone. We have analysed our data in terms of two model atom-atom intermolecular potentials, using an isotropic functional form and an anisotropic one. The anisotropic form gives an excellent representation of the IMPT potential energy surface, considerably better than the isotropic model, and is comprised entirely of theoretically justified, physically meaningful terms.
    Additional Material: 7 Ill.
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  • 92
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    Journal of Computational Chemistry 11 (1990), S. 694-699 
    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 relationships between atomic hardness, atomic electronegativity, and electronic energy are considered and emphasized. A new method for calculating atomic hardness is described. The concept of local hardness is quantified through the calculation of a new variable named alfahardness. Atomic hardness and alfahardness are used for the calculation of both the mean molecular and local properties. The results obtained are discussed and a comparison made with the analogous quantities presented by Pearson. An algorithm has been realized and transformed into a computer routine for use within a CAOS program.
    Additional Material: 5 Tab.
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  • 93
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    Journal of Computational Chemistry 11 (1990), S. 734-742 
    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 a force field extending Boyd and Kesner's molecule mechanics treatment of alkyl chlorides, fluorides and bromides to alkyl iodides: accordingly, as well as parameters for the potential energy of bond stretching and bending and for interactions between nonbonded atoms, the field includes parameters taking into account permanent and induced C-I dipoles, whose values have been estimated by fitting the model to experimental dipole moment data. The results of applying this force field to 22 organic iodides comprising several substitution series are reported, and the structural and energy trends in the various series are discussed. These results agree satisfactorily with available experimental data and with those obtained by A. Y. Meyer using a different kind of force field.
    Additional Material: 5 Tab.
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  • 94
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    Journal of Computational Chemistry 11 (1990), S. 765-790 
    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 anomeric effect of the functional groups X = C≡N, C≡CH, COOH, COO-, O—CH3, NH2, and NH+3 has been studied with ab initio techniques. Geometry effects upon rotation around the central C—O bond in X—CH2—O—CH3 have been compared in the various compounds. The energy differences between the conformers with a gauche and trans (X—C—O—C) arrangement were calculated at the 6-31G* level in the fully optimized 4-21G geometries. Energy differences calculated at the 4-21G level appeared not to be reliable, especially for the groups X that contain non-sp3 hybridized atoms. The 6-31G* energy differences indicate a normal anomeric effect for X = COO-, O—CH3, and NH2(g+) (ca. 13 kJ/mol) and a small anomeric effect for X = COOH, C≡N, and C≡CH (ca. 6 kJ/mol). For X = NH2(t) and NH+3 a reverse anomeric effect occurs. These observations are in line with experimental results and evidence is given for a competition among various stereoelectronic interactions that occur at the same anomeric center. Geometry variations can be understood in terms of simple rules associated with anomeric orbital interactions. Trends followed when the group X is varied cannot be related in a straightforward way to the energy differences between the trans and the gauche forms in these compounds. Only the variation in the gauche torsion angle X—C—O—C follows roughly the same trend.
    Additional Material: 6 Ill.
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  • 95
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    Journal of Computational Chemistry 11 (1990), S. 829-836 
    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 computer program is developed to compute distance polynomials of graphs containing up to 200 vertices. The code also computes the eigenvalues and the eigenvectors of the distance matrix. It requires as input only the neighborhood information from which the program constructs the distance matrix. The eigenvalues and eigenvectors are computed using the Givens-Householder method while the characteristic polynomials of the distance matrix are constructed using the codes developed by the author before. The newly developed codes are tested out on many graphs containing large numbers of vertices. It is shown that some cyclic isospectral graphs are differentiated by their distance polynomials although distance polynomials themselves are in general not unique structural invariants.
    Additional Material: 3 Ill.
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  • 96
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    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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  • 97
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    Journal of Computational Chemistry 11 (1990), S. 924-929 
    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, electronic structure, and photoelectron spectra of Sb2 and Sb4 have been investigated employing the LCGTO-MP-LSD method. For both molecules the geometrical and spectroscopic constants computed using the VWN potential are in very good agreement with the available experimental data. The HeI photoelectron spectra were computed with different potentials (Xα, GL, HL, BH, and VWN). The calculated spectra are in excellent agreement with the experimental ones and the use of the VWN potential gives the most accurate results. The reliable results for molecules complement those for the Sb atom and show that the proposed LSD Model Potential is able to give an accurate description of the structural and spectroscopic properties of the title molecules.
    Additional Material: 1 Ill.
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  • 98
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    Journal of Computational Chemistry 11 (1990), S. 909-923 
    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 strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point-charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO-3G and 6-31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6-31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6-31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6-31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.
    Additional Material: 5 Ill.
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  • 99
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    Journal of Computational Chemistry 11 (1990), S. 105-111 
    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 universal computational approach for evaluating integrals over gaussian basis functions for general operators of the form \documentclass{article}\pagestyle{empty}\begin{document}$$x^{k_x } y^{k_y } z^{k_z } \{ (\frac{\partial }{{\partial x'}})^{l_x } (\frac{\partial }{{\partial y'}})^{l_y } (\frac{\partial }{{\partial z'}})^{l_z } \frac{1}{{r'}}\} (\frac{\partial }{{\partial x}})^{m_x } (\frac{\partial }{{\partial y}})^{m_y } (\frac{\partial }{{\partial z'}})^{m_z } x^{n_x } y^{n_y } z^{n_z }$$\end{document} is presented. The implementation is open-ended with respect to the types of basis functions (s, p, d, f, g, h…) and with respect to the integers that specify the operator. These one-electron integrals comprise operators associated with electrical and magnetic properties of molecules and include those needed to find multipole polarizabilities, multipole susceptibilities, chemical shifts, and so on. The scheme also generates the usual kinetic, nuclear attraction, and overlap operators.
    Additional Material: 1 Ill.
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  • 100
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    Journal of Computational Chemistry 11 (1990), S. 121-151 
    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 procedure has been developed for global energy minimization of surface loops of proteins in the presence of a fixed core. The ECEPP potential function has been modified to allow more accurate representations of hydrogen bond interactions and intrinsic torsional energies. A computationally efficient representation of hydration free energy has been introduced. A local minimization procedure has been developed that uses a cutoff distance, minimization with respect to subsets of degrees of freedom, analytical second derivatives, and distance constraints between rigid segments to achieve efficiency in applications to surface loops. Efficient procedures have been developed for deforming segments of the initial backbone structure and for removing overlaps. Global energy minimization of a surface loop is accomplished by generating a sequence (or a trajectory) of local minima, the component steps of which are generated by searching collections of local minima obtained by deforming seven-residue segments of the surface loop. The search at each component step consists of the following calculations: (1) A large collection of backbone structures is generated by deforming a seven-residue segment of the initial backbone structure. (2) A collection of low-energy backbone structures is generated by applying local energy minimization to the resulting collection of backbone structures (interactions involving side chains that will be searched in this component step are not included in the energy). (3) One low-energy side-chain structure is generated for each of the resulting low-energy backbone structures. (4) A collection of low-energy local minima is generated by applying local energy minimization to the resulting collection of structures. (5) The local minimum with the lowest energy is retained as the next point of the trajectory. Applications of our global search procedure to surface segments of bovine pancreatic trypsin inhibitor (BPTI) and bovine trypsin suggest that component-step searches are reasonably complete. The computational efficiency of component-step searches is such that trajectories consisting of about 10 component steps are feasible using an FPS-5200 array processor. Our procedure for global energy minimization of surface loops is being used to identify and correct problems with the potential function and to calculate protein structure using a combination of sequence homology and global energy minimization.
    Additional Material: 7 Ill.
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