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  • 1
    ISSN: 1432-0533
    Keywords: Canine galactosialidosis ; Morphology ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary An adult-onset lysosomal storage disorder was diagnosed in a 5-year-old Schipperke dog with progressive cerebellar and central vestibular signs. It was characterized by cerebellar atrophy with extensive loss of Purkinje and granular cells, and hydrocephalus. Enlarged and vacuolated neurons were observed in spinal cord and brain; pancreatic centrolobular and islet cells were also vacuolated. Ultrastructurally, enlarged secondary lysosomes laden with lamellated membrane structures were present in neurons and empty enlarged vacuoles were found in pancreatic centroacinar, ductal, and islet cells. On frozen sections neurons stained with Ricinus communis agglutinin-I and wheat germ agglutinin. On paraffin sections neurons stained with luxol fast blue, periodic acid-Schiff, Concanavalia ensiformis agglutinin, and were autofluorescent. These findings indicate an accumulation of glycolipids containing terminal β-galactosyl and α-sialyl residues, and N-linked oligosaccharides. Tissue activity of lysosomal β-galactosidase was 50% of normal and the activity of β-hexosaminidase was elevated. Brain lipid-bound sialic acid was twice normal, with a small increase of GM1-ganglioside, but there was a significant elevation of GM2 (GD2) and GM3 (GD3). In addition, significant elevations of sialylated and non-sialylated oligosaccharides were noted. These clinical, biochemical and pathological findings are similar to those observed in human patients with adult-onset galactosialidosis.
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  • 2
    ISSN: 1432-0878
    Keywords: Gap junction ; Cell junction ; Immunocytochemistry ; Biochemistry ; Heliothis virescens (Insecta)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Subcellular fractions enriched in gap junctions with an ultrastructure similar to those in intact insect tissue have been obtained by extracting crude membranes from the tobacco budworm Heliothis virescens (Lepidoptera: Noctuidae) with 2.5 mM NaOH. n-Octyl-β-d-glucopyranoside (OG) was used to further purify integral membrane proteins in the NaOH-extracted fractions. A polyclonal antibody (R16) is described that specifically labels nonextracted and NaOH-extracted gap junctions in cell fractions by electron microscope immunocytochemistry. R16 immunostaining of sectioned Heliothis testis at the light-microscope level yields a pattern of immunoreactivity consistent with the distribution of gap junctions in the tissue. R16 identifies a 40-kDa protein as a candidate gap junction protein on immunoblots of crude membrane, NaOH-extracted and NaOH/OG-extracted fractions.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    The @Anatomical Record 235 (1993), S. 611-621 
    ISSN: 0003-276X
    Keywords: Peroxidase ; Parotid gland ; Salivary gland ; Rat ; Growth and development ; Biochemistry ; Cytochemistry ; Ultrastructure ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The course of development of salivary peroxidase, an enzyme that has an important role in oral defense mechanisms, has been well documented in rat submandibular glands. However, the only report on salivary peroxidase activity in the other major salivary glands of the rat has been a cytochemical study of the adult parotid gland. In the present investigation, the accumulation of salivary peroxidase activity in developing parotid glands of rats was followed both biochemically and cytochemically. Specific activity (units per mg protein) attributable to salivary peroxidase began at 1 day after birth, then rose rapidly but unevenly, with peaks at 21 and 70 days, and no difference between the sexes at any age. Activity per gland increased progressively to 42 days in both sexes and was significantly higher in males at 70 days. The cytochemical observations on peroxidase activity localized to the rough endoplasmic reticulum and secretory granules of the developing acini were well correlated with the biochemical findings. Peroxidase-negative cells occurred in immature acini at 1 and 7 days, but only in the intercalated ducts thereafter. This observation suggests that the acini are a source of some of the ductal cells, at least during early postnatal development. The developmental pattern of specific activity differed from those of other rat parotid secretory enzymes, indicating that control of their synthesis during development is noncoordinate. The patterns of specific activity of the parotid and submandibular glands were complementary, suggesting that their combined secretions may supply biologically significant peroxidase activity to the oral cavities of rats throughout postnatal development. © 1993 Wiley-Liss, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    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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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 237-245 
    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 affinity of a ligand for a receptor is usually expressed in terms of the dissociation constant (Ki) of the drug-receptor complex, conveniently measured by the inhibition of radioligand binding. However, a ligand can be an antagonist, a partial agonist, or a full agonist, a property largely independent of its receptor affinity. This property can be quantitated as intrinsic activity (1A), which can range from 0 for a full antagonist to 1 for a full agonist. Although quantitative structure-activity relationship (QSAR) methods have been applied to the prediction of receptor affinity with considerable success, the prediction of IA, even qualitatively, has rarely been attempted. Because most traditional QSAR methods are limited to congeneric series, and there are often major structural differences between agonists and antagonists, this lack of success in predicting IA is understandable. To overcome this limitation, we used the method of comparative molecular field analysis (CoMFA), which, unlike traditional Hansch analysis, permits the inclusion of structurally dissimilar compounds in a single QSAR model. A structurally diverse set of 5-hydroxytryptamine1A (5-HT1A) receptor ligands, with literature IA data (determined by the inhibition of 5-HT sensitive forskolin-stimulated adenylate cyclase), was used to develop a 3-D QSAR model correlating intrinsic activity with molecular structure properties of 5HT1A receptor ligands. This CoMFA model had a crossvalidated r2 of 0.481, five components and final conventional r2 of 0.943. The receptor model suggests that agonist and antagonist ligands can share parts of a common binding site on the receptor, with a primary agonist binding region that is also occupied by antagonists and a secondary binding site accommodating the excess bulk present in the sidechains of many antagonists and partial agonists. The CoMFA steric field graph clearly shows that agonists tend to be “flatter” (more coplanar) than antagonists, consistent with the difference between the 5-HT1A agonist and antagonist pharmacophores proposed by Hibert and coworkers. The CoMFA electrostatic field graph suggests that, in the region surrounding the essential protonated aliphatic amino group, the positive molecular electrostatic potential may be weaker in antagonists as compared to agonists. Together, the steric and electrostatic maps suggest that in the secondary binding site region increased hydrophobic binding may enhance antagonist activity. These results demonstrate that CoMFA is capable of generating a statistically crossvalidated 3-D QSAR model that can successfully distinguish between agonist and antagonist 5-HT1A ligands. To the best of our knowledge, this is the first time this or any other QSAR method has been successfully applied to the correlation of structure with IA rather than potency or affinity. The analysis has suggested various structural features associated with agonist and antagonist behaviors of 5-HT1A ligands and thus should assist in the future design of drugs that act via 5-HT1A receptors. © 1993 John Wiley & Sons, Inc.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 30-36 
    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 consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function-based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 19-29 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 106 scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 103-104 scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 45-53 
    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 antitumor drug cis-diamminedichloroplatinum(II) (cisplatin) binds preferentially to GpG and ApG sequences of DNA, forming N7,N7 intrastrand chelates. Molecular modeling of the intrastrand adducts have been handicapped, so far, by the lack of force-field data describing the Pt-guanine and Pt-adenine binding. We used ab initio calculations with relativistic pseudopotentials to evaluate three important parameters for the platinum-adenine model complex [Pt(NH3)3(Ade)]2+: (1) the force constant for the Pt—N7 bond bending out of the adenine plane; (2) the energy profile for the torsion about Pt—N7; (3) a set of fractional atomic charges that reproduce the ab initio potential for a number of space points placed around the adduct. A population analysis and comparative study on the tetrammine complex [Pt(NH3)4]2+ have shown that for platinum adenine is a better σ-donor than NH3, but its capacity as a π-acceptor is weak. © 1993 John Wiley & Sons, Inc.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 422-437 
    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 reported for the prediction of dense crystal structures of C-, H-, N-, O-, and F-containing organic compounds in the primitive triclinic, monoclinic, and orthorhombic space groups with Z ≤ 4. The crystal environments of molecules in 242 crystal structures have been analyzed to determine the common coordination sphere pattens. This led to the development of the MOLPAK (MOLecular PAcKing) program, which uses a rigid-body molecular structure probe to build packing arrangements (possible crystal structures) in the various space groups. A MOLPAK search, which involves the investigation of all unique orientations of a central molecule and the construction of the appropriate coordination patterns about the central molecule, provides a 3-D map of minimum unit cell volume as a function of the orientation of the central molecule. MOLPAK uses a repulsion-only potential and a preset threshold to place molecules in contact with each other. The 5-10 smallest volume packing arrangements from a search are subjected to a lattice energy minimization refinement with the WMIN program to yield possible crystal structures. The results are described from the analyses of several known compounds starting with the crystal molecular structures as the MOLPAK search probes in the P1, P21, P21/c, and P212121 space groups. In addition, several examples are given in which the search probes were created by AM1 geometry optimization of preliminary molecular models. More extensive data are given in supplementary tables. © 1993 John Wiley & Sons, Inc.
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  • 10
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 312-329 
    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 fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed-memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen-containing bonds but also all heavy-atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time-step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.
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  • 11
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 349-352 
    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 development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look-up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4-Å solvent probe, we in general underestimate the total solvent-accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley & Sons, Inc.
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  • 12
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 378-378 
    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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  • 13
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 728-735 
    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 is proposed for calculating the forces in path integral theory and tested on semiclassic systems. It takes the range of the classic and quantum interactions into account and uses a second table within the neighbors table for the nearest neighbors. This method is found to be much more efficient than either the standard direct method or the traditional neighbors table, the efficiency increasing with the size of the system. The method can also be applied to clusters whose interaction centers are much farther apart than the distances between two consecutive members of the cluster. © 1993 John Wiley & Sons, Inc.
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    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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  • 15
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 445-451 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parallelization of the SCF method for closed-shell molecules on the highly parallel transputer-based system PARAM is described. The parallelization has been implemented on three different hardware and software environments: (1) a network of bare 64 transputers; (2) configuration 1 plus a back-end file system (BFS); and (3) configuration 2 with one INTEL i860 processor. The evaluation of electron repulsion integrals (ERIs) and setting up of the Fock matrix is carried out in parallel on 64 nodes using minimal communication strategies. A good load balance is achieved for ERI evaluation with the help of bounds, local symmetry features, and the shell concept, as well as a data randomization technique, resulting into almost linear speedup (for ERI evaluation). In configurations 2 and 3, BFS is used for parallel storage and retrieval of ERIs. Further, in 3 matrix operations are implemented as remote procedure calls on the i860 processor. Routine techniques of level shifting and extrapolation are used for accelerating SCF convergence. The resulting package, INDMOL, has been tested for some randomly selected molecules having up to 255 contractions. Using configuration 3, a factor of 2 to 5 in computation time is obtained over 1, for the systems for which the ERIs cannot be stored in the distributed core memory. In summary, a heterogeneous system, as in configuration 3, can indeed be optimally exploited for programming peculiar diverse requirements of the SCF procedure. © 1993 John Wiley & Sons, Inc.
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 471-477 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: One of the features of the polypeptide backbone is that it represents a flexible chain that contains almost rigid CO—NH peptide bonds. One may try to substitute one or more such bonds by another relatively rigid unit to maintain the overall conformational properties of the backbone and at the same time modify some other properties of the molecule (“pseudopeptide”), such as the ability to form hydrogen bonds. By a detailed conformational analysis, it is shown that the carbon—carbon double bond is quite isosteric with the peptide bond and for this reason suitable for such a substitution. This is accomplished by applying molecular mechanics in calculation of the φ, ψ maps for pseudopeptide analogs of the N-acetyl-Ala-NHMe molecule. © 1993 John Wiley & Sons, Inc.
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  • 17
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 510-521 
    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 analytical expressions to calculate the gradient of the water-accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent-protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.
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  • 18
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 530-540 
    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 potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.
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  • 19
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 556-565 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling-relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all-atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA-type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence-Jones). © 1993 John Wiley & Sons, Inc.
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  • 20
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 928-933 
    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 index suitable for computing molecular similarity based upon the similarity of molecular properties such as electrostatic potentials or electrostatic fields is presented in two forms. For one form of the present index, general conditions are established for which a linear measure of similarity is obtained. An illustrative example is provided in which the electrostatic field and electrostatic potential of guanine obtained from different wave functions are compared. © 1993 John Wiley & Sons, Inc.
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  • 21
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 934-943 
    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 the MM2-87 program and parameter set, conformational analyses have been performed on cocaine (1), the potent analog 2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT, 2), and a group of dopamine reuptake blockers that contain two phenyl rings. The latter includes LU 19-005 (3), a 1-amino-4-phenyltetralin (4), a hexahydropyrrolo[2,1-a]isoquinoline (5), diclofensine (6), and a hexahydro[1,2-b]pyridine (7). Using different values for the dielectric constant, the global minimum of 1 and 2 is a conformer in which there is a favorable electrostatic interaction between the ammonium hydrogen and the carbonyl of the carbomethoxy group. The N-methyl groups in 1 and 2 are found to strongly prefer the equatorial position of the piperidine ring. These results were also related to four crystal structures of 1 and its close derivatives. Compounds 3-7 are found to have a common conformation that was used to define the pharmacophore for dopamine reuptake blockers including the required orientation of the ammonium hydrogen. The pharmacophore provides an explanation for why the tertiary amine analogs of 3 and 4 are less potent than the secondary amines because the added N-methyl group occupies the position required for the ammonium hydrogen. This explanation, however, does not work for 7, in which the tertiary amine is again less active than the secondary amine. However, this last series appears to have a number of anomalous features. Superposition of 2 with the pharmacophore suggests that its carbomethoxy may occupy the same region of the receptor as the second phenyl ring in compounds 3-7. © 1993 John Wiley & Sons, Inc.
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  • 22
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 970-976 
    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 defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N′-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed. © 1993 John Wiley & Sons, Inc.
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  • 23
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    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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  • 24
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    Journal of Computational Chemistry 14 (1993), S. 1007-1018 
    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 program AQUARIUS2 calculates probable positions for water molecules within the first hydration shell of any protein for which atomic coordinates are known. Like its predecessor, AQUARIUS, it uses a knowledge of water molecules sites from crystallographically determined protein structures. Energy calculations are not employed. It differs substantially from the original program in that a 3-D probability map (for solvent sites) is generated around the surface of the protein instead of the previously used discrete points. The accuracy of the program has been gauged by comparison with experimentally derived water molecule positions for proteins not used in the knowledge base of the program. It has also been tested by combining the probability density maps with crystallographically determined electron density maps for the protein porphobilinogen deaminase. This procedure filters the most likely solvent electron density peaks from the background noise and has been used in the determination of the solvent structure around the protein nerve growth factor. © John Wiley & Sons, Inc.
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  • 25
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    Journal of Computational Chemistry 14 (1993), S. 1036-1041 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Net atomic charges are derived from a least-squares fitting to electrostatic potentials at atomic sites. The method treats atoms in the molecule as having spherically averaged Hartree-Fock densities, the atomic densities overlapping with one another. The method has the advantage of best reproducing the electrostatic potentials at the atomic nuclei and avoiding the arbitrariness in choosing the points used in the fitting. We have written a FORTRAN program, CHELPN92 (Z. Su, Chemistry Department, SUNY at Buffalo, Buffalo, NY, 1992), based on the method and applied it to deuterated benzene, l-alanine, d,l-histidine, 2-methyl-4-nitroaniline, and deuterated pyridinium-1-dicyanomethylide using the molecular geometry and electrostatic potentials from analysis of accurate X-ray diffraction data. The derived charges are used to calculate the molecular dipole moments. While the charges from this method are in general significantly different from those from the kappa refinement [P. Coppens, T.N. Guru Row, P. Leung, E.D. Stevens, P.J. Becker, and Y.W. Yang, Acta Cryst. A, 35, 63 (1979)], the dipole moments obtained with the new method agree well with those from the kappa refinement. © John Wiley & Sons, Inc.
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  • 26
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    Journal of Computational Chemistry 14 (1993), S. 1050-1065 
    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 methods are available in the literature for the conformational analysis of small molecules. Each of these methods has some advantages and some disadvantages. Also, each of these methods may be expected to perform better or worse on different types of molecules. There is no clear calibration of each of these methods against a “standardized” set of molecules available in the literature. Such a reference work would be useful to the community because it would allow the choice of methods to be based on some facts. We attempted to provide a start to such a calibration in this article with an examination of the SYBYL SEARCH method. Methods for evaluating the performance of this method are described in detail and will be applied to all other available conformational analysis methods in future papers. © John Wiley & Sons, Inc.
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  • 27
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    Journal of Computational Chemistry 14 (1993), S. 1123-1123 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 28
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    Journal of Computational Chemistry 14 (1993), S. 1125-1135 
    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 quantifying similarity between crystal structures is transformed into the problem of comparing the associated X-ray powder diagrams. A smooth similarity measure between two powder diagrams, termed a “fold,” is defined. In contrast to conventional comparison methods, the introduced method is still applicable when the peaks of the spectra to be compared have no overlap. The main areas of application of the method are the construction of a molecular crystal structure when only the experimental powder diagram is available and the analysis of possible crystal packings predicted on the basis of molecular information only. A suitable empirical parameterization of the fold has been derived from a large set of experimental and force-field-generated crystals. The analysis of the outcome of an ab initio packing of a flexible molecule is given as an example. The algorithmic details of the method are given as a FORTRAN 77 code. © John Wiley & Sons, Inc.
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  • 29
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    Journal of Computational Chemistry 14 (1993), S. 1184-1193 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a new method for de novo design of molecules that bind to protein active sites. The method, CONCEPTS (Creation of Novel Compounds by Evaluation of Particles at Target Sites), places a group of atom-like particles in the site. The particles are free to move within the site to improve binding to the protein. A key innovation of this technique is that covalent connections are made among the particles in a stochastic and dynamically reversible manner. These changes in the topology are either accepted or rejected depending on their ability to improve the total energy of the enzyme-inhibitor complex. The method is applied to two test systems: The FK506 binding protein (FKBP-12) and HIV-1 aspartyl protease. In both cases, we are able to predict, de novo, drugs that have striking similarities to known potent inhibitors and that can successfully be used to generate “hits” of the known inhibitors from a data base. © John Wiley & Sons, Inc.
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  • 30
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    Journal of Computational Chemistry 14 (1993), S. 1203-1211 
    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 separation of the short- and long-range terms in the potentials generated by pairs of Slater functions is reformulated in the context of the Gauss transform method. Analytic expressions of the long-range potentials (in closed form) are derived for equal exponents and generalized (as expansion series) for different exponents. Additionally, the representation of these potentials from small sets of charges or lowest-order multipoles is examined, paying special attention to their values and optimal positions. Finally, numerical tests of the formal developments are presented. It is concluded that the long-range three- and four-center integrals can be calculated with high accuracy in a simple and relatively inexpensive manner. © John Wiley & Sons, Inc.
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  • 31
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    Journal of Computational Chemistry 14 (1993) 
    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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  • 32
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    Journal of Computational Chemistry 14 (1993), S. 1281-1289 
    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 compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of α-D-glucose anhydrate and monohydrate crystals were performed. Also, the long-range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X-ray diffraction. The force-field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. © John Wiley & Sons, Inc.
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  • 33
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    Journal of Computational Chemistry 14 (1993), S. 1301-1312 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Lithium parameters have been optimized for Stewart's standard PM3 method. The average deviation of the heats of formation calculated for 18 reference compounds is 6.2 kcal/mol from the experimental or high-level ab initio data; the average deviation with Li/MNDO is 18.9 kcal/mol. The average error in bond lengths is also reduced by a factor of two to three. Ionization potentials and dipole moments are reproduced with comparable accuracy than Li/MNDO. However, the mean deviation for the heats of formation of both methods increases when being applied to other systems, especially to small inorgnic molecules. The applicability of the new parameter set is demonstrated further for various compounds not included in the reference set, for the calculation of the activation barriers of several lithiation reactions, as well as for the estimation of oligomerization energies of methyl lithium (including the tetramer). Li/PM3 gives reliable results even for large dimeric complexes, like [{4-(CH3CR)C5H4N}Li]2, containing TMEDA or THF as coligands and reproduces the haptotropic interaction between Li+ and π-systems (e.g., in benzyl lithium) as well as the relative energies and structural features of compounds with “hypervalent” atoms (e.g., in lithiated sulfones). © John Wiley & Sons, Inc.
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  • 34
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    Journal of Computational Chemistry 14 (1993), S. 1333-1338 
    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 apply a recently developed method, the multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, metenkephalin is studied and the ergodicity problem, or multiple-minima problem, is shown to be overcome by this algorithm. The lowest-energy conformation obtained agrees with that determined by other efficient methods such as Monte Carlo simulated annealing. The superiority of the present method to simulated annealing lies in the fact that the relationship to the canonical ensemble remains exactly controlled. Once the multicanonical parameters are determined, only one simulation run is necessary to obtain the lowest-energy conformation and further the results of this one run can be used to calculate various thermodynamic quantities at any temperature. The latter point is demonstrated by the calculation of the average potential energy and specific heat as functions of temperature. © John Wiley & Sons, Inc.
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  • 35
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    Journal of Computational Chemistry 14 (1993), S. 1376-1384 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized geometries and total energies for the conformers of 3,6-dihydro-1,2-dithiin (2) and 3,6-dihydro-1,2-dioxin (3) were calculated at several ab initio MO levels: RHF/3-21G(*), RHF/6-31G*, MP2/6-31G*, and MP2/6-31G*/ /RHF/3-21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH3)2S2, whose optimized geometries agree closely with the observed structures, which is the gauche (C2 symmetry). For the disulfanes, the gauche geometries from RHF/3-21G(*) are in good agreement with the observed structure while the RHF/3-21G results best fit the dioxin. Pertinent structural data at the RHF/3-21G(*) for the half-chair (C2) dithiin are: bond lengths, —SS—, —CS—, —CC=, and —C=C—, 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, =CCS, and C=CS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half-chair dithiin at MP2/6-31G*//RHF/3-21G(*) is less than the planar (C2v) and the half-boat (Cs) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3-21G for the half-chair dioxin are: bond lengths, —OO—, —CO—, —CC=, and C=C, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, =CCO, and C=CO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half-chair dioxin at MP2/6-31G//RHF/3-21G is less than the planar and the half-boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C2 symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.
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  • 36
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    Journal of Computational Chemistry 14 (1993), S. 1417-1422 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A common problem in the solution of the Poisson-Boltzmann equation using finite difference methods is the self-energy of the system, also known as the grid energy. Because atoms are typically modeled as a point charge, the infinite self-energy of a point charge is likewise modeled. In this article, a simple, alternate treatment of atomic charge is described where each atom is represented as a sphere of uniform charge. Unlike the point charge model, this method converges as the grid spacing is reduced. The uniform charge model generates the same electrostatic field outside the atoms. In addition, the use of fine grids reduces the variations in the potential due to variations in the position of atoms relative to the grid. Calculations of Born ion solvation energies, small-molecule solvation energies, and the electrostatic field of superoxide dismutase are used to demonstrate that this method yields the same results as the point charge model. © John Wiley & Sons, Inc.
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  • 37
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    Journal of Computational Chemistry 14 (1993), S. 1454-1459 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is introduced that tests whether a proposed elementary reaction can be realized within a specified number of cleavages and formations of covalent bonds. This is related to the problem of computing the minimum chemical distance of a given stoichiometry, but differs from it in important ways that are exploited in the algorithm design. One application of the algorithm is as a filter in MECHEM - a computer aid for the elucidation of reaction pathways. In that application, reaction steps implying more changes to covalent bonds than a given threshold are ruled implausible, and in practice such tests need to be carried out many thousands of times. Future applications of the algorithm can be expected because the question addressed is a fundamental one: What elementary reactions can occur? © 1993 by John Wiley & Sons, Inc.
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  • 38
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    Journal of Computational Chemistry 14 (1993), S. 1272-1280 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small-and medium-sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50-4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley & Sons, Inc.
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  • 39
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    Journal of Computational Chemistry 14 (1993), S. 1320-1325 
    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 representation of the RKR (or IPA) diatomic potential by a simple analytic function is considered. This old problem has for a fairly good solution the Coxon-Hajigeorgiou function U(x) = D[1 - exp-fn(x)]2 with fn(x) = Σm = 1n amxm. The problem of the determination of the disposable parameters a1 … an [in order that U(r) fits the given RKR potential] is reduced to that of a set of linear equations in am where a standard least-squares technique is used. The application to several states (ground or excited) of several molecules shows that a fairly “good” fit is obtained for n ∼ 10, even for the state XOg - I2 bounded by 109 vibrational levels, for which the RKR potential is defined by the coordinates of 219 points. It is shown that the percentage deviation |U(r)RKR - U(r)| throughout the range of r values is about 0.04% for XΣ—Li2, 0.0005% for XΣ—HCl, 0.06% for XOg—I2, and 0.05% for BOu—I2 (as examples). This approach shows the same success for deep and shallow potentials. The comparison of the computed Ev (vibrational energy) and Bv (rotational constant) with their corresponding experimental values shows that a good agreement is reached even for high vibrational levels close to the dissociation. © John Wiley & Sons, Inc.
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  • 40
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.
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  • 41
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    Journal of Computational Chemistry 14 (1993), S. 1066-1076 
    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 nonbonded portion of a force field for lecithins was characterized by application to the study of the crystal packing geometry and energetics of eight different molecules. The molecules were either lecithin fragments or chosen to isolate particular intermolecular features to test the accuracy of the force field specifically for those interactions. In particular, the hydrocarbon interactions, hydrogen bonding, electrostatics, and phosphate interactions were critiqued. The results support previous findings that indicated that this force field is reasonably accurate for lecithins. For all molecules, a minimum was found near the experimentally determined crystal structure. Using D-glucitol as an example, it is shown that the structural effect of hydrogen bonding is better represented by a nonelectrostatic force-field model than by a purely electrostatic model. Results obtained with glycerylphosphocholine and four smaller organic phosphate molecules suggest that further study of nonbonded interactions of phosphate groups is needed. © John Wiley & Sons, Inc.
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  • 42
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    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 43
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    Journal of Computational Chemistry 14 (1993), S. 1396-1406 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is presented within the context of the calculation of the time-relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time-relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325-ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. © John Wiley & Sons, Inc.
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  • 44
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    Journal of Computational Chemistry 14 (1993), S. 1429-1439 
    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 developed parallel coupled-cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194, 84 (1992)] is extended to allow four-indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed-memory parallel processors. Quantities such as the double-excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2-hydroxypyridine/2-pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed-memory supercomputers. The largest coupled-cluster calculations contained over 2 million double-excitation amplitudes. © John Wiley & Sons, Inc.
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  • 45
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    Journal of Computational Chemistry 14 (1993), S. 1460-1467 
    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 the estimation of pKa from empirically calculated atomic charges has been developed and tested on a diverse set of organic oxyacids. The approach involves a comparison of the atomic charges calculated for both the acid and the negative ion that is formed after loss of the acidic proton. These charges have been used in conjunction with the familiar concepts of induction and resonance to develop an accurate formula to predict pKa. Results for a set of 135 compounds, including alcohols, phenols, and carboxylic acids, yielded a fit of pKa with r = 0.993 and an rms error of 0.455. © John Wiley & Sons, Inc.
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  • 46
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    Journal of Computational Chemistry 14 (1993), S. 13-18 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The principles of an efficient, fast algorithm for the calculation of diagrams appearing in Green function and many-body perturbation methods are discussed and timing examples are given. Within the suggested algorithm, the third order-diagrams required in the Green function approach are evaluated by arranging computations in such a way that the most inner loops contain only simple scalar products and multiplication of vector by scalar operations. The molecular symmetry is taken into account for abelian groups. © 1993 John Wiley & Sons, Inc.
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  • 47
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    Journal of Computational Chemistry 14 (1993), S. 67-74 
    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 CO, CO2, CS, CIF, and SO2 molecules were used to test the dependence of supplementary d and f function exponents to changes in bond lengths and bond angles in MO calculations utilizing Gaussian basis sets in Hartree-Fock and Moller-Plesset calculations. Using Dunning-Hay double zeta basis sets, optimizations were performed at internuclear separations from 100-200 pm and beyond. The energy cost of not reoptimizing d function exponents when bonds are stretched or compressed is much smaller for correlated calculations than for those at the Hartree-Fock level and is greatest at the lower end of the range of internuclear distances. The problem is much less serious at all levels when multiple sets of d functions are used. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 478-483 
    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 conformational analysis for a molecule is often performed by assuming that the total conformational energy is a function of two dihedral angles. The resulting conformational energy map is sometimes not easy to interpret because what counts is not energy differences but rather the probability distribution map at a given temperature. In the present article, an algorithm to calculate such a map is given. An example concerning N-substituted amino sugars shows how the conformational probability map may be interpreted. In addition, a similarity index is proposed to get a measure of similarity of the conformational properties of two molecules. The index is based upon the analysis of the conformational probability maps for both molecules. © 1993 John Wiley & Sons, Inc.
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  • 49
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    Journal of Computational Chemistry 14 (1993), S. 484-501 
    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 treatment of macromolecular electrostatics has been developed using the 3-D finite element method to numerically solve the linear Poisson-Boltzmann equation. The procedure is based upon a model where the macromolecule is represented at an atomic level of detail, while the solvent is treated in a continuum approximation. The finite element method has two major advantages over previous methods based upon the finite difference approach. First, charges are located on atomic centers rather than being distributed onto grid points. Second, an isoparameter model allows the use of noncubic grids, providing a more accurate description of molecular shape. The principal disadvantage of the finite element method has been its computational complexity, which arises from the use of large matrices. To overcome this difficulty, a new matrix representation has been formulated and an iterative solution procedure has been adopted. The combination of these two techniques drastically reduces the size of the system matrix and increases the overall computational efficiency of the algorithm, making the new treatment computationally competitive with the finite difference approach. Because of the mathematical rigor and physical sophistication of the finite element algorithm, the new treatment is able to give an accurate description of the electrostatic potential distribution in a macromolecular system. Results on test cases with simple geometries show that the new treatment is able to reach the same level of accuracy achieved by the finite difference method while using a lower grid density. Near changes and surfaces, our method is more accurate than the finite difference method. The overall maximum deviation between computed and analytic potentials is less than 3% except in regions surrounding charges. The applicaions of both the finite element and finite difference methods to the same biomolecular systems produce similar potential distributions that would become identical in the limit of infinitely fine grids. © 1993 John Wiley & Sons, Inc.
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  • 50
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    Journal of Computational Chemistry 14 (1993), S. 155-160 
    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 types of real (i.e., noninteger) local vertex invariants (LOVIs), denoted by ci and c′i and called distance-enhanced exponential connectivities, are defined via eqs. (1)-(3) and (1′)-(3′), respectively. Only the case when the exponent z equals 1 in eqs. (3) and (3′) is discussed in detail. Both these LOVIs span the range from 0-1, but their dependence upon topology is fairly different, as seen from Table II, where ci and c′i values for all heptane and octane isomers are displayed. From these LOVIs, by simple summation over all graph vertices two new topological indexes (TIs), denoted by XC and XC′, respectively, are obtained. Their intermolecular ordering of all alkanes with four to nine carbon atoms is discussed. On their basis, correlations with boiling points and critical pressures of alkanes are presented. © 1993 John Wiley & Sons, Inc.
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  • 51
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    Journal of Computational Chemistry 14 (1993), S. 161-185 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different microscopic and semimicroscopic approaches for calculations of electrostatic energies in macromolecules are examined. This includes the Protein Dipoles Langevin Dipoles (PDLD) method, the semimicroscopic PDLD (PDLD/S) method, and a free energy perturbation (FEP) method. The incorporation of these approaches in the POLARIS and ENZYMIX modules of the MOLARIS package is described in detail. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions, as well as the effects of the ionic strength and external pH. Determination of the hydrophobic energy involves an approach that considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. Ionic strength effects are studied by modeling the ionic environment around the given system using a grid of residual charges and evaluating the relevant interaction using Coulomb's law with the dielectric constant of water. The performance of the FEP calculations is significantly enhanced by using special boundary conditions and evaluating the long-range electrostatic contributions using the Local Reaction Field (LRF) model. A diverse set of electrostatic effects are examined, including the solvation energies of charges in proteins and solutions, energetics of ion pairs in proteins and solutions, interaction between surface charges in proteins, and effect of ionic strength on such interactions, as well as electrostatic contributions to binding and catalysis in solvated proteins. Encouraging results are obtained by the microscopic and semimicroscopic approaches and the problems associated with some macroscopic models are illustrated. The PDLD and PDLD/S methods appear to be much faster than the FEP approach and still give reasonable results. In particular, the speed and simplicity of the PDLD/S method make it an effective strategy for calculations of electrostatic free energies in interactive docking studies. Nevertheless, comparing the results of the three approaches can provide a useful estimate of the accuracy of the calculated energies. © 1993 John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 14 (1993), S. 603-619 
    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 develop a computer code that uses elegant bit-manipulation techniques for matrix multiplication and thus facilitates exhaustive generation of Skew-Hadamard matrices. Hadamard matrices are useful in spectroscopic applications (Hadamard transform spectroscopy) and in balanced chemical designs. Application of our code yields several Skew-Hadamard matrices up to order 100 × 100, although the combinatorial complexity of exhaustive generation increases exponentially. Our bit-manipulation-based codes took 124 h of CPU time to perform 7.79344 × 1011 matrix multiplications on an IBM RS 6000/560 system to generate all 100 × 100 matrices. This amounts to 5.7 × 10-7 s of CPU time per matrix multiplication. © 1993 John Wiley & Sons, Inc.
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  • 53
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    Journal of Computational Chemistry 14 (1993), S. 629-638 
    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 ab initio effective two-body potential that aims at mimicking the average copper-water interaction energy of the first solvation shell was developed. This new potential, together with the MCY water-water potential and a three-body ion-water-water induction potential, is tested in simulations of gas-phase clusters [Cu2+—(H2O)20] and diluted solutions [Cu2+—(H2O)200] at T = 298 K. The results of simulations with conventional ab initio pair potentials, with and without three-body induction corrections, are also presented. The different types of copper-water interaction potentials are evaluated comparatively and the efficiency of the newly proposed effective pair potential is discussed. © 1993 John Wiley & Sons, Inc.
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  • 54
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    Journal of Computational Chemistry 14 (1993), S. 620-626 
    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 computed the free energy of solvation for a series of ions and neutral molecules using two different continuum approaches. First, we used the AM1-SM1 technique, where the AM1 Fock matrix is modified to include a generalized Born contribution. Second, we applied the DelPhi approach, where the electrostatic component of the free energy of solvation is evaluated by resolving the Poisson-Boltzman equation by a finite difference method. Both methods appear equally reliable for ionic systems. For neutral compounds, AM1-SM1 performs better than DelPhi; however, the differences become less pronounced for compounds with larger free energies of solvation. In parallel, both methods were applied to study the influence of the solvation process in the overall drug receptor interaction for a series of closely related ligands for the D1 dopamine receptor. An inverse linear relationship was found between the free energy of solvation and the logarithm of the affinity of the ligands; nevertheless, electrostatic properties are likely to modulate affinity as well. © 1993 John Wiley & Sons, Inc.
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  • 55
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    Journal of Computational Chemistry 14 (1993), S. 655-666 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures of several sulfones, including dimethyl sulfone, methyl ethyl sulfone, methyl vinyl sulfone, and diphenyl sulfone, have been fit with the MM3 force field to existing experimental data from electron diffraction and microwave spectroscopy. The vibrational spectra have also been fit for six of these compounds. The torsional parameters for the aliphatic sulfones were fit to ab initio 6-31G data. Heats of formation were also fit. © 1993 John Wiley & Sons, Inc.
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  • 56
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    Journal of Computational Chemistry 14 (1993), S. 667-672 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Chemisorption on small, closed-ring CdS clusters and the electronic structure of the surface were studied using Hartree-Fock valence calculations based upon stepwise density matrix approximations. Detailed valence calculations gave stabilization energies similar to the all-electron results for the small CdS clusters, verifying our valence method in which the approximations of the density matrices were fitted against the atomic calculations. Chemisorption studies have shown that the 4d shell relaxation on the Cd atom plays a crucial role even though the 4d does not participate directly in the substrate-adsorbate bonds. Thus, the CdCl2 was found unbound to the surface in the case of implicit description of the 4d orbital of the Cd whereas treating the Cd 4d orbital explicitly in the variational calculation the CdCl2 bonds to the surface with the calculated adsorption energy of 107.4 kJ/mol. © 1993 John Wiley & Sons, Inc.
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  • 57
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    Journal of Computational Chemistry 14 (1993), S. 715-717 
    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 scheme for sprouting peptide side chains using X-PLOR is introduced using an example from the collagen system to show how reasonable starting structures for minimization studies may be created. © 1993 John Wiley & Sons, Inc.
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  • 58
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    Journal of Computational Chemistry 14 (1993), S. 410-421 
    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 to represent atomic electron charge densities [L. Fernandez Pacios, J. Phys. Chem., 95, 10653 (1991); J. Phys. Chem., 96, 7294 (1992)] is here generalized to obtain simple analytical functions for potential energy contributions. Based upon suitable functions to describe atomic electron densities in a physically meaningful form, the procedure is developed to define density-dependent analytical expressions for the electrostatic (classical) and exchange (quantum) potentials by means of proper approximate functionals. Calculations of correlation energies by using various density-functional approaches are also performed. The whole scheme is used to represent Hartree-Fock limit atomic wave functions by Clementi-Roetti. This way, a set of analytically simple, nonbasis set-dependent functions are defined with the aim to be further implemented in energy decomposition schemes for molecular interactions studies using atomic instead of electronic building blocks. © 1993 John Wiley & Sons, Inc.
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  • 59
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    Journal of Computational Chemistry 14 (1993), S. 755-768 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Studies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (R—O—O—H) and dialkyl peroxides (R1—O—O—R2). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 14 (1993), S. 1234-1239 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SCF and Møller-Plesset calculations were done for the systems AB6 (TeF6 and SeF6) and AB6E (TeF2-6 and SeF2-6) to determine their relative stabilities and geometric structures. The SCF calculations show that both TeF2-6 (as expected) and SeF2-6 (despite a small central atom) possess nonoctahedral shapes. However, at the Møller-Plesset level only the TeF2-6 ion, studied with a large valence basis set, retains nonoctahedral geometry. The calculated structural parameters of the ion in C3v symmetry (the bond lengths are 2.212 and 1.975 Å and the bond angles are 104.9 and 83.4 °) differ considerably from the octahedral values (2.101 Å and 90.0°), yet the corresponding total energy is only about 1 kcal/mol smaller. The results show significant dependence of the computational predictions on the basis sets used and indicate the need to include electron correlation effects in the studies devoted to establishing the stereochemical activity of the lone electron pair. © John Wiley & Sons, Inc.
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  • 61
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new approach to the computation of molecular electrostatic potentials based on the AM1 wave function is described. In contrast to the prevailing philosophy, but consistent with the underlying NDDO approximation, no deorthogonalization of the wave function is carried out. The integrals required for the computation of the electronic contributions to the molecular electrostatic potential are evaluated in a manner similar to that of the AM1 core-electron attraction integrals, while the nuclear contributions are computed using a new semiempirical function - ZA(SASA, SpSp)[1 + exp[ - ωA(RAi - δA)]] - where the atomic parameters ωA and δA are obtained by calibration against the results of ab initio HF/6-31G* calculations. Isopotential contour maps for guanine and cytosine obtained with the new method are qualitatively almost indistinguishable from their HF/6-31G* counterparts, while quantitative comparisons for the minima for a wide range of molecules are reproduced with an rms error of 5.2 kcal mol-1. The locations of the “lone-pair” minima for a wide range of heterosubstituted organic molecules generally fall within 0.02 Å of the corresponding HF/6-31G* minima while those in the π-regions of unsaturated molecules are generally within 0.2 Å. Because of the rapid integral evaluation, the fully semiempirical method described here is extremely economical. For example, for the guanine-cytosine base pair it is 〉500 times faster than calculations in which the complete integral matrix is computed analytically from the deorthogonalized AM1 wave function. © John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 14 (1993), S. 1149-1163 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: High-level ab initio calculations {QCISD(T)/6-311 +G**//MP2(fu)/6-31 +G**, with corrections for higher polarization [evaluated at MP2/6-311 +G(3df,2p)] and ΔZPE//MP2(fu)/6-31 +G**, i.e., comparable to Gaussian-2 theory} indicate concerted mechanisms for double- and triple-hydrogen exchange reactions in HF and HCl dimers and trimers, in mixed dimers and trimers containing one NH3, and in mixed dimers of HF, HCl, and NH3 with formic acid. All these reactions proceed via cyclic four- or six-center transition structures, the latter being generally more favorable. Calculated activation barriers (ΔHd̊ at 0 K, kcal/mol) are 42.3 for (HF)2, 20.3 for (HF)3, 41.2 for (HCl)2, 25.6 for (HCl)3, 36.0 for NH3-HF, 10.6 for NH3(HF)2, 19.9 for NH3-HCl, 2.3 for NH3(HCl)2, 9.7 for HCO2H-HF, 7.0 for HCO2H-HCl, and 11.3, for HCO2H-NH3. The barriers are lower for the more ionic systems and when more ion pair character is present. © John Wiley & Sons, Inc.
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  • 63
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    Journal of Computational Chemistry 14 (1993), S. 1172-1183 
    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 a detailed 3-D characterization of the shapes of molecular charge distributions is implemented in the form of a comprehensive package of computer programs, GSHAPE, and applied to a series of 10-electron hydrides to critically evaluate the methodology. Attention is paid to the effects of nuclear geometry and the size of basis on the molecular shape. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend on two continuous parameters: a density value defining the density contour and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is calculated at the ab initio level using basis sets ranging from STO-3G to 6-31G**. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visualization of the results is one option of our program using Application Visualization Software (AVS). For a given molecule, in a given nuclear geometry, the technique provides a 2-D shape map, displaying the distribution of the shape gruops as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, a variety of 2-D shape maps are discussed. © John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 14 (1993), S. 1523-1533 
    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 a 6-311G** basis set with estimation of correlation energy at the MP2 level, structural and energetic data for 40 molecular species containing magnesium have been calculated. For about half the species studied, further energetic data were obtained using Pople's G2 method. Enthalpy changes at 298.15 K were obtained for isogyric reactions and standard enthalpies of formation were derived from these. Comparison of the standard enthalpies of formation with the sparse literature data suggests the MP2/6-311G** standard enthalpies of formation are accurate to ± 15 kJ mol-1 and the corresponding G2 enthalpies accurate to ± 10 kJ mol-1. The calculated ΔH0f [MgN, g] revealed a gross error in the currently accepted value for this function. It is intended that these results will be used to parameterize the semiempirical molecular orbital package, MOPAC, for the element magnesium. © John Wiley & Sons, Inc.
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  • 65
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    Journal of Computational Chemistry 14 (1993), S. 1519-1522 
    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 diatomic matrix elements Mnn′ = 〈Ψn|Q|Ψn′〉 related to the anharmonic oscillator is considered for standard operators Q of the form x = r - re (r is the radial variable), powers of x, or exponentials, or combinations of such operators; the quantum numbers (n, n′) may be equal or not. A “full numerical” method to determine Mnn′ is presented for any type of the potential U, analytic like that of Morse or numerical like the RKR potential. This numerical method is a simplified version of the standard Cooley shooting method (CSM). The present simplified shooting method (SSM): (1) shoots in one direction only (instead of two); (2) avoids starting problems and matching problems; (3) determines the “end” point automatically (without prior guesses); and (4) reduces thus the number of grid points effectively needed. Examples for analytic (Morse) and RKR potentials are presented. The numerical application to a standard example used by Delgado-Barrio et al. [J. Comp. Chem., 7, 208 (1986)] using the CSM, and by Kobeissi et al. [J. Comp. Chem., 10, 358 (1989)] using the highly accurate “Canonical Functions” method, shows that when the SSM and CSM are used with the same integrator and the same mesh size the relative discrepancy ΔMnn′(between computed and exact M) is averaged for several (n, n′) to 5.4 × 10-4 for the CSM and to 8.5 × 10-6 for the present SSM. This improvement in accuracy is supplemented by a reduction in computer time consumption. © John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 1575-1579 
    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 density-functional theory (DFT)-based computational chemistry software package DMol was used to provide insight into the reductive potentials of a series of halomethanes. It is known that certain members of this series are readily reduced in vivo via catalysis by cytochrome P450. DMol was used to calculate the electron affinities of these molecules to be used as measures of their reduction potentials. Our results are consistent with experimental electrochemical reduction potentials and indicate that electron affinity is dependent upon the number and type of halogens present in the molecule. Calculated bond lengths and angles also compared favorably with experimental results and estimates derived from other ab initio methods of calculation. Concurrent with this study was the observation of a linear empirical relationship between electron affinity and the lowest unoccupied molecular orbital energy. It is possible that these values could be used as indicators of reductive potentials and ultimately of metabolic rates for use in PB-PK models designed to predict the dose associated with the toxicity of molecules of this and other classes. © John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 1136-1141 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We studied the transferability of the localized orbitals (LOs) of interacting Ne atoms using several basis sets. Both at SCF and at MP2 and MP3 levels, the contributions of the LOs have been calculated and discussed for the Ne2 and Ne3 systems. It was shown that for the LOs the transferability is satisfied to a good extent and due to the transferability the interaction energy at the correlated level can be calculated by using only the LOs of the supermolecule. The basis set superposition error (BSSE) is simply extracted from the intramolecular parts of the correlation energy. The two- and three-body interaction energies have been investigated for the studied systems. © John Wiley & Sons, Inc.
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  • 68
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    Journal of Computational Chemistry 14 (1993), S. 1164-1171 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: One task in the interpretation of the 2-D nuclear magnetic resonance (NMR) spectrum is to assign its signal patterns to their corresponding amino acids in proteins or polypeptides. To carry out this task of interpretation, one requires sufficient chemical knowledge and expertise to reason from a set of highly noisy data. We present a system called RUBIDIUM (a Rule-Based Identification in 2-D NMR Spectrum) to formulate the expertise and automate the process of interpretation. Given a protein or polypeptide with a known amino acid sequence and the 2-D NMR spectra (both COSY and NOESY), RUBIDIUM yields plausible assignments of lines that account for most signals observed in the spectrum and conform to prior chemical knowledge. Rules of pattern matching are used to detect plausible signal patterns. The expertise of the sequence-specific assignment task is formulated to assign a signal pattern to amino acids. To cope with ambiguities and noise, RUBIDIUM adopts various low-level data preprocessing techniques, the strategy of divide and conquer, and the relaxation technique to decrease the complexity and recover from overconstrained conditions. The polypeptides oxytocin and vasopressin are used to illustrate the performance of RUBIDIUM. © John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 1212-1233 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevin/implicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane demonstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes. © John Wiley & Sons, Inc.
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  • 70
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    Journal of Computational Chemistry 14 (1993) 
    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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  • 71
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    Journal of Computational Chemistry 14 (1993), S. 1-1 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 72
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    Journal of Computational Chemistry 14 (1993), S. 37-44 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO parameters for helium are derived from an optimization that employs only atomic and diatomic reference data. Comparisons with published high-level ab initio results indicate that MNDO correctly predicts the existence of covalently bonded helium compounds and normally reproduces the geometries of these small charged molecules reasonably well. Endohedral fullerene-helium complexes and the transition states for their formation are studied for C60, C60, and C602+. The calculated barriers are discussed and compared with those for the passage of helium through C6H6, C6H6+, and C6H62+. © 1993 John Wiley & Sons, Inc.
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  • 73
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    Journal of Computational Chemistry 14 (1993), S. 75-88 
    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 variety of computational methods, including the semiempirical techniques AM1, PM3, and MNDO, and the thermochemical basis sets of Benson and Stine, was used to calculate and compare heats of formation (ΔHf°) data for optimized geometries of a variety of aromatic and nonaromatic heterocycles. Detailed analyses, including 6-31G* and MP2/6-31G* ab initio calculations, were performed for the oxazole and thiazole heterocycles. The results indicate a scatter among the methods sensitive to the nature of the heterocycle. This was in particular evident in the oxazole molecule, where AM1 gave a singularly high value of ΔHf° consistent with longer calculated bond lengths, particularly about the oxygen atom. Aromatic stabilization energy appears to be addressed differently among the employed methods. Implications of this contrast applied to calculation of macromolecular systems containing heterocyclic units are discussed.
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  • 74
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    Journal of Computational Chemistry 14 (1993), S. 114-120 
    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 algorithms are introduced that show exceptional promise in finding molecular conformations using distance geometry on nuclear magnetic resonance data. The first algorithm is a gradient version of the majorization algorithm from multidimensional scaling. The main contribution is a large decrease in CPU time. The second algorithm is an iterative algorithm between possible conformations obtained from the first algorithm and permissible data points near the configuration. These ideas are similar to alternating least squares or alternating projections on convex sets. The iterations significantly improve the conformation from the first algorithm when applied to the small peptide E. coli STh enterotoxin. © 1993 John Wiley & Sons, Inc.
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  • 75
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    Journal of Computational Chemistry 14 (1993), S. 127-137 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe the development of Metropolis Monte Carlo algorithms for a general network of multiple instruction multiple data (MIMD) parallel processors. The implementation of farm, event, and systolic parallel algorithms on transputer-based computers is detailed and their relative performance discussed. Although the emphasis is on methodology, the application of such parallel algorithms will be important for addressing computational problems such as the determination of free energy differences in complex biologically important molecular systems. © 1993 John Wiley & Sons, Inc.
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  • 76
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    Journal of Computational Chemistry 14 (1993), S. 186-194 
    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 surface of HCP converting to HPC in its ground electronic state has been investigated with ab initio methods at levels up to MP2/6-311G**//MP4/6-311G** as well as TZV + + ** CASSCF. All geometries are fully optimized and compare favorably to previous theoretical and experimental values. The HCP molecule is predicted to be 85.4 kcal/mol lower in energy than its linear isomer at the-MP2/6-31G*//MP2/6-31G* level. The energy barrier for hydrogen rearrangement is found to be merely 2.3 kcal from the HPC end. CASSCF studies were initiated to clarify the low barrier and lent support to a flat surface as HPC converts to stable, linear HCP at the TZV + + ** level. CASSCF also predicts that HPC is unstable with respect to bending. Harmonic vibrational frequencies for HCP results in 5% accuracy or better. A bent triplet is found to be the lowest excited state using the CASSCF method. © 1993 John Wiley & Sons, Inc.
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  • 77
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    Journal of Computational Chemistry 14 (1993), S. 206-215 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested in Monte Carlo statistical mechanics simulations for the pure liquids of toluene, m-cresol, anisole, aniline, and benzonitrile at 25°C at 1 atm. The merged potential functions yielded acceptable thermodynamic results for the liquids except in the case of aniline, for which the error in the heat of vaporization was 12%. This was remedied by enhancing the polarity of the model to be more consistent with the observed dipole moment of aniline. Overall, the average errors in computed heats of vaporization and densities were then 2 and 1%, respectively. The structures of the liquids were characterized through energy and radial distribution functions. For m-cresol and aniline, the molecules participate in averages of 1.6 and 1.4 hydrogen bonds, respectively. Condensed phase effects on the torsional energies for anisole, m-cresol, and aniline were found to be small; m-cresol has a slightly enhanced tendency to be nonplanar in the liquid than in the gas phase, while anisole shows the opposite pattern. © 1993 John Wiley & Sons, Inc.
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  • 78
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    Journal of Computational Chemistry 14 (1993), S. 246-250 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An improved version of the “marching cubes” algorithm [W. Lorensen and H. Cline, Comp. Graph. 21, (1987)] for the generation of isosurfaces from 3D data fields is presented and applied to molecular surfaces. The new algorithm avoids inconsistent pattern definitions of the original one, which lead to artificial gaps. The advantage of a logarithmic interpolation procedure, in particular for data fields typically occurring in molecular science, is demonstrated. An example is the generation of molecular surfaces based upon electron density data. © 1993 John Wiley & Sons, Inc.
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  • 79
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    Journal of Computational Chemistry 14 (1993), S. 138-154 
    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 first ionization potential of an organic molecule containing electrons in nonbonding or π-type molecular orbitals can rapidly be calculated using parameters describing physical and chemical effects. These parameters include effective polarizability, resonance stabilization of a cation, π- and σ-charges, and electronegativity and are directly calculated from the structure of the compound. Correlation analyses with the first ionization potentials were carried out on various data sets classified into five groups to cover a wide range of organic molecules. The equations thus obtained were integrated into a system that automatically calculates the ionization potential of an organic compound from a connection table as obtained by a graphic input program. © 1993 John Wiley & Sons, Inc.
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  • 80
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    Journal of Computational Chemistry 14 (1993), S. 195-205 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested by computing free energies of hydration for toluene, p-xylene, phenol, anisole, benzonitrile, p-cresol, hydroquinone, and p-dicyanobenzene. The calculations featured Monte Carlo simulations at 25°C and 1 atm with statistical perturbation theory. The average difference between the computed results and experimental data for the absolute free energies of hydration is 0.5 kcal/mol. The AM1-SM2 method is also found to perform well in predicting the free energies of hydration for the substituted benzenes. In addition, the Monte Carlo simulations provided details on the hydration of the substituted benzenes, in particular for the solute-water hydrogen bonding. © 1993 John Wiley & Sons, Inc.
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  • 81
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    Journal of Computational Chemistry 14 (1993), S. 216-225 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A series of ab initio electronic structure calculations have been performed on the (H3Si)2O molecule using a range of basis sets. The accuracy of these calculations was evaluated by comparison with several experimental measurements. These calculations support earlier results indicating that polarization functions on the bridging oxygen atom are usually required to obtain a bent geometry for the Si-O-Si linkage in disiloxane. It was found that ab initio calculations utilizing effective core potentials and a double-ζ valence description augmented with polarization functions (CEP-31G*) provide results comparable in quality to those obtained using the all-electron 6-31G* basis set. To demonstrate the general utility of these effective core potential basis sets for theoretical studies of molecular silicates, calculations were performed on the (HO)3SiOSi(OH)3 molecule. The results obtained are in excellent agreement with previous experimental and ab initio calculations using all-electron basis sets. © 1993 John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 14 (1993), S. 251-251 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 83
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    Journal of Computational Chemistry 14 (1993), S. 278-284 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long-range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom-by-atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short-range truncation must be used, the ST2 switching function applied on a group-by-group basis was found to be the most realistic procedure. If atom-based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 John Wiley & Sons, Inc.
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  • 84
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The nature of the tetrahedral H42+ stationary point (minimum or triply degenerate saddle) depends remarkably upon the theoretical level employed. Harmonic vibrational analyses with, e.g., the 6-31G** (and 6-31 + +G**) and Dunning's [4s2p1d;2s1p] [D95(d,p)] basis sets using the standard p exponent suggest (erroneously) that the Td geometry is a minimum at both the HF and MP2 levels. This is not the case at definitive higher levels. The C3H42+ structure with an apical H is another example of the failure of the calculations with the 6-31G**, 6-311G**, and D95(d,p) basis sets. Even at MP2/6-31G** and MP2/ cc-pVDZ levels, the C3v structure has no negative eigenvalues of the Hessian. Actually, this form is a second-order saddle point as shown by the MP2/6-31G** calculation with the optimized exponent. The D4h methane dication structure is also an example of the misleading performance of the 6-31G** basis set. In all these cases, energy-optimized hydrogen p exponents give the correct results, i.e., those found with more extended treatments. Optimized values of the hydrogen polarization function exponents eliminate these defects in 6-31G** calculations. Species with higher coordinate hydrogens may also be calculated reliably by using more than one set of p functions on hydrogen [e.g., the 6-31G(d,2p) basis set]. Not all cases are critical. A survey of examples, also including some boron compounds, provides calibration. © 1993 John Wiley & Sons, Inc.
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  • 85
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    Journal of Computational Chemistry 14 (1993), S. 295-311 
    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 aqueous protein dynamics study, we compared the rms deviation relative to the crystal structure for distance-dependent and constant dielectric models with and without a nonbonded cutoff. The structures obtained from a constant dielectric simulation with a cutoff were substantially different from the structures obtained from a distance-dependent dielectric simulation, with and without cutoff, and a constant dielectric model without a cutoff. In fact, structures from the distance-dependent dielectric simulations were insensitive to the nonbonded cutoff and in good agreement with the structures generated from the constant dielectric simulation without a cutoff. In addition, the solute-solvent temperature differential and solvent evaporation artifacts, characteristic of the constant dielectric simulation with a cutoff, were not present for the distance-dependent dielectric simulations. In this current work, we explore whether this dielectric-dependent cutoff-sensitive behavior for a constant dielectric model arises from the discontinuities in the forces at the nonbonded cutoff or from neglecting the structure-stabilizing interactions beyond the nonbonded cutoff. We also examine the origin of the dielectric-dependent artifacts, and its potential influence on the structural disparity. Several protocols for protein dynamics simulations are compared using both constant and distance-dependent dielectric models, including implementation of a switching function and a nonbonded cutoff and two different temperature coupling algorithms. We show that the distance-dependent dielectric model conserves energy in the SPASMS molecular mechanics and dynamics software for the time steps and nonbonded cutoffs commonly used in macromolecule simulations. Although the switching function simulation also conserved energy over a range of commonly used cutoffs, the constant dielectric model with a switching function yielded conformational results more similar to a constant dielectric simulation without a switching function than to a constant dielectric model without a nonbonded cutoff. Therefore, the conformational disparity between the dielectric models arises from neglecting important structure-stabilizing interactions beyond the cutoff, rather than differences in energy conservation. © 1993 John Wiley & Sons, Inc.
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  • 86
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    Journal of Computational Chemistry 14 (1993), S. 363-370 
    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 outline a procedure that resolves ambiguities in fitting nonlinear data by power series. As is well known, the coefficients in the regression equations depend upon the truncation of the power series. We outline the procedure in which the coefficients of the regression using a power expansion are independent of the degree of the polynomials used. This is achieved by considering mutual regression of descriptors and using residuals as novel variables. The derived regression equations show unusual numerical stability, i.e., the coefficients of the regression equations are constant and independent of the truncation of the power series. The process is illustrated in an example to show all details and facilitate duplicating the process for interested readers. The method described here complements recently outlined procedures for construction of orthogonal descriptors for use in multivariate regression analysis. © 1993 John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 14 (1993), S. 392-400 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl-mercaptans (Cys-46, Cys-176), an imidazole (His-67), and a water. An imidazole (His-51) hydrogen bonded to a hydroxy-acetate (Ser-48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His-51) via hydrogen-bonded hydroxy-acetate (Ser-48), creating a proton relay system; and (2) the rate-limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc-bound OH- and by direct deprotonation of zinc-bound ethanol by imidazole via hydroxyacetate (Ser-48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner-sphere-pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results. © 1993 John Wiley & Sons, Inc.
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  • 88
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    Journal of Computational Chemistry 14 (1993), S. 54-66 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Energy optimization calculations have been carried out to determine the variability of optimum p, d, and f polarization function exponents in molecules containing first- and second-row elements and in normal valency and hypercoordinate species. Optimum exponents were determined for single sets of higher-order functions at both Hartree-Fock and correlated (Moller-Plesset) levels of theory using the Dunning-Hay double zeta and the McLean-Chandler triple zeta basis sets. More detailed calculations were used to test the response to nonoptimum d and f function exponents of the total energy, the optimum geometry, and harmonic stretching frequencies. The variability in optimum exponents and the size of the energy penalties incurred by adopting nonoptimum values reduces the utility of standard exponents for p, d, and f polarization functions. © 1993 John Wiley & Sons, Inc.
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  • 89
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    Journal of Computational Chemistry 14 (1993), S. 89-104 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-1 suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-1 imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 Å for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-1. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and O predict that donor strength follows the order F 〉 O 〉 N and acceptor strength follows the order N 〉 O 〉 F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H---N bond to be the strongest and the N-H---F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems. © 1993 John Wiley & Sons, Inc.
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  • 90
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    Journal of Computational Chemistry 14 (1993), S. 105-113 
    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 multigrid method is presented for the numerical solution of the linearized Poisson-Boltzmann equation arising in molecular biophysics. The equation is discretized with the finite volume method, and the numerical solution of the discrete equations is accomplished with multiple grid techniques originally developed for twodimensional interface problems occurring in reactor physics. A detailed analysis of the resulting method is presented for several computer architectures, including comparisons to diagonally scaled CG, ICCG, vectorized ICCG and MICCG, and to SOR provided with an optimal relaxation parameter. Our results indicate that the multigrid method is superior to the preconditioned CG methods and SOR and that the advantage of multigrid grows with the problem size. © 1993 John Wiley & Sons, Inc.
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  • 91
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    Journal of Computational Chemistry 14 (1993), S. 121-125 
    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 concept of molecular kurtosis as a dynamic molecular shape descriptor is introduced and used to compare the relative flexibilities of benzene and cyclohexane. For small torsional deformations (〈15°) the potential energy surfaces are similar, indicating both molecules are flexible. Using molecular kurtosis, the stiffness of benzene and cyclohexane are compared from gas-phase stochastic dynamics simulations and validated by distributions found in the Cambridge Structural Database. © 1993 John Wiley & Sons, Inc.
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  • 92
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    Journal of Computational Chemistry 14 (1993), S. 522-529 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Geometry optimizations at the HF/3-21G(*) and HF/6-31G* levels of ab initio theory have been carried out for various isomers of model disubstituted phosphoranes PH3XY(X, Y=OH, CH3, NH2, and SH). Reasonable agreement was obtained between the optimized geometries and available crystal structure data for analogous compounds. The isomers were further characterized by frequency calculations. The MP2/6-31G*//6-31G* + ZPE energy data reveal that the interactions between the ligands are relatively small (0-4 kcal mol-1) for the most stable conformations of the isomers. Hence, for these conformations the apicophilicities (based upon monosubstituted phosphoranes) are approximately additive. The less stable PH3XY conformations are in general transition states or higher-order saddle points, and their interligand interactions are larger in magnitude (up to 10 kcal mol-1); the results with these conformations suggest that apicophilicities may not be as additive for some highly substituted phosphoranes. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 541-548 
    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 our earlier molecular dynamics simulations, we found that there was a discrepancy between the predicted and experimental product ratios when norcamphor is hydroxylated by cytochrome P450cam. The experimental results suggest that there is a nearly equimolar ratio between the 5- and 6-hydroxynorcamphor (45% 5-, 47% 6-, and 8% 3-hydroxynorcamphor) [W.M. Atkins and S.J. Sligar, J. Am. Chem. Soc., 109, 3754 (1987)]. Our previous simulations predicted predominately from 68-88% 5-hydroxynorcamphor [M.B. Bass et al., Prot. Struct. Funct. Genet., 13, 26 (1992); M.B. Bass et al., Proc. Natl. Acad. Sci. U.S.A., submitted]. One possible explanation for this discrepancy is that the simulations were performed using D-norcamphor while the experiments were conducted with racemic norcamphor. The suggestion that norcamphor is the D-isomer was based upon the similarity with the native substrate D-camphor. Indeed, the reported crystallographic structure for norcamphor-bound P450cam models norcamphor as the D-isomer. Unfortunately, the two stereomers have never been separated. The simulations presented here model the L-isomer of norcamphor. Three simulations each of the L- and D-isomers of norcamphor bound to cytochrome P450cam were compared to account for the effects due to substrate orientation and the assignment of random velocities. The results presented here show that the L-isomer of norcamphor is predicted to give rise to predominately 6-hydroxynorcamphor, while the D-isomer gives rise to mainly 5-hydroxynorcamphor. From this data, we infer that racemic norcamphor will give rise to nonracemic 5- and 6-hydroxynorcamphors after oxidation by cytochrome P450cam. © 1993 John Wiley & Sons, Inc.
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  • 94
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    Journal of Computational Chemistry 14 (1993), S. 579-586 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program that calculates Born-Oppenheimer potential energy curves of diatomic molecules directly from spectroscopic data is presented. Rather than performing the usual preliminary fitting of the experimental data to a single polynomial in the variable (v + 1/2), where v is the vibrational quantum number, the program contains an accurate built-in interpolation routine by which each experimental input point belongs to its own polynomial. The program is tested on the ground state of the H2 molecule and results are compared with the most accurate ab initio calculations available. © 1993 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 95
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    Journal of Computational Chemistry 14 (1993), S. 587-602 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new methodology to compute molecular interaction potentials (MIPs) is developed and tested. The calculation of the MIP is based upon the generalization of the rigorous quantum mechanical molecular electrostatic potential (MEP) and further addition of a classical repulsion-dispersion term. As a result, the MIP is able to represent not only with high accuracy electrostatic interactions but also represent in a suitable way steric effects. The analysis of the results obtained for different molecules demonstrates the superiority of the MIP with regard to the standard MEP to describe nonbonded interactions, in particular hydrogen bonds. The comparison of results calculated at the ab initio I 6-31G* and semiempirical AM1 levels points out the suitability of semiempirical calculations to qualitatively reproduce the most relevant reactive features of the molecules. Finally, possible applications of the MIP in different fields are discussed. © 1993 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 96
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    Journal of Computational Chemistry 14 (1993), S. 647-654 
    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 importance of characterizing the stationary points of the intermolecular potential by means of Hessian eigenvalues is illustrated for the calculation of the benzene-benzene interaction using an atom-to-atom pair potential proposed by Fraga (FAAP). Two models, the standard one-center-per atom and another using three-centers-per atom due to Hunter and Sanders, are used to evaluate the electrostatic contributions and the results are compared. It is found in both cases that although using low-gradient thresholds allows optimization procedures to avoid many stationary points that are not true minima computing time considerations makes the usual procedure of using high-gradient thresholds [say, 10-2 kj/(mol Å)] as the most efficient. Moreover, this later procedure can be recommended because the actual minima can be characterized by means of Hessian eigenvalues even if these high-gradient thresholds are used, and further decreasing of the convergence criterion does not imply significant modifications in the geometric parameters of the minima. The possible advantages of using the three-centers-per-atom model for the calculation of molecular associations between delocalized systems are also discussed on the basis of the agreement of the benzene-benzene results with experimental and theoretical data taken from the literature. © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 97
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    Journal of Computational Chemistry 14 (1993), S. 680-684 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple procedure devised to obtain optimized point charges to represent the Madelung potential is reported and applied to six different crystal structures occurring in ionic systems. Their use in ab initio cluster model calculations is discussed through some selected examples and results compared with those arising from the use of the well-known Evjen method. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 98
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    Journal of Computational Chemistry 14 (1993), S. 691-698 
    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 stochastic (Monte Carlo) procedure, termed torsional flexing, has been devised for searching the conformational space of cyclic molecules. Torsional flexing causes a local, torsion angle-biased, distortion of a ring bond in a cyclic molecule. Because torsional flexing does not cause large atomic movements, even when it is applied to several bonds simultaneously, subsequent energy minimization generally proceeds rapidly. Nevertheless, the torsional flexing method is prone to generate structures that cross energy barriers so that the structure resulting after energy minimization is frequently a different conformer of the cyclic molecule. Conformational searches on cycloheptadecane, oxobrefeldin A, cyclopenta-L-alanine, and rifamycin SV based upon torsional flexing indicated that torsional flexing is among the best methods yet devised for searching the conformational space of flexible cyclic molecules. © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 99
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    Journal of Computational Chemistry 14 (1993), S. 775-789 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is suggested to improve the MNDO model by the explicit inclusion of valence-shell orthogonalization corrections, penetration integrals, and effective core potentials (ECPs) in the one-center part of the core Hamiltonian matrix. Guided by analytic formulas and numerical ab initio results, the orthogonalization corrections are expressed in terms of the resonance integrals that are represented by a new empirical parametric function. All two-center Coulomb interactions and ECP integrals are evaluated analytically in a Gaussian basis followed by a uniform Klopman-Ohno scaling. One particular implementation of the proposed NDDO SCF approach is described and parameterized for the elements H, C, N, O, and F. In a statistical evaluation of ground-state properties, this implementation shows slight but consistent improvements over MNDO, AM1, and PM3. Significant improvements are found for excited states, transition states, and strong hydrogen bonds. Possible further enhancements of the current implementation are discussed. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 100
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    Journal of Computational Chemistry 14 (1993), S. 818-830 
    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 use of a cluster of workstations as an alternative supercomputer resource is demonstrated using the ab initio direct SCF and RPA code DISCO. DISCO was implemented using several different mechanisms to achieve the requisite parallelization. The various parallel software mechanisms are characterized based upon several different criteria, including portability, ease of use, and relative efficiency. The application of direct SCF and RPA techniques to study the static polarizability of paranitroaniline is described. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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