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  • 1
    ISSN: 0192-8651
    Keywords: gas-phase proton affinity and basicity ; density functional computations ; protonation of DNA acid bases ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 989-1000, 1998
    Additional Material: 10 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 772-791 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    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.
    Additional Material: 5 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1019-1040 
    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 force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard-Jones parameters were made. Furthermore, a 10-12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water-saccharide intermolecular distances. STO-3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D-glucose and D-mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α-D-glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β-maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Fire and Materials 17 (1993), S. 79-90 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Four vinyl wire and cable materials were tested using five smoke toxic potency test methods: the NBS cup furnace test (in its flaming and non-flaming modes), the NIST radiant test, the NIBS IT50 test (also using the radiant apparatus) and the UPITT test. One of the materials is a standard poly(vinyl chloride) (PVC) flexible wire and cable material, used commercially for wire insulation. The three other materials tested represent a new family of vinyl thermoplastic elastomer alloys, which are advanced materials with good fire performance, particularly in terms of heat release and smoke obscuration. It was found that the smokes from all four materials are similar in terms of their toxic potencies, and that they are all within the ‘common’ range of toxic potency found. In particular, the toxic potencies of the smoke from the new vinyl thermoplastic elastomer alloys are not significantly different from those of other traditional vinyl wire and cable compounds. The results of the tests were also interpreted in terms of the toxicities and concentrations of the individual gases emitted. The fractional effective dose of the toxicants analysed was sufficient to account for the toxicity of the smoke for the NBS cup furnace and the NISt radiant test. It was not able to account for the toxicity found in the UPITT test. The adequacy of the test protocols themselves was also investigated. It was found that the UPITT and the NIBS IT50 method are inadequate for measurement of smoke toxicity. It was also found that the NIST radiant test protocol is the one most likely to lead to the smallest amount of future testing.
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  • 6
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 897-903 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    Philadelphia : Wiley-Blackwell
    Journal of Cellular and Comparative Physiology 8 (1936), S. 1-19 
    ISSN: 0095-9898
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 381-391 
    ISSN: 1075-2617
    Keywords: conformational analysis ; crystal structure ; folded structures ; pseudopeptides ; reduced peptides ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reduced dipeptides with the general formula RCO-Xaa- rXbb-N+HR′R′′ (rXbb, reduced analogue of residue Xbb: NH-Cα HR1 -Cr H2) are shown to adopt a folded conformation in solution and in the solid state. The protonated reduced amide bond is an active proton donor capable of interacting with a peptide carbonyl to give a strong hydrogen bond topologically equivalent to the i+2 or i+3⇒ i interaction. The resulting conformation is similar to the γ- or β-turn structure found in peptides and proteins.
    Additional Material: 7 Ill.
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  • 9
    ISSN: 0935-6304
    Keywords: supercritical fluid chromatography ; experimental design optimization ; Diesel fuel ; group-type analysis ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---An optimization procedure is presented for group-type analysis of diesel fuel by supercritical fluid chromatography using packed silica column and a mixed mobile phase. A set of five responses, four values of resolution of a performance mixture and analysis time, was modeled using a Doehlert matrix for experimental design. Optimized experimental conditions for the five responses were obtained from a response surfaces optimization, taking into account various constraints on SF6 content in mobile phase and analysis time. The predicted and experimental resolutions were in good agreement for the different optimized conditions and one of them was selected to for application to a given diesel fuel for comparison with the results obtained by SFC using pure CO2 and by HPLC. The conditions found in this study provide an alternative method for the determination of mono-, di-, and polyaromatic compounds in middle distillates.
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  • 10
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1399-1417 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by -29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer-Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); φ: 141° (86°). These represent half-chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche- conformation at C4′-C5′; the [p]T segment is anti, 3T4, trans. The C5′-O5′ torsion of the [p]T unit is -124.5°, and the C3′-O3′ torsion of the T[p] unit is -152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are -138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.
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