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  • Articles: DFG German National Licenses  (10)
  • 1995-1999  (10)
  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 1172-1181 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 7030-7039 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Structural and energetic properties of hydrogen bonded infinite chains and of two-dimensional infinite periodic networks of formamide molecules were investigated by the ab initio crystal orbital method using several, partly highly polarized, atomic basis sets of increasing size at the Hartree–Fock (HF) level and by including electron correlation effects in different orders of Møller–Plesset (MP) perturbation theory, up to the complete MP4 level. For comparison, calculations at the same theoretical levels were also performed for the monomer and for dimers in three different configurations (linear, zig–zag, and cyclic). Besides full structural optimizations, the intermolecular interaction energies were corrected for basis set superposition errors taking into account monomer relaxation effects as well. The results show that hydrogen bonding in the formamide crystal is a highly cooperative phenomenon, both from the structural and energetic points of view. The lengths of the hydrogen bonds, RHB, will be reduced by 0.12–0.18 A(ring) in the crystalline environment, as compared with dimers, both for HF and MP theories and the binding energies will be increased typically by 50%–60%. Electron correlation effects substantially influence the structural features (reducing, e.g., RHB by about 0.08–0.10 A(ring)) and contribute 15%–20% to the cohesion energy. The theoretical model explains why the RHB values for open-chain dimers become shorter in the crystal than those obtained for the cyclic ones (as opposed to free dimers), correctly predicts changes of bond lengths in going from the monomer to the crystal, and provides N–H...O bond lengths and lattice constants very close to experiments. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular medicine 75 (1997), S. 620-623 
    ISSN: 1432-1440
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 101 (1999), S. 180-185 
    ISSN: 1432-2234
    Keywords: Key words: Density functional theory ; Proton ; translocation ; Photocycle ; Opsin shift
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base in bR, the results show that Asp85 and Asp212, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced by the presence of the neighboring amino acids.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1572-8951
    Keywords: Water dimer ; PES ; DFT ; B3PW91 ; ab initio
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Conventional ab initio and density functional methods with extended basis sets were employed in the study of a path on the water-dimer potential energy surface. The results show that density functional methods do depend strongly on the type of exchange-correlation potential employed, as well as on the quality of the basis sets – similarly to conventional ab initio methods – and on the density of the grid. Gradient-corrected methods behave, as expected, better than uncorrected ones, the Becke–Lee–Yang–Parr (BLYP) potential being the one that gives the best results. However, too large chemical- and hydrogen-bond lengths and absolute energies, as well as too small relative total and correlation energies demonstrate that even BLYP calculations with a relative large basis set are not good as MP2 calculations of the same size. Adiabatically connected functionals (ACM), represented in this work by B3PW91, provide an improvement on the whole surface.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 253-267 
    ISSN: 0020-7608
    Keywords: DFT ; carbonyloxyl radicals ; CASPT2 ; chemical reactions ; isomerizations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the lowest electronic states of HCOO· in C2v and Cs symmetries were optimized employing density functional theory (DFT) methods with extended basis sets including up to f- (on C and O) and d- (on H) polarization functions. Generalized gradient functionals (BLYP) and adiabatically connected functionals (B3LYP and B3PW91) were employed for studying HCOO·, as well as the isomer HOCO· (trans), the dissociation limit H·+CO2, and the transition state for the decomposition. At the best DFT levels employed, the ground state of HCOO· is 2A1 (in C2v) with equal C—O bond lengths, while the low-lying 2B2 state is only about 4 kJ/mol above (without inclusion of zero-point energies). The broken-symmetry 2A′ state (with unequal C—O bond lengths, i.e., Cs symmetry) is predicted to be about 13 kJ/mol above the 2A1 state and to be a transition state for the isomerization HCOO· (2A1)→HOCO· (2A′), with the trans-HOCO· isomer about 55 kJ/mol more stable. These facts agree closely with the most recent CASPT2/ANO calculations on this system. Therefore, it is concluded that some DFT models can be used safely for the study of larger radicals of the same type (despite several drawbacks discussed at length in this study). B3PW91, using several basis sets, is subsequently applied to the study of the possible reaction mechanisms of acetyloxyl radical, which exhibits a much more complicated path than formyloxyl, due to the presence of the methyl group. The optimum structures of isomers with coplanar or perpendicular CH and CO bonds were obtained for CH3COO· and two saddle points identified on the path of decomposition into CH3· and CO2. On the other side, saddle points for isomerization into CH3OCO· and CH2COOH· were also located, and the decomposition of the former to CH3O·+CO investigated. Finally, the structure of the benzoyloxyl radical (C6H5COO·) and its possible decomposition products were investigated along the same lines.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 253-267, 1998
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1434-1444 
    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 genetic algorithm is used to minimize the energy of peptide analogues in the dihedral angle space. It is interfaced to MOPAC, which computes the energy employing the AM1 Hamiltonian. The genetic algorithm identified the global energy minimum of glycine dipeptide analogue, alanine dipeptide analogue, diglycine, and dialanine. It identified three low-energy conformations of tetraalanine, including the reported global minimum, all of which contained three hydrogen bonds. A structure with a lower energy than the reported global minimum has been generated in which one hydrogen bond is replaced by another one. © 1995 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 575-584 
    ISSN: 0192-8651
    Keywords: Boys-Bernardi scheme ; chemical Hamiltonian approach ; hydrogen bond ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A comparative study of intermolecular potential energy curves is performed on the complexes H2O(SINGLE BOND)HF, H2O(SINGLE BOND)H2O, H2O(SINGLE BOND)H2S, and H2S(SINGLE BOND)H2S using nine different basis sets at the MP2 and DFT (BLYP and B3LYP) levels of theory. The basis set superposition error is corrected by means of the counterpoise scheme and based on the “chemical Hamiltonian approach.” The counterpoise and CHA-corrected DFT curves are generally close to each other. Using small basis sets, the B3LYP functional cannot be favored against the BLYP one because the BLYP results sometimes get closer to the MP2 values than those of B3LYP. From the results - including the available literature data - we suggest that one has to use at least polarized-valence triple-zeta-quality basis sets (TZV, 6-311G) for the investigation of hydrogen-bonded complexes. Special attention must be paid to the physical nature of the binding. If the dispersion forces become significant DFT methods are not able to describe the interaction. Proper correction for the basis set superposition error is found to be mandatory in all cases.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 575-584, 1998
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 694-701 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We extended Mayer's chemical Hamiltonian approach methods to N interacting subsystems at the self-consistent field and density functional levels of theory and discussed an efficient algorithm for the implementation. As an example, the energetics of linear (HF)n chains (n varies from 2 to 8) were calculated. © 1997 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1508-1519 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium structure of the ammonia dimer has been investigated with density functional and MP2 calculations. We used Slater- and Becke-exchange functionals combined with correlation functionals as recommended by Vosko-Wilk-Nusair, by Perdew, and by Lee-Yang-Parr, respectively. The potential energy surfaces was investigated. The asymmetric cyclic “microwave” structure could be identified as a minimum. Optimization of the intermolecular parameters showed that this structure has nearly the same energy as the centrosymmetric cyclic structure. Full optimization transformed the asymmetric cyclic structure into the linear structure. The interaction energies in the dimer were corrected for the basis set superposition error using the Boys-Bernardi counterpoise method and the a priori chemical Hamiltonian approach, respectively. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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