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  • Computational Chemistry and Molecular Modeling  (12)
  • Wiley-Blackwell  (12)
  • Springer Nature
  • 1990-1994  (6)
  • 1985-1989  (6)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 27 (1985), S. 181-194 
    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: Ab initio SCF MO calculations at the STO-3G level have been carried out on CH2OHOPO3-H and CH2OHOPO32-, which have been considered as model systems for the Cl-phosphate moiety of sugars. The results predict higher anomeric energy for the phosphate moiety at Cl atom of pyranosides. Also a trans arrangement of the exocyclic O - P bond is preferred rather than a gauche arrangement, thus exhibiting a reverse exo-anomeric effect. A complete potential energy map has been constructed for CH3OPO3-H, a model system for C6-phosphate moiety. It is seen that the bond angle optimization brings down the relative energies of various conformations. The effect of the phosphate group on the preferred conformation of phosphate containing polysaccharides is also discussed.
    Additional Material: 5 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 29 (1986), S. 1177-1180 
    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 preferred conformations of the thyrotropin-releasing hormone (TRH) have been calculated by the global optimization method proposed earlier by us. [G. Subba Rao, R. S. Tyagi, and R. K. Mishra, J. Theor. Biol. 90, 377 (1981)]. The potential function used comprises the electrostatic, nonbonded, torsional and hydrogen-bonding terms. The results are in good agreement with the crystal structures of TRH. No intramolecular hydrogen bonding is found to occur.
    Additional Material: 1 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 34 (1988), S. 231-236 
    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 geometry of Mn5 in rare gas matrices has been proposed to be a planar pentagon with 25 unpaired electrons. Simple unrestricted Hartree-Fock (UHF) calculations have been carried out using a basis of STO-6G for 1s, 2s, and 2p orbitals with STO-4G for 3s, 3p, 3d, 4s, and 4p in the HONDO5 program. The structure is optimized at the UHF level using the analytic gradient formalism for a planar pentagon. Binding energies and spinmixing are given for the optimized structure.
    Additional Material: 3 Tab.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 34 (1988), S. 95-101 
    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: Residues 23-26 (Gly-, Phe-, Phe-, Tyr) of the B-chain of insulin constitute a critical area of the receptor-binding region of the molecule. Three chemically distinct mutant insulins have recently been identified in patients with NIDDM, each involving substitution of either B24 of B25 phenylalanine. Two of the mutations have been unambiguously characterized: a B25 phenylalanine-to-leucine substitution [B25(Phe → Leu)], and the other, a B24 phenylalanine-to-serine [B24 (Phe → Ser)]. We have calculated the preferred conformations of normal and mutant insulins using a global optimization method developed by us earlier. The mutant insulins exhibit significant alterations in conformation and in the average distances between amino acid side-chains as compared to normal insulin. Therefore, the decreased binding affinity of mutant insulin could be either due to an alteration in the nature of the substituted residue (hydrophilic in place of hydrophobic) or to the alteration in one or more critical side-chain distances in the case of a hydrophobic to hydrophobic substitution.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 32 (1987), S. 551-562 
    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: Pair-excitation multiconfigurational self-consistent field (PEMCSCF) treatment of 11 small molecules (LiH, BeH2, BH3, BF, CH4, C2H4, C2H2, CH2O, NH3, H2O, and HF) has been carried out in a minimum basis set of Slater Transform Preuss functions as fitted by six cartesian gaussians (STP-6G). The advantages of accuracy without using a split basis are shown by comparison to familiar 4-31G and 6-31G calculations using molecular geometries optimized with STO-6G basis sets. A benefit is shown for the use of minimum basis fitted to STP functions: they overemphasize long-tail radial dependence to achieve long range basis sensitivity without increasing the basis size at the AO-to-MO transformation step in the configuration interaction portion of the MCSCF algorithm. Fully optimized STP-6G parameters are given and appear to be transferable as shown for acrolein. A FORTRAN listing of the full least squares fitting algorithm is available* for in situ generation of STP-6G orbitals energetically superior to 4-31G, or a less accurate STP-6G 1S, 2S, and 2P basis may be scaled directly as if they were STO-6G functions, but with considerably lower energy that with an STO-6G basis.
    Additional Material: 9 Tab.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 34 (1988), S. 287-296 
    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 ground state energetics and equilibrium geometries of neutral and positively and negatively charged clusters of Li3, Li2H, Li2Na, Li2Mg, and Na2Li have been obtained from a self-consistent field-linear combination of atomic orbitals-molecular orbital calculations within the Hartree-Fock approximation. The correlation energies are included perturbatively using the Möller-Plesset scheme up to the fourth order. The geometries of all negatively charged clusters are found to be linear with bond lengths that are, in general, larger than their neutral or cationic counterparts. The adiabatic electron affinities and ionization potentials are calculated and compared with earlier theoretical results. The addition of an electron to the neutral cluster is found to stabilize the cluster further against dissociation. The spatial distribution of the electrons in these clusters is studied to determine the extent to which electrons added or taken out are localized in the clusters. Mulliken population analysis is also used to elaborate the charge state of the anionic and cationic clusters.
    Additional Material: 4 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 47 (1993), S. 437-448 
    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: In this paper, we present a symmetrical and adiabatic reaction path for hydrogen transfer from methane by methyl by an ab initio method using the 6-31G** basis set with the MP2 corrections for UHF/6-31G** optimized geometries. The theoretical barrier is fitted with the symmetric Eckart function. We, then, take thermal averages of the rate constant (k) considering the discrete nature of the C-H oscillators and the continuous character of the various low-frequency modes of the composite system. Finally, we present a linear relation between log k and temperature. It is shown that this relation gives a good description of the kinetic results of both thermal and photochemical H-transfer reactions in the region of low temperatures. © 1993 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 254-265 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab-initio self-consistent-field molecular-orbital (SCF MO) Hartree-Fock (HF) calculations using the STO-3G, 6-31G, and 6-31G* basis sets, were performed to model quasi-tetrahedral silicon species in silicon dioxide. Mostly nine-atom clusters, [Si(OH)4]qt, with charge number qt = 0 or + 1, were studied. The positions of the Si and O atoms were varied to achieve minimum total energies, while the protons were held fixed in the O-(neighboring)Si direction to simulate the rigid crystal surroundings. The α-quartz-type local symmetry C2 was found to be retained for the neutral cluster, but not for the ionic one. The unrestricted HF calculations indicate that the latter paramagnetic centre, (qt = +1), has its spin population almost entirely on one short-bonded oxygen ion bonded weakly to its neighboring Si, and is quite high in energy (9.55 eV with 6-31G) compared to the diamagnetic centre (qt = 0). The ionization energy is much higher than the self-trapping potential of the polaronic hole, a fact which may account for the failure so far to observe a [SiO4]+1 center in quartz by means of continuous-wave electron paramagnetic resonance spectroscopy. Calculations on the [SiO4]+1 center agree well with ultraviolet spectra, and with the [hole portion of a] proposed radiation-induced exciton in quartz. The hole in [Si(OH)4]+1 can be shifted from a short-bonded to a long-bonded oxygen to give the excited state [Si(OH)4]es+1. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [Si(OSiH3)4]qt. Comparisons with the known isoelectronic species [AlO4]0 were carried out.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 209-214 
    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 molecular modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 446-453 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF-MO Hartree-Fock calculations were performed using the STO-3G, 6-31G, and 6-31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine-atom clusters, [C(OH)4]qt, with charge number qt = 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the C—O bond lengths are appreciably longer than typical C—O bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0 model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed-proton model by 6.80 eV with the 6-31G* basis set. The free-H model compared favorably with the x-ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α-quartz. In the fixed-H models, the twofold local symmetry was found to be retained when qt is 0 but not when qt is + 1. For the latter ion, the unrestricted H-F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6-31G) compared to the diamagnetic neutral one. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [C(OSiH3)4]0.
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