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  • 1990-1994  (136)
  • 1990  (136)
  • Biochemistry  (136)
  • 101
    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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  • 102
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 103
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 104
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 181-193 
    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 computational scheme for the rational design of chiral stationary phases for the chromatographic separation of enantiomers has been established. The developed scheme was based on applying different interaction models (force field methods versus semi empirical quantum chemical methods), different docking algorithms (systematic grid search methods versus interactive methods guided by rules based on binding modes) and different levels of approximations (rigid versus flexible docking) to a representative test problem containing the 3,5-dinitrobenzoyl group. The computational methods in use covered the most sophisticated methods which could presently be applied to problems of such a size (about 80 atoms). It has been shown that the current computational approaches using rigid body approximations for the docked molecules and simple molecular mechanics (not taking pi-“effects” into account) are invalid in view of the required predictive precision of about 1-2 Kcal/mole for the differential binding energy. Another surprising result was the failure of the commonly used systematic search methods in determining the most favorable binding modes. Based on our calculations on the representative test problem we propose a new arrangement for the most stable complexes without parallel stacking of the aromatic pi-donor and the 3,5-dinitrobenzoyl pi-acceptor systems.
    Additional Material: 6 Ill.
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  • 105
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 223-235 
    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 novel efficient computer-oriented approach, based on the DAST (dualist angle-restricted spanning tree) code, is introduced for enumeration and generation of planar polyhex hydrocarbons. It is much faster than other approaches in the literature. The numbers of planar polyhex hydrocarbons with 14 hexagons are reported for the first time.
    Additional Material: 9 Ill.
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  • 106
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 242-248 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Variations of a procedure have been examined for minimization of the energies, calculated using MM2, of two docked molecules. After doing the intramolecular minimization of the individual molecules, randomized orientations of the rigid molecules were brought together to form complexes and the nonbonded energies of interaction were then minimized. Next, pairs having energies within 4.0 kcal/mol of the most stable pair were minimized further by atom-by-atom relaxation of the complex. Only two repetitions of the last two steps were found to give values within 0.001 kcal/mol in more than 90% of the cases. Compared to two other variations of the procedure, this method appeared to avoid erroneous (local, not global) minima. Finally, this overall procedure was tested against chromatographic data in the literature. Using only the most stable comformer of each species, the results appeared to be in qualitative agreement with fractionation data for enantiomeric aminoethanes on a chiral packing very similar to the one modeled here.
    Additional Material: 2 Ill.
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  • 107
    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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  • 108
    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 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.
    Additional Material: 6 Ill.
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  • 109
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 7 Ill.
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  • 110
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    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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  • 111
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    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.
    Additional Material: 1 Tab.
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  • 112
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 545-547 
    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 based on a small matrix approach to the solution of a system of inhomogeneous linear algebraic equations is developed and tested in this short communication. The solution is assumed to lie in an initial subspace and the dimension of the subspace is augmented iteratively by adding the component of the correction vector obtained from the Jacobi scheme on the coefficient matrix A (ATA, if the matrix A is nondefinite) that is orthogonal to the subspace. If the dimension of the subspace becomes inconveniently large, the iterative scheme can be restarted. The scheme is applicable to both symmetric and nonsymmetric matrices. The small matrix is symmetric (nonsymmetric), if the coefficient matrix is symmetric (nonsymmetric). The scheme has rapid convergence even for large nonsymmetric sparse systems.
    Additional Material: 1 Tab.
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  • 113
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    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.
    Additional Material: 1 Ill.
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  • 114
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 115
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 3 Ill.
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  • 116
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 117
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 118
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 576-588 
    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 extension of the Indirect Counterpoise (ICP) method, proposed in previous work, has been applied to the H2O—HF hydrogen-bonded system. The new version, which introduces important numerical changes is called EICP (Extended Indirect Counterpoise method). In their framework, the nonnegligible overestimation of the Counterpoise correction (CP) of Boys and Bernardi in the coupling component (MIX) of the interaction energy, computed via the Kitaura and Morokuma method is studied. Several basis sets, BS, were used to describe the oxygen, fluorine and hydrogen atoms that constitute the complex. The EICP results leads to more coherent values with the uncorrected energy than with the CP correction, which seems to be significantly affected by the size and type of the basis set used (especially for minimal basis sets).
    Additional Material: 8 Ill.
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  • 119
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 629-635 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An analytical procedure is presented for the determination of the proper dissociation configurations of a molecule. We illustrate this procedure by determining the proper dissociation configurations of many electronic states of the first-row diatomic molecules and ozone. Finally, a few simple guidelines are provided to help in the identification of the important configurations needed for proper dissociation of a molecule.
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  • 120
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 644-653 
    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 structural, conformational, and electronic properties of three triazine antifolates were determined by AM1 molecular orbital calculations, and the results were compared with other theoretical studies and with X-ray crystallographic studies of these and similar triazines both in the crystalline state and as complexes bound to dihydrofolate reductase. Calculated protonation energies confirm crystal structure data indicating N-protonation analogous to that reported for MTX in similar environments. Overall, the calculated structural and conformational properties are in good agreement with X-ray crystallographic results for these and similar triazines as found in the crystalline state and in enzymebound ternary complexes. However, for one triazine AM1 predicts a conformation with the bulky aromatic substituent twisted about 60° away from coplanarity with the triazine ring, in contrast to the nearly coplanar conformation found in the crystalline state. Intermolecular interactions favoring the coplanar conformation may thus be operative in the crystalline environment. The unique conformational preferences and greater conformation flexibility of triazines in general and of this triazine in particular may provide a key to understanding their biological activity.
    Additional Material: 3 Ill.
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  • 121
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 122
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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
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  • 123
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 9 Ill.
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  • 124
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 15 Ill.
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  • 125
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 819-828 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Complexes of alkali and alkaline earth cations with organic compounds are modeled by describing ionligand interaction energies with pair potentials and intraligand as well as interligand energies with the MM2 potential. New pair potentials for the interaction of Li+, Na+, K+, Mg2+, and Ca2+ ions are derived on the basis of 30,000 ab initio interaction energy values with 70 selected model ligand molecules. Various problems of the combination of these two basically different potentials are discussed. An application for the K+ complex of 18-crown-6 is presented. For more flexible ligands the introduction of three-body correction terms of the pair potentials seems necessary.
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  • 126
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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.
    Additional Material: 5 Ill.
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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.
    Additional Material: 15 Ill.
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  • 128
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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.
    Additional Material: 8 Tab.
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  • 129
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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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  • 130
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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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  • 131
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    Journal of Computational Chemistry 11 (1990), S. 1101-1110 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two new computational methods for the evaluation and partitioning of projected, planar, and averaged slab electron densities, implemented in the program PRODEN, are presented. The new algorithms for the projection, demarcation, and integration of electron densities are described and evaluated in terms of speed and numerical accuracy. Integrated Projected Populations are analyzed and some of the advantages and limitations of the methods are discussed.
    Additional Material: 4 Ill.
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  • 132
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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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  • 133
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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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  • 134
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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
    Type of Medium: Electronic Resource
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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.
    Additional Material: 15 Ill.
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    Journal of Electron Microscopy Technique 16 (1990), S. 93-114 
    ISSN: 0741-0581
    Keywords: Ultrastructure ; Biochemistry ; Maturation ; Comparative ; Oocytes ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Natural Sciences in General
    Notes: This review of the anatomical, histological, biochemical, and molecular biological literature on echinoderm oogenesis includes the entire developmental history of oocytes; from their inception to the time they become ova. This is done from a comparative perspective, with reference to members of the five extant echinoderm classes; crinoids, holothurians, asteroids, ophiuroids, and echinoids. I describe the anatomy and fine structure of the echinoderm ovary, with emphasis on both the cellular relationships of the germ line cells to the somatic cells of the inner epithelium, and on the neuromuscular systems. I review the literature on the growth of oogonia into fully formed oocytes, including the process of vitellogenesis, presenting an ultrastructural analysis of the organelles and extracellular structures found in fully formed echinoderm oocytes. Echinoderm oocyte maturation is reviewed and a description of the ultrastructural, biochemical and molecular biological changes thought to occur during this process is presented. Finally, I discuss oocyte ovulation, the severing of cellular connections between the oocyte and its surrounding somatic epithelial cells.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
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