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  • 1995-1999  (4)
  • 1990-1994  (8)
  • Analytical Chemistry and Spectroscopy  (8)
  • Computational Chemistry and Molecular Modeling  (4)
  • 1
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: The products from base-specific, dideoxy-nucleotide chain-termination DNA sequencing reactions catalyzed by the modified T7 DNA polymerase have been analyzed by using the technique of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. Preliminary experiments were performed to determine detection limits for a synthetic mixture of mixed-base single-stranded DNA which contained a 14-mer, a 21-mer, and a 41-mer; acceptable spectra, showing peaks for each component, were obtainable for samples that contained as little as 5 fmol per component. Initial sequencing reactions were therefore carried out on 2-pmol amounts of a short synthetic template that was 45 nucleotides in length, employing 2 pmol of 12-mer as the primer strand. This provided readable sequence information out to the 19th base past the primer. Using a 21-mer primer, nearly the entire sequence of the template could be read.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 22 (1993), S. 319-325 
    ISSN: 1052-9306
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: A novel procedure based on electrospray tandem mass spectrometry (ESI-MS/MS) has been used in the diagnosis of organic acidemias. The method is based on the determination of acylcarnitine profiles from blood spots collected on Guthrie cards. The acylcarnitines are extracted with methanol, derivatized to their butyl esters and analyzed by ESI-MS/MS. Precursor-ion scanning of the common fragment at m/z 85 of the butyl esters yields highly diagnostic acylcarnitine profiles. Analysis time is one minute per sample and is fully automated. Examples are given of normal profiles, of profiles from two patients with fatty acid oxidation defects, and of a case of propionic acidemia. The technique is simple, rapid and specific, and shows potential for routine application in neonatal screening of organic acidemias.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: A termination synthesis approach has been developed to encode each resin bead in support-bound combinatorial peptide libraries with the information needed to establish the sequence of the full-length products also contained on the beads. Matrix-assisted laser desorption ionization mass spectrometry was then used to rapidly read the appropriate sequences. In addition to rapid peptide sequencing, the technique allows direct assessment of the quality of the synthetic library, since deletion peptides, side-reaction products and incomplete-deprotection products are readily observed. An anti-gp120 monoclonal antibody was screened against a hexapeptide library, and eight active peptides were isolated. Six of the eight peptides were shown to possess the exact recognition sequence for the antibody.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Rapid Communications in Mass Spectrometry 8 (1994), S. 371-376 
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: Analysis by thermospray of glucuronide and glutathione conjugates as the corresponding methyl-, propyl-, or hexyl esters is demonstrated to yield a remarkable increase in positive pseudomolecular ion production and to result in a dramatic improvement in detectability of these thermally labile compounds as intact molecular structures. In the most extreme examples a 450-fold increase in the [M + NH4]+ ion intensity was observed for mycophenolic acid glucuronide bis-propyl esters vs. the native conjugate and an 860-fold increase in the [M + H]+ ion intensity was achieved for acetaminophen glutathione bis-hexyl ester vs. the native conjugate. Following esterification, seventeen of the eighteen glucuronide esters analyzed demonstrated an increase in totalion-current yield ranging from 1.1- to 8.3-fold while eighteen of the twenty-one glutathione esters examined demonstrated an increase in totalion-current yield from 2.0- to 26.3-fold. For both types of conjugates a trend in increased relative abundance of the positive pseudomolecular ion intensity is observed as the hydrophobicity of the ester increases from methyl to hexyl. For the glutathione conjugate esters, the [M + H]+ ion represented the base peak in the mass spectra of the majority of samples analyzed. This approach improves the protonated- or ammoniated-molecular-ion abundances of the conjugates to such an extent that it provides a means for unambiguous molecular weight assignments to be made. Although the exact mechanism(s) for the observed phenomenon is not known, it appears that the improvement in sensitivity for the conjugate esters over the corresponding native conjugates involves an increase in pseudomolecular-ion stability and also in part an increased ionization efficiency of the esterified molecule.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Rapid Communications in Mass Spectrometry 8 (1994), S. 65-70 
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: Liquid secondary-ion mass spectrometry (LSIMS) experiments were performed on a series of model quaternary ammonium chlorides [MQ+Cl-] in order to develop a strategy, via an understanding of cluster-ion formation, for recognition of quarternary ammonium structures. Model structures contained a single quaternary site and various other structural features (for example, conjugated quaternary systems and carboxylic acid groups), using amine hydrochlorides as controls. Cluster ions were examined with both positive- and negative-ion LSIMS, using a range of matrix modifiers. Precursor scans, or ‘molecular weight confirmation scans’, of MQ+ (the charged molecular ion of quaternary ammonium compounds) and [M+H]+ ions were used to assist in the observation of cluster ions and to unambiguously demonstrate precursor/product relationships. Positive-ion experiments typically showed dimeric clusters of [2MQ+ A]+ (A=anion) and [2MQ-H]+ ions, while negative ion experiments produced [MQ + 2A]- ions. Observation of these cluster ions coupled with the lack of an [M-H]- ion are a distinguishing feature of quaternary amines. Additional cluster ions were targeted for distinguishing between protonated amines and quaternary amonium compounds containing a carboxylic acid group. A strategy for recognizing and distinguishing quaternary ammonium structures using LSIMS is proposed, and some initial experiments with thermospray and electrospray are discussed.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1076-5174
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: In a study designed to examine the nature of short-lived, electrophilic intermediates liberated during decomposition of N,N′-bis(2-chloroethyl)-N-nitrosourea (BCNU) in vitro and also on administration of BCNU (140 μmol i.p.) to rats in vivo, both on-line and off-line LC/MS/MS techniques were employed to detect and characterize the corresponding glutathione (GSH) adducts present in incubation media and excreted into bile, respectively. In vitro, four GSH conjugates were formed and these were identified, on the basis of their product ion spectra, as products of S-and N-carbamoylation and alkylation reactions. Although the relative proportions of these in vitro adducts were found to depend on the molar ratios of GSH and BCNU, the major adduct under all conditions studied proved to be S-(2-chloroethylcarbamoyl)glutathione (SCG). Analysis of untreated bile samples by means of on-line LC/MS/MS with constant neutral loss (129 u) and precursor ion (m/z 179) scanning techniques again led to the detection of four GSH conjugates, although only one of these (SCG) was common to the group of adducts identified in vitro. All of the GSH conjugates detected in bile represented products of S-carbamoylation, indicating that the alkylating moiety released from BCNU undergoes reactions in vivo with nucleophiles other than GSH.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Density functional theory is tested on a large ensemble of model compounds containing a wide variety of functional groups to understand better its ability to reproduce experimental molecular geometries, relative conformational energies, and dipole moments. We find that gradient-corrected density functional methods with triple-ζ plus polarization basis sets reproduce geometries well. Most bonds tend to be approximately 0.015 Å longer than the experimental results. Bond angles are very well reproduced and most often fall within a degree of experiment. Torsions are, on average, within 4 degrees of the experimental values. For relative conformational energies, comparisons with Hartree-Fock calculations and correlated conventional ab initio methods indicate that gradient-corrected density functionals easily surpass the Hartree-Fock approximation and give results which are nearly as accurate as MP2 calculations. For the 35 comparisons of conformational energies for which experimental data was available, the root mean square (rms) deviation for gradient-corrected functionals was approximately 0.5 kcal mol-1. Without gradient corrections, the rms deviation is 0.8 kcal mol-1, which is even less accurate than the Hartree-Fock calculations. Calculations with extended basis sets and with gradient corrections incorporated into the self-consistent procedure generate dipole moments with an rms deviation of 5%. Dipole moments from local density functional calculations, with more modest basis sets, can be scaled down to achieve roughly the same accuracy. In this study, all density functional geometries were generated by local density functional self-consistent calculations with gradient corrections added in a perturbative fashion. Such an approach generates results that are almost identical to the self-consistent gradient-corrected calculations, which require significantly more computer time. Timings on scalar and vector architectures indicate that, for moderately sized systems, our density functional implementation requires only slightly less computer resources than established Hartree-Fock programs. However, our density functional calculations scale much better and are significantly faster than their MP2 counterparts, whose results they approach. © 1995 John Wiley & Sons, Inc.
    Additional Material: 8 Tab.
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  • 9
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A combined theoretical and experimental study of the binding and interaction of valproic acid (VPA) with the bacterial cytochrome P450cam enzyme and the determination of regio- and stereoselective hydroxylation product distribution was performed. From the experiments, C4—;OH VPA was found to be the predominant hydroxylation product with a small amount of C5—OH VPA formed. The experimental stereoselectivity of hydroxylation was 2R4S 〉 ∼ 2S4R 〉 2R4R 〉 ∼ 2S4S and 2S5 〉 ∼ 2R5. The overall goals of the theoretical study were twofold: (1) to characterize as completely as possible, using energy optimization and molecular dynamics simulations, the interactions of flexible ligands with their target proteins, and (2) to determine the extent to which these results could be used to develop criteria to predict or explain the experimentally observed regio- and stereoselectivity of hydroxylation of the flexible ligands. Among the useful insights into the behavior of flexible ligands upon binding to their traget proteins obtained are (1) a large change in conformation occurs for many conformers of VPA upon binding to P450cam, (2) low- energy conformers of VPA do not necessarily lead to optimum interactions with the target protein, and (3) the most favorable mode of interaction of this flexible ligand with the protein binding site has been identified and found to be a result of strong electrostatic interactions between VPA and both Tyr96 and Asp297. For the study of the hydroxylated VPA products, the challenging aspect of this problem was to determine criteria for weighing the contribution of each of the possible protein-ligand complexes. To this end, various possibilities were examined and compared with the experimental results. No single complex was found to reproduce the observed experimental regio- and stereoselectivity. This result indicates that more than one bioactive form of VPA contributes to its oxidation. Results most consistent with experiment are obtained by using the interaction energy of the protein-ligand complex as a criterion for including its contribution to product formation. Although there are remaining disparities between predicted and observed product distributions, the combined theoretical and experimental effort has led to insights into the modes of interaction of this flexible ligand that lead to its observed product specificity. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Mass Spectrometry Reviews 14 (1995), S. 353-382 
    ISSN: 0277-7037
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: Foundations of isotope effects are examined in terms of concepts, models, and theories. Leading instrumental methods for bimoleculur reactions are reviewed: the guided ion beum mass spectrometer (GIBMS) and the selected ion flow tube (SIFT). In their most elaborate forms, both methods can select the translational energies of the reacting ions and the temperatures of the neutral molecules. This capability gives extraordinary control over bimolecular ion/molecule reactions. Experiments on simple systems can sometimes identify the effects of particular forms of internal energy. Isotope effects appear in numerous reaction types and behave in several ways as functions of ion translational energy and temperature. For endothermic reactions, they can become very large at low temperatures, a matter of much interest in astrophysics. © 1996 John Wiley & Sons, Inc.
    Additional Material: 23 Ill.
    Type of Medium: Electronic Resource
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