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  • 1990-1994  (136)
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  • 1990  (136)
  • Biochemistry  (136)
  • 101
    Electronic Resource
    Electronic Resource
    A stringent formulation of the overall rotational diffusion in molecules and other flexible assemblies (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 64-66 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110107
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  • 102
    Electronic Resource
    Electronic Resource
    Evaluation of a finite multipole expansion technique for the computation of electrostatic potentials of dibenzo-p-dioxins and related systems (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 112-120 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic 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.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110114
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  • 103
    Electronic Resource
    Electronic Resource
    Ab initio study of substituent effect on the addition of hydrogen fluoride to fluoroethylenes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 170-180 
    Details
    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.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110203
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  • 104
    Electronic Resource
    Electronic Resource
    Numerical solution of a partial differential equation system describing chemical kinetics and diffusion in a cell with the aid of compartmentalization (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 194-204 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110205
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  • 105
    Electronic Resource
    Electronic Resource
    Relaxed potential energy surfaces of N-linked oligosaccharides: The mannose-α(1 → 3)-mannose case (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 205-216 
    Details
    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 report calculations of potential energy surfaces where all the internal coordinates of the disaccharide Man-α(1 → 3)-Man-α-O-Me were relaxed and minimized through an extensive molecular mechanics scheme. Flexibility within the mannopyranose rings plays a crucial role. Introduction of the relaxed principle into the conformational description of the disaccharide does not greatly alter the overall shape of the low-energy domains but it reveals new local minima. However, its principle effect is the lowering of energy barriers in the potential energy surface. New conformational transitions about the glycosidic bonds appear, permiting pathways among the low energy sections. This occurs with only little variation of the classical 4C1 conformation of the mannopyranose residues. All the conformations observed in the solid state, along with those already predicted through the joint use of NMR and modeling techniques, fall into the populations of stable conformers calculated in the present work. Moreover, a satisfactory agreement is reached between previously observed NOE values, and the theoretical one, calculated from the averaging of more than 500 microstates. The present results reconciliate most of the apparently conflicting data previously reported; they provide strong support for the application of the concept of conformational averaging to solution behavior. Some limitations of the proposed methodology are also discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110206
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  • 106
    Electronic Resource
    Electronic Resource
    Distance geometry and molecular conformation, by G. M. Crippen and T. F. Havel, Research Studies Press, Taunton, England, John Wiley and Sons, New York, 1988. pp. 541 + x pp. Price: $142.00 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 265-266 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110212
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  • 107
    Electronic Resource
    Electronic Resource
    Announcement (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 268-268 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110214
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  • 108
    Electronic Resource
    Electronic Resource
    Derivation of net atomic charges from molecular electrostatic potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 297-310 
    Details
    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 dependence of net atomic charges, as derived from least-squares fitting to electrostatic potentials, on molecular orientation and potential site location is critically examined. A unique rotationally invariant algorithm, in which the charges may be constrained to reproduce the molecular dipole moment, is presented and the results for several basis sets compared to previous work. Significant improvements in dipole moments derived from the unconstrained charges are noted.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110304
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  • 109
    Electronic Resource
    Electronic Resource
    Theoretical study of the proton affinities of 2-, 3-, and 4-monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 269-290 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110302
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  • 110
    Electronic Resource
    Electronic Resource
    Extended basis sets for the transition metals yttrium through cadmium (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 518-523 
    Details
    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.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110410
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  • 111
    Electronic Resource
    Electronic Resource
    Reply to “Comments on a comparison of AM1 with the recently developed PM3 method” (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 543-544 
    Details
    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 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110414
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  • 112
    Electronic Resource
    Electronic Resource
    H/He Molecules in strong electric fields (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 548-559 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Floating spherical Gaussian orbitals are used within a split-shell description to calculate the properties of H, He, He+, H2, H+2, HeH+, and H+3 in a strong uniform electric field. Accurate polarizabilities including their field strength dependence are obtained with two basis functions at most. Critical field strengths for ionization and deprotonation are determined for different orientations of molecules. Electron tunneling is described within the time dependent approach using floating Gaussian orbitals also.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110503
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  • 113
    Electronic Resource
    Electronic Resource
    A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 560-568 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey-Bradley-Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm-1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C—N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.
    Additional Material: 11 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110504
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  • 114
    Electronic Resource
    Electronic Resource
    Overestimation of the coupling component in the CP technique. Application of the indirect counterpoise correction to the H2O—HF hydrogen-bonded system (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 576-588 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110507
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  • 115
    Electronic Resource
    Electronic Resource
    On proper dissociation configurations of a molecule (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 629-635 
    Details
    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.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110511
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  • 116
    Electronic Resource
    Electronic Resource
    AM1 molecular orbital studies of the structures, conformations, protonation energies, and electronic properties of triazine dihydrofolate reductase inhibitors (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 644-653 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110513
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  • 117
    Electronic Resource
    Electronic Resource
    A new method for the calculation of atomic and local hardness (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 694-699 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110604
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  • 118
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110701
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  • 119
    Electronic Resource
    Electronic Resource
    Adaptation of D2h ab initio computer code to higher-symmetry point groups (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 636-643 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110512
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  • 120
    Electronic Resource
    Electronic Resource
    Free energy calculation of a soft sphere solid using an adaptive, importance sampling Monte Carlo algorithm (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 511-517 
    Details
    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.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110409
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  • 121
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110501
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  • 122
    Electronic Resource
    Electronic Resource
    Molecular modeling studies of novel heteroarotinoids (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 531-540 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles φ1 and φ2 in closest agreement with the crystal structure, and all three computational methods yield values of φ1 and φ2 within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus φ1 and φ2 indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110412
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  • 123
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    Electronic Resource
    Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 791-804 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110703
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    MM2 study of 20-hydroxy-4,7,13,16-tetraoxa-1,10-diazabicyclo [8,8,3] heneicosane and its formation controlled by hydrogen bonding (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 837-847 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110707
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  • 125
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    The theoretical reaction path for the cation radical vinylcyclobutane rearrangement: A concerted SR path (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 896-898 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio reaction path calculations for the cation radical vinylcyclobutane rearrangement at the MP2/ 6-31G*//3-21G level reveal a concerted, sr reaction path with an activation energy of 9.4 kcal/mol. The vinylcyclobutane cation radical itself, at both the MP2 and MP3 levels of theory has predominant olefin cation radical character but with modest stretching of one of the adjacent ring carbon - carbon bonds.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110710
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  • 126
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    On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 909-923 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110803
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  • 127
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    Different approaches to conformational analysis: A comparison of completeness, efficiency, and reliability based on the study of a nine-membered lactam (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1021-1028 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110904
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  • 128
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    An ab initio method for approximation of the frozen molecular fragment (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1072-1075 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110909
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  • 129
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    Four-Index transformation on distributed-memory parallel computers (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1151-1159 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111006
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  • 130
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    Construction and molecular modeling of phospholipid surfaces (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1181-1186 
    Details
    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.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111010
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    Announcement (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1247-1247 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540111016
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  • 132
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    An improved empirical force field for saturated hydrocarbons (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1125-1138 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111003
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  • 133
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    Theoretical studies on the intramolecular cyclization of alkyl halide anions (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1119-1124 
    Details
    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 intramolecular cyclization reactions of alkyl fluoride and chloride anions1 were investigated theoretically using the AM1 method. Formation of five-membered ring was the most reactive and that of three-membered ring was the least reactive process in both series. For the fluoride series the reactivity order of n = 5 〉 6 〉 7 〉 4 〉 3 was dictated by the enthalpy (ΔH≠) effect while for the chloride series the entropy (ΔS≠) effect was found to play somewhat greater role due to the much better leaving ability of the chloride anion leading to the reactivity order of n = 5 〉 6 〉 4 〉 7 〉 3. For both series, BEP principle held and the degree of bond formation was greater with the fluoride series owing to the poor electron acceptor ability of the cleaving bond.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111002
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  • 134
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    The bond order - bond length relationship (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1160-1163 
    Details
    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.)
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111007
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  • 135
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    Electronic Resource
    An algorithm for the simultaneous superposition of a structural series (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1187-1192 
    Details
    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.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111011
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  • 136
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    A review of echinoderm oogenesis (1990)
    New York, NY : Wiley-Blackwell
    Journal of Electron Microscopy Technique 16 (1990), S. 93-114 
    Details
    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
    URL: http://dx.doi.org/10.1002/jemt.1060160203
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