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  • Computational Chemistry and Molecular Modeling  (16)
  • 1990-1994  (16)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 46 (1993), S. 137-144 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Silicon analogs of aromatic monocyclic ions, (SiH)3+ (4), (SiH)42+ (5), and (SiH)5- (6) have been studied ab initio at MP2(full)/6-31G*. The D3h structure of Si3H3+ is the global minimum, whereas other two ions are nonplanar. The D2d structure of (SiH)42+ is less folded than the carbon analog and possesses a higher stabilization energy. Stabilization energies for the monocharged ions are diminished with respect to the corresponding carbons © 1993 John Wiley & Sons, Inc.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 46 (1993), S. 119-125 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The lowest-energy N4 is computed ab initio to be the planar C2h(3Bu) open-chain structure 13. The open-chain N4 singlet-state structures dissociate on geometry optimization. The tetraazatetrahedrane Td structure 1 and the tetrazete D2h structure 2 are minima at MP2/6-31G*. However, both are higher in energy than 13 (24.1 and 21.2 Kcal/mol [UQCISD) (T)(full)/6-311+G*//MP2/6-31G* + ZPE(MP2/6-31G)*, respectively]. The energy of 13 is 157.5 kcal/mol higher than that of two N2(1∑g+ molecules [UQCISD(T)(Full)/6-311+G*//MP2/6-31G*] © 1993 John Wiley & Sons, Inc.
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  • 3
    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 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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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1065-1076 
    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 Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below -10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below -10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.
    Additional Material: 16 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 997-1003 
    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 closely related Cs (1) and C2v (3) structures of CH5+ have been reinvestigated at many ab initio levels using MP2/6-31G** and MP2/6-311 + + G(2df, 2pd) geometries. The largest basis sets employed were 6-311G(3df, 2p), 6-311 + + G(3df, 3pd), and the Dunning “correlation consistent” polarized triple-split valence basis set (cc-pVTZ). Electron correlation was probed at the MP4 level, but the QCISD method was also used with the largest basis sets. While electron correlation favors 3 over 1 by about 2 kcal/mol, the correlated relative energies with all basis sets employed range from 0.36-1.03 kcal/mol in favor of 1. The best estimate of this difference, 0.86 kcal/mol, is essentially identical with the (scaled) zero-point energy difference, 0.84 kcal/mol, favoring 3 over 1. These results indicate that 1 and 3 have almost exactly the same energy at 0 K. Our best value for the dissociation energy of CH5+ is 42.0 kcal/mol [QCISD(T)/6-311 + + G(3df, 3pd)//MP2(fu)/6-311 + + G(2df, 2pd), corrected to 298 K], which agrees very well with the experimental value. © 1992 by 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. 1-1 
    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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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 596-626 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effects of substituents (X) on the structures and stabilities of CH2X- anions for groups comprised of fourth- and fifth-period main group elements (X = K, CaH, GaH2, GeH3, AsH2, SeH, Br, Rb, SrH, InH2, SnH3, SbH2, TeH, and I) have been investigated by ab initio pseudopotential calculations. Full geometry optimizations have been carried out on the CH2X- anions and the corresponding neutral parent molecules, CH3X, at HF/DZP + and MP2/DZP + levels. Results for substituents from the second (X = Li—F) and third (X = Na—Cl) periods provide comparisons of substituent effects of the main group elements of the first four rows of the periodic table on methyl anions. Frequency calculations characterize the nature of stationary points and show pyramidal CH2X- anion structures to be the most stable unless π acceptor interactions (e.g., with BH2, AlH2, GaH2, and InH2 favor planar geometries. The CH2X- stabilization energies [at QCISD(T)/DZP + /MP2/DZP + + ZPE level for X = K—I and QCISD(T)/6-31 + G*/MP2/6-31 + G* + ZPE level] for X = Li—Cl) also show strong π-stabilizing effects for the same substituents. With the exception of CH3 and NH2, all substituents stabilize methyl anions, although the σ stabilization by OH and F is small. The SiH3—PH2—SH—Cl, GeH3—AsH2—SeH—Br, and SnH3—SbH2—TeH—I sets of substituents give stabilization energies between 19 and 30 kcal/mol. The stability of methyl anions substituted by the halogens and the chalcogens (X = OH, SH, SeH, and TeH) increases down a group in accord with the increasing substituent polarizability, while for π acceptors (BH2, AlH2, GaH2, and InH2) the stability decreases down a group in line with their π-accepting ability. © 1994 by John Wiley & Sons, Inc.
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