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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-04-03
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crow, J F -- New York, N.Y. -- Science. 1999 Mar 12;283(5408):1651-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, University of Wisconsin, Madison, WI 53706, USA. jfcrow@facstaff.wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10189318" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Carrier Proteins/*genetics/physiology ; Cell Nucleus/metabolism ; Cloning, Molecular ; Drosophila/*genetics/physiology ; *Drosophila Proteins ; *GTPase-Activating Proteins ; *Genes, Insect ; Male ; *Meiosis ; Nuclear Proteins/*genetics/physiology ; Sperm Maturation ; Spermatozoa/*physiology
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-12-28
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wickelgren, I -- New York, N.Y. -- Science. 1999 Nov 12;286(5443):1265-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10610528" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Astrocytes/*enzymology ; Brain/*enzymology ; Cloning, Molecular ; Glutamic Acid/metabolism ; Neurons/metabolism ; Racemases and Epimerases/*genetics/metabolism ; Rats ; Receptors, N-Methyl-D-Aspartate/metabolism ; Serine/*biosynthesis/metabolism ; Stereoisomerism ; Synapses/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-03-26
    Beschreibung: The carboxyl-terminal domain of colicin E5 was shown to inhibit protein synthesis of Escherichia coli. Its target, as revealed through in vivo and in vitro experiments, was not ribosomes as in the case of E3, but the transfer RNAs (tRNAs) for Tyr, His, Asn, and Asp, which contain a modified base, queuine, at the wobble position of each anticodon. The E5 carboxyl-terminal domain hydrolyzed these tRNAs just on the 3' side of this nucleotide. Tight correlation was observed between the toxicity of E5 and the cleavage of intracellular tRNAs of this group, implying that these tRNAs are the primary targets of colicin E5.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogawa, T -- Tomita, K -- Ueda, T -- Watanabe, K -- Uozumi, T -- Masaki, H -- New York, N.Y. -- Science. 1999 Mar 26;283(5410):2097-100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10092236" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Anticodon/*metabolism ; Bacterial Proteins/biosynthesis/genetics/pharmacology ; Base Sequence ; Cloning, Molecular ; Colicins/genetics/*metabolism/pharmacology ; Escherichia coli/drug effects/metabolism ; *Escherichia coli Proteins ; Guanine/analogs & derivatives/analysis ; Molecular Sequence Data ; RNA, Bacterial/chemistry/*metabolism ; RNA, Ribosomal, 16S/metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; RNA, Transfer, Asn/chemistry/metabolism ; RNA, Transfer, Asp/chemistry/metabolism ; RNA, Transfer, His/chemistry/metabolism ; RNA, Transfer, Tyr/chemistry/metabolism ; Ribonucleases/genetics/*metabolism/pharmacology ; Ribosomes/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-31
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wong, V -- Goodenough, D A -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10428705" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Calcium Channels/metabolism ; Cell Membrane/metabolism/ultrastructure ; Claudins ; Cloning, Molecular ; Humans ; Ion Channels ; Ion Transport ; Kidney Diseases/genetics/*metabolism ; Kidney Tubules/*metabolism/ultrastructure ; Lipid Bilayers/metabolism ; Magnesium/blood/*metabolism ; Magnesium Deficiency/genetics/*metabolism ; Membrane Proteins/genetics/*physiology ; Mutation ; Tight Junctions/*metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 5
    Publikationsdatum: 1999-01-05
    Beschreibung: CmPP16 from Cucurbita maxima was cloned and the protein was shown to possess properties similar to those of viral movement proteins. CmPP16 messenger RNA (mRNA) is present in phloem tissue, whereas protein appears confined to sieve elements (SE). Microinjection and grafting studies revealed that CmPP16 moves from cell to cell, mediates the transport of sense and antisense RNA, and moves together with its mRNA into the SE of scion tissue. CmPP16 possesses the characteristics that are likely required to mediate RNA delivery into the long-distance translocation stream. Thus, RNA may move within the phloem as a component of a plant information superhighway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xoconostle-Cazares, B -- Xiang, Y -- Ruiz-Medrano, R -- Wang, H L -- Monzer, J -- Yoo, B C -- McFarland, K C -- Franceschi, V R -- Lucas, W J -- New York, N.Y. -- Science. 1999 Jan 1;283(5398):94-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Plant Biology, Division of Biological Sciences, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9872750" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Biological Transport ; Cloning, Molecular ; Cucumis sativus ; Cucurbitaceae/genetics/*metabolism ; Microinjections ; Molecular Sequence Data ; Plant Leaves/metabolism ; Plant Proteins/chemistry/genetics/*metabolism ; Plant Roots/metabolism ; Plant Stems/metabolism ; Plant Viral Movement Proteins ; RNA, Antisense/metabolism ; RNA, Messenger/*metabolism ; RNA, Plant/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Signal Transduction ; Viral Proteins/chemistry/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 6
    Publikationsdatum: 1999-07-03
    Beschreibung: Epithelia permit selective and regulated flux from apical to basolateral surfaces by transcellular passage through cells or paracellular flux between cells. Tight junctions constitute the barrier to paracellular conductance; however, little is known about the specific molecules that mediate paracellular permeabilities. Renal magnesium ion (Mg2+) resorption occurs predominantly through a paracellular conductance in the thick ascending limb of Henle (TAL). Here, positional cloning has identified a human gene, paracellin-1 (PCLN-1), mutations in which cause renal Mg2+ wasting. PCLN-1 is located in tight junctions of the TAL and is related to the claudin family of tight junction proteins. These findings provide insight into Mg2+ homeostasis, demonstrate the role of a tight junction protein in human disease, and identify an essential component of a selective paracellular conductance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simon, D B -- Lu, Y -- Choate, K A -- Velazquez, H -- Al-Sabban, E -- Praga, M -- Casari, G -- Bettinelli, A -- Colussi, G -- Rodriguez-Soriano, J -- McCredie, D -- Milford, D -- Sanjad, S -- Lifton, R P -- F.1/Telethon/Italy -- R01DK51696/DK/NIDDK NIH HHS/ -- TGM06S01/Telethon/Italy -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):103-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10390358" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Calcium/urine ; Chromosomes, Human, Pair 3/genetics ; Claudins ; Cloning, Molecular ; Female ; Genes, Recessive ; Homeostasis ; Humans ; Kidney Diseases/*genetics/metabolism ; Kidney Tubules/chemistry ; Loop of Henle/chemistry/*metabolism ; Magnesium/blood/*metabolism ; Magnesium Deficiency/*genetics/metabolism ; Male ; Membrane Proteins/analysis/chemistry/genetics/*physiology ; Molecular Sequence Data ; Mutation ; Pedigree ; Physical Chromosome Mapping ; Tight Junctions/*metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 7
    Publikationsdatum: 1999-04-16
    Beschreibung: Mutation of the VHL tumor suppressor is associated with the inherited von Hippel-Lindau (VHL) cancer syndrome and the majority of kidney cancers. VHL binds the ElonginC-ElonginB complex and regulates levels of hypoxia-inducible proteins. The structure of the ternary complex at 2.7 angstrom resolution shows two interfaces, one between VHL and ElonginC and another between ElonginC and ElonginB. Tumorigenic mutations frequently occur in a 35-residue domain of VHL responsible for ElonginC binding. A mutational patch on a separate domain of VHL indicates a second macromolecular binding site. The structure extends the similarities to the SCF (Skp1-Cul1-F-box protein) complex that targets proteins for degradation, supporting the hypothesis that VHL may function in an analogous pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stebbins, C E -- Kaelin, W G Jr -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):455-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Structural Biology, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205047" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Binding Sites ; Cell Cycle Proteins/chemistry/metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; *Ligases ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mutation, Missense ; Neoplasms/genetics ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/metabolism ; S-Phase Kinase-Associated Proteins ; Surface Properties ; Transcription Factors/*chemistry/metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Von Hippel-Lindau Tumor Suppressor Protein ; von Hippel-Lindau Disease/*genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 8
    Publikationsdatum: 1999-09-08
    Beschreibung: Photoperiodic responses in plants include flowering that is day-length-dependent. Mutations in the Arabidopsis thaliana GIGANTEA (GI) gene cause photoperiod-insensitive flowering and alteration of circadian rhythms. The GI gene encodes a protein containing six putative transmembrane domains. Circadian expression patterns of the GI gene and the clock-associated genes, LHY and CCA1, are altered in gi mutants, showing that GI is required for maintaining circadian amplitude and appropriate period length of these genes. The gi-1 mutation also affects light signaling to the clock, which suggests that GI participates in a feedback loop of the plant circadian system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, D H -- Somers, D E -- Kim, Y S -- Choy, Y H -- Lim, H K -- Soh, M S -- Kim, H J -- Kay, S A -- Nam, H G -- GM56006/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Sep 3;285(5433):1579-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10477524" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Arabidopsis/*genetics/*physiology ; *Arabidopsis Proteins ; *Circadian Rhythm ; Cloning, Molecular ; Crosses, Genetic ; DNA-Binding Proteins/genetics ; Darkness ; Feedback ; Gene Expression Regulation, Plant ; *Genes, Plant ; Light ; Molecular Sequence Data ; Mutation ; Photoperiod ; Plant Leaves/physiology ; Plant Proteins/chemistry/*genetics/physiology ; Plant Structures/physiology ; Sequence Deletion ; Transcription Factors/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 9
    Publikationsdatum: 1999-07-03
    Beschreibung: An estimated 170 million persons worldwide are infected with hepatitis C virus (HCV), a major cause of chronic liver disease. Despite increasing knowledge of genome structure and individual viral proteins, studies on virus replication and pathogenesis have been hampered by the lack of reliable and efficient cell culture systems. A full-length consensus genome was cloned from viral RNA isolated from an infected human liver and used to construct subgenomic selectable replicons. Upon transfection into a human hepatoma cell line, these RNAs were found to replicate to high levels, permitting metabolic radiolabeling of viral RNA and proteins. This work defines the structure of HCV replicons functional in cell culture and provides the basis for a long-sought cellular system that should allow detailed molecular studies of HCV and the development of antiviral drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lohmann, V -- Korner, F -- Koch, J -- Herian, U -- Theilmann, L -- Bartenschlager, R -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):110-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Virology, Johannes-Gutenberg University Mainz, Obere Zahlbacher Strasse 67, 55131 Mainz, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10390360" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Carcinoma, Hepatocellular ; Cloning, Molecular ; Drug Resistance ; *Genome, Viral ; Gentamicins/pharmacology ; Hepacivirus/genetics/*physiology ; Hepatitis C/virology ; Humans ; Liver Neoplasms ; RNA, Viral/*biosynthesis/genetics ; *Replicon ; Transfection ; Tumor Cells, Cultured/*virology ; Viral Nonstructural Proteins/analysis/genetics ; Virus Cultivation ; *Virus Replication
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-12-28
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1999 Nov 26;286(5445):1655.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10610555" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Biotechnology/*legislation & jurisprudence ; California ; Cloning, Molecular ; *Human Growth Hormone/genetics ; *Patents as Topic ; Universities/*legislation & jurisprudence
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 11
    Publikationsdatum: 1999-03-19
    Beschreibung: In higher plants, organogenesis occurs continuously from self-renewing apical meristems. Arabidopsis thaliana plants with loss-of-function mutations in the CLAVATA (CLV1, 2, and 3) genes have enlarged meristems and generate extra floral organs. Genetic analysis indicates that CLV1, which encodes a receptor kinase, acts with CLV3 to control the balance between meristem cell proliferation and differentiation. CLV3 encodes a small, predicted extracellular protein. CLV3 acts nonautonomously in meristems and is expressed at the meristem surface overlying the CLV1 domain. These proteins may act as a ligand-receptor pair in a signal transduction pathway, coordinating growth between adjacent meristematic regions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fletcher, J C -- Brand, U -- Running, M P -- Simon, R -- Meyerowitz, E M -- New York, N.Y. -- Science. 1999 Mar 19;283(5409):1911-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10082464" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Arabidopsis/*cytology/genetics/growth & development/metabolism ; *Arabidopsis Proteins ; Cell Differentiation ; Cell Division ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; In Situ Hybridization ; Ligands ; Meristem/*cytology/growth & development/metabolism ; Molecular Sequence Data ; Mutation ; Phenotype ; Plant Proteins/chemistry/genetics/*metabolism ; Plant Shoots/cytology ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Receptor Protein-Tyrosine Kinases/genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 12
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-10
    Beschreibung: Drug resistance of pathogens is an increasing problem whose underlying mechanisms are not fully understood. Cellular uptake of the major drugs against Trypanosoma brucei spp., the causative agents of sleeping sickness, is thought to occur through an unusual, so far unidentified adenosine transporter. Saccharomyces cerevisiae was used in a functional screen to clone a gene (TbAT1) from Trypanosoma brucei brucei that encodes a nucleoside transporter. When expressed in yeast, TbAT1 enabled adenosine uptake and conferred susceptibility to melaminophenyl arsenicals. Drug-resistant trypanosomes harbor a defective TbAT1 variant. The molecular identification of the entry route of trypanocides opens the way to approaches for diagnosis and treatment of drug-resistant sleeping sickness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maser, P -- Sutterlin, C -- Kralli, A -- Kaminsky, R -- New York, N.Y. -- Science. 1999 Jul 9;285(5425):242-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Swiss Tropical Institute, CH-4002 Basel, Switzerland. Biozentrum, University of Basel, CH-4056 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10398598" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Adenosine/*metabolism ; Amino Acid Sequence ; Animals ; Arsenicals/metabolism/pharmacology ; Biological Transport ; Carrier Proteins/chemistry/genetics/*metabolism ; Cloning, Molecular ; Drug Resistance/genetics ; Genes, Protozoan ; Membrane Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Nucleoside Transport Proteins ; Nucleosides/metabolism ; Purines/metabolism/pharmacology ; Saccharomyces cerevisiae/genetics ; Substrate Specificity ; Trypanocidal Agents/metabolism/*pharmacology ; Trypanosoma brucei brucei/*drug effects/genetics/*metabolism ; Trypanosomiasis, African/drug therapy/parasitology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 13
    Publikationsdatum: 1999-10-16
    Beschreibung: Analysis of rhesus macaque leukocytes disclosed the presence of an 18-residue macrocyclic, tridisulfide antibiotic peptide in granules of neutrophils and monocytes. The peptide, termed rhesus theta defensin-1 (RTD-1), is microbicidal for bacteria and fungi at low micromolar concentrations. Antibacterial activity of the cyclic peptide was threefold greater than that of an open-chain analog, and the cyclic conformation was required for antimicrobial activity in the presence of 150 millimolar sodium chloride. Biosynthesis of RTD-1 involves the head-to-tail ligation of two alpha-defensin-related nonapeptides, requiring the formation of two new peptide bonds. Thus, host defense cells possess mechanisms for synthesis and granular packaging of macrocyclic antibiotic peptides that are components of the phagocyte antimicrobial armamentarium.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Y Q -- Yuan, J -- Osapay, G -- Osapay, K -- Tran, D -- Miller, C J -- Ouellette, A J -- Selsted, M E -- AI22931/AI/NIAID NIH HHS/ -- DK33506/DK/NIDDK NIH HHS/ -- DK44632/DK/NIDDK NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1999 Oct 15;286(5439):498-502.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, College of Medicine, University of California, Irvine, CA 92697, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10521339" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Animals ; Anti-Bacterial Agents ; Anti-Infective Agents/chemistry/*metabolism/pharmacology ; Bacteria/drug effects ; Cloning, Molecular ; Defensins ; Disulfides/chemistry ; Fungi/drug effects ; Humans ; Leukopoiesis ; Macaca mulatta ; Molecular Sequence Data ; Monocytes/*metabolism ; Neutrophils/*metabolism ; Oligopeptides/chemistry/genetics/metabolism ; Osmolar Concentration ; Peptides, Cyclic/*biosynthesis/chemistry/genetics/pharmacology ; *Protein Biosynthesis ; Protein Conformation ; Protein Precursors/chemistry/genetics/metabolism ; Protein Processing, Post-Translational ; Proteins/chemistry/genetics/pharmacology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 14
    Publikationsdatum: 1999-06-18
    Beschreibung: Cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. A 60-kilodalton fucosyltransferase (FTase) that adds this residue was purified from pea epicotyls. Peptide sequence information from the pea FTase allowed the cloning of a homologous gene, AtFT1, from Arabidopsis. Antibodies raised against recombinant AtFTase immunoprecipitate FTase enzyme activity from solubilized Arabidopsis membrane proteins, and AtFT1 expressed in mammalian COS cells results in the presence of XG FTase activity in these cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perrin, R M -- DeRocher, A E -- Bar-Peled, M -- Zeng, W -- Norambuena, L -- Orellana, A -- Raikhel, N V -- Keegstra, K -- New York, N.Y. -- Science. 1999 Jun 18;284(5422):1976-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Michigan State University-Department of Energy (MSU-DOE) Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10373113" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Animals ; Arabidopsis/*enzymology/genetics ; COS Cells ; Carbohydrate Conformation ; Cell Wall/*metabolism ; Cloning, Molecular ; DNA, Complementary ; Expressed Sequence Tags ; Fucosyltransferases/chemistry/genetics/isolation & purification/*metabolism ; Genes, Plant ; *Glucans ; Molecular Sequence Data ; Peas/*enzymology ; Polysaccharides/*biosynthesis/chemistry ; *Xylans
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 15
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    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-10-16
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takahashi, J S -- New York, N.Y. -- Science. 1999 Sep 24;285(5436):2076-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Neurobiology and Physiology, Northwestern University, Evanston, IL 60208-3520, USA. j-takahashi@nwu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10523205" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Chromosome Mapping ; Circadian Rhythm ; Cloning, Molecular ; Dogs ; Homeostasis ; Hypothalamus/metabolism ; Ligands ; Mice ; Mice, Knockout ; Narcolepsy/*genetics/physiopathology ; Neurons/metabolism ; Neuropeptides/metabolism ; Orexin Receptors ; Receptors, G-Protein-Coupled ; Receptors, Neuropeptide/chemistry/*genetics/physiology ; *Sleep/physiology ; Sleep, REM
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 16
    Publikationsdatum: 1999-09-08
    Beschreibung: A mevalonate-independent pathway of isoprenoid biosynthesis present in Plasmodium falciparum was shown to represent an effective target for chemotherapy of malaria. This pathway includes 1-deoxy-D-xylulose 5-phosphate (DOXP) as a key metabolite. The presence of two genes encoding the enzymes DOXP synthase and DOXP reductoisomerase suggests that isoprenoid biosynthesis in P. falciparum depends on the DOXP pathway. This pathway is probably located in the apicoplast. The recombinant P. falciparum DOXP reductoisomerase was inhibited by fosmidomycin and its derivative, FR-900098. Both drugs suppressed the in vitro growth of multidrug-resistant P. falciparum strains. After therapy with these drugs, mice infected with the rodent malaria parasite P. vinckei were cured.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jomaa, H -- Wiesner, J -- Sanderbrand, S -- Altincicek, B -- Weidemeyer, C -- Hintz, M -- Turbachova, I -- Eberl, M -- Zeidler, J -- Lichtenthaler, H K -- Soldati, D -- Beck, E -- New York, N.Y. -- Science. 1999 Sep 3;285(5433):1573-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, Academic Hospital Centre, Justus-Liebig-University, Friedrichstrasse 24, D-35392 Giessen, Germany. hassan.jomaa@biochemie.med.uni-giessen.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10477522" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Aldose-Ketose Isomerases/*antagonists & inhibitors/chemistry/genetics/metabolism ; Amino Acid Sequence ; Animals ; Antimalarials/*pharmacology ; Cloning, Molecular ; Enzyme Inhibitors/pharmacology ; Fosfomycin/*analogs & derivatives/pharmacology ; Genes, Protozoan ; *Hemiterpenes ; Malaria/*drug therapy/parasitology ; Malaria, Falciparum/drug therapy/parasitology ; Mevalonic Acid/metabolism ; Mice ; Molecular Sequence Data ; Multienzyme Complexes/*antagonists & inhibitors/chemistry/genetics/metabolism ; Organelles/drug effects/metabolism ; Organophosphorus Compounds/metabolism ; Oxidoreductases/*antagonists & inhibitors/chemistry/genetics/metabolism ; Pentosephosphates/*metabolism ; Plasmodium falciparum/*drug effects/genetics/metabolism ; Recombinant Proteins/antagonists & inhibitors/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Terpenes/*pharmacology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 17
    Publikationsdatum: 1999-07-20
    Beschreibung: A phytochrome-like protein called Ppr was discovered in the purple photosynthetic bacterium Rhodospirillum centenum. Ppr has a photoactive yellow protein (PYP) amino-terminal domain, a central domain with similarity to phytochrome, and a carboxyl-terminal histidine kinase domain. Reconstitution experiments demonstrate that Ppr covalently attaches the blue light-absorbing chromophore p-hydroxycinnamic acid and that it has a photocycle that is spectrally similar to, but kinetically slower than, that of PYP. Ppr also regulates chalcone synthase gene expression in response to blue light with autophosphorylation inhibited in vitro by blue light. Phylogenetic analysis demonstrates that R. centenum Ppr may be ancestral to cyanobacterial and plant phytochromes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Z -- Swem, L R -- Rushing, B G -- Devanathan, S -- Tollin, G -- Bauer, C E -- GM 40941/GM/NIGMS NIH HHS/ -- R01 GM040941/GM/NIGMS NIH HHS/ -- R01 GM053940/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 16;285(5426):406-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Jordan Hall, Bloomington, IN 47405, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10411503" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Acyltransferases/genetics ; Amino Acid Sequence ; Apoproteins/chemistry/metabolism ; Bacterial Proteins/*chemistry/genetics/physiology ; Chemotaxis ; Cloning, Molecular ; Coumaric Acids/metabolism ; Gene Expression Regulation, Bacterial ; Light ; Molecular Sequence Data ; Mutation ; Phosphorylation ; *Photoreceptors, Microbial ; Phylogeny ; Phytochrome/*chemistry ; Protein Kinases/metabolism ; Rhodospirillum/*chemistry/genetics/physiology ; Sequence Alignment
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 18
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    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-10-16
    Beschreibung: Annotation of large-scale gene sequence data will benefit from comprehensive and consistent application of well-documented, standard analysis methods and from progressive and vigilant efforts to ensure quality and utility and to keep the annotation up to date. However, it is imperative to learn how to apply information derived from functional genomics and proteomics technologies to conceptualize and explain the behaviors of biological systems. Quantitative and dynamical models of systems behaviors will supersede the limited and static forms of single-gene annotation that are now the norm. Molecular biological epistemology will increasingly encompass both teleological and causal explanations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boguski, M S -- New York, N.Y. -- Science. 1999 Oct 15;286(5439):453-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10521334" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Base Sequence ; Cloning, Molecular ; *Computational Biology ; Databases, Factual ; *Genetic Techniques ; *Genome ; Genome, Human ; Human Genome Project ; Humans ; Molecular Biology ; *Proteome ; *Sequence Analysis, DNA
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 19
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-31
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finkel, E -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):33-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10428697" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Antineoplastic Agents/therapeutic use ; Clinical Trials as Topic ; Cloning, Molecular ; *Glucuronidase ; Glycoside Hydrolases/*antagonists & inhibitors/*genetics/isolation & ; purification/metabolism ; Humans ; Mice ; Neoplasm Metastasis/*prevention & control ; Rats ; Tumor Cells, Cultured
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 20
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    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-03
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1999 Jun 11;284(5421):1752-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10391787" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Biotechnology/*legislation & jurisprudence ; California ; Cloning, Molecular ; Genetic Vectors ; *Human Growth Hormone/genetics ; Humans ; *Patents as Topic ; Publishing ; Universities/*legislation & jurisprudence
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 21
    Publikationsdatum: 1999-06-05
    Beschreibung: We purified, cloned, and expressed aggrecanase, a protease that is thought to be responsible for the degradation of cartilage aggrecan in arthritic diseases. Aggrecanase-1 [a disintegrin and metalloproteinase with thrombospondin motifs-4 (ADAMTS-4)] is a member of the ADAMTS protein family that cleaves aggrecan at the glutamic acid-373-alanine-374 bond. The identification of this protease provides a specific target for the development of therapeutics to prevent cartilage degradation in arthritis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tortorella, M D -- Burn, T C -- Pratta, M A -- Abbaszade, I -- Hollis, J M -- Liu, R -- Rosenfeld, S A -- Copeland, R A -- Decicco, C P -- Wynn, R -- Rockwell, A -- Yang, F -- Duke, J L -- Solomon, K -- George, H -- Bruckner, R -- Nagase, H -- Itoh, Y -- Ellis, D M -- Ross, H -- Wiswall, B H -- Murphy, K -- Hillman, M C Jr -- Hollis, G F -- Newton, R C -- Magolda, R L -- Trzaskos, J M -- Arner, E C -- New York, N.Y. -- Science. 1999 Jun 4;284(5420):1664-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Inflammatory Diseases Research, DuPont Pharmaceuticals Company, Wilmington, DE 19880-0400, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10356395" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): ADAM Proteins ; Aggrecans ; Amino Acid Sequence ; Arthritis/drug therapy ; Cartilage/metabolism ; Catalytic Domain ; Cloning, Molecular ; Disintegrins/chemistry/metabolism ; *Extracellular Matrix Proteins ; Humans ; Hydroxamic Acids/pharmacology ; Interleukin-1/pharmacology ; Lectins, C-Type ; Metalloendopeptidases/*chemistry/*genetics/isolation & purification/metabolism ; Molecular Sequence Data ; Procollagen N-Endopeptidase ; Protease Inhibitors/pharmacology ; Protein Sorting Signals ; Proteoglycans/metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Analysis
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 22
    Publikationsdatum: 1999-04-02
    Beschreibung: Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsiantis, M -- Schneeberger, R -- Golz, J F -- Freeling, M -- Langdale, J A -- GM14578/GM/NIGMS NIH HHS/ -- GM42610/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 2;284(5411):154-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3BR, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10102817" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Cloning, Molecular ; DNA-Binding Proteins/chemistry/*genetics ; Down-Regulation ; *Gene Expression Regulation, Plant ; *Genes, Homeobox ; Genes, Plant ; Homeodomain Proteins/*genetics/metabolism ; In Situ Hybridization ; Molecular Sequence Data ; Mutation ; Phenotype ; Plant Development ; Plant Leaves/cytology/genetics/*growth & development/metabolism ; Plant Proteins/chemistry/*genetics ; Plants/*genetics/metabolism ; *Proto-Oncogene Proteins c-myb ; Repressor Proteins/chemistry/*genetics/physiology ; Sequence Alignment ; Zea mays/*genetics/growth & development/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 23
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    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-11-05
    Beschreibung: Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in three loci [NPH2, root phototropism 2 (RPT2), and NPH3] disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene, now cloned, encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motchoulski, A -- Liscum, E -- New York, N.Y. -- Science. 1999 Oct 29;286(5441):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10542152" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; *Arabidopsis Proteins ; Cell Membrane/metabolism ; Cloning, Molecular ; Escherichia coli ; Molecular Sequence Data ; Phosphoproteins/genetics/*metabolism ; Photoreceptor Cells, Invertebrate/*metabolism ; Phototropism ; Plant Proteins/genetics/*metabolism ; Protein Binding ; Two-Hybrid System Techniques
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 24
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-06-26
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seeburg, P H -- New York, N.Y. -- Science. 1999 May 28;284(5419):1465-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10383323" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Biotechnology/*legislation & jurisprudence ; California ; Cloning, Molecular ; Genetic Vectors ; *Human Growth Hormone ; Humans ; Patents as Topic/*legislation & jurisprudence ; Periodicals as Topic ; Plasmids ; Publishing ; Universities/*legislation & jurisprudence
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 25
    Publikationsdatum: 1999-06-26
    Beschreibung: Ethylene regulates plant growth, development, and responsiveness to a variety of stresses. Cloning of the Arabidopsis EIN2 gene identifies a central component of the ethylene signaling pathway. The amino-terminal integral membrane domain of EIN2 shows similarity to the disease-related Nramp family of metal-ion transporters. Expression of the EIN2 CEND is sufficient to constitutively activate ethylene responses and restores responsiveness to jasmonic acid and paraquat-induced oxygen radicals to mutant plants. EIN2 is thus recognized as a molecular link between previously distinct hormone response pathways. Plants may use a combinatorial mechanism for assessing various stresses by enlisting a common set of signaling molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alonso, J M -- Hirayama, T -- Roman, G -- Nourizadeh, S -- Ecker, J R -- New York, N.Y. -- Science. 1999 Jun 25;284(5423):2148-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10381874" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Arabidopsis/chemistry/genetics/growth & development/*physiology ; *Arabidopsis Proteins ; Carrier Proteins/chemistry ; *Cation Transport Proteins ; Cloning, Molecular ; Cyclopentanes/metabolism/pharmacology ; *Defensins ; Ethylenes/*metabolism/pharmacology ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Complementation Test ; Herbicides/pharmacology ; *Iron-Binding Proteins ; Membrane Proteins/chemistry/genetics/*physiology ; Microsomes/metabolism ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/physiology ; Oxylipins ; Paraquat/pharmacology ; Plant Growth Regulators/*metabolism/pharmacology ; Plant Proteins/chemistry/genetics/*physiology ; Plants, Genetically Modified ; Protein Biosynthesis ; Protein Structure, Secondary ; Receptors, Cell Surface/chemistry/genetics/*physiology ; *Signal Transduction ; *Transcription Factors
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 26
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-27
    Beschreibung: Candida glabrata is an important fungal pathogen of humans that is responsible for about 15 percent of mucosal and systemic candidiasis. Candida glabrata adhered avidly to human epithelial cells in culture. By means of a genetic approach and a strategy allowing parallel screening of mutants, it was possible to clone a lectin from a Candida species. Deletion of this adhesin reduced adherence of C. glabrata to human epithelial cells by 95 percent. The adhesin, encoded by the EPA1 gene, is likely a glucan-cross-linked cell-wall protein and binds to host-cell carbohydrate, specifically recognizing asialo-lactosyl-containing carbohydrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cormack, B P -- Ghori, N -- Falkow, S -- New York, N.Y. -- Science. 1999 Jul 23;285(5427):578-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild D039, 299 Campus Drive, Stanford, CA 94305-5124, USA. bcormack@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10417386" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Animals ; Calcium/metabolism ; Candida/*genetics/*pathogenicity/physiology ; Candidiasis, Vulvovaginal/microbiology ; Carbohydrates/pharmacology ; Cell Adhesion ; Cloning, Molecular ; Epithelial Cells/*microbiology ; Female ; *Fungal Proteins ; Genes, Fungal ; Humans ; Lectins/chemistry/*genetics/metabolism ; Ligands ; Mice ; Mice, Inbred DBA ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mutation ; Plasmids ; Polymerase Chain Reaction ; Transformation, Genetic ; Tumor Cells, Cultured ; Virulence/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 27
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-06-26
    Beschreibung: Segmentation of the hindbrain and branchial region is a conserved feature of head development, involving the nested expression of Hox genes. Although it is presumed that vertebrate Hox genes function as segment identifiers, responsible for mediating registration between elements of diverse embryonic origin, this assumption has remained untested. To assess this, retroviral misexpression was combined with orthotopic grafting in chick embryos to generate a mismatch in Hox coding between a specific rhombomere and its corresponding branchial arch. Rhombomere-restricted misexpression of a single gene, Hoxb1, resulted in the homeotic transformation of the rhombomere, revealed by reorganization of motor axon projections.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, E -- Wingate, R J -- Lumsden, A -- N01-HD-7-3263/HD/NICHD NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1999 Jun 25;284(5423):2168-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Neurobiology, King's College London, Guy's Hospital, London SE1 9RT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10381880" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Axons/physiology ; Branchial Region/*embryology/innervation/metabolism ; Cell Differentiation ; Cell Movement ; Chick Embryo ; Cloning, Molecular ; DNA-Binding Proteins/genetics ; GATA2 Transcription Factor ; *Gene Expression Regulation, Developmental ; *Genes, Homeobox ; Genetic Vectors ; Homeodomain Proteins/*genetics/physiology ; Membrane Glycoproteins/genetics ; Motor Neurons/cytology/physiology ; Rhombencephalon/*embryology/metabolism/transplantation ; Transcription Factors/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 28
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-04-16
    Beschreibung: The five members of the phytochrome photoreceptor family of Arabidopsis thaliana control morphogenesis differentially in response to light. Genetic analysis has identified a signaling pathway that is specifically activated by phytochrome A. A component in this pathway, SPA1 (for "suppressor of phyA-105"), functions in repression of photomorphogenesis and is required for normal photosensory specificity of phytochrome A. Molecular cloning of the SPA1 gene indicates that SPA1 is a WD (tryptophan-aspartic acid)-repeat protein that also shares sequence similarity with protein kinases. SPA1 can localize to the nucleus, suggesting a possible function in phytochrome A-specific regulation of gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoecker, U -- Tepperman, J M -- Quail, P H -- GM-47475/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):496-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205059" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Arabidopsis/genetics/growth & development/*metabolism ; *Arabidopsis Proteins ; Cell Cycle Proteins/*chemistry/*physiology ; Cell Nucleus/metabolism ; Cloning, Molecular ; Darkness ; Gene Expression Regulation, Plant ; *Light ; Molecular Sequence Data ; Morphogenesis ; Mutation ; Nuclear Localization Signals ; Phytochrome/*metabolism ; Phytochrome A ; Plant Proteins/*chemistry/genetics/physiology ; Protein Kinases/chemistry ; RNA, Messenger/genetics/metabolism ; Repetitive Sequences, Amino Acid ; Repressor Proteins/chemistry ; Sequence Alignment ; *Signal Transduction
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 29
    Publikationsdatum: 1999-10-26
    Beschreibung: Cerebral deposition of amyloid beta peptide (Abeta) is an early and critical feature of Alzheimer's disease. Abeta generation depends on proteolytic cleavage of the amyloid precursor protein (APP) by two unknown proteases: beta-secretase and gamma-secretase. These proteases are prime therapeutic targets. A transmembrane aspartic protease with all the known characteristics of beta-secretase was cloned and characterized. Overexpression of this protease, termed BACE (for beta-site APP-cleaving enzyme) increased the amount of beta-secretase cleavage products, and these were cleaved exactly and only at known beta-secretase positions. Antisense inhibition of endogenous BACE messenger RNA decreased the amount of beta-secretase cleavage products, and purified BACE protein cleaved APP-derived substrates with the same sequence specificity as beta-secretase. Finally, the expression pattern and subcellular localization of BACE were consistent with that expected for beta-secretase. Future development of BACE inhibitors may prove beneficial for the treatment of Alzheimer's disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vassar, R -- Bennett, B D -- Babu-Khan, S -- Kahn, S -- Mendiaz, E A -- Denis, P -- Teplow, D B -- Ross, S -- Amarante, P -- Loeloff, R -- Luo, Y -- Fisher, S -- Fuller, J -- Edenson, S -- Lile, J -- Jarosinski, M A -- Biere, A L -- Curran, E -- Burgess, T -- Louis, J C -- Collins, F -- Treanor, J -- Rogers, G -- Citron, M -- New York, N.Y. -- Science. 1999 Oct 22;286(5440):735-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Amgen, Inc., One Amgen Center Drive, M/S 29-2-B, Thousand Oaks, CA 91320-1799, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10531052" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Alzheimer Disease/drug therapy/*enzymology ; Amino Acid Motifs ; Amino Acid Sequence ; Amyloid Precursor Protein Secretases ; Amyloid beta-Peptides/*biosynthesis ; Amyloid beta-Protein Precursor/*metabolism ; Animals ; Aspartic Acid Endopeptidases/chemistry/genetics/*isolation & ; purification/*metabolism ; Binding Sites ; Brain/enzymology/metabolism ; Cell Line ; Cloning, Molecular ; Endopeptidases ; Endosomes/enzymology ; Gene Expression ; Gene Library ; Golgi Apparatus/enzymology ; Humans ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oligonucleotides, Antisense/pharmacology ; Peptides/metabolism ; Protease Inhibitors/pharmacology ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Transfection
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 30
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-02-26
    Beschreibung: Although broken chromosomes can induce apoptosis, natural chromosome ends (telomeres) do not trigger this response. It is shown that this suppression of apoptosis involves the telomeric-repeat binding factor 2 (TRF2). Inhibition of TRF2 resulted in apoptosis in a subset of mammalian cell types. The response was mediated by p53 and the ATM (ataxia telangiectasia mutated) kinase, consistent with activation of a DNA damage checkpoint. Apoptosis was not due to rupture of dicentric chromosomes formed by end-to-end fusion, indicating that telomeres lacking TRF2 directly signal apoptosis, possibly because they resemble damaged DNA. Thus, in some cells, telomere shortening may signal cell death rather than senescence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karlseder, J -- Broccoli, D -- Dai, Y -- Hardy, S -- de Lange, T -- GM49046/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Feb 26;283(5406):1321-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10021, USA. Cell Genesys, Foster City, CA 94405, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10037601" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Adenoviridae/genetics/physiology ; Animals ; *Apoptosis ; Ataxia Telangiectasia/pathology ; Ataxia Telangiectasia Mutated Proteins ; B-Lymphocytes/cytology ; Cell Cycle Proteins ; Cell Line ; Cells, Cultured ; Cloning, Molecular ; DNA Damage ; DNA-Binding Proteins/chemistry/genetics/*physiology ; Genetic Vectors ; Humans ; In Situ Nick-End Labeling ; Mice ; Mitosis ; Phosphorylation ; *Protein-Serine-Threonine Kinases ; Proteins/metabolism ; T-Lymphocytes/cytology ; Telomere/*physiology ; Telomeric Repeat Binding Protein 2 ; Tumor Cells, Cultured ; Tumor Suppressor Protein p53/*metabolism ; Tumor Suppressor Proteins
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 31
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-31
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cleaver, J E -- New York, N.Y. -- Science. 1999 Jul 9;285(5425):212-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Dermatology and Pharmaceutical Chemistry, UCSF Cancer Center, University of California, San Francisco, CA 94143-0808, USA. jcleaver@cc.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10428720" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Cloning, Molecular ; DNA Damage ; DNA Repair ; *DNA Replication ; DNA-Binding Proteins ; DNA-Directed DNA Polymerase/*genetics/metabolism ; Humans ; Mutation ; Pyrimidine Dimers/metabolism ; Ultraviolet Rays ; Xeroderma Pigmentosum/*genetics/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 32
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-06-26
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hagmann, M -- New York, N.Y. -- Science. 1999 Jun 4;284(5420):1600-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10383332" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): ADAM Proteins ; Animals ; Antineoplastic Agents ; Antirheumatic Agents ; Arthritis/*drug therapy ; Binding Sites ; Cloning, Molecular ; Enzyme Precursors/chemistry/metabolism ; Gelatinases/antagonists & inhibitors/*chemistry/metabolism ; Humans ; Matrix Metalloproteinase 2 ; Metalloendopeptidases/antagonists & inhibitors/*chemistry/genetics/metabolism ; Mice ; Models, Molecular ; Neoplasms/*drug therapy ; Procollagen N-Endopeptidase ; Protease Inhibitors/*pharmacology ; Protein Conformation ; Protein Structure, Secondary
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 33
    Publikationsdatum: 1999-06-26
    Beschreibung: Motilin is a 22-amino acid peptide hormone expressed throughout the gastrointestinal (GI) tract of humans and other species. It affects gastric motility by stimulating interdigestive antrum and duodenal contractions. A heterotrimeric guanosine triphosphate-binding protein (G protein)-coupled receptor for motilin was isolated from human stomach, and its amino acid sequence was found to be 52 percent identical to the human receptor for growth hormone secretagogues. The macrolide antibiotic erythromycin also interacted with the cloned motilin receptor, providing a molecular basis for its effects on the human GI tract. The motilin receptor is expressed in enteric neurons of the human duodenum and colon. Development of motilin receptor agonists and antagonists may be useful in the treatment of multiple disorders of GI motility.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feighner, S D -- Tan, C P -- McKee, K K -- Palyha, O C -- Hreniuk, D L -- Pong, S S -- Austin, C P -- Figueroa, D -- MacNeil, D -- Cascieri, M A -- Nargund, R -- Bakshi, R -- Abramovitz, M -- Stocco, R -- Kargman, S -- O'Neill, G -- Van Der Ploeg, L H -- Evans, J -- Patchett, A A -- Smith, R G -- Howard, A D -- New York, N.Y. -- Science. 1999 Jun 25;284(5423):2184-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Metabolic Disorders, Department of Medicinal Chemistry, Merck Research Laboratories, Building RY-80Y-265, 126 East Lincoln Avenue, Rahway, NJ 07065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10381885" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Alternative Splicing ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Calcium/metabolism ; Cell Line ; Chromosome Mapping ; Chromosomes, Human, Pair 13 ; Cloning, Molecular ; Colon/*metabolism ; Erythromycin/metabolism ; GTP-Binding Proteins/metabolism ; Humans ; In Situ Hybridization ; Intestine, Small/*metabolism ; Ligands ; Molecular Sequence Data ; Motilin/analogs & derivatives/*metabolism ; Receptors, Gastrointestinal Hormone/*chemistry/*genetics/metabolism ; Receptors, Neuropeptide/*chemistry/*genetics/metabolism ; Stomach/*metabolism ; Thyroid Gland/metabolism ; Transfection
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 34
    Publikationsdatum: 1999-11-05
    Beschreibung: The Caenorhabditis elegans heterochronic genes control the relative timing and sequence of many events during postembryonic development, including the terminal differentiation of the lateral hypodermis, which occurs during the final (fourth) molt. Inactivation of the heterochronic gene lin-42 causes hypodermal terminal differentiation to occur precociously, during the third molt. LIN-42 most closely resembles the Period family of proteins from Drosophila and other organisms, proteins that function in another type of biological timing mechanism: the timing of circadian rhythms. Per mRNA levels oscillate with an approximately 24-hour periodicity. lin-42 mRNA levels also oscillate, but with a faster rhythm; the oscillation occurs relative to the approximately 6-hour molting cycles of postembryonic development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeon, M -- Gardner, H F -- Miller, E A -- Deshler, J -- Rougvie, A E -- GM50227/GM/NIGMS NIH HHS/ -- HD007480/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 5;286(5442):1141-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10550049" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Alleles ; Amino Acid Sequence ; Animals ; Caenorhabditis elegans/*chemistry/genetics/growth & development ; *Caenorhabditis elegans Proteins ; Cell Cycle Proteins ; Cell Differentiation ; *Circadian Rhythm ; Cloning, Molecular ; *Drosophila Proteins ; Evolution, Molecular ; Exons ; Genes, Helminth ; Helminth Proteins/*chemistry/*genetics/physiology ; Humans ; Insect Proteins/chemistry/genetics ; Intracellular Signaling Peptides and Proteins ; Molecular Sequence Data ; Molting ; Mutation ; Nuclear Proteins/chemistry/genetics/physiology ; Period Circadian Proteins ; RNA, Helminth/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Repetitive Sequences, Amino Acid ; Sequence Alignment ; Transcription Factors/chemistry/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 35
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 1999-07-20
    Beschreibung: Although polymorphic inversions in Drosophila are very common, the origin of these chromosomal rearrangements is unclear. The breakpoints of the cosmopolitan inversion 2j of D. buzzatii were cloned and sequenced. Both breakpoints contain large insertions corresponding to a transposable element. It appears that the two pairs of target site duplications generated upon insertion were exchanged during the inversion event, and that the inversion arose by ectopic recombination between two copies of the transposon that were in opposite orientations. This is apparently the mechanism by which transposable elements generate natural inversions in Drosophila.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Caceres, M -- Ranz, J M -- Barbadilla, A -- Long, M -- Ruiz, A -- New York, N.Y. -- Science. 1999 Jul 16;285(5426):415-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departament de Genetica i de Microbiologia, Universitat Autonoma de Barcelona, 08193 Bellaterra (Barcelona), Spain. mariocs@cc.uab.es〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10411506" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Chromosome Inversion ; Cloning, Molecular ; *DNA Transposable Elements ; DNA, Complementary ; Drosophila/*genetics ; Gene Expression ; Genes, Insect ; In Situ Hybridization ; Models, Genetic ; Open Reading Frames ; Polymerase Chain Reaction ; Recombination, Genetic ; Sequence Alignment
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 36
    Publikationsdatum: 1999-12-30
    Beschreibung: Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walhout, A J -- Sordella, R -- Lu, X -- Hartley, J L -- Temple, G F -- Brasch, M A -- Thierry-Mieg, N -- Vidal, M -- 1 R21 CA81658 A 01/CA/NCI NIH HHS/ -- 1 RO1 HG01715-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2000 Jan 7;287(5450):116-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10615043" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Caenorhabditis elegans/*genetics/growth & development/*metabolism ; *Caenorhabditis elegans Proteins ; Cloning, Molecular ; Databases, Factual ; Female ; Genes, Helminth ; Genetic Vectors ; *Genome ; Helminth Proteins/*genetics/*metabolism ; Mutation ; Open Reading Frames ; Phenotype ; Repressor Proteins/genetics/metabolism ; Retinoblastoma Protein/genetics/metabolism ; *Two-Hybrid System Techniques ; Vulva/growth & development
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 37
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 203-214 
    ISSN: 0192-8651
    Schlagwort(e): structure ; stability ; B+13 clusters ; B3LYP/6-31G* density functional theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The structures and energies of B+13, observed experimentally to be an unusually abundant species among cationic boron clusters, have been studied systematically with B3LYP/6-31G* density functional theory. The most thermodynamically stable B+12 and B+13 clusters are confirmed to have planar or quasiplanar rather than globular structures. However, the computed dissociation energies of the 3-dimensional B+13 clusters are much closer to the experimental values than those of the planar or quasiplanar structures. Hence, planar and 3-dimensional B+13 may both exist.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 203-214, 1998
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 38
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 232-239 
    ISSN: 0192-8651
    Schlagwort(e): endohedral metallofullerenes ; cage structures and symmetry ; metal positions and motion ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The structural determination of endohedral metallofullerenes has attracted special attention in disclosing the formation mechanism and developing new routes to bulk production. Recent advances in the theoretical and experimental studies are summarized with representative mono- and dimetallofullerenes such as M@C82 (M=Ca, Sc, Y, and La), Sc2@C84, and La2@C80.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 232-239, 1998
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 39
    ISSN: 0192-8651
    Schlagwort(e): protein folding ; multibody interactions ; electrostatic interactions ; cumulant expansion ; potential of mean force ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci., 2, 1697 (1993)], a cumulant expansion of the average free energy of the system of freely rotating peptide-group dipoles tethered to a fixed α-carbon trace is derived. A graphical approach is presented to find all nonvanishing terms in the cumulants. In particular, analytical expressions for three- and four-body (correlation) terms in the averaged interaction potential of united peptide groups are derived. These expressions are similar to the cooperative forces in hydrogen bonding introduced by Koliński and Skolnick [J. Chem. Phys., 97, 9412 (1992)]. The cooperativity arises here naturally from the higher order terms in the power-series expansion (in the inverse of the temperature) for the average energy. Test calculations have shown that addition of the derived four-body term to the statistical united-residue potential of our earlier work [Liwo et al., J. Comput. Chem., 18, 849, 874 (1997)] greatly improves its performance in folding poly-L-alanine into an α-helix.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 259-276, 1998
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 40
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 308-318 
    ISSN: 0192-8651
    Schlagwort(e): tellurium tetrachloride ; ab initio calculations ; density functional theory ; vibrational analysis ; scaled quantum mechanical method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Vibrational analysis of tellurium tetrachloride, TeCl4, was performed with Hartree-Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6-31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A2 (ν4) fundamental, where the results of the best methods were within 4 cm-1. The best force fields were obtained with the following methods: Becke3-Lee-Yang-Parr and Becke3-Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl4; however, it provides poor results with correlated methods.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 308-318, 1998
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 41
    ISSN: 0192-8651
    Schlagwort(e): Broyden-Fletcher-Goldfarb-Shanno formula ; update Hessian formula ; transition structures ; optimization ; saddle points ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Based on a study of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) update Hessian formula to locate minima on a hypersurface potential energy, we present an updated Hessian formula to locate and optimize saddle points of any order that in some sense preserves the initial structure of the BFGS update formula. The performance and efficiency of this new formula is compared with the previous updated Hessian formulae such as the Powell and MSP ones. We conclude that the proposed update is quite competitive but no more efficient than the normal updates normally used in any optimization of saddle points.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 349-362, 1998
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 42
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 396-403 
    ISSN: 0192-8651
    Schlagwort(e): Monte-Carlo simulation ; catalytic processes ; stochastic kinetic model ; solid surfaces ; graphic representation ; catalysis by metal ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A Monte-Carlo model for the simulation of alkene hydrogenation on metallic catalysts has been developed and implemented in Fortran language. We describe the model employed for ethylene hydrogenation on platinum and show the flow chart of the program. Computational characteristics such as number of necessary calculations to reach steady state, running times on different platforms, and effect of the size of the catalyst matrix, are presented. Good correlation between simulated and experimental data was observed. A subroutine allows for visual observation of the reaction. This approach is very useful for obtaining a personal impression of the important factors governing the reaction. By using this example the advantages of Monte-Carlo simulation to test the level of understanding of catalytic phenomena are discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 396-403, 1998
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 43
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 418-429 
    ISSN: 0192-8651
    Schlagwort(e): Lacks-Gordon exchange functional ; Lee-Yang-Parr correlation functional ; conventional density functional ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We present an analysis of the numerical performances of the exchange functional proposed by Lacks and Gordon, which we have implemented in the Gaussian series of programs. This functional has been built with the double aim of respecting most of the known scaling and asymptotic properties and of giving good numerical performances, especially as concerns noncovalent interactions. We have found that the coupling of the Lacks-Gordon exchange and Lee-Yang-Parr correlation functionals provides a reliable conventional density functional approach. The corresponding parameter-free adiabatic connection model, in which the ratio between Hartree-Fock and Lacks-Gordon exchange is determined a priori from purely theoretical considerations, allows us to obtain remarkable results for both covalent and noncovalent interactions in a satisfactory theoretical scheme, encompassing the free electron gas limit and most of the known scaling conditions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 418-429, 1998
    Zusätzliches Material: 3 Ill.
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  • 44
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 488-503 
    ISSN: 0192-8651
    Schlagwort(e): density functional theory ; electron density ; shell structure ; Fukui function ; atomic hardnesses ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: An approximation to the Fukui function in atoms recently proposed in the form of a gradient correction to the local density approximation expression is here investigated. The spatial behavior of this function is analyzed, focusing on the gradient correction term. Physical information on the shell structure of atoms is shown to be conveyed by the radial distribution of that term. The analytically modeled densities (AMD) procedure is also implemented, and global atomic hardnesses are calculated with Hartree-Fock and AMD representations of atomic electron densities.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 488-503, 1998
    Zusätzliches Material: 10 Ill.
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  • 45
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 512-523 
    ISSN: 0192-8651
    Schlagwort(e): molecular mechanics ; force field ; transition metal compounds ; coordinated ligands ; organic backbone ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A new molecular mechanics force field has been developed that takes into account the fact that, upon coordination to a transition metal ion, the redistribution of electron density leads to small but significant structural changes in the organic backbone of the ligand. Structural studies indicate that the perturbation by coordination to a metal ion extends to the α-carbon atom of the donor, the perturbation is roughly independent of the metal center for M2+ and M3+ and negligible for M+, and the perturbation of the Cα(SINGLE BOND)Cα′ bond is roughly independent of the donor atom. New parameter sets for oxalates, imidazoles, and pyrazoles are also presented. The refined parameters have been validated with a large number of monodentate, multidentate, and macrocyclic ligands.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 512-523, 1998
    Zusätzliches Material: 2 Ill.
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  • 46
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 548-573 
    ISSN: 0192-8651
    Schlagwort(e): surface loops ; structure prediction ; global energy minimization ; energy functions ; hydration free energy ; atomic multipoles ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree-Fock/6-31G* level.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 548-573, 1998
    Zusätzliches Material: 3 Ill.
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  • 47
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 575-584 
    ISSN: 0192-8651
    Schlagwort(e): Boys-Bernardi scheme ; chemical Hamiltonian approach ; hydrogen bond ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: 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
    Zusätzliches Material: 4 Ill.
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  • 48
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 610-627 
    ISSN: 0192-8651
    Schlagwort(e): natural resonance theory ; resonance theory ; valency ; bond order ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Resonance weights derived from the Natural Resonance Theory (NRT), introduced in the preceding paper are used to calculate “natural bond order,” “natural atomic valency,” and other atomic and bond indices reflecting the resonance composition of the wave function. These indices are found to give significantly better agreement with observed properties (empirical valency, bond lengths) than do corresponding MO-based indices. A characteristic feature of the NRT treatment is the description of bond polarity by a “bond ionicity” index (resonance-averaged NBO polarization ratio), which replaces the “covalent-ionic resonance” of Pauling-Wheland theory and explicity exhibits the complementary relationship of covalency and electrovalency that underlies empirical assignments of atomic valency. We present ab initio NRT applications to prototype saturated and unsaturated molecules methylamine, butadiene), polar compounds (fluoromethanes), and open-shell species: (hydroxymethyl radical) to demonstrate the numerical stability, convergence, and chemical reasonableness of the NRT bond indices in comparison to other measures of valency and bond order in current usage.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 610-627, 1998
    Zusätzliches Material: 4 Ill.
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  • 49
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 658-672 
    ISSN: 0192-8651
    Schlagwort(e): full configuration interaction ; ab initio methods ; acetylene molecule ; parallel computation ; message passing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A parallel full configuration interaction (FCI) code, implemented on a distributed memory MPP computer, has been modified in order to use a direct algorithm to compute the lists of mono- and biexcitations each time they are needed. We were able to perform FCI calculations on the ground state of the acetylene molecule with two different basis sets, corresponding to more than 2.5 and 5 billion Slater determinants, respectively. The calculations were performed on a Cray-T3D and a Cray-T3E, both machines having 128 processors. Performance and comparison between the two computers are reported and discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 658-672, 1998
    Zusätzliches Material: 9 Ill.
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  • 50
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 716-725 
    ISSN: 0192-8651
    Schlagwort(e): NMR ; boron nitride ; solid state ; theoretical chemistry ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Hydrogen-saturated cut-outs of hexagonal boron nitride have been used to model the solid state. Model compounds have been geometry optimized by means of density functional theory, whereas chemical shift calculations have been carried out at the coupled-perturbed Hartree-Fock level of theory employing gauge-including atomic orbital (GIAO) basis sets. The reliability of results has been tested against experimental values for chemical shifts in stable molecules with similar structural elements. With increasing cluster size, viz. a vanishing influence of the saturating hydrogens on the innermost nitrogen atoms, we find a convergence of 15N chemical shifts. A classification scheme for the chemical environment of a nitrogen atom has been set up according to its bonding graph including the second coordination sphere. For a given connectivity, chemical shifts vary within a few parts per million, thus enabling us to predict a 15N-NMR chemical shift of -285 ± 5 ppm for solid α-boron nitride.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 716-725, 1998
    Zusätzliches Material: 6 Ill.
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  • 51
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 754-768 
    ISSN: 0192-8651
    Schlagwort(e): molecular mechanics ; spectroscopically determined force field ; infrared intensities ; electrostatic model ; alkanes ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A new electrostatic model for the calculation of infrared intensities in molecular mechanics and molecular dynamics is presented. The model is based on atomic charges, atomic charge fluxes, and internal coordinate dipoles and their fluxes. The internal coordinate dipoles are used instead of atomic dipoles, thus simplifying the derivation of parameters. The model is designed to reproduce ab initio dipole derivatives, and the parameters can be obtained by (iterative) transformations from these, or by linear least squares fitting to them. A first application to linear alkanes has been made. For these molecules, the intensities can be predicted with an average accuracy of 30-40%.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 754-768, 1998
    Zusätzliches Material: 4 Ill.
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  • 52
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 847-857 
    ISSN: 0192-8651
    Schlagwort(e): exchange-repulsion ; methane ; methane dimer ; anisotropic model potential ; potential energy surface ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The procedure previously proposed for the parameterization of the exchange-repulsion energy using probe atom calculations is applied here to the study of the methane dimer and refined to give a very accurate anisotropic model potential in terms of atomic parameters. The most accurate model uses sites on C and H atoms and requires 12 parameters, but a description using just four isotropic sites shifted inward from the H atoms by 15% of the bond length is almost as accurate and is very simple in form.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 847-857, 1998
    Zusätzliches Material: 8 Tab.
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  • 53
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1-20 
    ISSN: 0192-8651
    Schlagwort(e): crystal structure prediction ; polymorphism ; atom-atom potential method ; force fields ; crystal structure solution ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The approach of Karfunkel and Gdanitz has been used to predict possible crystal structures of acetic acid and three of its monohalogenated analogs starting with the molecular structure alone. The results demonstrate that this approach is capable of finding many, if not all, of the possible packing arrangements of molecules of this size, but that it is not currently capable of correctly ranking these structures in terms of their enthalpy. This deficiency is probably due to inadequacies in the force field used to minimize the structures. The inadequacies relate to the description of acidic hydrogen bonds and halogen-halogen interactions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1-20, 1998
    Zusätzliches Material: 13 Ill.
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  • 54
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 21-37 
    ISSN: 0192-8651
    Schlagwort(e): antisteroid antibody ; progesterone ; thrombin ; NAPAP ; flexible docking ; MSNI ; MCM ; finite-difference Poisson-Boltzmann technique ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A novel procedure for docking ligands in a flexible binding site is presented. It relies on conjugate gradient minimization, during which nonbonded interactions are gradually switched on. Short Monte Carlo minimization runs are performed on the most promising candidates. Solvation is implicitly taken into account in the evaluation of structures with a continuum model. It is shown that the method is very accurate and can model induced fit in the ligand and the binding site. The docking procedure has been successfully applied to three systems. The first two are the binding of progesterone and 5β-androstane-3,17-dione to the antigen binding fragment of a steroid binding antibody. A comparison of the crystal structures of the free and the two complexed forms reveals that any attempt to model binding must take protein rearrangements into account. Furthermore, the two ligands bind in two different orientations, posing an additional challenge. The third test case is the docking of Nα-(2-naphthyl-sulfonyl-glycyl)-D-para-amidino-phenyl-alanyl-piperidine (NAPAP) to human α-thrombin. In contrast to steroids, NAPAP is a very flexible ligand, and no information of its conformation in the binding site is used. All docking calculations are started from X-ray conformations of proteins with the uncomplexed binding site. For all three systems the best minima in terms of free energy have a root mean square deviation from the X-ray structure smaller than 1.5 Å for the ligand atoms.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 21-37, 1998
    Zusätzliches Material: 6 Ill.
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  • 55
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 86-93 
    ISSN: 0192-8651
    Schlagwort(e): molecular dynamics simulation ; ortho-terphenyl ; 1,3,5-tri-α-naphthyl benzene ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A computer code was prepared for the molecular dynamics (MD) simulation of a multimolecular system to atomic resolution. Based on a widely accepted force field and aided by simulated annealing of single molecules, $\tilde V$ and $\tilde E$ were computed for ortho-terphenyl and 1,3,5-tri-α-naphthyl benzene across an extended range of temperatures. Although neither the simulation time (40-100 ps) nor the system size (27 and 64 molecules) appeared to affect the computational results to an appreciable extent, it was clear that a longer simulation time or a larger system tended to yield a more consistent set of data. In comparison to experimental observations, simulation was capable of representing $\tilde V$ to within 2-7%, Tg to within 10 K, and ΔCp across Tg to within 10%.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 86-93, 1998
    Zusätzliches Material: 6 Ill.
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  • 56
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 102-111 
    ISSN: 0192-8651
    Schlagwort(e): QSHAKE ; bond constraints ; semirigid molecules ; molecular dynamics simulations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on “SHAKE-ing” bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its performance compared with SHAKE for liquid octane. QSHAKE is significantly more efficient whenever SHAKE requires triangles (or tetrahedra) of constraints to maintain molecular shape. Efficiencies are gained because QSHAKE reduces the number of holonomic constraints that must be solved iteratively and requires fewer iterations to obtain convergence. The gains in efficiency are most noticeable when a high degree of precision is imposed on the constraint criteria. QSHAKE is also stable at larger time steps than SHAKE, thus allowing for even more efficient exploration of phase space for semirigid molecules.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 102-111, 1998
    Zusätzliches Material: 5 Ill.
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  • 57
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 123-128 
    ISSN: 0192-8651
    Schlagwort(e): gas phase structures ; conformational properties ; gas electron diffraction ; theoretical calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Theoretical calculations in combination with experimental gas phase structure research can be performed in two ways. The first is to support and improve experimental analyses by including additional data from theoretical calculations. This is to the advantage of the experiment. The second way is a comparison of geometric structures and conformational properties obtained with different theoretical methods with the experimental result. This comparison indicates which theoretical method or methods are suitable for a specific compound. This approach is to the advantage of the theory.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 123-128, 1998
    Zusätzliches Material: 2 Ill.
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  • 58
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 833-846 
    ISSN: 0192-8651
    Schlagwort(e): continuum solvation models ; ab initio calculations ; solvation free energy ; solute-solvent interactions ; cavity errors ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We present a formal and numerical analysis of the errors related to the use of molecular cavities in the continuum description of solute-solvent electrostatic interactions. In this approximation the solvent response is fully described by an apparent charge distribution induced on the cavity surface. The latter is then discretized into a set of point charges that are generally affected by errors of different origin but all depending on the definition of the cavity boundaries, and the way its surface is partitioned. The numerical analysis is based on results obtained for a set of couples of neutral/anionic solutes obtained with various versions of PCM methods, exploiting different correction procedures, as well as with two recently developed continuum methods, complementing PCM.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 833-846, 1998
    Zusätzliches Material: 4 Ill.
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  • 59
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 144-153 
    ISSN: 0192-8651
    Schlagwort(e): molecular dynamics simulations ; clay mineral adsorption ; clay mineral parameter development ; trichloroethene adsorption on clay minerals ; organic chlorine electrostatic charges ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The adsorption of trichloroethene, C2HCl3, on clay mineral surfaces in the presence of water has been modeled as an example describing a general program that uses molecular dynamics simulations to study the sorption of organic materials at the clay mineral/aqueous solution interface. Surfaces of the clay minerals kaolinite and pyrophyllite were hydrated at different water levels corresponding to partial and complete monolayers of water. In agreement with experimental trends, water was found to outcompete C2HCl3 for clay surface sites. The simulations suggest that at least three distinct mechanisms coexist for C2HCl3 on clay minerals in the environment. The most stable interaction of C2HCl3 with clay surfaces is by full molecular contact, coplanar with the basal surface. This kind of interaction is suppressed by increasing water loads. A second less stable and more reversible interaction involves adsorption through single-atom contact between one Cl atom and the surface. In a third mechanism, adsorbed C2HCl3 never contacts the clay directly but sorbs onto the first water layer. To test the efficacy of existing force field parameters of organic compounds in solid state simulations, molecular dynamics simulations of several representative organic crystals were also performed and compared with the experimental crystal structures. These investigations show that, in general, in condensed-phase studies, parameter evaluations are realistic only when thermal motion effects are included in the simulations. For chlorohydrocarbons in particular, further explorations are needed of atomic point charge assignments.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 144-153, 1998
    Zusätzliches Material: 5 Ill.
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  • 60
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 189-194 
    ISSN: 0192-8651
    Schlagwort(e): fullerene, ab initio ; carbon-13 ; nuclear magnetic resonance ; density functional ; buckyball ; MM3 ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Ab initio studies at the HF/6-31G* and B3LYP/6-31G* levels are reported for two bowl-shaped hydrocarbons related to C60: C30H12 and C36H12, of C3 and C3v symmetry, respectively. The former has an approximate heat of formation of 211 kcal/mol. Bowl-to-bowl interconversion may occur through a planar (C3h) form of ca. 64 kcal/mol greater energy having one imaginary vibrational frequency. The larger C36H12 bowl has a calculated ΔH°f of 265 kcal/mol. Its HF/6-31G*, B3LYP/6-31G*, and MM3 bond lengths are in good agreement with a recent X-ray structure. Chemical shifts for both compounds calculated by the GIAO method are in good agreement with the measured NMR spectra. The observed 13C chemical shifts increase with the extent of pyramidalization.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 189-194, 1998
    Zusätzliches Material: 4 Ill.
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  • 61
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 222-231 
    ISSN: 0192-8651
    Schlagwort(e): vinylcyclopropane ; sigmatropic shift ; cyclopropane stereo-mutations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The thermal isomerization of vinylcyclopropane to cyclopentene was discovered in 1960 and soon recognized as the simplest known example of a [1,3] sigmatropic shift. Experimental observations for the parent rearrangement and for isomerizations shown by substituted systems suggest that diradical transition structures are involved; recent theoretical treatments of the reaction find no minima corresponding to diradical intermediates. The common dichotomy opposing concerted versus diradical and thus necessarily stepwise mechanisms appears inappropriate. The reaction of vinylcyclopropane may involve four energetically concerted paths traversed by different conformational forms of nearly isoenergetic diradical species leading through four isometric diradical transition structures to cyclopentene.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 222-231, 1998
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  • 62
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 250-257 
    ISSN: 0192-8651
    Schlagwort(e): fluorosulfonic acid ; protonation energies ; solvation ; acidities ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Electrostatic solvation free energies were computed for several small neutral bases and their conjugate acids using a continuum solvation model called the self-consistent isodensity polarizable continuum model (SCIPCM). The solvation energies were computed at the restricted Hartree-Fock (RHF) and second-order Møller-Plesset (MP2) levels of theory, as well as with the Becke3-Lee-Yang-Parr (B3LYP) density functional theory, using the standard 6-31G** Gaussian basis set. The RHF solvation energies are similar to those computed at the correlated MP2 and B3LYP theoretical levels. A model for computing protonation enthalpies for neutral bases in fluorosulfonic acid solvent leads to the equation ΔHprot, HSO3F(B)=-PA(B)+ΔEt(BH+)-ΔEt(B)+β, where PA(B) is the gas phase proton affinity for base B, ΔEt(BH+) is the SCIPCM solvation energy for the conjugate acid, and ΔEt(B) is the solvation energy for the base. A fit to experimental values of ΔHprot, HSO3F(B) for 10 neutral bases (H2O, MeOH, Me2O, H2S, MeSH, Me2S, NH3, MeNH2, Me2NH, and PH3) gives β=238.4±2.9 kcal/mol when ΔΔEt is computed using the 0.0004 e⋅bohr-3 isodensity surface for defining the solute cavity at the RHF/6-31G** level. The model predicts that for carbon monoxide ΔHprot, HSO3F(CO)=10 kcal/mol. Thus, protonation of CO is endothermic, and the conjugate acid HCO+ (formyl cation) behaves as a strong acid in fluorosulfonic acid.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 250-257, 1998
    Zusätzliches Material: 2 Ill.
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  • 63
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 277-289 
    ISSN: 0192-8651
    Schlagwort(e): ab initio molecular orbital theory ; density functional theory ; ozone depletion problem ; halon replacement ; fire suppression mechanism ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Ab initio molecular orbital theory and density functional theory calculations have been carried out on the reactions of the trifluoromethyl radical with the hydroxyl and the hydrogen radicals. These reactions are key reactions that underlie a new fire extinguishing mechanism of non-bromine-containing halon replacements. The activation energies calculated by the MP2 and QCISD methods are in good agreement with the experimental values. The B3LYP, as well as MP2 and QCISD, give good results for the calculations of the heats of reactions. The GAUSSIAN-1 and GAUSSIAN-2 theory calculations present the most acxcurate results on both the activation energies and the heats of reactions. The effects of the scaling factors on the activation energies and the heats of reactions are also evaluated.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 277-289, 1998
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  • 64
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 319-333 
    ISSN: 0192-8651
    Schlagwort(e): solvation energy ; solvent accessible surface area ; atomic solvation parameters ; Monte Carlo simulation ; FANTOM ; avian pancreatic polypeptide ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described. The new surface routine, GETAREA, finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the accessible surface area by the Gauss-Bonnet theorem. The surface routine was implemented in FANTOM, a program for energy minimization and Monte Carlo simulation, and tested for accuracy and efficiency in extensive energy minimizations of Met-enkephalin, the α-amylase inhibitor tendamistat, and avian pancreatic polypeptide (APP). The CPU time for the exact calculation of the accessible surface areas and their gradients has been reduced by factors of 2.2 (Met-enkephalin) and 3.2 (tendamistat) compared with our previous approach. The efficiency of our exact method is similar to the recently described approximate methods MSEED and SASAD. The performance of several atomic solvation parameter sets was tested in searches for low energy conformations of APP among conformations near the native X-ray crystal structure and highly distorted structures. The protein solvation parameters from Ooi et al. [Proc. Natl. Acad. Sci. USA, 84, 3086 (1987)] and from Wesson and Eisenberg [Prot. Sci., 1, 227 (1992)] showed a good correlation between solvation energies of the conformations and their root-mean-square deviations from the X-ray crystal structure of APP.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 319-333, 1998
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  • 65
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 377-395 
    ISSN: 0192-8651
    Schlagwort(e): atomic charges ; copper complexes ; electrostatic potential charges ; molecular simulation ; rank-deficiency problems ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Four methods for deriving partial atomic charges from the quantum chemical electrostatic potential (CHELP, CHELPG, Merz-Kollman, and RESP) have been compared and critically evaluated. It is shown the charges strongly depend on how and where the potential points are selected. Two alternative methods are suggested to avoid the arbitrariness in the point-selection schemes and van der Waals exclusion radii: CHELP-BOW, which also estimates the charges from the electrostatic potential, but with potential points that are Boltzmann-weighted after their occurrence in actual simulations using the energy function of the program in which the charges will be used, and CHELMO, which estimates the charges directly from the electrostatic multipole moments. Different criteria for the quality of the charges are discussed. The CHELMO method gives the best multipole moments for small and medium-sized polar systems, whereas the CHELP-BOW charges reproduce best the total interaction energy in actual simulations. Among the standard methods, the Merz-Kollman charges give the best moments and potentials, but they show an appreciable dependence on the orientation of the molecule.We have also examined the recent warning that charges derived by a least-squares fit to the electrostatic potential normally are not statistically valid. It is shown that no rank-deficiency problems are encountered for molecules with up to 84 atoms if the least-squares fit is performed using pseudoinverses calculated by singular value decomposition and if constraints are treated by elimination.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 377-395, 1998
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  • 66
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 459-474 
    ISSN: 0192-8651
    Schlagwort(e): crystal structure prediction ; distributed multipoles ; molecular dynamics ; symmetry constraints ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Possible crystal structures of acetic acid were generated, considering eight space groups and assuming one molecule in the asymmetric unit. Our grid-search method was compared with a Monte Carlo approach as implemented in the Biosym/MSI Polymorph Predictor. This revealed no sampling deficiencies. A large number of possible crystal structures were found (∼100 within only 5 kJ/mol), including the experimental structure. Energy minimizations were done with a united-atoms force field (GROMOS), an all-atoms force field (AMBER), and a potential that describes the electrostatic interactions with distributed multipoles (DMA). In all cases, the experimental structure had a low lattice energy. The number of hypothetical crystal structures was reduced considerably by removing space-group symmetry constraints, or by a primitive molecular dynamics shake-up. Nevertheless, sufficient structures of equal or lower energy compared with the experimental structure remained to suggest that other factors need to be considered for genuine structure prediction.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 459-474, 1998
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  • 67
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 430-458 
    ISSN: 0192-8651
    Schlagwort(e): force fields ; amides ; conformations ; ab initio ; quantum chemistry ; molecular mechanics ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: As the field of biomolecular structure advances, there is an ever-growing need for accurate modeling of molecular energy surfaces to simulate and predict the properties of these important systems. To address this need, a second generation amide force field for use in simulations of small organics as well as proteins and peptides has been derived. The critical question of what accuracy can be expected from calculations in general, and with this class II force field in particular, is addressed for structural, dynamic, and energetic properties. The force field is derived from a recent methodology we have developed that involves the systematic use of quantum mechanical observables. Systematic ab initio calculations were carried out for numerous configurations of 17 amide and related compounds. Relative energies and first and second derivatives of the energy of 638 structures of these compounds resulted in 140,970 ab initio quantum mechanical observables. The class II peptide quantum mechanical force field (QMFF), containing 732 force constants and reference values, was parameterized against these observables. A major objective of this work is to help establish the role of anharmonicity and coupling in improving the accuracy of molecular force fields, as these terms have not yet become an agreed upon standard in the ever more extensive simulations being used to probe biomolecular properties. This has been addressed by deriving a class I harmonic diagonal force field (HDFF), which was fit to the same energy surface as the QMFF, thus providing an opportunity to quantify the effects of these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess the range of applicability (transferability) of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcal/mol with the class II force field, and 2.30 kcal/mol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it approaches a (rotational) barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of ever-increasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm-1 was achieved with the coupled anharmonic force field, as compared to 105 cm-1 with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides.    © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 430-458, 1998
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  • 68
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 524-534 
    ISSN: 0192-8651
    Schlagwort(e): ab initio conformational analysis ; cyclooctane molecule ; potential energy surface ; Hartree-Fock theory ; Møller-Plesset theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The potential energy surface (PES) for the cyclooctane molecule was comprehensively investigated at the Hartree-Fock (HF) level of theory employing the 3-21G, 6-31G, and 6-31G* basis sets. Six distinct true minimum energy structures (named B, BB, BC, CROWN, TBC, and TCC1), characterized through harmonic frequency analysis, were located on the multidimensional PES. Two transition state structures were also located on the PES for the cyclooctane molecule. Electron correlation effects were accounted for using the Møller-Plesset second-order perturbation theory (MP2) approach. The predicted global minimum energy structure on the ab initio PES for the cyclooctane molecule is the BC conformer. A gas phase electron diffraction study at 300 K suggested a conformational mixture while an NMR study in solution at 161.5 K predicted the BC conformer as the predominant form. The equilibrium constants reported in the present study, which were evaluated from the ab initio calculated total Gibbs free energy change values, were in good agreement with both experimental investigations. The ab initio results showed that the low temperature condition significantly favored the BC conformer while above room temperature both BC and CROWN structures can coexist.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 524-534, 1998
    Zusätzliches Material: 4 Ill.
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  • 69
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 593-609 
    ISSN: 0192-8651
    Schlagwort(e): natural resonance theory ; resonance theory ; natural bond orbitals ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We present a new quantum-mechanical resonance theory based on the first-order reduced density matrix and its representation in terms of natural bond orbitals (NBOs). This “natural” resonance theory (NRT) departs in important respects from the classical Pauling-Wheland formulation, yet it leads to quantitative resonance weights that are in qualitative accord with conventional resonance theory and chemical intuition. The NRT variational functional leads to an optimal resonance-weighted approximation to the full density matrix, combining the “single reference” limit of weak delocalization (incorporating diagonal population changes only) with the full “multireference” limit of strong delocalization (incorporating off-diagonal couplings between resonance structures. The NRT variational functional yields an error measure that serves as an intrinsic criterion of accuracy of the resonance-theoretic description. The NRT program structure, algorithms, and numerical characteristics are described in supplementary material, and detailed chemical applications are presented in two companion papers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 593-609, 1998
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  • 70
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 647-657 
    ISSN: 0192-8651
    Schlagwort(e): simulated annealing ; molecular dynamics ; Tsallis machine ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We propose a stochastic optimization technique based on a generalized simulated annealing (GSA) method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by coupling a classical molecular force field (THOR package) with a GSA procedure. Unlike the usual molecular dynamics (MD) method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by applying it to examples of simple molecules (H2O and H2O3) and to polypeptides. The results obtained for H2O and H2O3 using Tsallis thermostatistics suggest that the GSA approach is faster than the other two conventional methods (Boltzmann and Cauchy machines). The results for polypeptides show that pentalanine does not form a stable α-helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an α-helix structure. We obtain this structure simulating all Φ, Ψ pairs using only a few steps, as compared with conventional methods.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 647-657, 1998
    Zusätzliches Material: 5 Ill.
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  • 71
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 695-715 
    ISSN: 0192-8651
    Schlagwort(e): nucleic acid ; multivariate analysis ; Ramachandran plots ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A method to construct the equivalent of multidimensional Ramachandran plots for nucleic acids on the basis of singular value decomposition (SVD) is presented. For this purpose, a data matrix containing 244 DNA dinucleoside monophosphate steps, represented by nine torsion angles, was decomposed into a score and loading matrix. It is shown that biplots, containing both score points and loading vectors, provide a simple tool to interpret the principles of DNA class separation. Scores separate the data matrix into one A-DNA class, two different B-DNA classes, and one so-called crankshaft class. Loading vectors correlate torsion angles. The projections of scores on loading vectors indicate which torsion angles play a dominant role in DNA class separation. The results of the biplots are supported by (simple) physical interpretations. From a three-dimensional score space the nine original torsion angles can be reconstructed. Hence, the potential to create the multidimensional equivalent of a Ramachandran plot is available; that is, forbidden and accessible regions in the reduced space reflect these same regions in the nine-dimensional original space.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 695-715, 1998
    Zusätzliches Material: 12 Ill.
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  • 72
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 673-684 
    ISSN: 0192-8651
    Schlagwort(e): molecular interaction potential ; molecular electrostatic potential ; dibenzo-p-dioxin ; induced molecular dipole moments ; π-charge interaction ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Interaction with the ligand binding domain of receptors for natural chemicals present one potential mechanism for the biological effects of environmental chemicals. Evidence suggests that the electrostatic interaction between the ligand and the receptor is an important component for binding to some of the relevant receptors. The presence of charged residues near the binding site suggests that the charge distribution of the free ligand may be different from the charge distribution of the ligand as it approaches the binding domain of the protein. In this study a new type of potential is computed for a series of dibenzo-p-dioxin (dioxin) ligands. This quantum mechanically computed potential results from interaction between the ligand and a trimethyl ammonium probe at a set of grid points. This interaction potential is compared with the molecular electrostatic potential computed from the wave function of the isolated ligands. Three types of local minima are found: (1) above the oxygen; (2) above the conjugated ring; and (3) above the chlorine(s). The molecular electrostatic potential emphasizes the minima associated with the chlorine atoms and, in that potential, the minima associated with the oxygen atoms disappear with chlorination. In the new potential, the minima over the oxygen atoms are maintained even in tetrachlorodioxin. As chlorination is increased the differences between the two potentials increases. The new potential shows the influence of the π-cation interaction, which is largest when there is little substitution on the ring. The presence of the probe induces a dipole component of 1 debye perpendicular to the plane of the ligand. Local minima in the interaction potential are then used as starting structures for the determination of the most stable ligand-probe complexes. The most stable structures are obtained from the minima associated with the oxygen atoms. These structures are stabilized by a hydrogen bond formation between the probe and the oxygen and the molecule is bent by 30° about the O(SINGLE BOND)O axis. For this series of molecules, the new potential retains some of the features that determine the hydrogen bond whereas the molecular electrostatic potential does not.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 673-684, 1998
    Zusätzliches Material: 9 Ill.
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  • 73
    ISSN: 0192-8651
    Schlagwort(e): solvation free energies ; GB/SA solvent model ; energy minimization calculations ; AMBER force field ; macromodel ; thermodynamic cycle perturbation (TCP) calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 769-780, 1998
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  • 74
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 797-808 
    ISSN: 0192-8651
    Schlagwort(e): van der Waals surface area (vdWSA) ; solvent-accessible surface area (SASA), numerical calculation ; neighbor list ; united- and all-atom representations ; protein structures ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A general, fast, and exact optimization, called neighbor-list reduction (NLR), is presented, which can be used to accelerate the computation of hard-sphere molecular surface areas. NLR allows selected neighbors of a central atom to be removed from the computation in a preprocessing step, thus allowing the calculation of the atom's surface area to proceed with a shorter list of neighbors. The atoms removed are those having intersections with the central atom falling entirely within unions of other atoms' intersections with the central atom. We describe explicit methods for two levels of neighbor-list reduction: 3NLR considers three hard spheres at a time - the central atom, the candidate for removal, and one other neighbor; whereas 4NLR considers two other neighbors. We demonstrate the correctness and efficiency of this optimization by means of a modified version of the NACCESS program, which computes atomic and molecular surface areas numerically. As test cases we used compounds of different size and class, with and without explicit hydrogens. When van der Waals surface (vdWSA) is computed, the NLR methods reduce the length of the neighbor list by as much as 41%; when solvent-accessible surface area (SASA) is computed, the reduction is as great as 74%. The overall speed improvement due to these reductions is a factor of only about 1.2 for vdWSA, but is about 2.0 for the computation of SASA, in the context of this particular program. All 39,554 calculated atomic surface areas (vdWSA and SASA) were found to be identical to within 0.001 Å2 to those obtained without NLR.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 797-808, 1998
    Zusätzliches Material: 8 Ill.
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  • 75
    ISSN: 0192-8651
    Schlagwort(e): cryptophanes ; molecular dynamics ; free energy perturbation ; preorganization ; binding selectivity ; solvent effects ; molecular recognition ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Quantitative assessment of the “best fit” between neutral molecules and the cavity of a “rigid” neutral receptor is a challenging task in supramolecular chemistry, drug design, and biology. We investigate this question by molecular dynamics and free-energy perturbation simulations performed on the macrocyclic ligand cryptophane-E (L) and its L·S complexes with three tetrahedral guests (S=CH2Cl2, CHCl3, and CCl4) in the gas phase and in chloroform solution. The van der Waals interactions are shown to play a crucial role in the calculated complexation selectivity. Calculations using Lennard-Jones 6-12 potentials and “standard” OPLS R*Cl and εCl parameters for the Cl atoms of S lead to a preference for CCl4, in contrast to the selectivities observed experimentally in solution (CHCl3 〉 CH2Cl2 〉 CCl4). Based on systematic investigations of the relative free energies of binding of CHCl3/S, we derive a set of R*Cl and εCl van der Waals parameters that account for experimental binding data. Although the complexes are of the van der Waals type, their electrostatic representation is also crucial for correct calculation of relative stabilities. Thus, the recognition of the “best guest” stems from a subtle balance of distance and time-dependent, cumulative noncovalent interactions between atoms of S and of L, which require an accurate representation. In addition, even in a weakly polar solvent, like chloroform, solvation effects are shown to modulate the recognition of the neutral substrates.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 820-832, 1998
    Zusätzliches Material: 12 Ill.
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  • 76
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1596-1603 
    ISSN: 0192-8651
    Schlagwort(e): direct perturbation theory ; MP2 gradients ; density functional theory ; relativistic effects ; nonadditivity of relativity and correlation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The evaluation of the first-order scalar relativistic corrections to MP2 energy based on either direct perturbation theory or the mass-velocity and Darwin terms is discussed. In a basis set of Lévy-Leblond spinors the one- and two-electron matrix elements of the relativistic Hamiltonian can be decomposed into a nonrelativistic part and a relativistic perturbation. Thus, a program capable of calculating nonrelativistic energy gradients can be used to calculate the cross-term between relativity and correlation. The method has been applied to selected closed-shell atoms (He, Be, Ne, and Ar) and molecules (CuH, AgH, and AuH). The calculated equilibrium distances and harmonic frequencies were compared with results from first-order relativistic density functional calculations. It was found that the cross-term is not the origin of the nonadditivity of relativistic and correlation effects.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1596-1603, 1998
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  • 77
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1623-1631 
    ISSN: 0192-8651
    Schlagwort(e): docking ; genetic algorithms (GA) ; simulated annealing (SA) ; Monte Carlo (MC) ; molecular dynamics (MD) ; scoring functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We assess the efficiency of molecular dynamics (MD), Monte Carlo (MC), and genetic algorithms (GA) for docking five representative ligand-receptor complexes. All three algorithms employ a modified CHARMM-based energy function. The algorithms are also compared with an established docking algorithm, AutoDock. The receptors are kept rigid while flexibility of ligands is permitted. To test the efficiency of the algorithms, two search spaces are used: an 11-Å-radius sphere and a 2.5-Å-radius sphere, both centered on the active site. We find MD is most efficient in the case of the large search space, and GA outperforms the other methods in the small search space. We also find that MD provides structures that are, on average, lower in energy and closer to the crystallographic conformation. The GA obtains good solutions over the course of the fewest energy evaluations. However, due to the nature of the nonbonded interaction calculations, the GA requires the longest time for a single energy evaluation, which results in a decreased efficiency. The GA and MC search algorithms are implemented in the CHARMM macromolecular package.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1623-1631, 1998
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  • 78
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 947-960 
    ISSN: 0192-8651
    Schlagwort(e): olefin polymerization ; Ziegler-Natta catalysis ; quantum chemical methods ; ethylene ; TiH2CH3+ ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Insertion of ethylene into the Ti-methyl bond in TiH2CH+3 is chosen as a model reaction for investigating the performance of a range of contemporary quantum chemical models in polymerization studies. Basis set effects are investigated at the self-consistent-field level, covering Hartree-Fock, pure DFT, and hybrid DFT. In agreement with findings in part I of this study, the basis set sensitivity of ethylene is shown to introduce a bias in computed energetics, amounting to 2-3 kcal/mol when DZP bases are used to compute the overall heat of monomer insertion. The geometry of stationary points relevant to the insertion reaction is determined using hybrid density functional theory. Based on these structures, the energy profile of the insertion reaction is computed using a range of popular quantum chemical approximations. The methods include Hartree-Fock and Møller-Plesset (MP) perturbation theory up through the fourth order in spin-restricted, spin-unrestricted, and spin-projected formalisms. Furthermore, configuration-interaction-based methods are included, of which the top level method is singly and doubly excited coupled clusters with a perturbative estimate of the contribution from triply excited configurations added [CCSD(T)]. The performance of the methods just mentioned, as well as three pure density functional and three hybrid density functional methods, are compared with respect to “best” relative energies, defined through extrapolation of CCSD(T) correlation energies according to the PCI scheme of Siegbahn and coworkers. Even though the MP series show poor convergence, spin-projected MP2, as well as two pure DFT methods (BPW91, BP86) and PCI-78 based on the MCPF method, show similar and very good agreement with best relative energies for the insertion reaction.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 947-960, 1998
    Zusätzliches Material: 4 Ill.
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  • 79
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 989-1000 
    ISSN: 0192-8651
    Schlagwort(e): gas-phase proton affinity and basicity ; density functional computations ; protonation of DNA acid bases ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: 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
    Zusätzliches Material: 10 Ill.
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  • 80
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1030-1038 
    ISSN: 0192-8651
    Schlagwort(e): pseudospectral ; parallel ; localized Møller-Plesset, scalable ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We have developed a parallel version of our pseudospectral localized Møller-Plesset electronic structure code. We present timings for molecules up to 1010 basis functions and parallel speedup for molecules in the range of 260-658 basis functions. We demonstrate that the code is scalable; that is, a larger number of nodes can be efficiently utilized as the size of the molecule increases. By taking advantage of the available distributed memory and disk space of a scalable parallel computer, the parallel code can calculate LMP2 energies of molecules too large to be done on workstations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1030-1038, 1998
    Zusätzliches Material: 2 Ill.
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  • 81
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1758-1776 
    ISSN: 0192-8651
    Schlagwort(e): DefPol ; molecular surfaces ; continuum solvation methods ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We present a method to define van der Waals, solvent-accessible, and solvent-excluding molecular surfaces with their partition in nonoverlapping surface portions (tesserae). The procedure is more efficient than those available in the literature to describe solvent effects on molecular systems of large size, and it can also be applied to solutes of small size without reducing the accuracy of the output and without increasing computational times. All the tesserae are expressed in terms of spherical triangles, having all the characterizing elements (vertices, centers, etc.) analytically defined. The method was tested by comparing the results for the surface area and the solvation free energy (decomposed in electrostatic, dispersion, and steric contributions) obtained using the GEPOL procedure within the framework of the polarizable continuum model solvation method. These comparisons regard 87 molecules at the molecular mechanics level and 28 molecules at the ab initio Hartree-Fock level: the results are quite satisfactory.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1758-1776, 1998
    Zusätzliches Material: 9 Ill.
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  • 82
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1805-1815 
    ISSN: 0192-8651
    Schlagwort(e): molecular surface ; molecular graphics ; molecular recognition ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1805-1815, 1998
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 83
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1853-1861 
    ISSN: 0192-8651
    Schlagwort(e): pyrrolizidine alkaloids ; necine bases ; retronecine ; heliotridine ; conformational analysis ; molecular structure ; hydrogen bond ; molecular mechanics ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Molecular mechanics calculations were applied to the conformational analysis of two diasteroisomers, the pyrrolizidine alkaloids (PAs) retronecine and heliotridine. The application of reoptimized parameters for H bonding corrected the tendency of MM3(92) calculations to give unrealistic H(DOTTED BOND)O distances for intramolecular OH interactions occurring in both diasterisomers. Inversions in the H-bond direction of exo-retronecine and in the relative stability of heliotridine endo-exo conformers were also observed with the application of the new parameters. A set of probable conformers was obtained for each diasterisomer, based on conformational and Boltzmann population analysis. Only exo-puckered conformers were found in the retronecine set, whereas both exo- and endo-puckered conformers were obtained for heliotridine. Transition state conformations supplied arguments supporting the design of models for H-bond interconversion in the case of exo-retronecine and for the exo-endo interconversion of heliotridine. Reactivity behaviors and 1H-NMR data of both diasterisomers were elucidated in light of the theoretical results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1853-1861, 1998
    Zusätzliches Material: 3 Ill.
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  • 84
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1862-1876 
    ISSN: 0192-8651
    Schlagwort(e): protonation of glycine ; ab initio calculations ; conformational analysis ; gas-phase basicity ; amino acids ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller-Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH3+ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)2+. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0-10 and 30-40 kcal mol-1. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1862-1876, 1998
    Zusätzliches Material: 4 Ill.
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  • 85
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1887-1898 
    ISSN: 0192-8651
    Schlagwort(e): Hartree-Fock exchange plus correlation functionals SCF calculations ; two-body density ; ionization potentials ; electron affinities ; polarizabilities ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Self-consistent field calculations are done using two-body density functionals for the correlation energy. The corresponding functional derivatives are obtained and used in pseudo-eigenvalue equations analogous to the Kohn-Sham ones. The examples studied include atomic systems from He to Ar. The values obtained for ionization potentials, electron affinities, dipole polarizabilities, and virial ratios from these calculations are given, and the effect of exchange is addressed. The results obtained are in good agreement with experimental values, and are of the same quality as those given by accurate exchange-correlation functionals.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1887-1898, 1998
    Zusätzliches Material: 6 Tab.
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  • 86
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 858-865 
    ISSN: 0192-8651
    Schlagwort(e): generator coordinate Hartree-Fock method ; adapted Gaussian basis sets ; total energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We have applied a discretized version of the generator coordinate Hartree-Fock method to generate adapted Gaussian basis sets for atoms Cs (Z=55) to Lr (Z=103). Our Hartree-Fock total energy results, for all atoms studied, are better than the corresponding Hartree-Fock energy results attained with previous Gaussian basis sets. For the atoms Cs to Lr we have obtained an energy value within the accuracy of 10-4 to 10-3 hartree when compared with the corresponding numerical Hartree-Fock total energy results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 858-865, 1998
    Zusätzliches Material: 3 Tab.
    Materialart: Digitale Medien
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  • 87
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 363-367 
    ISSN: 0192-8651
    Schlagwort(e): solution structuring ; radial distribution functions ; available volume ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The traditional method of analyzing solution structuring properties of solutes using atom-atom radial distribution functions (rdfs) can give rise to misleading interpretations when the volume occupied by the solute is ignored. It is shown by using the examples of O(4) in α- and β-D-allose that a more reliable interpretation of rdfs can be obtained by normalising the rdf using the available volume, rather than the traditional volume of a spherical shell.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 363-367, 1998
    Zusätzliches Material: 4 Ill.
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  • 88
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 368-376 
    ISSN: 0192-8651
    Schlagwort(e): general coupling operator ; coupling operator ; wave functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We comment on the convergence of the general coupling operator for all types of one-configuration or multiconfigurational wave functions that still preserve the one-configuration structure for the energy expression. The choice on the best arbitrary real and antisymmetric parameters inherent in the coupling operator methodology is discussed, giving a theoretical reason. Another type of coupling operator is defined, presented, and analyzed. Finally, we give some numerical examples related to the low-lying electronic states of a cluster model for K2NiF4 solid.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 368-376, 1998
    Zusätzliches Material: 2 Tab.
    Materialart: Digitale Medien
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  • 89
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 404-417 
    ISSN: 0192-8651
    Schlagwort(e): geometry optimization ; polarizable continuum model ; density functionals ; fixed cavity ; mobile cavity ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A new implementation of analytical gradients for the polarizable continuum model is presented, which allows Hartree-Fock and density functional calculations taking into account both electrostatic and nonelectrostatic contributions to energies and gradients for closed and open shell systems. Simplified procedures neglecting the derivatives of the cavity surface and/or using single spheres for XHn groups have also been implemented and tested. The solvent-induced geometry relaxation has been studied for a number of representative systems in order to test the efficiency of the procedure and to investigate the role of different contributions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 404-417, 1998
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 90
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 475-487 
    ISSN: 0192-8651
    Schlagwort(e): molecular mechanics ; correlation energies ; conjugated polyenes ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Electron correlation at the Møller-Plesset second-order level was incorporated into the π-system portion of MM3 calculations for several conformers of [10]annulene, [18]annulene, bicyclo[5.3.1]undecapentaene, and bicyclo[4.4.1]undecapentaene. The conformers with “localized” C(SINGLE BOND)C π bonds (strongly alternating bond lengths) were found to be of lower energy than their counterparts with “delocalized” C(SINGLE BOND)C π bonds (similar bond lengths) before correlation energy was included. Correlation always lowered the energies of the delocalized conformation more than it did that of the localized conformation, such that often the latter was found to be more stable after correlation energy was included in the calculation. When a delocalized structure was not at a stationary point on the MM3 energy surface, such comparison could not be made. An example is the porphin molecule.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 475-487, 1998
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 91
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 504-511 
    ISSN: 0192-8651
    Schlagwort(e): geometry optimization ; natural internal coordinates ; connectivity ; graph theory ; ring systems ; intermolecular interactions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A simple, customizable connectivity scheme is rigorously defined in which pairs of atoms are classified into three categories. The tools of graph theory are used to analyze the molecular graph and to efficiently find rings and ring assemblies through a combination of pruning and homeomorphic reduction. The definition of natural internal coordinates is extended in a nonredundant fashion for the various cases of weakly interacting components and for fused ring systems. The ring system coordinates were tested and found to be superior to Z-matrix coordinates.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 504-511, 1998
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 92
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 535-547 
    ISSN: 0192-8651
    Schlagwort(e): force field parametrization ; liquid alkanes ; van der Waals interactions ; molecular dynamics ; GROMOS96 ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The derivation of the van der Waals parameters for the aliphatic CHn united atoms of the GROMOS96 force field is presented. The parameters have been adjusted to reproduce the experimental enthalpies of vaporization and vapor pressures or densities of a set of nine alkanes in the liquid state at 298 K (or at the boiling point in the case of methane), using a cutoff radius for the van der Waals interactions of 1.6 nm. Force fields to be used in molecular simulations are bound to the conditions chosen for their parametrization, for example, the temperature, the densities of the systems included in the calibration set, or the cutoff radius used for the nonbonded interactions. Van der Waals parameters for the CHn united atoms of earlier GROMOS force fields were developed using a cutoff radius of 0.8 nm for the van der Waals interactions. Because the van der Waals interaction energy between aliphatic groups separated by distances between 0.8 and 1.4 nm is not negligible at liquid densities, the use of these parameters in combination with longer cutoffs leads to an overestimation of the attractive van der Waals interaction energy. The relevance of this excess attraction depends on the size of the groups that are interacting, as well as on their local densities. Free energies of hydration have been calculated for five alkanes.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 535-547, 1998
    Zusätzliches Material: 1 Ill.
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  • 93
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 585-592 
    ISSN: 0192-8651
    Schlagwort(e): semiempirical calculations ; electronic spectra ; conformational analysis ; 2,5-distyrylpyrazine laser dye ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Semiempirical (MNDO and PM3) molecular orbital calculations have been undertaken to study the structures of the ground and excited states of 2,5-distrylpyrazine dye to assess its activity as a laser dye. In the ground and first excited singlet states, the trans-trans structure of C2h symmetry is the most stable structure in the gas phase and in DMSO, which agrees with the experimental findings. Upon excitation, the flexibility of the molecule decreases, leading to a subsequent decrease in the radiationless deactivation pathway and this increases the fluorescence efficiency of DSP. The absorption, excitation, and emission spectra have been calculated at the MNDO level using the PM3 optimized geometries in DMSO. At this level the agreement between theory and experiment is quite good. An estimated absorption band at 377 nm (expt 380 nm) is assigned to the S0→S1 transition. The excited state absorption band at 457 nm (expt 460 nm) is assigned to the S1→S12 transition. The emission band at 458 nm (expt 460 nm) is assigned to the S′1→S′0 transition. The overlap between the emission and the excited-state absorption spectra is presumably the main reason behind the reduced laser activity of the investigated dye.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 585-592, 1998
    Zusätzliches Material: 4 Ill.
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  • 94
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 628-646 
    ISSN: 0192-8651
    Schlagwort(e): natural resonance theory ; resonance theory ; bonding ; chemical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We describe quantitative numerical applications of the natural resonance theory (NRT) to a variety of chemical bonding types, in order to demonstrate the generality and practicality of the method for a wide range of chemical systems. Illustrative applications are presented for (1) benzene and polycyclic aromatics; (2) CO2, formate, and related acyclic species; (3) ionic and polar compounds; (4) coordinate covalent compounds and complexes; (5) hypervalent and electron-deficient species; (6) noncovalent H-bonded complex; and (7) a model Diels-Alder chemical reaction surface. The examples exhibit the general harmony of NRT weightings with qualitative resonance-theoretic concepts and illustrate how these concepts can be extended to many new types of chemical phenomena at a quanitative ab initio level.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 628-646, 1998
    Zusätzliches Material: 4 Ill.
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  • 95
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1141-1145 
    ISSN: 0192-8651
    Schlagwort(e): internal rotation ; ethane ; energy pathways ; broken symmetry ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Computational studies of the minimum energy pathway for internal rotation of a methyl group are often made by constraining one dihedral angle at a sequence of values and optimizing all other parameters. When this is done, the methyl group adopts an asymmetric configuration at intermediate values of the torsion angle, with unequal bond lengths, bond angles, and torsion angles, even though the moiety against which it is rotating is another methyl group. The potential surface leading to this phenomenon is investigated using Hartree-Fock SCF calculations at the 6-31G* and 6-311G** levels and the detailed structural behavior of the methyl group during the course of the internal rotation is examined. It is shown that the nature of the constraint governs the resulting deformation of the methyl group symmetry.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1141-1145, 1998
    Zusätzliches Material: 3 Ill.
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  • 96
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1179-1186 
    ISSN: 0192-8651
    Schlagwort(e): liquid water ; density ; Monte Carlo simulations ; water models ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Monte Carlo statistical mechanics simulations have been carried out with the TIP3P, SPC, and TIP4P models for liquid water at 13 temperatures from -50°C to 100°C at 1 atm. Long runs with 512 water molecules provided definitive results for densities. Although the TIP4P model yields a flat region in the density profile and a temperature of maximum density near -15°C, the SPC and TIP3P models show monotonically increasing density with decreasing temperature. Results for heats of vaporization, isothermal compressibilities, and coefficients of thermal expansion and their convergence characteristics are also reported.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1179-1186, 1998
    Zusätzliches Material: 10 Ill.
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  • 97
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1215-1228 
    ISSN: 0192-8651
    Schlagwort(e): configuration interaction ; parallel computation ; quantum chemistry ; electronic structure ; electron correlation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A parallel implementation of the internally contracted (IC) multireference configuration (MRCI) module of the MOLPRO quantum chemistry program is described. The global array (GA) toolkit has been used in order to map an existing disk-paging small-memory algorithm onto a massively parallel supercomputer, where disk storage is replaced by the combined memory of all processors. This model has enabled a rather complicated code to be ported to the parallel environment without the need for the wholesale redesign of algorithms and data structures. Examples show that the parallel ICMRCI program can deliver results in a fraction of the time needed for equivalent uncontracted MRCI computations. Further examples demonstrate that ICMRCI computations with up to 107 variational parameters, and equivalent to uncontracted MRCI with 109 configurations, are feasible. The largest calculation demonstrates a parallel efficiency of about 80% on 128 nodes of a Cray T3E-300.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1215-1228, 1998
    Zusätzliches Material: 12 Tab.
    Materialart: Digitale Medien
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  • 98
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1268-1277 
    ISSN: 0192-8651
    Schlagwort(e): molecular surface ; marching tetrahedra ; meshing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A method is presented to generate and triangulate molecular surfaces rapidly. It is based on the ‘marching tetrahedra’ approach. The method is fast, simple and easy to implement. Our approach is not analytical in nature. Hence no special treatment is required for complications with singularity, degeneracy, or with self-intersecting re-entrant surfaces. A quick test for determining the solvent accessibility of a point in space forms an important part of the method. This test has potential use outside of the surface generation algorithm such as in molecular field analysis where the solvent accessibility of a point needs to be determined. The triangulated surface generated is suitable for molecular graphics display as well as boundary element continuum dielectric calculations.   © 1998, Government of Canada. Exclusive worldwide publication rights in the article have been transferred to John Wiley & Sons, Inc. in perpetuity.   J Comput Chem 19: 1268-1277, 1998
    Zusätzliches Material: 12 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 99
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1284-1293 
    ISSN: 0192-8651
    Schlagwort(e): reference program ; molecular calculations ; Slater-type orbitals ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A program for computing all the integrals appearing in molecular calculation with Slater-type orbitals is reported. The program is mainly intended as a reference for testing and comparing other algorithms and techniques. An analysis of the performance of the program is presented, paying special attention to the computational cost and the accuracy of the results. Results are also compared with others obtained with Gaussian basis sets of similar quality.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1284-1293, 1998
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 100
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1325-1336 
    ISSN: 0192-8651
    Schlagwort(e): cyanate ; isocyanate ; ambident ; ion pair ; SN2 reaction ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The structure of lithium and sodium cyanates and isocyanates and their related ion pair SN2 reactions were investigated using molecular quantum mechanics at the Hartree-Fock (HF)/6-31G**//HF/6-31G** level. Extensive further calculations of some of the lithium systems at higher levels gave no significant changes in relative properties. The isocyanate ion pairs are the most stable monomeric forms. The lowest energy dimers are planar eight-membered rings. For the ionic SN2 reaction of cyanate ion and methyl fluoride and chloride, methyl isocyanate is the predicted major product. The monomer ion pair inversion mechanism is predicted to preferentially form methyl cyanate but the calculations also indicate that reaction with dimeric ion pairs have no clear preference for forming methyl cyanate or isocyanate.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1325-1336, 1998
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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