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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 83 (1985), S. 5727-5734 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The perturbational method developed in the present paper is applied to the interaction between a polymer and a small molecule using a few simple model systems. The validity of our method is studied by comparing the results obtained with the perturbation method and the tight binding SCF crystal orbital method. The total electronic energies and charge distributions obtained are in good agreement with each other for the two methods. This result leads to the conclusion that the present perturbational approach is promising for application to interactions between real polymers and impurities.
    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 113 (2000), S. 6566-6572 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present an improved version of our recent algorithm [B. Paizs, G. Fogarasi, and P. Pulay, J. Chem. Phys. 109, 6571 (1998)] for optimizing the geometries of large molecules. The approximate Cholesky factorization technique has been generalized to the case of redundant coordinates, and an alternative approach involving use of the B†B matrix in the iterative coordinate back transformation is described. The generalized full Cholesky factors of B†B are very sparse and the corresponding force and geometry transformations are fast and numerically stable, permitting us to apply this technique for internal coordinate geometry optimization of molecules containing thousands of atoms. As an example we present optimization data on alpha-helical alanine polypeptides, and various globular proteins. Results for the alanine polypeptides indicates that internal coordinate optimization is clearly superior to the first-order Cartesian optimization techniques generally used in force field calculations. The largest system investigated is alpha-helical Ac-(Ala)999-NH2 containing 9999 atoms, which was successfully optimized using less than a megaword of memory. Optimization of various globular proteins shows that our procedure can easily deal with highly redundant (including full primitive) coordinate sets. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 9766-9782 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: As a step toward the first principles quantum mechanical modeling of the structural and electronic properties of ice, hydrogen-bonded periodic infinite chains of water molecules have been investigated by the ab initio crystal orbital method at the Hartree–Fock (HF) level and by including electron correlation up to the complete fourth order of Møller–Plesset perturbation theory (MP4). The Bloch functions of the crystal have been expanded in a series of high quality atomic orbital basis sets complemented by extended sets of polarization functions, up to TZ(3d2f,3p2d). Basis set superposition errors have been (partly) eliminated by the counterpoise method and the infinite lattice sums have been computed using the multipole expansion technique. The systematically increasing size of the basis sets has allowed the extrapolation of structural and electronic indices of this ice model to the limit of an infinite atomic basis at both the HF and various correlated levels, respectively. For each theoretical model, detailed comparisons have been made with the corresponding physical properties of water monomers, dimers, and some larger linear oligomers.The results convincingly prove that hydrogen bonding in ice is a highly cooperative phenomenon, both from the structural and energetic points of view. The cohesive energy per hydrogen bond of the crystal is −5.30 kcal/mol at the HF level (with RHFO,O=2.88 A(ring)) as compared with the dimer value of −3.60 kcal/mol (at the optimized distance of 3.03 A(ring)). At the MP2 level of theory, the crystalline binding energy decreases to −6.60 kcal/mol and the lattice contracts to RMP2O,O=2.73 A(ring) (compared with −4.50 kcal/mol at 2.88 A(ring) for the dimer). The correlation corrections at third and fourth order slightly expand the crystal lattice (to RMP4O,O=2.75 A(ring)) and reduce the cohesion by 0.15 kcal/mol. A decomposition of the intermolecular interactions according to different terms of MP4 theory suggests that the cohesive energy of ice results from a delicate balance between different repulsive and attractive terms in third and fourth order, which exhibit different long-range behaviors. The detailed study of the role of high-energy virtual energy bands in computing electron correlation effects in ice provides further insight into the important role that basis set flexibility plays in such investigations. The resulting cohesive energy of −6.83 kcal/mol at the MP4 level is in reasonable agreement with the experimental energy per hydrogen bond in ice I, −6.7 kcal/mol. © 1994 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    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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  • 5
    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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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 10808-10823 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The elongation method to synthesize the electronic states of polymers is developed at the level of the density functional theory using the linear combination of Gaussian-type orbitals local spin density method. In this treatment, the interactions between the localized molecular orbitals of a cluster and the canonical molecular orbitals of an attacking monomer are successively included, where the Kohn–Sham equation is self-consistently solved instead of the Hartree–Fock equation in the conventional ab initio method. In the process of the cluster extension, an efficient treatment is implemented to calculate the matrix elements of Coulomb integral and exchange-correlation potential. The reliability and the efficiency of this method are examined via applications to hydrogen molecule cluster, linear water cluster (H2O)n and formamide cluster (CHONHH2)n. It was shown that the present method saves significantly the computational time and disk storage in the large cluster calculations, and provides good agreements with the results by the conventional density functional treatment for the whole system. © 1994 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    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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  • 8
    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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  • 9
    ISSN: 1432-2234
    Keywords: (HF)n-chains ; (H2O)n-chains ; Hydrogen bond energies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Energy band structures of one-dimensional (HF)n- and (H2O)n-chains have been calculated (1) by extrapolation of CNDO/2-MO levels to infinite chain length and (2) by the CNDO/2 crystal orbital (CO) method. In the CO-calculations interactions up to fifth neighbours have been taken into account. Both types of calculations were performed using experimental geometries and CNDO/2 minimum geometries of the corresponding dimers (HF)2 and (H2O)2. With the same geometries CO calculations on two-dimensional sheets of hydrogen bonded chains were performed too. Due to end-effects the extrapolated MO bands are much broader than the bands obtained by the CO method. In the CO calculations further neighbour interactions play a non-negligible role and hence the nearest neighbour approximation is not sufficient for an accurate description of crystals containing hydrogen bonds. MO calculations on one-dimensional chains of both systems show that the hydrogen bond energies increase with the number of monomers indicating the presence of cooperative effects. The hydrogen bond energies calculated with the CO method are usually somewhat larger than those extrapolated from the MO results. In three-dimensional networks of (H2O)n, however, the additional stabilization of clusters with respect to dimers is drastically diminished.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 51 (1979), S. 323-329 
    ISSN: 1432-2234
    Keywords: Biopolymer constituents, protonation of ∼
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Side-chain proton affinities for a series of peptide-forming amino acids have been calculated using ab initio Hartree-Fock-Roothaan SCF method; the order of proton affinities is Arg 〉 His 〉 Ser ≈ Tyr ≫ Lys. Protonation of some side-chains in a protein may introduce new energy levels in the band gaps thus fundamentally altering the conduction properties of the proteins.
    Type of Medium: Electronic Resource
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