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• 1985-1989  (529)
• Biochemistry  (529)
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• 1
Electronic Resource
Springer
Pharmacy world & science 11 (1989), S. 146-150
ISSN: 1573-739X
Keywords: Agonists ; Antagonists ; Biochemistry ; Central nervous system ; Ligands ; Pharmacology ; Receptors, histamine
Source: Springer Online Journal Archives 1860-2000
Topics: Chemistry and Pharmacology
Notes: Abstract The role of histamine in brain function is discussed. A brief review is presented on the three types of histamine receptors with regard to their biochemistry and functions, as well as on specific ligands, both agonists and antagonists. It is concluded that several aspects of the pharmacology of histamine in the central nervous system are still a matter of empirism and speculations. The recent publications on the brain-penetrating H2 antagonist zolantidine and the selective H3 agonists and antagonists are expected to contribute to the knowledge of the histaminergic pathways in the brain. Therapeutical areas within the central nervous system are related to behaviour (including wake-sleep), neuroendocrinal processes, the control of muscle activity and cerebral circulation.
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• 2
Electronic Resource
Springer
Pharmacy world & science 11 (1989), S. 3-8
ISSN: 1573-739X
Keywords: Biochemistry ; Clofazimine ; Dapsone ; Ethionamide ; Isoniazide ; Mechanism of action ; Mycobacterium leprae ; Prothionamide ; Quinolones ; Ribonucleotide reductase inhibitors ; Rifampicin
Source: Springer Online Journal Archives 1860-2000
Topics: Chemistry and Pharmacology
Notes: Abstract From a pharmacochemical point of view the existing anti-leprotics as well as possible innovations in the chemotherapy of leprosy are discussed. Of the main anti-leprotics, which are used nowadays — dapsone, rifampicin, clofazimine, isoniazide, ethionamide and prothionamide — the mechanism of action, the main problems in their application and possibilities to develop improved variants are reviewed. Based on the chemistry ofMycobacterium leprae, the target systems for new anti-leprotics are identified. These systems include the cell wall, the catabolism of reactive oxygen species, the metabolisms of carbon sources, the amino acid metabolism and the uptake of iron. Two possible new lead structures from other fields, 4-quinolones and mycobacterial ribonucleotide reductase inhibitors are presented.
Type of Medium: Electronic Resource
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• 3
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989)
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Type of Medium: Electronic Resource
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• 4
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 35-54
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: An unusual type of π-electron delocalization in Y-shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO-3G and 3-21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen-substituted guanidine series (urea, carbamic, and carbonic acids); “extended-guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended-guanidine group is incorporated (3-amino-1,2,4-triazole, 2,4-diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π-bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended-guanidinium group resemble those of the group when incorporated within 6-membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.
Type of Medium: Electronic Resource
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• 5
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 99-103
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: For a series of simple alkyldisilanes, 3-21G (*) full gradient geometry optimizations have been performed to yield both structural and conformational energy data which was suitable for calibrating the MM2 force field for disilanes. We have examined several model structures which yielded sufficient information about the rotational potential around the Si-Si bond to enable us to revise and augment those reported by Frierson. These parameters were questioned by us in the course of MM2 studies of 1,2-disilacyclobutanes. We report new Si-Si torsion parameters as well as pertinent structural data from 3-21G(*) geometry optimizations and relative conformational energies derived from Møller-Plesset (MP2/MP3) calculations at the 6-31(*)/3-21G(*) level. The new parameters were applied to the 1,2-dimethyl-1,2-disilacyclohexane system and those results are also reported.
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• 6
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 136-136
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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• 7
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 118-135
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 theory of atoms in molecules defines an unambiguous partitioning of the three-dimensional electron density into atomic basins based on the zero-flux surfaces of the gradient of the electron density, ∇(r). Integrations of the electron density within such basins yield integrated Bader populations (IBP) that have a rigorous foundation in quantum mechanics. In the density integration technique based on the two-dimensional electron density projection function, P(x,z), integrated projection populations (IPP) are obtained by integration within regions demarked by steepest descent lines Dp of P(x,z). These density integration techniques are compared by an analysis of the electron density of diatomic molecules that is based on the properties of the zero-flux surface that partitions the electron density between the atoms. The conventional method for the partitioning of regions of P(x,z) approximates the virial partitioning. Differences between IPP and IBP can be quantitatively described by two terms. One term reflects the error intrinsic to projection populations as a result of the loss of all information about the electron distribution in the third dimension in the calculation of P(x,z). The second term accounts for the effects of the displacement of the demarcation lines Dp toward the less polarizable atom compared with the cross-section of the density with the plane of projection, Dd. The analysis suggests the definition of a projection population IPP2 that is based on the cross-section Dd instead of the demarcation lines Dp. Relations between the populations IPP, IPP2, and IBP are derived for diatomic molecules and numerical results are presented for a series of diatomic molecules. Several polyatomic anions are also discussed. The values of IPP are found to be good approximations of IBP in highly polar diatomic molecules. In cases where the bonding involves comparatively little intramolecular charge transfer IPP2 is the better and equally satisfactory projection population. In the intermediate semipolar bonding situations projection populations provide qualitatively correct descriptions of the charge distributions but the numerical agreement with the IBP values is less satisfactory.
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• 8
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 344-345
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: In self-consistent field (SCF) calculations the construction of the Fock matrix is most time-consuming step. The Fock matrix construction may formally be seen as a matrix-vector multiplication, where the matrix is the supermatrix,Pijkl, and the vector is the first-order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the P matrix, typically in the order of 106-108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.
Type of Medium: Electronic Resource
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• 9
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 358-366
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: The problem of the computation of the matrix elements \documentclass{article}\pagestyle{empty}\begin{document}$$I(v,v';k) = \int_0^x {\Psi _v (r)(r - r_e )} ^k \Psi _{v'} (r)dr,$$\end{document} is considered when Ψv(r) and Ψv(r) are eigenfunctions related to a diatomic potential of the RKR type (defined by the coordinates of its turning points Pi with polynomial interpolations). The eigenfunction Ψ(r) is computed by the canonical functions method making use of the abscissas ri of Pi uniquely. This limited number of points allows the storage of ψv(ri) for all the required levels v, and reduces greatly the computational effort when v, ν′, and k are varying. The present method maintains all the advantages of a highly accurate numerical method (even for levels near the dissociation), and reduces greatly the computing time. Furthermore, it is shown that it may be extended to analytical potentials like Morse and Lennard-Jones functions, to vibrational-rotational eigenfunctions and to matrix elements between eigenfunctions related to two different potentials. Numerical applications are presented and discussed.
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• 10
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 380-385
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Prolog is applied to calculate the zero- through the sixth-order molecular connectivity indexes. A description of the program is given. Enumeration of substructure fragments, which is the most time-consuming part for this calculation, can be executed quite compactly by Prolog. For this execution, molecular structures and substructures are represented by Prolog facts and rules. An example of calculation is presented for a polycyclic structure. In addition, the method to increase the calculation speed is demonstrated.
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• 11
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 495-502
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Basis sets ranging in size from (16, 10, 7) to (20, 14, 11) have been derived for the atoms Y-Cd. Separate sets represent the energy optimized wave functions for each of the s2dn, s1dn+1, and s0dn+2 configurations. The energies from the largest sets are within 3 mhartrees of the values obtained in numerical Hartree-Fock calculations. Reasonable Hartree-Fock s2dn- s1dn+1 and s2dn- s0dn+2 excitation energies may be obtained either using the largest basis sets, or using d-orbitals optimized for the s0dn+2 configurations. The basis sets are slightly unbalanced in favor of the s-functions and in disfavor of the d-functions, but various alternative basis sets may be derived by combining parts of the five parent sets. The convergence of radial expectation values is discussed.
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• 12
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 529-551
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 method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
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• 13
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 552-567
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 SCF calculation has been performed on C63H113N11O12, a derivative of the immuno-suppressive drug cyclosporin, using a 3-21G basis set and a Direct SCF method. A distributed multipole analysis has been performed on the resulting charge density to give a set of multipoles at each atomic site, which are used to calculate the electrostatic potential around the molecule. The potential maxima and minima on the accessible surface of the molecule are compared with those predicted using the corresponding Mulliken charges, and also using a potential-derived point-charge model based on the force-field of Kollman et al. The Mulliken charges give a misleading picture of the electrostatic potential around this peptide. The potential-derived charges give results which are in far better agreement with the ab initio distributed multipole model, despite being derived from calculations on smaller molecules with different basis sets and geometries. The limitations of point-charge models for describing the electrostatic interactions of polypeptides are discussed.
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• 14
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 17-34
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: The procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO-3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO-3G and 6-31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.
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• 15
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 63-76
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.
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• 16
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 77-93
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Radial dielectric constant (permittivity) functions for ionic solute, polar solvent systems of the type obtainable from the Lorentz-Debye continuum field formulations are reexamined. Major interest is focused on the assumptions underlying these formulations and their expression in limiting field behavior. The analysis is extended to dipolar solutes and the importance of two types of corrections are evaluated. The first draws connections with the concept of the reaction field as employed by Onsager. This correction is shown to be significant as regards range of predicted saturation effects and for dipole moment self-consistency, for the same type molecule serving as solute and solvent. The second type correction involves the phenomenon of electrostriction whose effects appear much more limited both in range and on the intensity of the fields necessary for its observation. Application of the permittivity functions developed to compute modified Born model hydration energies for a variety of ions is illustrated. Excellent asymptotic approximations for all radial permittivity equations of interest are also presented which should enhance their future utility.
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• 17
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 104-111
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Three improvements on the direct self-consistent field method are proposed and tested which together increase CPU-efficiency by about 50%: (i) selective storage of costly integral batches; (ii) improved integral bond for prescreening; (iii) decomposition of the current density matrix into a linear combination of previous density matrices - for which the two-electron contributions to the Fock matrix are available - and a remainder ΔD, which is minimized; construction of the current Fock matrix only requires processing of the small ΔD which enhances prescreening.
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• 18
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 137-137
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
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• 19
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989)
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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• 20
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 488-494
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Monte Carlo simulations have been performed to study the conformations of the pentapeptide fragments of normal adult (Thr-Pro-Glu-Glu-Lys) and sickle-like anemia hemoglobin (Thr-Pro-Val-Glu-Lys). The results show that the energy optimized conformation of normal adult hemoglobin-fragment agrees with the X-ray experiment and the theoretically determined conformation of the sickle-like anemia hemoglobin-fragment is identical with the conformation of the normal adult hemoglobin-fragment.
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• 21
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 520-528
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 method for calculating the number of rotamers of a linear alkane and of the number of rotamers with a given number of gauche conformations along the chain as a function of the total number of atoms in the chain, using general equations, is presented. A graphical method for generating individual rotamers was applied to the homologs up to decane, which has 1134 rotamers. The steric energies calculated by molecular mechanics (MM2 force field) were used as measures of the heat of formation for the coiled conformations relative to the anti conformer for each molecule, whereas the statistical entropy differences were calculated for classes of coiled rotamers grouped by the number of gauche bonds and steric energy. The free energy values calculated from these components show that already at 400 K hexane exists preferentially in conformations containing gauche bonds. For larger chains the free energy advantage for the coiled chains increases very steeply. The implications for the question of reactions of linear alkanes occurring on the surface or inside the channels of small- and medium-pore zeolites are briefly examined.
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• 22
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 568-592
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 gas-phase analogs of the classical SN1 and SN2 reactions of nucleophiles with a series of protonated oxiranes bearing the substituents CN, Cl, Me, and Ph were studied using MNDO semiempirical molecular orbital theory. The transition states for nucleophilic attack on the intact rings are calculated to become progressively more “SN1-like,” as the ability of the substituent group to stabilize the corresponding ring opened carbenium ion increases. At the same time the activation barriers become progressively smaller and their relative values for different nucleophiles approach the order expected on the basis of a purely electrostatic attraction between the reacting moieties. Exactly the opposite trends are calculated for the transition states for nucleophilic attack on the intermediate carbenium ions. As the stabilities of the latter increase the extent of bond formation, and transfer of charge to the incoming nucleophile also increase. Here, the relative barriers for attack by different nucleophiles approach the order expected on the basis of a superposition of both covalent and electrostatic interactions in which the former dominate. These results support a previously suggested rationalization for the enhanced reactivities of certain alkylating agents towards the exocyclic oxygen atoms, rather than the ring nitrogens, of the nucleic acid bases. They also suggest a new explanation for the tendencies of aralkylating electrophiles to modify the exocyclic amino groups of the nucleic acid bases: sites which are unreactive towards simple alkylating agents.
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• 23
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 616-627
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: We present a simple computational method for the evaluation of solute-solvent dispersion energy contributions in dilute isotropic solutions, supplementing the method with an analysis of its sensitivity with respect to several parameters (or features of the solvation model) which are left free in the general formulation. The method is a natural complement of the electrostatic solvation procedure described in preceding articles.
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• 24
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 683-697
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: An algorithm for obtaining the matching polynomial of an arbitrary catacondensed unbranched benzenoid molecule is presented. It is based on multiplication of only three 5 x 5 transfer matrices I, J, K, and an appropriate terminal vector. The choice of the matrices is dictated by the history of the growth of the hexagonal “animals” (i.e., by the pattern of the successive fusions of the benzene rings). The approach also gives the number of Kekule valance structures, the count of conjugated circuits, the values of the topological index Z, and the characteristic polynomials.
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• 25
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 698-710
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Computational algorithms are described which provide for constructing the set of associated edge-weighted directed graphs such that the average of the characteristic polynomials of the edge-weighted graphs gives the matching polynomial of the parent graph. The weights were chosen to be unities or purely imaginary numbers so that the adjacency matrix is hermitian. The computer code developed earlier by one of the authors (K.B.) is generalized for complex hermitian matrices. Applications to bridged and spirographs, some lattices and all polycyclic graphs containing up to four cycles are considered.
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• 26
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 718-732
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 enantioselective binding of optical analytes on chiral stationary phases used in column chromatography is investigated with molecular modeling techniques. By rolling the analytes over the van der Waals surface of the phase, configurations are sampled and free energies of transient diastereomeric complexes are computed. These free energies allow us to compute chromatographic separability factors and a linear relationship between computed and observed values is found. The intermolecular potential energy surfaces of these diastereomeric complexes are flat with gentle rolling hills and multiple minima. The binding sites are ill-defined and the analytes are found to freely slide over the chiral stationary phases. An energy partitioning algorithm is used to determine how much of the total binding energy is attributable to a given molecular fragment on the phase. It is found that the fragments of the phase bearing the stereogenic carbons are the least cognizant of differences between optical antipodes.
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• 27
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 753-769
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 well-tempered Gaussian basis sets (14s 10p) for atoms from lithium to neon were contracted and used in restricted Hartree-Fock calculations on 13 systems: Li2(Σ), B2(Σ), C2(Σ), N2(Σ), O2(Σ), F2(Σ), Ne2(Σ), LiF(Σ), BeO(Σ), BF(Σ), CN-(Σ), CO(Σ), and NO+(Σ). Spectroscopic constants (Re, ωe, ωexe, Be, αe, and ke) and one-electron properties (dipole, quadrupole, and octupole moments at the center of mass and electric field, electric field gradient, potential, and electron density at the nuclei) were evaluated and compared with the Hartree-Fock results. The largest contracted basis set (7s6p3d) gives results very close to the Hartree-Fock values; the remaining differences are attributed to the absence of the f functions in the present basis sets. For Ne2, the interaction energy was calculated; the magnitude of the basis-set superposition error was found to be very small (less than 3 μEh at 2.8 a0 and less than 2 μEh at 5.0 a0).
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• 28
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 817-831
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 that generates random conformations of a protein chain, and then applies energy minimization to find the structure of lowest energy, is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. Each state corresponds to a rectangular region in the φ, ψ map. The conformation of an entire chain is then represented by a sequence of single-residue conformational states. The distinct “chain-states” in this representation correspond to multidimensional rectangular regions in the conformational space of the whole protein. A set of highly-probable chain-states can be predicted from the amino acid sequence using the pattern recognition procedure developed in the first two articles of this series. The importance-sampling minimization procedure of the present article is then used to explore the regions of conformational space corresponding to each of these chain-states. The importance-sampling procedure generates a number of random conformations within a particular multidimensional rectangular region, sampling most densely from the most probable, or “important,” sections of the φ, ψ map. All values of φ and ψ are allowed, but the less-probable values are sampled less often. To achieve this, the random values of φ and Φ are generated from bivariate gaussian distributions that are determined from known X-ray structures. Separate gaussian distributions are used for proline residues in the α and ∊ states, for glycine residues in the α, ∊, α*, and ∊* states, and for ordinary residues involved in 29 different tripeptide conformations. Energy minimization is then applied to the randomly-generated structures to optimize interactions and to improve packing. The final energy values are used to select the best structures. The importance-sampling minimization procedure is tested on the avian pancreatic polypeptide, using chain-states predicted from the amino acid sequence. The conformation having the lowest energy is very similar to the X-ray conformation.
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• 29
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 832-849
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: The geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3-21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.
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• 30
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 869-874
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: In a previous article (J. Fernández Rico, R. López and G. Ramírez, J. Comp. Chem., 9, 790 (1988)) we have proposed the calculation of molecular integrals involving STOs by means of some recurrence relations which use two sets (h and H) of overlap integrals (basic matrices). In the present paper, we derive explicit expressions of these integrals employing the two-range expansion of the 0s-function. This approach yields equations for the elements of the two basic matrices in terms of two further matrices, k(x,y) and i(x,y), and some auxiliary functions. Relations between the elements of these matrices and the functions are thoroughly explored and numerical tests are included for illustrating the behavior of the method.
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• 31
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 896-902
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: There are many methods in the literature for calculating conformations of a molecule subject to geometric constraints, such as those derived from two-dimensional NMR experiments. One of the most general ones is the EMBED algorithm, based on distance geometry, where all constraints except chirality are converted into upper and lower bounds on interatomic distances. Here we propose a variation on this where the molecule is assumed to have fixed bond lengths, vicinal bond angles and chiral centers; and these holonomic constraints are enforced separately from the experimental constraints by being built into the mathematical structure of the problem. The advantages of this approach are: (1) for molecules having large rigid groups of atoms, there are substantially fewer variables in the problem than all the atomic coordinates; (2) rigid groups achieve in the end more accurate local geometry (e.g., planar aromatic rings are truly planar, chiral centers always have their correct absolute chirality); (3) it is easier to detect inconsistencies between the holonomic and the experimental constraints; and (4) when generating a random sampling of conformers consistent with all constraints, the probability of achieving satisfactory structures tends to be greater.
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• 32
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 163-175
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 potential energy surfaces for the proton transfer processes in H+(H2O)n with n=2 ∼ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H+ (H2O)n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.
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• 33
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989)
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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• 34
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 287-294
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 presented earlier [T. Kikuchi, G. Némethy, and H.A. Scheraga, (1986) J. Comput. Chem. 7, 67] for the classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain has been extended to nonplanar proteins. The procedure described earlier was applicable only to proteins termed planar, i.e., with a connexity of the crosslinks (e.g., disulfide bonds) that can be represented in a planar diagram. The procedure described in the present work is applicable to any (planar or nonplanar) pattern of crosslinking. The classification is based on a systematic and objective method of enumeration of spatial geometric arrangements of loops (SGAL) using no information other than the location of the disulfide bonds in the amino acid sequence. Various SGAL classes correspond to the presence of different ways of mutual penetration of loops, called thrustings and entanglements. Information on SGAL classes can be of use in structural predictions of folding patterns of proteins.
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• 35
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 1-13
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: A computer code and nonnumerical algorithm are developed to construct the edge group of a graph and to enumerate the edge colorings of graphs of chemical interest. The edge colorings of graphs have many applications in nuclear magnetic resonance (NMR), multiple quantum NMR, enumeration of structural isomers of unsaturated organic compounds, and in the construction of configurational integral expansion series in statistical mechanics. The code developed is applied to many NMR graphs, complete graphs containing up to 10 vertices, and the Petersen graph.
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• 36
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 14-16
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 the geometry-optimized total energies and bond distances for the closo-carborane isomers 3,5-C2B6H8, 1,7-C2B7H9, and 1,2-C2B7H9 calculated by the ab initio SCF MO method using the STO-3G basis set. Relative energies are compared with those of the other carborane isomers in the 8- and 9- atom classes. These results complete the set of calculations at the same level of theory for all deltahedral carborane isomers except for those of the 11-atom class.
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• 37
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 595-602
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 recognition in Rebek's cleft was studied with the MM2 force field. A new computational protocol was used to determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate-receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic π-stacking on the exterior of the cleft.
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• 38
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 603-615
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Hartree-Fock 6-31G(d) structures for the neutral, positive ion, and negative ion bimolecular complexes of NH3 with the first- and second-row hydrides AHn (AHn = NH3, OH2, FH, PH3, SH2, and ClH) have been determined. All of the stable neutral complexes except (NH3)2, the positive ion complexes with NH3 as the proton acceptor, and the negative ion complexes containing first-row anions exhibit conventional hydrogen bonded structures with essentially linear hydrogen bonds and directed lone pairs of electrons. The positive ion complex NH4+ … OH2 has the dipole moment vector of H2O instead of a lone pair directed along the intermolecular line, while the complexes of NH4+ with SH2, FH, and ClH have structures intermediate between the lone-pair directed and dipole directed forms. The negative ion complexes containing second-row anions have nonlinear hydrogen bonds. The addition of diffuse functions on nonhydrogen atoms to the valence double-split plus polarization 6-31G(d,p) basis set usually decreases the computed stabilization energies of these complexes. Splitting d polarization functions usually destabilizes these complexes, whereas splitting p polarization functions either has no effect or leads to stabilization. The overall effect of augmenting the 6-31G(d,p) basis set with diffuse functions on nonhydrogen atoms and two sets of polarization functions is to lower computed stabilization energies. Electron correlation stabilizes all of these complexes. The second-order Møller-Plesset correlation term is the largest term and always has a stabilizing effect, whereas the third and fourth-order terms are smaller and often of opposite sign. The recommended level of theory for computing the stabilization energies of these complexes is MP2/6-31+G(2d,2p), although MP2/6-31+G(d,p) is appropriate for the negative ion complexes.
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• 39
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 635-647
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 mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
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• 40
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 673-682
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 and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time-consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three-region site then as a single region site, but never as a two-region site.
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• 41
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 417-425
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Algorithms and codes based on the method of Schur functions and Frobenius' theorem are used to generate the character tables of the symmetric groups (Sn) containing n! elements. The codes developed can generate characters of Sn up to n = 20.
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• 42
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 426-433
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 annular tautomerism of 1,2,3-triazole and 3(5)-methylpyrazole is discussed by means of a combination of theoretical calculations and experimental (ICR) gas-phase basicities and acidities. In the gas phase 1,2,3-triazole exists as the 2H-tautomer, whereas both tautomers of 3(5)-methylpyrazole are of similar energy. The solvent effects on these prototropic equilibria are discussed taking into account solvent properties as polarity/polarizability, acidity, and basicity. In nonhydrogen bonding solvents, the difference in dipole moments between both tautomers plays a role that has usually been underestimated.
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• 43
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 176-185
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: A new method of eliminating the finite-time-step error inherent in diffusion quantum Monte Carlo is presented, utilizing an improved version of the existing differential techniques. An implementation is described and results of several small but representative calculations are discussed. The pertinent computation requirements on these systems were reduced by up to a factor of five by the new algorithm. It is speculated that this method may be easily applied to other quantum Monte Carlo and discretized path integral Monte Carlo techniques having related finite step-size errors with a possibility of obtaining similar good results.
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• 44
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 152-162
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 alternative route toward developing basis sets for post-Hartree-Fock calculations, the hybrid bond polarization function method, is investigated. Two new basis sets, denoted 6-31G(d, p)+ B and 6-31 + G(d,p)+B, are defined for the first-row hydrides. The dissociation energies of the first-row hydride species in their respective ground states are computed using full fourth-order Møller-Plesset theory, and compared with results obtained with large polarized basis sets containing no bond functions. It is shown that results are competitive even with basis sets as large as 6-311++G(3df,3pd), while computation times are reduced by a factor of 4 to 20. On empirical grounds, the basis set superposition error should be neglected entirely.
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• 45
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 221-264
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: MNDO/AM1-type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO-PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.
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• 46
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 302-308
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 of haloperidol as free base in its C(13) - C(14) trans form is optimized using Pulay's gradient method and a 4-21G basis set without any geometrical constraints. The resulting structure is compared with the experimental structure of the free base in the C(13) - C(14) gauche form and with the experimental structure of the HBr salt of haloperidol in the C(13) - C(14) trans form. Apart from the obvious differences, the two rotameric forms of the free base show many similarities. This, together with the manner in which the differences of the two experimental structures are distributed over the haloperidol molecule, leads to the conclusion that the conspicuous differences between the experimental structures are caused by inaccuracies in the X-ray determination of the HBr salt. Deviations of phenyl ring geometries from D6h symmetry and the asymmetry of the conformation around C(1) - C(9) could be rationalized by intramolecular effects.
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• 47
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 903-910
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: The recently reported Random Incremental Pulse Search (RIPS) technique has been used to probe the conformational energy surface of cyclononane. The stochastic method permits searching of the potential energy surface for all minimum-energy conformations. The search located all previously reported structures together with three additional conformations that were not found by earlier, primitive searching techniques. Two of these structures are high-nergy skew forms, and the third is a low-energy conformer that should contribute significantly to the overall equilibrium set of cyclononane conformations. The global minimum has been found to be the D3 symmetrical twist chair-boat (TBC) form in accordance with previous studies. The newly discovered low-energy structure, which lies only 2.2 kcal/mol above the global minimum, has been designated twist chair-twist chair (TCTC). The two higher energy conformers are skewed chair-chair (SCC) and skewed boat-boat (SBB) forms that are 5.7 kcal/mol and 10.4 kcal/mol above the global minimum, respectively. The seven reported conformations were reanalyzed quantum mechanically (AM1), and a comparison between MM2 and AM1 results is presented.
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• 48
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 935-938
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Explicit formulas are given for the characters of symmetric and antisymmetric powers of an arbitrary representation up to the sixth, and a general method for obtaining the higher ones is described. The results allow, among others, the determination of nonvanishing higher force constants in symmetrical molecules. The benzene molecule, for instance, has 237 nonvanishing cubic and 1890 quartic force constants. Other potential applications are a general method for the symmetry species of vibrational overtones, the determination of the number of independent centrifugal distortion constants, and the symmetry classification of vibrational multiplets.
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• 49
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 939-950
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Several improvements have been made to the gradient algorithms commonly used to optimize equilibrium and transition-state geometries at the semiempirical level. A gradient algorithm derived from a combination of a variable metric method (Davidon-Fletcher-Powell/Broyden-Fletcher-Goldfarb-Shanno) and Pulay's direct inversion in the iterative subspace method for geometry optimization (GDIIS) is compared with the variable metric method combined with an accurate linear search algorithm. The latter method is used routinely in the standard semiempirical program packages, MNDO, MOPAC, and AMPAC. The combined variable metric and GDIIS algorithm is also compared with GDIIS which uses a static metric. The performance of these algorithms is examined for a wide range of systems with respect to both choice of coordinate system (for cyclic molecules) and guess for the initial Hessian. The results show that the GDIIS method is up to ca. 40% more efficient than the variable metric combined with accurate line search algorithm: however, the exact savings vary depending on the coordinate system and initial Hessian. For noncyclic systems, variable-metric GDIIS is usually equal or superior to static-metric GDIIS, and consistently performs ca. 30% more efficiently than the variable metric combined with accurate line search algorithm. For the optimization of cyclic molecules, an improved estimate of the initial Hessian has increased the efficiency by at least a factor of two. Greater efficiencies (usually 〉40%) are also obtained when static-metric GDIIS is used to refine the geometry after the initial application of a transition-state search based on the variable metric combined with line search algorithm. On the basis of these results, we recommend several changes to the algorithms as currently implemented in the standard semiempirical program packages.
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• 50
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 975-981
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 potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.
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• 51
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 1016-1030
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 representation of atom valence state energy (E(nj), j = 1,…4; E(nj) is a nonlinear function of orbital occupancy numbers nj) is proposed and explicitly derived for H—Ar; the values of electronegativity calculated based on E(nj) agree within truncation error with those of Hinze and Jaffe. However, in our representation, orbital electronegativity χ and hardness parameters η of a given orbital always include nonlinear contributions from other orbitals, hence accounting for their influence on χ and η. An atomic charge calculation procedure based on E(nj) is also described and shown to perform well.
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• 52
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 1038-1052
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 molecular mechanics is used to investigate the structural and electrostatic features of molecular recognition by β-cyclodextrin and capped β-cyclodextrin models of α-chymotrypsin. Since capped β-cyclodextrin has been shown to be the more effective biomimetic catalyst, these features of molecular recognition can be interpreted in terms of the relationship between molecular structure and catalytic function. Calculations in vacuo show that the addition of an N-methylformamide “cap” substituent to each glucose unit appears to change the relative orientation of some glucose fragments from that found in the X-ray structure of the β-cyclodextrin macrocycle. These results indicate that certain structural components of molecular recognition, such as the orientation of the secondary hydroxyls and the related orientation of the caps, may be implicated in the catalysis. In addition, the electrostatic component of molecular recognition was investigated by the analysis of molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms. The results indicate that the addition of the caps to the β-cyclodextrin macrocycle subtly alters the pattern of the maps in each plane. However, the general qualitative features of electrostatic recognition by β-cyclodextrin and capped β-cyclodextrin are similar.
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• 53
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 921-927
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 proposed for the evaluation of nonbonded interactions in Molecular Dynamics simulations. The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test calculations show significant savings in CPU time and storage compared to commonly used algorithms for systems containing in excess of ca. 600 atoms.
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• 54
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 951-956
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: We present a simple recipe for calculating and differentiating cosine of bond angle and dihedral angle expressions. The resulting formulas can be incorporated in a straightforward manner into the bond angle and dihedral angle components of potential energy functions. These formulas rely only on expressions and derivatives of dot products, and, in particular, they avoid cross products as well as excessive Fortran function references. Consequently, the expressions derived in this article can be written compactly and evaluated rapidly.
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• 55
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989)
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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• 56
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New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 1013-1015
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 methods of bivariate interpolation suitable for experimental designs are summarized. The methods use experimental data obtained in usual manner. The programs are short and rapid and are often more accurate on test functions than the standard method.
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• 57
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 1031-1037
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: A continuum and a discrete-continuum models are used to determine the solvation energies of FCH2COO-, FCH2COOH, and F2CHCOO-. For the anions, the continuum model provides results closer to the experiment, while for the acid, the addition of one water molecule improves the continuum-only energy.
Type of Medium: Electronic Resource
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• 58
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 55-62
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: The determination of minima and saddle points on the potential energy surfaces of the hydrogen bonded species O2-HF and O2-H2O is performed with unrestricted Hartree-Fock calculations. Geometries, electron density distributions, and relative energies for every stationary point are reported. Only one true minimum is found for O2-HF and for O2-H2O, and this approximately corresponds to a structure where the partially positive hydrogen atom is located along one of the superoxide ion electron lone-pair directions. Calculated ΔH, ΔS, and ΔG values for the reaction between O2- and H2O are in good agreement with experimental data.
Type of Medium: Electronic Resource
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• 59
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 94-98
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Theoretical analysis of the electronic effect of aromatic substituents was done with the use of the AM1 computational procedure. The gas-phase acidity of substituted benzoic acids was linear with the difference in the heat of formation between corresponding benzoic acids and benzoate anions, the energy of the highest occupied molecular orbital, and the net charge on the acidic oxygen atoms of the corresponding benzoate anions. The Hammett σ constant was linearly correlated with the net charge on the atoms of the acid moiety of substituted benzoic acids. The AM1 computational procedure satisfactorily reproduced the electronic properties of a wide variety of substituents.
Type of Medium: Electronic Resource
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• 60
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 112-117
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Practical methods of generating reliable and economic basis sets for relativistic self-consistent fields (RSCF) calculations are developed. Large component basis sets are generated from constrained optimizations of exponents in the nonrelativistic atomic calculations for light atoms. For heavy atoms, large component basis sets for inner core orbitals are generated by fitting numerical atomic spinors of Dirac-Hartree-Fock calculations with appropriate number of Slater-type functions. Small component basis sets are obtained by using the kinetic balance condition and other computational criteria. With judicious selections of the basis sets, virtual orbitals in RSCF calculations become very similar to those in nonrelativistic calculations, implying that relativistic virtual orbitals can be used in electron correlation calculations in the same manner as the conventional nonrelativistic virtual orbitals. It is also evident that the Koopmans' theorem is also valid in RSCF results.
Type of Medium: Electronic Resource
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• 61
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 138-138
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Type of Medium: Electronic Resource
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• 62
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 145-151
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: Results of molecular orbital (MO) calculations by the complete neglect of differential overlap (CNDO/2) method on 50 small molecules are reported. The summation of calculated atomic polarizabilities are equated with molecular polarizabilities, and these are compared with experimentally determined values. It is found that there is very good agreement between calculated and experimental molecular polarizability. This provides a reliable method for the determination of molecular polarizabilities for compounds for which experimental values are not known. The relationship between log P and polarizability is discussed and analyzed in terms of contributions from electronic components to the partitioning energy.
Type of Medium: Electronic Resource
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• 63
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 203-208
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 stochastic search method was used to seek all of the conformations for 32 bicyclic hydrocarbons. Since the size of the random kick used is sufficient to invert the configurations of carbon atoms, the out, out, in, out, and in, in conformations were all found in a single stochastic run for each hydrocarbon. The lowest energy conformer obtained in each category is reported. A modification of the program to prevent inversion of configuration was developed. It was found, in some cases, that in, in and out, out isomers for some bicyclic hydrocarbons were interconverted by this modified program, presumably through the “homeomorphic isomerization” process described by Park and Simmons. A statistical formula for estimating the approximate chances of finding (or missing) any conformer as a function of the number of random kicks given is derived and presented.
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• 64
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 209-220
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: A new method for obtaining optimized parameters for semiempirical methods has been developed and applied to the modified neglect of diatomic overlap (MNDO) method. The method uses derivatives of calculated values for properties with respect to adjustable parameters to obtain the optimized values of parameters. The large increase in speed is a result of using a simple series expression for calculated values of properties rather than employing full semiempirical calculations. With this optimization procedure, the rate-determining step for parameterizing elements changes from the mechanics of parameterization to the assembling of experimental reference data.
Type of Medium: Electronic Resource
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• 65
Electronic Resource
New York, NY [u.a.] : Wiley-Blackwell
Journal of Computational Chemistry 10 (1989), S. 186-202
ISSN: 0192-8651
Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology , Computer Science
Notes: π-Electron delocalization in neutral and protonated “doubly-extended-guanidine,” (H2N)2C=N—CH=N - CH=NH, has been studied by ab initio methods at the self-consistent field (SCF) STO-3G and 3-21G levels for a large number of tautomeric, rotameric, pseudocyclic, and monocyclic (disubstituted triazine) forms. These π systems have been characterized in terms of a number of structural and energetic parameters: degree of single/bond character from bond lengths and π bond orders, electron distributions, and tautomer, rotamer, and protonation energies. The acyclic neutral forms exhibit largely alternant single-double bond patterns as predicted by classical bonding structures but with, however, significant deviations due to conjugation. The acyclic protonated forms exhibit bond patterns consistent with resonance delocalized structures extending over the whole molecule (“doubly-extended guanidinium”) or part of the molecule (“extended-guanidinium”) or guanidinium . All systems showed alternant charge distributions with electron-deficient carbons. The energy results have been analyzed in terms of possible contributions from steric interactions, lone-pair repulsions, purportive electrostatic interactions in pseudocyclic forms, overall π-system conformation (extended, kinked, or folded), and specific through-space π-overlap interactions in some pseudocyclic forms. It was found that these other interactions usually dominate the specifically π effects so that the general concept of preferential π delocalization in straight lines does not hold for the acyclic systems. Some interesting examples of pseudocyclic forms exhibiting strongly stabilizing intramolecular interactions attributed to π through-space coupling are identified. These systems with incipient-ring characteristics present intermediate bonding models between the acyclic and closed-ring π systems. The extent of stabilization of the guanidinium-type cations by resonance delocalization in cyclic systems depended on whether it reinforced or interfered with the overall ring delocalization.