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  • Cell & Developmental Biology  (25,032)
  • Theoretical, Physical and Computational Chemistry  (1,576)
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  • Wiley-Blackwell  (26,608)
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  • 1
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    Electronic Resource
    Extensive apoptotic death of rat colonic cells deprived of crypt habitat (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 377-386 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Apoptosis in cells of different lineages is restrained by survival signals which depend upon cell-to-cell communication. The aim of this study was to determine whether colonic cells deprived of crypt ambient are doomed to die prior to their normal chronological demise. Apoptosis was studied in rat whole colonic tissue, in isolated intact crypts, and in colonic cell populations collected from the crypt axis at different stages of proliferation and differentiation. In a number of experiments, cell harvest was performed in the presence of either a tetrapeptide (YVAD-CMK) inhibitor of interleukin-1β-converting enzyme (ICE), or tyrphostin A25, a protein tyrosine kinase inhibitor, or sodium-orthovanadate, a phosphatase inhibitor. DNA fragmentation was assessed by electrophoretic and nonisotopic-labeling procedures. The ultrastructure of colonic tissue specimens and isolated cells was examined by transmission electron microscopy. Apoptosis in whole colonic tissue and in isolated crypts was confined predominantly to cells resident in the upper crypt regions. In contrast, extensive apoptotic death was observed in isolated colonic cells, irrespective of their developmental stage and positional hierarchy within the crypt continuum at harvest time. An apoptotic gradient, however, was evident. Exposure to YVAD-CMK resulted in a marked decrease in the number of apoptotic cells. Treatment with tyrphostin A25 caused a sharp rise in the apoptotic index; conversely, vanadate significantly impeded apoptosis. Cumulatively, these results indicate that disordered intercellular communication provokes unscheduled ICE-mediated apoptosis of colonocytes, and that local signals along the crypt continuum control both the reprieve from death and the timely demise of distinct colonic cell populations. Attenuation of tyrosine phosphorylation may be a contributory event in the acquisition of the apoptotic phenotype. J. Cell. Physiol. 177:377-386, 1998. © 1998 Wiley-Liss, Inc.
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  • 2
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    Integration of the central death pathway in cellular decision-making (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 518-524 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: No abstract.
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  • 3
    Electronic Resource
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    Molecular genetics of the germinal center reaction (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 525-534 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: No abstract.
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  • 4
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    In vivo evaluation of hsp27 as an inhibitor of actin polymerization: Hsp27 limits actin stress fiber and focal adhesion formation after heat shock (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 575-584 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The role of hsp27 as an inhibitor of actin polymerization was considered in the context of the actin cytoskeleton and its relationship with focal adhesion formation. The aim of this study was to evaluate the potential effects of hsp27 on focal adhesion formation as a relevant biological consequence of actin stress fiber formation. When hsp27 was overexpressed in stably transfected cells, cell attachment was delayed and recovery of disrupted stress fibers and focal adhesions was limited. In ROS 17/2.8 cells, heat shock caused the reversible disruption of stress fibers and focal adhesions. The loss of stress fibers and focal adhesions was associated with reduced phosphotyrosine on the focal adhesion kinase (FAK). Microinjection of recombinant 6-His hsp27 and phosphorylated 6-His hsp27 was used to demonstrate that nonphosphorylated hsp27 prevented the recovery of stress fibers and focal adhesions. These results provide in vivo evidence that hsp27 acts as an inhibitor of actin polymerization that can alter cellular interactions with extracellular environments by perturbation of stress fibers, and subsequently focal adhesions. J Cell Physiol 177:575-584, 1998. © 1998 Wiley-Liss, Inc.
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  • 5
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    Long-term expression of differentiated functions in hepatocytes cultured in three-dimensional collagen matrix (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 553-562 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Hepatocytes entrapped in collagen gel and cultured in serum-free conditions survived longer than cells cultured on plastic (5 days vs. 3 weeks), showed fewer signs of early cell senescence (no increase in c-fos oncoprotein expression), and maintained the expression of differentiated hepatic metabolic functions over a longer period of time. Cells cultured in collagen gels retained their ability to respond to hormones. The insulin-stimulated glycogen synthesis rate remained fairly constant during 18 days in culture (between 5.4 ± 0.37 and 9 ± 2.7 nmol glucose/h/μg DNA). Collagen-cultured hepatocytes recovered glycogen stores to levels similar to those found in liver, or in hepatocytes isolated from fed rats. Urea synthesis from ammonia remained stable for more than 2 weeks (average value, 23 ± 4 nmol urea/h/μg DNA). The rate of albumin synthesis in collagen-entrapped cells was maintained above the day-1 level during 18 days in culture. Cells showed high levels of glutathione (GSH) (1,278 ± 152 pmol/μg DNA). Biotransformation activities CYP4501A1, CYP4502A2, CYP4502B1, and CYP4503A1 remained fairly stable in collagen-cultured hepatocytes. CYP4502E1 and CYP4502C11 decreased but were still measurable after 18 days. After 4 days in culture, GST activity returned to levels observed in isolated hepatocytes. In contrast with plastic cultures, cells responded to CYP450 inducers (methylcholanthrene for CYP4501A1, CYP4501A2, and gluthatione-transferase, and ethanol for CYP4502E1) for more than 2 weeks. CYP4501A1, CYP4501A2, and glutathione-transferase A2 (GST A2) induction was preceded by an increase in specific mRNA, while the effects on CYP4502E1 seemed to be at a posttranslational level. Analysis of the expression of relevant hepatic genes by reverse Northern and semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that culturing hepatocytes in collagen gels results in a sustained higher expression of key liver transcription factor genes DBP, C/EBP-α and -β, and HNF-1 and -4, as well as specific liver enzyme genes (phosphoenol pyryvate carboxykinase, and carbamoylphosphate-synthetase I). J Cell Physiol 177:553-562, 1998. © 1998 Wiley-Liss, Inc.
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  • 6
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    Physiological signals and oncogenesis mediated through Crk family adapter proteins (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 535-552 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The viral Crk oncogene (v-Crk) is known to induce sarcomas in chicken and its cellular homologs c-Crk I, c-Crk II, and Crk-like (CRKL) have been implicated in many signal transduction events. These include cell differentiation, cell migration, and the induced nonresponsiveness of T-cells to stimulation of the T-cell receptor (TCR), a state known as anergy. CRKL is also the most prominent substrate of the Bcr-Abl oncoprotein which causes human chronic myelogenous leukemias (CML). The modular composition of the Crk family adapters which largely consist of Src homology (SH2 and SH3) domains has prompted an intensive search for physiological and pathological upstream and downstream signalling partners which selectively bind to these adapters. Upstream proteins include various receptors and large multisite docking proteins, while several protein kinases and guanine nucleotide release proteins (GNRPs) have been suggested to function downstream of c-Crk and CRKL. Most Crk/CRKL SH2- and SH3-binding proteins contain several docking sites with considerable sequence similarity. Thus the binding requirements of Crk/CRKL SH2 and SH3 domains are now well defined, providing a basis for the design of small inhibitory molecules to block the function of these adapter proteins. The enzymatic cascades activated through Crk family adapters are only partially known, but stress kinases (SAPKs/JNKs) and the GTPase Rap1, as well as the B-Raf isoform of the Raf protein kinases, are affected in some systems. Several yet unidentified, highly selective Crk interacting proteins detectable in specific cell types remain to be studied. More detailed analyses of the enzymatic activities triggered through Crk-type adapters will also be crucial to fully define the signalling pathways controlled by this protein family. J Cell Physiol 177:535-552, 1998. © 1998 Wiley-Liss, Inc.
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  • 7
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    Regulation of the collagenase-3 receptor and its role in intracellular ligand processing in rat osteoblastic cells H.W.W. and P.T.C. contributed equally to this work. (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 563-574 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have previously described a specific, saturable receptor for rat collagenase-3 in the rat osteosarcoma cell line, UMR 106-01. Binding of rat collagenase-3 to this receptor is coupled to the internalization and eventual degradation of the enzyme and correlates with observed extracellular levels of the enzyme. In this study we have shown that decreased binding, internalization, and degradation of 125I-rat collagenase-3 were observed in cells after 24 h of parathyroid hormone treatment; these activities returned to control values after 48 h and were increased substantially (twice control levels) after 96 h of treatment with the hormone. Subcellular fractionation studies to identify the route of uptake and degradation of collagenase-3 localized intracellular accumulation of 125I-rat collagenase-3 initially in Golgi-associated lysosomes and later in secondary lysosomes. Maximal lysosomal accumulation of the radiolabel and stimulation of general lysosomal activity occurred after 72 h of parathyroid hormone treatment. Preventing fusion of endosomes with lysosomes (by temperature shift, colchicine, or monensin) resulted in no internalized 125I-collagenase-3 in either lysosomal fraction. Treatment of UMR cells with the above agents or ammonium chloride decreased excretion of 125I-labeled degradation products of collagenase-3. These experiments demonstrated that degradation of collagenase-3 required receptor-mediated endocytosis and sequential processing by endosomes and lysosomes. Thus, parathyroid hormone regulates the expression and synthesis of collagenase-3 as well as the abundance and functioning of the collagenase-3 receptor and the intracellular degradation of its ligand. The coordinate changes in the secretion of collagenase-3 and expression of the receptor determine the net abundance of the enzyme in the extracellular space. J Cell Physiol 177:563-574, 1998. © 1998 Wiley-Liss, Inc.
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  • 8
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    Metabolic depletion inhibits the uptake of nontransferrin-bound iron by K562 cells (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 585-592 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The effect of metabolic inhibitors on nontransferrin bound iron transport by K562 cells was investigated. Incubation with 1 μM rotenone, 10 μM antimycin, or 0.5 mM 2,4-dinitrophenol effectively reduced ATP levels by ∼50%. Both the rate and extent of Fe+3 uptake were impaired in ATP-depleted cells, which display a reduced Vmax for uptake. K562 cell ferrireductase activity was also lowered by metabolic inhibitors, suggesting that the apparent energy requirements for transport reside in the reduction of Fe+3 to Fe+2. However, ATP depletion was found to inhibit the rate and extent of Fe+2 uptake as well. Thus, the transbilayer passage of Fe+2 and/or Fe+3 appears to be an energy-requiring process. These features possibly reflect properties of the transport mechanism associated with a recently identified K562 cell transport protein, called SFT for “Stimulator of Fe Transport,” since exogenous expression of its activity is also affected by ATP depletion. J Cell Physiol 177:585-592, 1998. © 1998 Wiley-Liss, Inc.
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  • 9
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    Differential regulation of the clusterin gene by Ha-ras and c-myc oncogenes and during apoptosis (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 593-605 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Clusterin (ApoJ) is an extracellular glycoprotein expressed during processes of tissue differentiation and regression that involve programmed cell death (apoptosis). Increased clusterin expression has also been found in tumors, however, the mechanism underlying this induction is not known. Apoptotic processes in tumors could be responsible for clusterin gene activation. Alternatively, oncogenic mutations could modulate signal transduction, thereby inducing the gene. We examined the response of the rat clusterin gene to two oncogenes, Ha-ras and c-myc, in transfected Rat1 fibroblasts. While c-myc overexpression did not modify clusterin gene activity, the Ha-ras oncogene produced a seven to tenfold repression of clusterin mRNA; this down-regulation was also observed in the presence of c-myc. Since no induction of the clusterin gene was observed by the two oncogenes, we tested the alternative mechanism involving apoptosis. Growth factor withdrawal induced apoptosis, as shown by DNA degradation and micronuclei formation in the floating cells. Concomittantly we observed a three to tenfold increase in the amount of clusterin mRNA in the adhering cells of Rat1 and the c-myc transformed cell lines, and a weaker induction in the Ha-ras transformed cell line. On the basis of our results, we suggest that clusterin gene induction in the vital cells is produced by signaling molecules that are generated by the apoptotic cells. We conclude that apoptotic processes, not oncogenic mutations, are responsible for increased clusterin expression in tumors. J Cell Physiol 177:593-605, 1998. © 1998 Wiley-Liss, Inc.
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  • 10
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    Enterocytic differentiation of the human Caco-2 cell line correlates with alterations in integrin signaling (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 618-627 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We previously reported that the enterocytic differentiation of human colonic Caco-2 cells correlated with down-regulation of fibronectin (FN) and laminin (LN), two extracellular matrix components interacting with cell surface integrin receptors. We now investigated whether Caco-2 cell differentiation was associated with alterations in integrin signaling with special interest in the expression and activity of focal adhesion kinase (FAK) and mitogen-activated protein (MAP) kinase. The differentiation of Caco-2 cells was associated with: (1) down-regulation of β1 integrin expression at the mRNA and protein levels; (2) increased FAK expression together with decreased FAK autophosphorylation; (3) decreased FAK's ability to associate with PI3-kinase and pp60c-src; and (4) increased MAP kinase expression along with decreased MAP activity. In addition, we show that FAK and MAP kinase belong to distinct integrin signaling pathways and that both pathways remain functional during Caco-2 cell differentiation since the coating of differentiating cells on FN and LN but not on polylysine increased the tyrosine phosphorylation of FAK and of its endogenous substrate paxillin, and stimulated MAP kinase activity. In conclusion, our results provide evidence that FAK and MAP kinase, two signaling molecules activated independently by β1 integrins in Caco-2 cells, undergo alterations of both expression and activity during the enterocytic differentiation of this cell line. J Cell Physiol 177:618-627, 1998. © 1998 Wiley-Liss, Inc.
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  • 11
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    Growth factor regulation of the amylase promoter in a differentiating salivary acinar cell line This article is a US Government work and, as such, is in the public domain in the United States of America. (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 628-635 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Salivary glands contain two major epithelial cell types: acinar cells which produce the primary salivary secretion, including amylase, and ductal cells which reabsorb electrolytes but also secrete kallikrein. Here we investigated salivary acinar cell differentiation in vitro using the activity of the salivary amylase and tissue kallikrein promoters as markers of acinar cell and ductal cell differentiation, respectively. Each of the promoter sequences was cloned into a replication-deficient adenoviral vector containing the luciferase reporter gene. Previous studies showed that a human submandibular gland cell line (HSG) differentiated into acinar cells when cultured on a reconstituted basement membrane matrix (Matrigel). The luciferase activity of the amylase promoter vector (AdAMY-luc) was low in HSG cells cultured on plastic, where they grow as an epithelial monolayer. The promoter activity increased approximately tenfold when HSG cells were cultured on Matrigel and developed an acinar phenotype. Under the same conditions, the luciferase activity of the kallikrein promoter (AdKALL-luc) was not induced. Because HSG cells demonstrate acinar cell morphology, but not amylase gene expression, when cultured on laminin-1, certain soluble components of Matrigel were tested for their ability to induce the amylase promoter during in vitro differentiation of acinar cells. We find that epidermal growth factor (EGF) and transforming growth factor-alpha (TGF-α), which are present in the basement membrane, and hepatocyte growth factor (HGF) increase activity of the amylase promoter. Other basement membrane-derived growth factors such as TGF-β, basic fibroblast growth factor (bFGF), and platelet-derived growth factor (PGDF), as well as tumor necrosis factor (TNF-α), keratinocyte growth factor (KGH), nerve growth factor (NGF) and interferon gamma (IFN-γ) were inactive. This system will be further exploited to study the mechanisms by which extracellular matrix molecules and growth factors regulate salivary acinar cell differentiation. J Cell Physiol 177:628-635, 1998. Published 1998 Wiley-Liss, Inc.
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  • 12
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    Expression of HSP27 results in increased sensitivity to tumor necrosis factor, etoposide, and H2O2 in an oxidative stress-resistant cell line (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 606-617 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The role of HSP27 in cell growth and resistance to stress was investigated using murine fibrosarcoma L929 cells (normally devoid of constitutively expressed small HSPs) and human osteoblast-like SaOS-2 cells stably transfected with a human hsp27 expression vector. Our data showed that our L929 cells were more resistant to oxidative stress than generally observed for this line. Production of HSP27 in these cells led to a marked decrease in growth rate associated with a series of phenotypical changes, including cell spreading, cellular and nuclear hypertrophy, development of an irregular outline, and a tremendous accumulation of actin stress fibers. By contrast, none of these changes was observable in SaOS-2/hsp27 transfectants overexpressing the protein product. Together, these observations are consistent with a cause-to-effect cascade relationship between increased (or induced) HSP27 expression, changes in cytoskeletal organization, and decreased growth. On the other hand, whereas the transfection of the hsp27 gene increased the cell resistance to heat in both cell lines, only in SaOS-2 cells was this associated with protection to the cytotoxic action of tumor necrosis factor-alpha (TNF-α) and etoposide. Unexpectedly, L929/hsp27 transfectants exhibited an increased sensitivity to both agents and also to H2O2. These data thus imply that different mechanisms are involved in the cell resistance to heat shock and to the cytotoxic action of TNF-α, etoposide, and H2O2. They also plead against the simple view that overexpression of a phosphorylatable HSP27 would necessarily be beneficial in terms of increased cell resistance to any type of stress. Our data further indicate that the role of HSP27 in cellular resistance to stress and in cell proliferation involves different targets and that the ultimate result of its interference with these processes depends on the intracellular context in which the protein is expressed. J Cell Physiol 177:606-617, 1998. © 1998 Wiley-Liss, Inc.
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  • 13
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    Isolation and characterization of a cDNA clone encoding a novel peptide (OSF) that enhances osteoclast formation and bone resorption (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 636-645 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Using an expression cloning approach, we identified and cloned a novel intracellular protein produced by osteoclasts that indirectly induces osteoclast formation and bone resorption, termed OSF. Conditioned media from 293 cells transiently transfected with the 0.9 kb OSF cDNA clone stimulated osteoclast-like cell formation in both human and murine marrow cultures in the presence or absence 10-9 M 1,25-dihydroxyvitamin D3. In addition, conditioned media from 293 cells transfected with the OSF cDNA clone enhanced the stimulatory effects of 1,25-(OH)2D3 on bone resorption in the fetal rat long bone assay. In situ hybridization studies using antisense oligomers showed expression of OSF mRNA in highly purified osteoclast-like cells from human giant cell tumors of the bone. Northern blot analysis demonstrated ubiquitous expression of a 1.3 kb mRNA that encodes OSF in multiple human tissues. Sequence analysis showed the OSF cDNA encoded a 28 kD peptide that contains a c-Src homology 3 domain (SH3) and ankyrin repeats, suggesting that it was not a secreted protein, but that it was potentially involved in cell signaling. Consistent with these data, immunoblot analysis using rabbit antisera against recombinant OSF demonstrated OSF expression in cell lysates but not in the culture media. Furthermore, recombinant OSF had a high affinity for c-Src, an important regulator of osteoclast activity. Taken together, these data suggest that OSF is a novel intracellular protein that indirectly enhances osteoclast formation and osteoclastic bone resorption through the cellular signal transduction cascade, possibly through its interactions with c-Src or other Src-related proteins. J Cell Physiol 177:636-645, 1998. © 1998 Wiley-Liss, Inc.
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  • 14
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    Atomic calculations with an augmented Fourier basis (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 189-197 
    Details
    ISSN: 0020-7608
    Keywords: atomic Hartree-Fock ; augmented Fourier basis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a scheme for Hartree-Fock and related calculations on atoms using a Fourier basis augmented by an exponential function. All multiple sums in the variational energy expression are written as single sums over combinations of multiplications and convolutions. The computational cost of the method is thus practically linear in the number of basis functions. The results compare favorably with the most precise published results of numerical grid methods and variational calculations.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 189-197, 1998
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    Symmetry aspects of nonrigid molecules and transition structures in chemical reactions (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 205-217 
    Details
    ISSN: 0020-7608
    Keywords: potential energy surface ; transition structure ; nonrigid molecule ; symmetry group ; reaction path ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The symmetry group of a nonrigid molecule is related to that of the transition structure that is related to the rearrangement process which contributes to the “nonrigidity” of the molecular system. The resulting permutation/rotation/reflection groups for nonrigid molecules can be much larger in order than the usual Longuet-Higgins permutation/inversion group. A few examples are presented to illustrate the definition of the symmetry group for nonrigid molecules.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 205-217, 1998
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    Some recent developments of high-order response theory (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 219-239 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We review some recent developments of high-order response theory and illustrate the utility of this theory for a selection of nonlinear properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 219-239, 1998
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    Density functional investigations of carboxyl free radicals: Formyloxyl, acetyloxyl, and benzoyloxyl radicals (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 253-267 
    Details
    ISSN: 0020-7608
    Keywords: DFT ; carbonyloxyl radicals ; CASPT2 ; chemical reactions ; isomerizations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the lowest electronic states of HCOO· in C2v and Cs symmetries were optimized employing density functional theory (DFT) methods with extended basis sets including up to f- (on C and O) and d- (on H) polarization functions. Generalized gradient functionals (BLYP) and adiabatically connected functionals (B3LYP and B3PW91) were employed for studying HCOO·, as well as the isomer HOCO· (trans), the dissociation limit H·+CO2, and the transition state for the decomposition. At the best DFT levels employed, the ground state of HCOO· is 2A1 (in C2v) with equal C—O bond lengths, while the low-lying 2B2 state is only about 4 kJ/mol above (without inclusion of zero-point energies). The broken-symmetry 2A′ state (with unequal C—O bond lengths, i.e., Cs symmetry) is predicted to be about 13 kJ/mol above the 2A1 state and to be a transition state for the isomerization HCOO· (2A1)→HOCO· (2A′), with the trans-HOCO· isomer about 55 kJ/mol more stable. These facts agree closely with the most recent CASPT2/ANO calculations on this system. Therefore, it is concluded that some DFT models can be used safely for the study of larger radicals of the same type (despite several drawbacks discussed at length in this study). B3PW91, using several basis sets, is subsequently applied to the study of the possible reaction mechanisms of acetyloxyl radical, which exhibits a much more complicated path than formyloxyl, due to the presence of the methyl group. The optimum structures of isomers with coplanar or perpendicular CH and CO bonds were obtained for CH3COO· and two saddle points identified on the path of decomposition into CH3· and CO2. On the other side, saddle points for isomerization into CH3OCO· and CH2COOH· were also located, and the decomposition of the former to CH3O·+CO investigated. Finally, the structure of the benzoyloxyl radical (C6H5COO·) and its possible decomposition products were investigated along the same lines.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 253-267, 1998
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  • 18
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    Spectroscopic constants and bonding features of the low-lying states of LiB and LiB+: Comparative study of VBSCF and MO theory (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 283-290 
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    ISSN: 0020-7608
    Keywords: LiB ; spectroscopic constants ; excited states ; VBSCF ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The common correspondence between molecular orbital theory and resonance theory in the description of the electronic structure of a molecule is used to select valence bond (VB) structures constructing wave functions of the low-lying states of LiB and LiB+. The spectroscopic parameters of the low-lying states of LiB and LiB are determined by using the valence bond self-consistent field (VBSCF) method. For comparison, multconfiguration SCF (MCSCF) calculations for LiB are also carried out. If the overlap-enhanced orbitals are employed, a compact VB wave function can correctly describe bond making and bond breaking in the entire dissociation process for the low-lying electronic states of LiB. All calculations locate the ground state as 3Π. The VB calculation with 14 VB structures at the level of the basis set DH(s, p) predicts an excellent dissociation energy of 1.16 eV and vibrational frequency of 527 cm-1 for the ground state, which is in good agreement with previous high-level calculations with a large basis set. The effect of the basis set on the numerical quality of the VBSCF calculation is investigated. It is important for improving accuracy of the VB calculation to enlarge the basis set, although the VB treatment including more VB structures with a relatively small basis set needed in the nonorthogonal VB calculation can reasonably describe dissociation behavior for systems with few electrons. The chemical bonds in the ground state 3Π and the excited state (1)3Σ- have ionicities of 63.4 and 65.1%, respectively, while chemical bond in the first excited state 1Σ+ is mainly covalent. Other several low-lying states are also investigated by the VB and MCSCF methods.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 283-290, 1998
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    Difficulties of density functional theory in predicting the torsional potential of 2,2′-bithiophene (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 303-312 
    Details
    ISSN: 0020-7608
    Keywords: bithiophene ; internal rotation ; DFT calculations ; MP2 calculations ; Fourier-fitted torsional potentials ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The internal rotation of 2,2′-bithiophene was investigated within the density functional theory (DFT) approach. Fully optimized DFT torsional potentials are compared with Møller-Plesset (MP2) results which predict a fourfold potential with s-cis- and s-trans-gauche minima. DFT calculations fail in describing the energetics of the internal rotation because they favor planar vs. perpendicular conformers. Gradient-corrected functionals provide torsional potentials where the gauche minima have almost vanished and the s-cis↔s-trans interconversion barriers are twice as high as the barriers obtained at the MP2 level. The use of local functionals augments the shortcomings of the DFT approach. The gauche minima completely disappear and the rotational barriers are now about three times higher than the MP2 barriers. As an efficient computational approach, we suggest having geometries optimized at the DFT level and conformational energies evaluated via single-point MP2 calculations. The fitting of MP2//DFT energies to truncated Fourier expansions allows one to predict the torsional angles and the relative energies of the critical points of the rotational potential with an accuracy similar to that afforded by MP2 calculations including full geometry optimization.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 303-312, 1998
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    Ab initio study on the reaction 2NH2→NH+NH3 (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 321-329 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The geometries of the reactant, products, and transition state of the title reaction were optimized at the UHF and UMP2 levels with the double and triple zeta basis sets as well as polarization functions by using the energy-gradient method. The potential-energy barrier for this reaction is 3.73 kcal/mol at the UMP-SAC4 level of theory. The intrinsic reaction coordinate (IRC) was performed at the UMP2/6-311G** level. The changes of the geometry and the bound vibrational modes along the IRC were analyzed. To obtain a more reliable potential-energy curve for the study of the reaction dynamics, the UMP2 energy profile was refined along the IRC with the UQCISD(T) and UMP-SAC4 levels of theory. The theoretical rate constants calculated by the conventional and the variational transition-state theories at the UMP-SAC4 level agree approximately with the experimental values in the high-temperature range from 2000 to 3000 K and are not affected by the variation and quantum effects.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 321-329, 1997
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    Electronic structure of alumina surface (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 341-350 
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    ISSN: 0020-7608
    Keywords: alumina ; periodic SCF ; surface potential ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic structure of the (001) and (110) α-alumina surfaces was determined by periodic Hartree-Fock method in statically relaxed geometries. Both (001) and (110) surfaces generate specific surface states into the energy gap. Significant influence of charge-transfer effect on the surface-adsorbate potential is possible in both cases studied. The inclusion of the exponential part to the standard potential forms was suggested for the description of the interaction potential in such cases.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 341-350, 1998
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    Theoretical models for γ-Al2O3 (110) surface hydroxylation: An ab initio embedded cluster study (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 359-365 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A theoretical analysis of γ-Al2O3 (110) surface hydroxylation based on ab initio Hartree-Fock embedded cluster calculations was carried out. Both tetrahedral and octahedral Al sites were considered. These sites were modeled by a series of clusters of increasing size: Al8O3, Al12O5, and Al16O8, embedded in an array of point charges. The adsorption of water was found to be dissociative or nondissociative depending on the cluster size, although the mechanism clearly converges toward dissociation for the more reliable models in agreement with the experiment. This dependence can be explained in light of the basicity modification of surface oxide ions induced by the environment as well as by surface relaxation. Comparison of chemisorption energies suggests that the preferred site for hydroxylation is a low coordination tetrahedral aluminum.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 359-365, 1998
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    Electronic structure and catalytic properties of Waugh-type anion (NiMo9O32)6- (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 375-378 
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    ISSN: 0020-7608
    Keywords: electronic structure ; catalytic properties ; Wangh-type anion ; heteropoly compounds ; DV-Xα method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic structure of Waugh anion (NiMo9O32)6- has been calculated by the DV-Xα method. The electronic structure and catalytic behavior of the Waugh anion are discussed. At the same time, the difference in electronic structure and relationship in catalytic behavior between Waugh and Keggin anions are compared.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 375-378, 1998
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    Ab initio relative stability of a few conformers of bilirubin in vacuo and in aqueous solution (PCM) (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 395-405 
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    ISSN: 0020-7608
    Keywords: intramolecular H bonds ; gas-phase stability ; continuum solvent ; solvation free energy ; point charge model ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational properties of bilirubin present a considerable interest from the medical and biological points of view, because of the toxic pigment peculiar solubility features. Therefore, ab initio geometry optimizations at the 3-21G/SCF level were carried out on a few model-built structures of bilirubin, after substituting the methyl groups on the heteroaromatic rings with H atoms. The structures obtained show a varied network of H bonds, ranging from 0 to 6 H bonds for the lowest-energy conformer in vacuo. This conformer assumes a “ridge-tile” shape previously found in both MM/MD simulations [D. A. Lightner et al., J. Am. Chem. Soc. 114, 10123 (1992)] and semiempirical calculations [W. H. Shelver et al., Int. J. Quantum Chem. 44, 141 (1992)], but at the ab initio level, its computed H-bond geometrical parameters are fairly consistent with the X-ray observed ones. The relative stability of all the structures is compared in vacuo and in aqueous solution using the polarizable continuum model (PCM) of the solvent, whose stabilizing effect, however, is not sufficient to fill the large energy gap between the less lipophilic conformers and the most stable one in vacuo, in agreement with previous CD measurements. The energetic cost imposed to the solvent effect by each intramolecular H bond is almost constant if the other structural features do not change appreciably. The trend of the purely electrostatic results obtained employing a partial charge model of bilirubin is analogous to that produced by its polarized ab initio charge distribution.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 395-405, 1998
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    Products of arbitrary class-sums in the symmetric group (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 429-440 
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    ISSN: 0020-7608
    Keywords: symmetric group ; class-sums ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An algorithm for the evaluation of products of arbitrary conjugacy class-sums in the symmetric group is conjectured. This algorithm generalizes a procedure presented sometime ago, which deals with products in which at least one of the class-sums involved consists of a single cycle (and an appropriate number of fixed points). Let the support size of a conjugacy class be the number of indices that are not fixed points. The algorithm proposed implies that the coefficient of the class-sum C in the product of the class-sums A and B is given in terms of a well-defined enumeration problem within the symmetric group Sp, where p is the smallest of the support sizes of A, B, and C.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 429-440, 1998
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    Femtosecond quantum fluid dynamics of helium atom under an intense laser field (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 441-474 
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    ISSN: 0020-7608
    Keywords: quantum fluid dynamics ; atom-laser interaction ; femtosecond dynamics ; density functional theory ; high harmonic generation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comprehensive, nonperturbative, time-dependent quantum mechanical (TDQM) approach is proposed for studying the dynamics of a helium atom under an intense, ultrashort (femtoseconds) laser pulse. The method combines quantum fluid dynamics (QFD) and density functional theory. It solves a single generalized nonlinear Schrödinger equation of motion (EOM), involving time and three space variables, which is obtained from two QFD equations, namely, a continuity equation and an Euler-type equation. A highly accurate finite difference scheme along with a stability analysis is presented for numerically solving the EOM. Starting from the ground-state Hartree-Fock density for He at t=0, the EOM yields the time-dependent (TD) electron density, effective potential surface, difference density, difference effective potential, ground-state probability, 〈r〉, magnetic susceptibility, polarizability, flux, etc. By a Fourier transformation of the TD dipole moment along the linearly polarized-field direction, the power and rate spectra for photoemission are calculated. Eleven mechanistic routes for photoemission are identified, which include high harmonic generation as well as many other spectral transitions involving ionized, singly excited, doubly excited (autoionizing), and continuum He states, based on the evolution of the system up to a particular time. Intimate connections between photoionization and photoemission are clearly observed through computer visualizations. Apart from being consistent with current experimental and theoretical results, the present results offer certain predictions on spectral transitions which are open to experimental verification.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 441-474, 1998
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    Full variational molecular orbital method: Application to the positron-molecule complexes (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 491-501 
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    ISSN: 0020-7608
    Keywords: positron-molecule complex ; positron affinity ; full variational molecular orbital method ; nuclear wave function ; orbital relaxation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Optimal Gaussian-type orbital (GTO) basis sets of positron and electron in positron-molecule complexes are proposed by using the full variational treatment of molecular orbital (FVMO) method. The analytical expression for the energy gradient with respect to parameters of positronic and electronic GTO such as the orbital exponents, the orbital centers, and the linear combination of atomic orbital (LCAO) coefficients, is derived. Wave functions obtained by the FVMO method include the effect of electronic or positronic orbital relaxation explicitly and satisfy the virial and Hellmann-Feynman theorems completely. We have demonstrated the optimization of each orbital exponent in various positron-atomic and anion systems, and estimated the positron affinity (PA) as the difference between their energies. Our PA obtained with small basis set is in good agreement with the numerical Hartree-Fock result. We have calculated the OH- and [OH-; e+] species as the positron-molecular system by the FVMO method. This result shows that the positronic basis set not only becomes more diffuse but also moves toward the oxygen atom. Moreover, we have applied this method to determine both the nuclear and electronic wave functions of LiH and LiD molecules simultaneously, and obtained the isotopic effect directly.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 491-501, 1998
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    Ring currents in condensed ring systems (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 503-513 
    Details
    ISSN: 0020-7608
    Keywords: ring currents ; conjugated molecules ; Pariser-Parr-Pople model ; valence bond method ; correction vector technique ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied magnetism and aromaticity of polycyclic ring systems by analyzing ring currents for different circulations in these molecules. The technique employed for calculating ring currents uses correction vectors which implicitly includes all the eigenstates of the Hamiltonian in the space of the chosen configurations. We have employed the Pariser-Parr-Pople Hamiltonian and have carried out full configuration interaction (CI) calculations for small systems and approximate CI calculations for large systems. The systems studied include polyacenes, nonaromatic ring systems including the C60 fragments pyracylene, fluoranthene, and corannulene, and heteroatomic systems with upto two six-membered rings. We find that in polyacenes, the aromaticity of the extreme phenyl rings reduces with increasing number of phenyl rings in the system, and it saturates at ≈⅔ the benzene value. In systems containing nonaromatic rings, we find paramagnetic or diamagnetic behavior for different circulations depending upon the number of atoms in the chosen ring cycle, in agreement with the 4n+2 rule. In corannulene, the largest fragment of C60 we have studied, the five-membered ring is weakly diamagnetic while the six-membered ring is more diamagnetic, although much less than in isolated benzene. The ring structures with heteroatoms studied are pyridine, pyrimidine, and its isomers, s-triazine, quinoline and its isomer, and quinazoline and its isomers. All these have similar ring currents as in their purely carbon counterparts, although ions of these molecules show interesting behavior.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 503-513, 1998
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    Molecular surface electrostatic potentials of anticonvulsant drugs (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1137-1143 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The computed molecular surface electrostatic potentials of a group of anticonvulsants of various chemical types were investigated with the objective of identifying common features that may be related to their activities. The calculations were carried out with the density functional B3P86/6-31G* procedure, using HF/STO-3G*-optimized geometries. Analysis of several statistically based properties of the surface potentials indicates that the negative regions are of primary importance and that an optimum intermediate level of local polarity, or internal charge separation, is required.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1137-1143, 1998
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    Studies on the hydrogenation steps of the nitrogen molecule at the Azotobacter vinelandii nitrogenase site (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1159-1168 
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    ISSN: 0020-7608
    Keywords: nitrogenase ; nitrogen fixation ; INDO ; DFT ; PM3tm ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We follow the initial activation of the nitrogen molecule at the FeMo cofactor of nitrogenase and subsequently model the hydrogenation of N2 up to the fourth protonation step using the intermediate neglect of differential overlap quantum-chemical model. The results obtained favor a reaction mechanism going through hydrazido intermediates on the 4-Fe surfaces, externally to the FeMo cofactor. Calculations using density functional theory on smaller model systems also support the suggested mechanism over other possible schemes that involve early release of the first molecule of ammonia as a product of the enzymatic reaction. We also demonstrate that dielectric stabilization due to the protein around the cofactor could lower markedly the barrier for the product release as an ammonium ion.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1159-1168, 1998
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    Phytochrome structure: A new methodological approach (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1145-1157 
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    ISSN: 0020-7608
    Keywords: phytochrome ; absorption spectra ; semiempirical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Higher plants use the protein phytochrome as a photosensor. In physiological temperatures phytochrome exists in two forms: Pr and Pfr. The chromophore of phytochrome is an open-chain tetrapyrrole. On the pathway from Pr to Pfr four intermediates (Lumi-R, Meta-Ra, Meta-Rb, and Meta-Rc) can be distinguished, while only two (Lumi-F and Meta-F) can be seen on the way back from Pfr to Pr. We have used the x-ray structure of the C-Phycocyanin protein Fremyella diplosiphon bacteria as a template to build a model (∼200 atoms) that includes only the chromophore and five amino acids of the phytochrome (Arg316-Cys321-His322-Leu323-Gln324) around it. Using the existing experimental evidences, we have proposed a three-dimensional (3D) structure for Pr, Pfr, and intermediates and a mechanism for the photoisomerization as well. Structures were fully optimized using AM1 (Unichem package on a Cray J90-NACAD). Using the INDO/S method of Zerner and co-workers, we calculated the absorption spectra of the model compounds and compared them with the experimental data. The oscillator strength ratio is an indicator of the chomophore conformation in biliproteins. The calculated spectra reproduces well the spectra of the phytochrome (Pr, Pfr, and intermediates) except for the lower energy band. This result is attributed to the small number of amino acids in the models. The calculated ratios (fVIS/fUV-fosc of visible band over fosc of UV band and f2/f1-fosc of second absorption band over fosc of first absorption band) for the models match very well the experimental ratios obtained for the phytochrome (Pr, Pfr, and intermediates). This supports the proposed mechanism for the photoisomerization process.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1145-1157, 1998
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    RHF conformational analysis of the auxin phytohormones n-ethyl-indole-3-acetic acid (n=4, 5, 6) (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1169-1175 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: RHF/6-31G* investigations of 4-, 5-, and 6-ethyl(Et)-indole-3-acetic acid (IAA) yielded 11 symmetry-unique local minima with syn-periplanar orientation of the —COOH group for each of these compounds. The global minima are of C1 symmetry in all cases. Comparison with earlier results shows that ethylation or chlorination in position 5 or 6 introduces only minor changes on the orientation of the acetic acid side group, with no effect on the reaction paths related to this group. For 4-Et-IAA, the deviations from unsubstituted IAA are larger but preserve the pattern of reaction paths that is present in unsubstituted IAA, which is in contrast to 4-Cl-IAA, where local minima and reaction paths are completely different.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1169-1175, 1998
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    Parametric transform and moment indices in the molecular dynamics of n-alkanes (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1185-1194 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The integrated molecular transform (FTm) is a unitary numerical index of structure that is capable of uniquely representing different molecular structure conformations with the exception of enantiomers. Other molecular indices have been derived from FTm as well as from the normalized molecular moment (Mn), for example, the analogous electronic and charge transforms (FTe and FTc) and moments (Me and Mc). In this study, each of these indices was calculated for up to 10 sampled conformations of each of the C1-C10 normal alkanes as they were subjected to a standard annealing process. Statistical analyses of the resulting data in the individual series and subsequent box plots, permitting facile examination of those results, indicated that the respective transform indices (FTm, FTe, FTc) are unique, that is, with no statistically significantly overlap across the series. For the Mn and Me indices, the numerical values for methane overlapped those of ethane in the first instance and both ethane and propane in the second. The Mc index values overlapped in several instances in the series. Inasmuch as the noted molecular indices are based only on parameters of structural origin, these results have profound implications for the correlation and estimation of properties derived not only from a general structure representation, but also for those properties which may be dependent on specific molecular conformations. This includes the potential for indices of molecular flexibility and conformationally dependent atomic electron densities.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1185-1194, 1998
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    Optimal molecular connectivity descriptors for nitrogen-containing molecules (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1209-1215 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report on optimal molecular connectivity descriptors for nitrogen atoms in amines for use in structure-property correlations. The descriptors represent generalized molecular connectivity indices with adjusted diagonal entries in the adjacency matrices of the corresponding molecular graphs, such that the standard error in a regression for boiling points in a set of amines is minimized. Advantages of the so-optimized descriptors for multivariate regression analysis in structure-property-activity studies are discussed.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1209-1215, 1998
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    Unambiguous exchange-correlation energy density for Hooke's atom (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 583-589 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, we used Helmholtz's theorem to construct an unambiguous exchange-correlation energy density for use in density functional theory. This energy density requires only knowledge of the density dependence of the exchange-correlation energy functional, EXC, for its calculation. We calculate this energy density for Hooke's atom in three different regimes: the high-density (or weakly correlated) limit; a moderate density, comparable to that of the He atom; and a low density, in which the system is strongly correlated. We compare the exact unambiguous energy density with approximate energy densities found from approximate energy functionals. The exchange-correlation energy can be deduced directly from the density in the highly correlated limit and a new formula for the high-density limit of the correlation energy is given.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 583-589, 1998
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    Nonconventional partitioning of the many-body Hamiltonian for studying correlation effects (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 571-581 
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    ISSN: 0020-7608
    Keywords: partitioning ; level shift ; quasi-degenerate PT ; Dyson equation ; geminals ; excited states ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For the treatment of electron correlation, one most often uses the Møller-Plesset (MP) partition which defines the zero-order Hamiltonian through the spectral resolution of the Fockian. We investigate how the MP partitioning can be improved while still using the Hartree-Fock (HF) reference state; and how the HF wave function can be substituted by a correlated one preserving the formal simplicity of the HF-based approach. To improve the MPn result, we introduce a fine tuning of energy denominators replacing the HF orbital energies with the ionization potentials obtained from the second-order Dyson equation. As this equation usually tends to close the gaps, a slight decrease of the denominators is expected, inducing an improvement of low-order correlation energies. We keep the simplicity of the MP partitioning and handle Dyson corrections as simple level shifts. Substituting doubly filled HF orbitals by strongly orthogonal geminals, one introduces a correlated reference state which is variational, size-consistent, and properly describes single-bond dissociation. This wave function, the antisymmetrized product of strongly orthogonal geminals (APSG), offers a good starting point for further corrections. We show that the use of an APSG reference state in the equation-of-motion technique leads to Tamm-Dankoff approach (TDA) equations which account for correlation effects in electronic excitation energies.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 571-581, 1998
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    3,5-contracted Schrödinger equation: Determining quantum energies and reduced density matrices without wave functions (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 557-570 
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    ISSN: 0020-7608
    Keywords: electron correlation ; reduced density matrices ; N-representability ; cumulants ; particle-hole duality ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Through the 3,5-contracted Schrödinger equation (3,5-CSchE) quantum energies and 3-particle reduced density matrices (3-RDMs) are determined directly without wave functions. Since the 3,5-CSchE involves the 5-RDM, its solution is indeterminate without N-representability conditions. However, the indeterminacy of the 3,5-CSchE may be removed through a reconstruction strategy for building the 4- and 5-RDMs from the 3-RDM. We present a systematic procedure for obtaining corrections for Valdemoro's reconstruction functionals from two complementary approaches, the particle-hole duality and the theory of cumulants. With the cumulants we are able to demonstrate that we have obtained all terms in the reconstruction functionals which may be written as antisymmetric products of the lower rdms. The cumulants allow us to understand the reconstruction functionals in terms of a renormalized many-body perturbation theory. The reconstruction functionals also lead to a natural generalization of Wick's theorem for evaluating expectation values of fermionic annihilation and creation operators with respect to correlated reference states. Previous work [Phys. Rev. A 57, 4219 (1998)] has explored the determination of correlation energy and 2-RDMs through the 2,4-CSchE, also known as the density equation. Because the reconstruction functionals employed with the 3,5-CSchE depend only on the antisymmetric products of lower RDMs in constrast to those used with the 2,4-CSchE, the 3,5-CSchE method presented here does not require the solution of systems of linear equations during reconstruction or the storage of the reconstructed RDMs. Application of the 3,5-CSchE technique to a quasi-spin model generates ground-state energies and 2-RDMs similar in accuracy to single-double configuration interaction (SDCI). We employ a simple iterative procedure for the solution of the 3,5-CSchE without traditional diagonalization. The CSchE techniques offer an approximate solution of the N-representability problem and a new approach to electron correlation.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 557-570, 1998
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    More about the leaky aquifer function (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 623-626 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The leaky aquifer function W(x, y) is an incomplete Bessel function which has had application in hydrology and more recently in electronic-structure calculations. This article presents an expansion which improves the efficiency of the calculation of W in the only part of its range not treated adequately by previously published methods, namely, the regime where x and y are both larger than unity but one is much larger than the other.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 623-626, 1998
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    Excitation energies in Brillouin-Wigner-based multireference perturbation theory (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 613-622 
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    ISSN: 0020-7608
    Keywords: excitation energies ; dynamic correlation effects ; perturbation theory ; MBPT ; multireference perturbation theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present the formalism for the treatment of several states of the same symmetry in basis-set reduction (BSR), a form of second-order Brillouin-Wigner multireference perturbation theory, which incorporates the first-order correction of the primary-space wave function with respect to its orthogonal complement. We benchmark this method for some valence and some Rydberg excitations of four small molecules (O2, CO, ethene, and ozone). In direct comparison with the underlying MR-SDCI benchmark results, we find an average accuracy of 0.2 eV or better for the excitation energies of the molecules considered and demonstrate the stability of the method with increasing size of the basis set and primary space. We argue that the configuration-based approach in BSR allows an accurate description of dynamical correlation effects with minimal primary space wave functions, containing far fewer configurations than are required for a CASSCF-based perturbative treatment of the molecules.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 613-622, 1998
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    Approximate Brueckner orbitals and shakeup operators in electron propagator calculations: Applications to F- And OH- (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 651-658 
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    ISSN: 0020-7608
    Keywords: electron propagator ; propagator theory ; Brueckner orbitals ; anions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vertical electron detachment energies of F- and OH- have presented difficulties for perturbative electron propagator methods. A recently derived, nondiagonal, renormalized approximation and two additional improvements are studied here. These improvements are replacement of the Hartree-Fock reference determinant by a determinant of approximate Brueckner orbitals generated by a coupled-cluster doubles calculation and retention of correlation terms in the 2hp-2hp block of the superoperator Hamiltonian matrix. Agreement with experiment is significantly better with these methods. When Hartree-Fock orbitals are used, electron detachment energies are underestimated, but approximate Brueckner orbitals lead to overestimates.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 651-658, 1998
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    Excited states in density functional theory (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 681-691 
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    ISSN: 0020-7608
    Keywords: excited states ; Kato's theorem ; adiabatic connection ; optimized potential method ; KLI approximation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Density functional theory for a single excited state is presented using Kato's theorem and the concept of adiabatic connection. The degenerate case is also detailed. The optimized potential method is generalized. The generalized Krieger, Li, and Iafrate (KLI) approximation is derived.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 681-691, 1998
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    A density functional study of small nickel clusters (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 693-701 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small nickel clusters up to the tetramer are investigated within the framework of the local spin density functional theory. Several competitive states are studied for the dimer. Both the geometry and the spin state are optimized for several starting symmetries in the case of the trimer and the tetramer. Moreover, all those calculations are followed by a vibrational analysis in order to discriminate between real minima and saddle points on the potential energy surface. It is found that Jahn-Teller deformations play an important role in determining transition-metal cluster geometries. Equilibrium geometries, electronic configurations, binding energies, magnetic moments, and harmonic frequencies are reported in this work.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 693-701, 1998
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    Excited electronic states of carotenoids: Time-dependent density-matrix-response algorithm (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 711-727 
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    ISSN: 0020-7608
    Keywords: density matrix response functions ; N-scaling ; time-dependent Hartree-Fock ; nonlinear response ; bosonization ; carotenoids ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The response of the single-electron density matrix of a many-electron system to an external field is calculated using the time-dependent Hartree-Fock (TDHF) technique. A procedure for inverting the resulting nonlinear response functions to obtain an effective quantum multilevel system that has the same response is developed. The number of effective states is gradually increased as higher-order nonlinearities are computed. The complete set of intrastate and interstate density matrices and excited-state energies can be calculated. A favorable N-scaling of computational effort with size can be obtained making use of the localization of the optical transitions in real space.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 711-727, 1998
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    Effect of heavy atom on the second hyperpolarizability of tetrahydrofuran homologs investigated by ab initio molecular orbital method (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 737-743 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Static second hyperpolarizabilities were calculated for molecules including tetrahydrofuran homologs by ab initio molecular orbital methods at the Hartree-Fock and various correlation levels. Substitution of the heteroatom with a heavier atom is found to be effective for increase of the second hyperpolarizability of these homologs. Comparison between the present results and previous results for furan homologs shows that π-conjugation is not effective for the increase of second hyperpolarizability of the molecules when the heteroatom is heavier.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 737-743, 1998
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    Structure dependence of the low-lying excited states and the first dipole hyperpolarizability of phenol blue (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 745-750 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (CH3)2NC6H4NC6H4O is a merocyanine dye that exists in resonance between the two extreme conformations of a keto and an eno form. The keto form is more stable in the gas phase and the eno form is believed to be more stable in solution. We show that the keto form can prevail in nonpolar solvents, but in polar solvents like chloroform, the eno form should be dominant. Analysis is made of the solvent effects in the low-lying absorption transition and its consequence in the first dipole hyperpolarizability. We show by explicit calculations that the hyperpolarizability of the eno form is one order of magnitude greater than in the keto form. We then contend that this structure dependence may also lead to very large changes of the hyperpolarizability of similar molecules and polymers in solvents.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 745-750, 1998
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    Theory and calculations of electric field effects on hyperfine interactions (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 771-778 
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    ISSN: 0020-7608
    Keywords: electric field effects ; hyperfine interactions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A recently published theory of electric field effects on electron spin resonance hyperfine couplings [Phys. Ref. Lett. 79, 379, (1997)] is extended to nuclear quadrupole coupling. With the use of the ab initio coupled Hartree-Fock approach and augmented Sadlej basis set, results are obtained for the first-order corrections to the isotropic and anisotropic parts of hyperfine coupling tensor and the electronic part of the electric field gradient tensor for 17O and 2H nuclei in OH radical. The first-order coefficients exhibit a number of interesting features. The calculated results, in general, appear to be insensitive to the bond-centered polarization functions used in the calculation.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 771-778, 1998
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    Differential equations for ground-state electron density and Slater sum in atoms and molecules with and without external fields (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 779-788 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ground-state density amplitude {ρ(r)}1/2 for atoms and molecules satisfies a Schrödinger equation in which the customary one-body potential energy V(r) of density functional theory is supplemented by the addition of the Pauli potential Vp(r). Since neither the exchange-correlation potential Vxc or Vp are presently known as functionals of the electron density ρ(r), approximations are currently unavoidable. Here, widespread use is made of semiclassical approximations, within a self-consistent field framework both with and without magnetic fields. The importance of low-order gradient quantities ∇2ρ/ρ and (∇ρ/ρ)2 is one focal point, while a generalized low-density approximation is another. New relativistic differential equations are given. Then, the arguments are generalized to embrace the so-called Slater sum P(r, β) : β=(kβT)-1, of statistical mechanics, generated by the one-body potential V(r). This is a generalized partition function, and differential equations are set up for this quantity P(r, β) with and without external fields. Finally, some potentially fruitful directions for treating cylindrically symmetric inhomogeneous electron liquids are outlined, following the very recent work of Amovilli and March. These include modeling the Slater sum along the electric field direction for the Stark effect in a hydrogenlike atom.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 779-788, 1998
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    Some aspects of data processing for an optical absorption experiment in a pulsed 1000-Tesla magnet (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 797-804 
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    ISSN: 0020-7608
    Keywords: pulsed magnetic field ; Zeeman effect ; quadruple metal bonds ; octachlorodirhenate ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A procedure is given for the analysis of optical absorption data acquired in the hostile environment of a pulsed 1000-Tesla magnet.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 797-804, 1998
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    Relativistic effects on the structural phase stability of molybdenum (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 825-830 
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    ISSN: 0020-7608
    Keywords: molybdenum ; phase stability ; relativity ; Douglas-Kroll ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The body-centered cubic-face-centered cubic (bcc-fcc) structural phase stability of molybdenum (Mo) is studied as a function of volume with both nonrelativistic and scalar-relativistic linear combinations of Gaussian-type orbitals-fitting functions (LCGTO-FF) calculations. It is demonstrated that relativity has a significant, albeit small effect, on the bcc-fcc structural energy difference, which increases with pressure. The scalar-relativistic structural energy difference curve is shown to be in excellent agreement with an earlier scalar-relativistic calculation using the full-potential linear muffin-tin orbital (FP-LMTO) method, clearly demonstrating the ability of the scalar-relativistic LCGTO-FF method to resolve an extremely subtle relativistic effect. It is argued that relativity will tend to delay pressure-induced structural phase transitions that are triggered by electron band reordering.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 825-830, 1998
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    Water cluster approach to study hydrogen-bonded pattern in liquid water: Ab initio orientational defects in water hexamers and octamers (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 831-853 
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    ISSN: 0020-7608
    Keywords: Liquid water ; H-bond pattern ; orientational defect ; water cluster ; “dangling” bond ; ab initio HF/6-311(d, p) calculation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fifteen different structures of the water hexamer found ab initio within the 6-311G(d, p) basis set in the interval of 1.75 kcal/mol above the global minimum represent an unprecedented wide range of conformational plasticity of liquid water. The present work also provides the first ab initio demonstration of the existence of pentacoordinated water clusters of an orientational defect type and elaborates their properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 831-853, 1998
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    Intramolecular hydrogen bonding in resonance-stabilized systems (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 863-875 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 3-substituted-2-methoxybenzoic acid system exhibits resonance-stabilized intramolecular hydrogen bonding between the 2-methoxy oxygen and the adjacent carboxylic acid. This intramolecular hydrogen bond can be disrupted by adding another substituent with variable size on the neighboring 3-position of the ring. To relieve steric strain, the system must sacrifice hydrogen bonding and/or resonance stabilization. Full-energy optimizations have been done at HF/D95V (valence double-zeta Dunning-Huzinaga), HF/6-31G* (Pople), HF/D95 (full double-zeta Dunning-Huzinaga), HF/D95V(d, p), and HF/6-31+G(d, p). Further single-point calculations were done at MP2/D95V, MP2/6-31G*, MP2/D95, MP2/D95V(d, p), and MP2/6-31+G(d, p). The thermal populations of various conformational states including the hydrogen-bonding conformation are presented. The computational results were compared with the experimental thermal population of hydrogen bonding determined by nuclear magnetic resonance (NMR) and infrared (IR) spectroscopies. Results indicate that polarization of the second-row elements in intramolecular hydrogen bonding and perturbation-theory calculations that correct for electron correlations are very important for intramolecular hydrogen bonding. Adding polarization and diffuse functions to the hydrogens, while useful, are quite costly for these systems and do not seem to be as important.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 863-875, 1998
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    The interface of electronic structure and dynamics for reactions in solution (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 887-896 
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    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We compare two systematic approaches to the calculation of reaction rates in liquid solutions: the separable equilibrium solvation (SES) approximation and the equilibrium solvation path (ESP) approximation. These approaches are tested for two reactions, ClCH3+NH3→Cl-+H3CNH3+ (R1) and NH4+…N′H3→NH3…N′H4+ (R2), both in aqueous solution. The first reaction illustrates the importance of variational optimization of the transition state, and the second illustrates the importance of tunneling. Free energies of solvation are calculated by the Solvation Model 5. All calculations are carried out by the new AMSOLRATE program, which is an interface of the AMSOL and POLYRATE programs.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 887-896, 1998
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    Single-electron-capture cross sections by alpha-particles from ground state K(4s) and Rb(5s): A molecular-state approach (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 909-917 
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    ISSN: 0020-7608
    Keywords: charge transfer ; α-particles ; alkali atoms ; MO expansion ; close coupling ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cross sections for single-electron capture by α-particles from ground state K and Rb were calculated in the low-to-intermediate energy region by employing the molecular expansion method in the framework of impact parameter formulation. The colliding partners are treated as a pseudo-one-electron system and the technique of the pseudopotential is used to account for their mutual interactions. The molecular wave function of the quasimolecule formed during the collision is expanded in terms of basis sets of atomic orbitals on two centers. The resulting coupled equations are solved semiclassically where a straight-line trajectory describes the relative motion of the two nuclei. The effect of electron translation is also suitably incorporated. The calculated cross sections, both total and partial, are presented and compared with the available experimental measurements.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 909-917, 1998
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    Enhanced proliferation of human fibroblasts, in the presence of dexamethasone, is accompanied by changes in p21Waf1/Cip1/Sdi1 and the insulin-like growth factor type 1 receptor (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 396-401 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The addition of dexamethasone (dex) to human fibroblast cultures has been found to elicit enhanced proliferation. This enhancement is manifested by an increase in the initial growth rate, saturation density, and proliferative life span of WI-38 fibroblast cultures grown in the presence of dex. We examined the acute effects of dex on a number of growth-related genes in WI-38 cells. Our results show a decrease in the level of the cyclin-dependent kinase inhibitor p21Waf1/Cip1/Sdi1 in response to dex. In addition, the level of the insulin-like growth factor type 1 receptor (IGF-1R) is increased in dex-treated cells. These changes are correlated with changes in the activity of the p21Waf1/Cip1/Sdi1 and IGF-1R promoters. The results presented in this report suggest that dex may delay growth arrest in response to contact inhibition, as well as during cellular senescence. Thus, dex may act at multiple levels to enhance cellular proliferation in WI-38 cells: first, to decrease the level of an inhibitor of cell-cycle progression, and second, to increase the sensitivity of WI-38 cells to the proliferative effects of IGF-1. These acute effects may cooperate with other, as yet uncharacterized effects, to result in the enhanced proliferation seen in the presence of dex. J. Cell. Physiol. 177:396-401, 1998. © 1998 Wiley-Liss, Inc.
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    Potassium channel inhibition reduces cell proliferation in the GH3 pituitary cell line (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 402-410 
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    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Potassium (K+) conductances are known to be involved in cell proliferation of a number of nonexcitable cell types. The nature of the mechanism by which K+ channel inhibition reduces cell proliferation has remained elusive despite intensive search. We investigated whether such a phenomenon could be demonstrated in excitable cells, using the GH3 pituitary cell line as a cell model. Our aims were: (1) to study the effect of K+ channel inhibition on the proliferation of GH3 cells; and (2) to investigate the putative intracellular signals involved in this inhibition. Tetraethylammonium chloride (TEA), a blocker of the calcium (Ca2+)-dependent K+ conductances of GH3, was found to reversibly inhibit cell proliferation, as measured by 3H-thymidine incorporation. Cell cycle block specifically occurred at the G1/S phase of the cell cycle. This inhibition of proliferation was observed for 1-4 mM TEA, which suppressed most of the Ca2+-activated K+ current and part of the inward rectifying K+ current, as shown by electrophysiological experiments. Increasing extracellular K+ concentrations with KCl also inhibited cell proliferation in a dose-dependent manner. Both TEA and KCl depolarized the cells and increased intracellular Ca2+ levels ([Ca2+]i), showing that, in this type of excitable cell, inhibition of cell proliferation can be associated with elevated Ca2+ levels. Ca2+ and membrane resting potential (MRP) were considered as possible messengers of this inhibition. Our results suggest that cell cycle arrest of GH3 cells by K+ channel block probably involves an additional pathway, distinct from those of Ca2+ and MRP. J. Cell. Physiol. 177:402-410, 1998. © 1998 Wiley-Liss, Inc.
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    Autocrine TGFα expression in the regulation of initiation of human colon carcinoma growth (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 387-395 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Previously, we reported that unaggressive, growth factor-dependent FET human colon carcinoma cells downregulated their transforming growth factor alpha (TGFα) expression in a quiescent state (G0/G1) induced by growth factor and nutrient deprivation (Mulder, 1991, Cancer Res., 51:2256-2262). In contrast, highly aggressive, growth factor-independent HCT116 human colon carcinoma cells aberrantly upregulated this autocrine activity in the quiescent state (Mulder, 1991, Cancer Res., 51:2256-2262; Howell et al., 1998, Mol. Cell. Biol., 18:303-313). In this report, the role of autocrine TGFα and the mechanism of its regulation of expression during reentry into the cell cycle from a noncycling growth state were determined in FET cells. Optimal induction of DNA synthesis from a quiescent state in FET cells is dependent upon autocrine TGFα as well as exogenous transferrin and insulin. Reentry into the cell cycle resulting from treatment with exogenous transferrin and insulin resulted in ∼3-fold induction of TGFα expression within 1 hr. TGFα induction was controlled at the transcription level, and the cis-controlling element was localized to the region between bp -370--201 relative to the translation start codon within the TGFα promoter. Thus neutralization of autocrine TGFα protein revealed that the induced TGFα autocrine activity was necessary for DNA synthesis and acted only in the early G1 phase of the cell cycle. Blockade of autocrine TGFα expression early in the cell cycle resulted in the reduction of DNA synthesis, whereas treatment with neutralization antibody at later times had no effect. This suggested that autocrine TGFα functions to initiate cell growth from noncycling states. This was further confirmed by the dependence of FET cells upon autocrine TGFα for colony formation in experiments where the plating density was sufficiently low to generate a lag phase in tissue culture. In contrast, TGFα autocrine activity was not required for exponential phase cells, as evidenced by the failure of TGFα neutralizing antibody to inhibit proliferation in this growth state. Taken together, these results suggest that autocrine TGFα acts primarily in the process of growth initiation by moving cells from a noncycling state back into the cell cycle, rather than supporting cell growth already initiated. J. Cell. Physiol. 177:387-395, 1998. © 1998 Wiley-Liss, Inc.
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    Overexpression of basic fibroblast growth factor in MCF-7 human breast cancer cells: Lack of correlation between inhibition of cell growth and MAP kinase activation (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 411-425 
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    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Basic fibroblast growth factor (bFGF, FGF-2) is progressively lost from mammary epithelial cells as they become malignant. To investigate the effects of restoring the expression of bFGF in breast cancer cells, we constructed MCF-7 cells that permanently overexpress 18-kD cytoplasm-localizing bFGF (MCF-7/ΔAFGF(18) cells) and cells that express both the 18-kD along with the 22- and 24-kD nucleus-localizing bFGF peptides (MCF-7/NCFFGF(18,22,24) cells), using retroviral transduction. These stable cell constructs grew more slowly and had a larger fraction of their populations in the G0/G1 phase of the cell cycle than control cells. All forms of bFGF were eluted from MCF-7/NCFFGF(18,22,24) cell monolayers with 2 M NaCl, in contrast to fibroblasts that were demonstrated to secrete only the 18-kD bFGF isoform. High-affinity binding of 18-kD 125I-bFGF to these cells was significantly decreased, probably because of competitive binding by the autocrine-secreted bFGF. Recombinant 18-kD bFGF that was previously demonstrated in our laboratory to inhibit proliferation, activate MAP kinase, and induce the cyclin-dependent kinase inhibitor p21WAF1/CIP1 in MCF-7 cells, further inhibited MCF-7/ΔAFGF(18) cells but had no effect on MCF-7/NCFFGF(18,22,24) cells. The total cellular content of the high-affinity FGF receptors 1-3 was unchanged, but FGF receptor 4 was decreased in MCF-7/NCFFGF(18,22,24) cells. Both cell types overexpressing bFGF isoforms had elevated levels of the cyclin-dependent kinase inhibitor p27Kip1 but not that of p21WAF1/CIP1. In MCF-7/ΔAFGF(18) cells, FGFR1 and MAP kinase were constitutively phosphorylated. Exogenous recombinant 18-kD bFGF did not accentuate these effects but did induce an increase in the levels of p21WAF1/CIP1 corresponding to the further inhibition induced by exogenous bFGF in these cells. In MCF-7/NCFFGF(18,22,24) cells, FGFR1 and MAP kinase were not phosphorylated at baseline nor upon stimulation with recombinant bFGF, and exogenous bFGF only had a minimal effect on low steady-state p21WAF1/CIP1 levels. However, stimulation of these cells with phorbol ester or insulin did result in MAP kinase phosphorylation. While growth-inhibited in the G1 phase of the cell cycle, MCF-7/NCFFGF(18,22,24) cells retained active isoforms of cdk2 and the hyperphosphorylated form of Rb. These data suggest that high molecular weight forms of bFGF overexpressed in MCF-7 cells do not activate the receptor-mediated MAP kinase pathway, and do not induce p21WAF1/CIP1 in an autocrine manner, but inhibit proliferation through other, possibly direct nuclear signalling mechanisms. J. Cell. Physiol. 177:411-425, 1998. © 1998 Wiley-Liss, Inc.
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    Receptor tyrosine kinase expression in human bone marrow stromal cellsThis article is a US Government work and, as such, is in the public domain in the United States of America. (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 426-438 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Bone marrow stromal cells (BMSCs) are a heterogeneous population of cells derived from colony-forming units-fibroblastic (CFU-Fs). These cells reside in the bone marrow cavity and are capable of differentiating into several cell phenotypes including osteoblasts, chondroblasts, hematopoiesis-supporting stromal cells, and adipocytes. However, the factors that regulate the proliferation and differentiation of the BMSC population are for the most part unknown. Since many members of the receptor tyrosine kinase (RTK) family have been shown to participate in growth control of various mesenchymal cell populations, in this study we examined the expression and function of RTKs in the BMSC population. Degenerate oligonucleotides corresponding to two conserved catalytic domains of the RTK family and RT-PCR were used initially to determine which RTKs are expressed in the human BMSC (hBMSC) system. After subcloning the amplification product generated from mRNA of a multicolony-derived hBMSC strain, PDGF receptor (β), EGF receptor, FGF receptor 1, and Axl were identified by DNA sequencing of 26 bacterial colonies. Furthermore, PDGF and EGF were found to enhance BMSC growth in a dose-dependent manner and to induce tyrosine phosphorylation of intracellular molecules, including the PDGF and EGF receptors themselves, demonstrating the functionality of these receptors. On the other hand, bFGF was found to have little effect on proliferation or tyrosine phosphorylation. Since single colony-derived hBMSC strains are known to vary from one colony to another in colony habit (growth rate and colony structure) and the ability to form bone in vivo, the expression levels of these RTKs were determined in 18 hBMSC clonal strains by semiquantitative RT-PCR and were found to vary from one clonal strain to another. While not absolutely predictive of the osteogenic capacity of individual clonal strains, on average, relatively high levels of PDGF-receptor were found in bone-forming strains, while on average, nonbone-forming strains had relatively high levels of EGF-receptor. Taken together, these results indicate that RTKs play a role in the control of hBMSC proliferation, and that the differential pattern of RTK expression may be useful in correlating the biochemical properties of individual clonal strains with their ability to produce bone in vivo. J. Cell. Physiol. 177:426-438, 1998. © 1998 Wiley-Liss, Inc.
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    Vascular endothelial growth factor (VEGF)-C synergizes with basic fibroblast growth factor and VEGF in the induction of angiogenesis in vitro and alters endothelial cell extracellular proteolytic activity (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 439-452 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Vascular endothelial growth factor-C (VEGF-C) is a recently characterized member of the VEGF family of angiogenic polypeptides. We demonstrate here that VEGF-C is angiogenic in vitro when added to bovine aortic or lymphatic endothelial (BAE and BLE) cells but has little or no effect on bovine microvascular endothelial (BME) cells. As reported previously for VEGF, VEGF-C and basic fibroblast growth factor (bFGF) induced a synergistic in vitro angiogenic response in all three cells lines. Unexpectedly, VEGF and VEGF-C also synergized in the in vitro angiogenic response when assessed on BAE cells. Characterization of VEGF receptor (VEGFR) expression revealed that BME, BAE, and BLE cell lines express VEGFR-1 and -2, whereas of the three cell lines assessed, only BAE cells express VEGFR-3. We also demonstrate that VEGF-C increases plasminogen activator (PA) activity in the three bovine endothelial cell lines and that this is accompanied by a concomitant increase in PA inhibitor-1. Addition of α2-antiplasmin to BME cells co-treated with bFGF and VEGF-C partially inhibited collagen gel invasion. These results demonstrate, first, that by acting in concert with bFGF or VEGF, VEGF-C has a potent synergistic effect on the induction of angiogenesis in vitro and, second, that like VEGF and bFGF, VEGF-C is capable of altering endothelial cell extracellular proteolytic activity. These observations also highlight the notion of context, i.e., that the activity of an angiogenesis-regulating cytokine depends on the presence and concentration of other cytokines in the pericellular environment of the responding endothelial cell. J. Cell. Physiol. 177:439-452, 1998. © 1998 Wiley-Liss, Inc.
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    HiNF-D (CDP-cut/CDC2/cyclin A/pRB-complex) influences the timing of IRF-2-dependent cell cycle activation of human histone H4 gene transcription at the G1/S phase transition (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 453-464 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Cell cycle control of histone H4 gene transcription is mediated by the multipartite promoter domain H4-Site II, which supports transcriptional activation at the G1/S phase transition and modulates basal H4 gene transcription. Proliferation-specific transcription is determined by the integrated activities of three distinct promoter factors interacting with H4-Site II: the interferon regulatory factor IRF-2 (synonymous with HiNF-M), HiNF-D (a complex between the homeodomain protein CDP-cut and the cell cycle mediators CDC2, cyclin A and pRB), as well as HiNF-P/H4TF-2. However, the contribution of HiNF-D to the enhancement and/or suppression of H4 gene transcription at specific cell cycle stages remains to be established. We used a panel of synchronized HeLa S3 cell lines containing stably integrated H4 promoter/CAT reporter gene constructs with mutations in H4-Site II. The temporal regulation of CAT mRNA accumulation under the control of the H4 promoter was analyzed by RNase protection analysis. Our main finding is that mutation of the HiNF-D/CDP-cut binding site alters the timing of histone gene activation during the cell cycle. Furthermore, our data indicate that HiNF-P/H4TF-2 may functionally compensate for HiNF-M/IRF-2 at Site II to regulate histone H4 gene transcription in HeLa S3 cervical carcinoma cells during early S phase. We postulate that HiNF-D (CDP-cut/cyclin A/CDC2/pRB containing complex) promotes HiNF-M/IRF-2 (and/or HiNF-P/H4TF-2) dependent histone H4 gene activation at the G1/S phase transition and attenuates H4 gene transcription at later cell cycle stages. The mechanistic division in the gene regulatory functions of the three H4-Site II binding proteins may ensure that histone H4 gene expression is stringently coupled with the onset of S phase in response to growth factor/cytokine-induced cell cycle progression. J. Cell. Physiol. 177:453-464, 1998. © 1998 Wiley-Liss, Inc.
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    Hyaluronic acid stimulates human fibroblast proliferation within a collagen matrix (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 465-473 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Human dermal fibroblasts suspended in a collagen matrix exhibit a 4-day delay in cell division, while the same cells in monolayer divided by day 1. The initial rates of 3H-thymidine incorporation by cells in monolayer or suspended in collagen were not significantly different. When suspended in collagen, there was a threefold increase in the proportion of cells in a tetraploidal (4N) DNA state compared to the same cells in monolayer. Flow cytometry analysis and 3H-thymidine incorporation studies identified the delay of cell division as a consequence of a block in the G2/M of the cell cycle and not an inhibition of DNA synthesis. The inclusion of 150 μ/ml of hyaluronic acid (HA) in the manufacture of fibroblast populated collagen lattices (FPCL) caused a stimulation of cell division, as determined by cell counting; increased the expression of tubulin, as determined by Western blot analysis; and reduced the proportion of cells in a 4N state, as determined by flow cytometry. HA added to the same cells growing in monolayer produced a minimal increase in the rate of cell division or DNA synthesis. HA supplementation of FPCLs stimulated cell division as well as tubulin concentrations, but it did not enhance lattice contraction. The introduction of tubulin isolated from pig brain or purchased tubulin into fibroblasts by electroporation prior to their transfer into collagen lattices promoted cell division in the first 24 hours and enhanced FPCL contraction. It is proposed that tubulin protein, the building blocks of microtubules, is limited in human fibroblasts residing within a collagen matrix. When human fibroblasts are suspended in collagen, one effect of added HA may be to stimulate the synthesis of tubulin which assists cells through the cell cycle. J. Cell. Physiol. 177:465-473, 1998. © 1998 Wiley-Liss, Inc.
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    Keratinocyte growth arrest is associated with activation of a transcriptional repressor element in the human cdk1 promoter (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 474-482 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In this study we examined the regulation of cdk1 expression in normal human epidermal keratinocytes (HEKs) and neoplastic keratinocytes. Keratinocytes were growth-arrested by allowing the cells to grow to confluence or by treating them with interferon-gamma (IFNγ) or 12-O-tetradecanoyl phorbol-13-acetate (TPA). RT-PCR and Western blot analysis demonstrated that cdk1 was profoundly reduced in growth-arrested HEKs when compared with dividing HEKs. In contrast, a squamous carcinoma cell line, SCC25, did not growth-arrest in response to growth inhibitors and did not downregulate cdk1 expression. Transfection of HEKs with a reporter gene driven off a 2.5-kb fragment of the human cdk1 promoter indicated that the downregulation of cdk1 upon growth arrest was transcriptional. Deletion mapping of the cdk1 promoter indicated that a repressor region was located between -949--722 bp. This repressor region was not operative in the SCC25 cells. Examination of DNA:protein binding complexes by gel-shift analysis indicated that nuclear factors from both proliferative and growth-arrested cells bound to the DNA fragment spanning -949--722 bp. Further analysis revealed that this binding could be resolved into a constitutive and growth arrest-specific complex that bound in a similar fashion to regions spanning -892--831 bp and -831--774 bp, respectively. The putative growth arrest-specific complex was not found in contact-inhibited fibroblasts and was found at very low levels in SCC25 cells, indicating that the putative repressor binding was growth arrest-specific and possibly keratinocyte-specific. The binding complexes bound to these two fragments were localized, by competition analysis, to regions -874--853 bp and -830--800 bp. This is the first report of a transcriptional repressor being operative during keratinocyte growth arrest. J. Cell. Physiol. 177:474-482, 1998. © 1998 Wiley-Liss, Inc.
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    Diamide-induced cytotoxicity and thermotolerance in CHO cells (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 483-492 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Treatment with the sulfhydryl oxidant diamide denatures and aggregates cellular proteins, which prior studies have implicated as an oxidative damage that activates the heat shock transcription factor and induces thermotolerance. This study was initiated to further characterize cellular response to diamide-denatured proteins, including their involvement in diamide cytotoxicity. Cytotoxic diamide exposures at 37.0°C denatured and aggregated cellular proteins in a manner that was proportional to cell killing, but this correlation was different than that established for heated cells. Diamide exposures at 24.0°C were orders of magnitude less cytotoxic, with little additional killing occurring after diamide was removed and cells were returned to 37.0°C. Thus, protein denaturation that occurred at 37.0°C, after proteins were chemically destabilized by diamide at 24.0°C [Freeman et al., J. Cell. Physiol., 164:356-366 (1995) Senisterra et al., Biochemistry 36: 11002-11011 (1997)], had little effect on cell killing. Thermotolerance protected cells against diamide cytotoxicity but did not reduce the amount of denatured and aggregated protein observed immediately following diamide exposure. However, denatured/aggregated proteins in thermotolerant cells were disaggregated within 17 h following diamide exposure, while no disaggregation was observed in nontolerant cells. This more rapid disaggregation of proteins may be one mechanism by which thermotolerance protects cells against diamide toxicity, as it has been postulated to do against heat killing. As with heat shock, nontoxic diamide exposures induced maximal tolerance against heat killing; however, there was no detectable, increased synthesis of heat shock proteins. Thus, diamide treatment proved to be a reproducible procedure for inducing a phase of thermotolerance that does not require new heat shock protein (HSP) synthesis, without having to use transcription or translation inhibitors to suppress HSP gene expression.These results complement those from studies with other stresses to establish the importance of protein denaturation/aggregation as a cytotoxic consequence of stress and a trigger for thermotolerance induction. The data also illustrate that differences in how proteins are denatured and aggregated can affect their cytotoxicity and the manner in which thermotolerance is expressed. J. Cell. Physiol. 177:483-492, 1998. © 1998 Wiley-Liss, Inc.
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    Erratum: Smith, Karol R, Percival, Susan S. (1998): Manganese enhances phosphorylation of a 47 kD protein in retinoic acid-induced HL-60 cells. J. Cell. Physiol. 176:188-195 (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 499-499 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: No abstract.
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    CDK9 (PITALRE): A multifunctional cdc2-related kinase (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 501-506 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: CDK9 is a cdc2-related kinase protein. Previously named PITALRE, this protein is a serine-threonine kinase involved in many physiological processes. Unlike most of the cdc2-like kinases, its activity is not cell cycle-regulated. CDK9 acts preferentially in processes different from cell-cycle regulation, such as differentiation. Its cyclin partners, cyclins of T family, recently have been isolated. CDK9 immunoprecipitates with several unidentified polypeptides that may regulate its kinase activity. CDK9 has been shown to associate with the HIV-Tat protein, suggesting a possible involvement in AIDS. CDK9 recently was shown to be responsible for the kinase activity associated with the TAK complex and with the P-TEFb complex, suggesting activity also in the transcription process. J Cell Physiol 177:501-506, 1998. © 1998 Wiley-Liss, Inc.
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    Dose-dependent induction of IL-12 but not IL-10 from human keratinocytes after exposure to ultraviolet light A (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 493-498 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Ultraviolet light A (UVA) is shown to play an augmentative or synergistic role with UVB in pathophysiological conditions induced by solar radiation. Thus, UVA would contribute significantly to the development of skin malignancies. It remains unclear, however, how UVA contributes to solar radiation-induced immune suppression. Keratinocytes (KC) produce cytokines which are a significant mediator of inflammatory and immunologic reactions in skin exposed to solar radiation and are a potent mediator in the induction of immune suppression. To examine if UVA alters the expression and production of cytokines from KC, normal human keratinocytes (HuSK) were cultured and exposed to UVA at doses ranging between 2.5 and 20 kJ/m2. Constitutive expression of the p35 subunit of interleukin (IL)-12 was detected by reverse transcription-polymerase chain reaction (RT-PCR) and the p40 subunit was induced by UVA irradiation dose dependently. IL-12 protein was also detected in the supernatants from UVA-irradiated HuSK by enzyme-linked imuunosorbent assay (ELISA) and confirmed by a bioassay. On the other hand, the same doses of UVA did not induce IL-10 mRNA or IL-10 protein which has been shown to be one of the cytokines responsible for the induction of UVB-induced immunosuppression. Considering that IL-12 promotes activation of Th1 cells and prevents the activation of Th2 cells and that administration of IL-12 has been shown to block the induction of immune suppression in UV-irradiated animals, our results suggest that UVA modulates skin immune function distinctively from UVB by affecting the balance between IL-10 and IL-12 produced from KC. J. Cell. Physiol. 177:493-498, 1998. © 1998 Wiley-Liss, Inc.
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    Signal transduction pathways in the mitogenic response to G protein-coupled neuropeptide receptor agonists (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 507-517 
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    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Neuropeptides, including mammalian bombesin-like peptides, act as potent cellular growth factors and have been implicated in a variety of normal and abnormal processes, including development, inflammation, and malignant transformation. These signaling peptides exert their characteristic effects on cellular processes by binding to specific G protein-coupled receptors (GPCR) on the surface of their target cells. Typically, the binding of a neuropeptide to its cognate GPCR triggers the activation of multiple signal transduction pathways that act in a synergistic and combinatorial fashion to relay the mitogenic signal to the nucleus and promote cell proliferation. A rapid increase in the synthesis of lipid-derived second messengers with subsequent activation of protein phosphorylation cascades is an important early response to neuropeptides. An emerging theme in signal transduction is that these agonists also induce rapid and coordinate tyrosine phosphorylation of cellular proteins including the nonreceptor tyrosine kinase p125fak and the adaptor proteins p130cas and paxillin. This tyrosine phosphorylation pathway depends on the integrity of the actin cytoskeleton and requires functional Rho. The purpose of this article is to review recent advances in unraveling the pathways that play a role in transducing mitogenic and migratory responses induced by G protein-coupled neuropeptide receptor agonists. J Cell Physiol 177:507-517, 1998. © 1998 Wiley-Liss, Inc.
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    Intracellular targeting of the endoplasmic reticulum/nuclear envelope by retrograde transport may determine cell hypersensitivity to verotoxin via globotriaosyl ceramide fatty acid isoform traffic (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 177 (1998), S. 646-660 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The pentameric B subunit of verotoxin (VT) mediates the attachment to cell surface globotriaosyl ceramide (Gb3) to facilitate receptor-mediated endocytosis of the toxin. In highly toxin-sensitive tumor cells, the holotoxin and VT1 B subunit is targeted intracellularly to elements of the endoplasmic reticulum (ER)/nuclear membrane. In less sensitive cells, the toxin is targeted to components of the Golgi apparatus. We have studied two cell systems: the induced VT hypersensitivity of human astrocytoma cell lines cultured in the presence of sodium butyrate (compared to sodium propionate and capronate) and the increased VT sensitivity of multiple drug-resistant mutants as compared to parental human ovarian carcinoma cells. In both cases, a difference in the intracellular retrograde transport of the receptor-bound internalized toxin to the ER/nuclear envelope, as opposed to the Golgi, correlated with a 〉1,000-fold increase in cell sensitivity to VT. This change in intracellular routing may be due to sorting of Gb3 fatty acid isoforms, since nuclear targeting was found in turn to correlate with the preferential synthesis of Gb3 containing shorter chain (primarily C16) fatty acid species. We propose that the isoform-dependent traffic of Gb3 from the cell surface to the ER/nuclear membrane provides a new signal transduction pathway for Gb3 binding proteins. J Cell Physiol 177:646-660, 1998. © 1998 Wiley-Liss, Inc.
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    Kramers' unrestricted Hartree-Fock and second-order Møller-Plesset perturbation methods using relativistic effective core potentials with spin-orbit operators: Test calculations for HI and CH3I (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 91-98 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Kramers' restricted Hartree-Fock (KRHF) and second-order Møller-Plesset perturbation (KRMP2) methods using relativistic effective core potentials (RECP) with spin-orbit operators and two-component spinors are extended to the unrestricted forms, KUHF and KUMP2. As in the conventional unrestricted methods, the KUHF and KUMP2 methods are capable of qualitatively describing the bond breaking for a single bond. As a result, it is possible to estimate spin-orbit effects along the dissociation curve at the HF and MP2 levels of theory as is demonstrated by the test calculations on the ground states of HI and CH3I. Since the energy lowering due to spin-orbit interactions is larger for the I atom than for the closed-shell molecules, dissociation energies are reduced and bond lengths are slightly elongated by the inclusion of the spin-orbit interactions.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 91-98, 1998
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    The conscious mind: In search of a fundamental theory (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 107-108 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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    Construction and applications of symmetrized valence bond wave functions (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 1-7 
    Details
    ISSN: 0020-7608
    Keywords: Symmetry ; projection operator ; VB wave function ; transition energy ; chemical bonds ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method constructing symmetry-adapted bonded Young tableau bases is proposed, based on the symmetry properties of bonded tableaus and the projection operator associated with a point group. Several examples including the ground states and π excited states of O3-, O3, O3+, and C3- are shown for instruction to construct the symmetrized valence bond (VB) wave function. Excitation energies of transitions from the ground states to π excited states of O3-, C3H5, and C3- are calculated with an optimized symmetrized valence bond wave function in the σ-π separation approximation. Good agreement between the VB and experimental excitation energies is observed. The bonding features of the ground state and the first π excited singlet and triplet states for S3 are discussed according to bonding populations from VB calculations. Both the singlet-biradical and the dipole structures have significant contributions to the ground state X 1A1 of S3, while the excited state 1 1B2 is essentially composed of the dipole structures, and the 1 3B2 excited state is comprised from a triplet-biradical structure.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 1-7, 1998
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    Comparative theoretical study of transition structures, barrier heights, and reaction energies for the intramolecular tautomerization in acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 9-24 
    Details
    ISSN: 0020-7608
    Keywords: keto/enol and imine/enamine tautomerizations ; intramolecular hydrogen shift ; transition structures ; comparison of several calculation methods ; asynchronous process ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The transition structures associated with the possible intramolecular tautomerization for acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems as models of keto/enol and imine/enamine interconversion processes, respectively, were characterized. The relative stabilities of the tautomers and the associated barrier heights were calculated. Ab initio analytical gradients and second derivatives at the HF level of theory and 3-21G, 6-31G, 6-31G**, 6-31++G**, and 6-311++G** basis-set, DFT (BP86/6-311++G** and BLYP/6-311++G**), and semiempirical (AM1 and PM3) procedures were used to identify the stationary points. Correlation effects were estimated using the perturbational approach at MP2/6-31G**, MP2/6-311++G**, and MP2/6-311++G (3df,2p) levels. The geometry, electronic structure, harmonic vibrational frequencies, and transition vector associated with the transition structures as well as the relative stabilities of different isomers and barrier heights were analyzed. The dependence of these properties upon theoretical methods is analyzed and discussed. The transition structures are four-membered rings and the corresponding transition vectors are associated to collective fluctuations. The 1,3 intramolecular hydrogen migration is much more advanced than are the hybridization changes on donor and acceptor centers at the transition structure. The corresponding barrier heights can be related to the change of bond orders and acid/base properties of these centers. A comparison of the results obtained with different methods renders that the nature of the transition structure seems to be a rather robust entity.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 9-24, 1998
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    Upper- and lower-bound Hylleraas-CI calculations for the nonrelativistic Po states of the 4He isotope (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 25-30 
    Details
    ISSN: 0020-7608
    Keywords: Hylleraas-CI ; P states of 4He ; variance minimization ; upper and lower bounds ; perturbation theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Extensive Hylleraas-CI calculations for the lowest Po states of 4He were performed. The dependence of the variational energy values Eκ on the mass parameter κ given by κ=mHe2+/me- is discussed. Furthermore, lower bounds to Eκ were calculated using variance minimization.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 25-30, 1998
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    Calculation of magnetic properties of HF, H2O, NH3, and CH4 molecules using a longitudinal gauge for the vector potential (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 31-45 
    Details
    ISSN: 0020-7608
    Keywords: magnetic susceptibility ; magnetic shielding tensor ; gauge invariance ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A transformation of the transverse Coulomb vector potential was implemented to calculate molecular magnetic properties via the random-phase approximation (RPA) within the framework of a “longitudinal gauge.” In this gauge, the diamagnetic contribution to magnetic susceptibility is a tensor with equal diagonal components as in atoms, irrespective of molecular symmetry, whereas diagonal and average diamagnetic contributions to the nuclear magnetic shielding are the same as in the Coulomb gauge. Near-Hartree-Fock magnetic susceptibility and nuclear magnetic shielding tensors were evaluated for a set of small molecules, HF, H2O, NH3, and CH4, employing extended Gaussian basis sets. The peculiar features of the longitudinal gauge, and the fulfillment of a series of sum rules involving the virial operator, which must be satisfied to guarantee gauge invariance of total magnetic tensors, were exploited to check the degree of convergence of theoretical values and to estimate the corresponding Hartree-Fock limit for the properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 31-45, 1998
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    A comparative three-dimensional Hartree-Fock crystal orbital study of double-stack organic charge-transfer (semi)conductors: TTF-TCNQ, TTF-DCNQI, and TTF-2,5-Me2-DCNQI (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 47-68 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Three-dimensional crystal structures of the charge-transfer complexes of tetrathiafulvalene (TTF) with tetracyanoquinodimethane (TCNQ), (N,N′-dicyanbenzoquinondiimine (DCNQI), and N,N′-dicyan-2,5-dimethyl-1,4-benzoquinondiimine (2,5-Me2-DCNQI) were studied within the ab initio Hartree-Fock crystal orbital approximation using the CRYSTAL92 routine package. A qualitative agreement with the experimental data was achieved, and a definite border between one-electron and many-electron effects in the specific physical properties of the crystals under study was drawn. The calculations led to the tentative conclusion that the true chemical reaction corresponding to the charge transfer in such systems is a two-step transfer of two electrons from the donor's HOMO to the acceptor's LUMO and not only single-electron transfer, as usually believed. Then, whether the system is conductive or semiconductive depends upon the degree of the charge transfer (one, two, or no electrons, respectively). But the final degree of the charge transfer and the density of states on the Fermi level should be determined by many-electron effects. The theoretical approach used in this work seems to be of crucial importance in designing organic crystals with specific physical properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 47-68, 1998
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    Calculation of rovibrational energy levels of diatomic molecules by Dunham method with potential obtained from ab initio calculations (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 94-101 
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    ISSN: 0192-8651
    Keywords: Dunham method ; rovibrational energy levels ; rovibrational Schrödinger equation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A numerical algorithm of the Dunham method for the solution of the rovibrational Schrödinger equation is proposed. It uses a new quasi-Hermitian method of constructing the optimal approximate polynomial for the tabularly defined potential curve of a diatomic molecule obtained from an ab initio calculation. In this method the optimal polynomial approximates the potential curve and its derivatives, but it uses only information about the potential curve for its construction. This property of the new method arises from analysis of a spectral representation of the optimal polynomial to determine how well it approximates the potential curve and its derivatives. Appropriate derivatives of the potential curve, needed in the Dunham method, are calculated by recurrence relations. Comparison with the finite-difference method shows that the precision of both methods is similar, while the Dunham method is hundreds of times faster.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 94-101, 1998
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    Editor's preface (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. v 
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    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
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    Molecular structures and conformations: Experiment and theory (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 123-128 
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    ISSN: 0192-8651
    Keywords: gas phase structures ; conformational properties ; gas electron diffraction ; theoretical calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Theoretical investigations of NMR chemical shifts and reactivities of oxovanadium(v) compounds (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 113-122 
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    ISSN: 0192-8651
    Keywords: density-functional theory ; 51V ; chemical shift calculations ; mechanism of ethylene polymerization ; barriers for ethylene insertion ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Employing gradient-corrected levels of density-functional theory (DFT), medium-sized basis sets, and optimized geometries, chemical shifts are calculated for [VOClnF3-n] (n=0-3), VF5, [VO(OCH2CH2)3N], [V(CO)6]-, [V(CO)5(N2)]-, as well as for the model compounds [VO(OMe)nMe3-n] (n=0-3) and their AlH3 adducts. Experimental trends in δ(51V) are well reproduced with DFT-based methods; for example, the slopes of the δ(51V)calc vs. δ(51V)expt linear regression lines are 0.92 and 1.03 at the GIAO-BP86 and GIAO-B3LYP levels, respectively. Ethylene polymerization observed with [V(O⋅⋅⋅AlX3)(OR)nR′3-n] (X, R, R′=bulky alkyl, aryl, or silyl groups) is shown for model systems (X=H, R=R′=Me) to proceed by insertion of the olefin into a V - C bond via a transition state with approximate square-pyramidal coordination about vanadium. For the tri- and dialkyl derivatives (n=0, 1), similar activation barriers of ca. 19 kcal/mol are computed (BP86 level including zero-point energies), whereas that of the monoalkyl species (n=2) is predicted to be much higher, ca. 30 kcal/mol. The relevance of these results for the apparent relationship between δ(51V) and catalytic activities is discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 113-122, 1998
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    Organometallic chemistry of fullerenes: η2- and η5-(π)complexes (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 139-143 
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    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The reactivity of the fullerenes is primarily a function of their strain, as measured by the pyramidalization angle or curvature of the conjugated carbon atoms. A consideration of the orientation of the π-orbitals shows that η2-complexation reactions lead to reaction products with the fullerenes that are very similar to those obtained from unstrained alkenes. Furthermore, a large amount of strain energy is released in this reaction, so it is clear just why this reaction is important in fullerene chemistry. On the other hand, it is shown that the π-orbitals of C60 are poorly oriented for overlap with an exohedral metal atom centered over the five- or six-membered rings, but well disposed for overlap with an endohedral metal atom centered under the five- or six-membered rings.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 139-143, 1998
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    Effect of nonproximate atomic substitution on excited state intramolecular proton transfer (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 129-138 
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    ISSN: 0192-8651
    Keywords: ab initio ; formimidol ; H-bond ; energy barrier ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The central C atom of the OCCCO skeleton of the malonaldehyde molecule is replaced by N, and the effects upon the intramolecular H-bond and the proton transfer are monitored by ab initio calculations in the ground and excited electronic states. The H-bond is weakened in the singlet and triplet states arising from n→π* excitation in both molecules, which is accompanied by a heightened barrier to proton transfer.3ππ* behaves in the same manner, but the singlet ππ* state has a stronger H-bond and lower barrier. Replacement of the central C atom by N strengthens the intramolecular H-bond. Although the proton transfer barrier in the ground state of formimidol is lower than in malonaldehyde, the barriers in all four excited states are higher in the N-analog. The latter substitution also dampens the effect of the n→π* excitation upon the H-bond and increases the excitation energies of the various states, particularly ππ*.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 129-138, 1998
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    Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 144-153 
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    ISSN: 0192-8651
    Keywords: 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
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Theoretical study of reaction of trifluoromethyl radical with hydroxyl and hydrogen radicals (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 277-289 
    Details
    ISSN: 0192-8651
    Keywords: ab initio molecular orbital theory ; density functional theory ; ozone depletion problem ; halon replacement ; fire suppression mechanism ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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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    United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 259-276 
    Details
    ISSN: 0192-8651
    Keywords: protein folding ; multibody interactions ; electrostatic interactions ; cumulant expansion ; potential of mean force ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Comparison of methods for deriving atomic charges from the electrostatic potential and moments (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 377-395 
    Details
    ISSN: 0192-8651
    Keywords: atomic charges ; copper complexes ; electrostatic potential charges ; molecular simulation ; rank-deficiency problems ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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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    Implementation and validation of the Lacks-Gordon exchange functional in conventional density functional and adiabatic connection methods (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 418-429 
    Details
    ISSN: 0192-8651
    Keywords: Lacks-Gordon exchange functional ; Lee-Yang-Parr correlation functional ; conventional density functional ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 548-573 
    Details
    ISSN: 0192-8651
    Keywords: surface loops ; structure prediction ; global energy minimization ; energy functions ; hydration free energy ; atomic multipoles ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Quantum chemical studies on structures and spectra of 2,5-distyrylpyrazine (DSP) laser dye (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 585-592 
    Details
    ISSN: 0192-8651
    Keywords: semiempirical calculations ; electronic spectra ; conformational analysis ; 2,5-distyrylpyrazine laser dye ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Full configuration interaction algorithm on a massively parallel architecture: Direct-list implementation (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 658-672 
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    ISSN: 0192-8651
    Keywords: full configuration interaction ; ab initio methods ; acetylene molecule ; parallel computation ; message passing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 769-780 
    Details
    ISSN: 0192-8651
    Keywords: 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
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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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    Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 989-1000 
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    ISSN: 0192-8651
    Keywords: gas-phase proton affinity and basicity ; density functional computations ; protonation of DNA acid bases ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 989-1000, 1998
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    Directional hydrogen bonding in the MM3 force field: II (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1001-1016 
    Details
    ISSN: 0192-8651
    Keywords: ab initio ; molecular mechanics ; hydrogen bond ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6-31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide-water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1001-1016, 1998
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    van der Waals host-guest complexes: Can one predict complexation selectivity of neutral guests by a cryptophane? MD-FEP studies in gas phase and chloroform solution (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 820-832 
    Details
    ISSN: 0192-8651
    Keywords: cryptophanes ; molecular dynamics ; free energy perturbation ; preorganization ; binding selectivity ; solvent effects ; molecular recognition ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Parallel pseudospectral electronic structure: I. Hartree-Fock calculations (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1017-1029 
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    ISSN: 0192-8651
    Keywords: pseudospectral ; parallel ; Hartree-Fock ; gradient ; scalable ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an outline of the parallel implementation of our pseudospectral electronic structure program, Jaguar, including the algorithm and timings for the Hartree-Fock and analytic gradient portions of the program. We also present the parallel algorithm and timings for our Lanczos eigenvector refinement code and demonstrate that its performance is superior to the ScaLAPACK diagonalization routines. The overall efficiency of our code increases as the size of the calculation is increased, demonstrating actual as well as theoretical scalability. For our largest test system, alanine pentapeptide [818 basis functions in the cc-pVTZ(-f) basis set], our Fock matrix assembly procedure has an efficiency of nearly 90% on a 16-processor SP2 partition. The SCF portion for this case (including eigenvector refinement) has an overall efficiency of 87% on a partition of 8 processors and 74% on a partition of 16 processors. Finally, our parallel gradient calculations have a parallel efficiency of 84% on 8 processors for porphine (430 basis functions).   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1017-1029, 1998
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    Comparison of ab initio and density functional methods for vibrational analysis of TeCl4 (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 308-318 
    Details
    ISSN: 0192-8651
    Keywords: tellurium tetrachloride ; ab initio calculations ; density functional theory ; vibrational analysis ; scaled quantum mechanical method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    An investigation of the quantum chemical description of the ethylenic double bond in reactions: II. Insertion of ethylene into a titanium-carbon bond (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 947-960 
    Details
    ISSN: 0192-8651
    Keywords: olefin polymerization ; Ziegler-Natta catalysis ; quantum chemical methods ; ethylene ; TiH2CH3+ ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Effect of available volumes on radial distribution functions (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 363-367 
    Details
    ISSN: 0192-8651
    Keywords: solution structuring ; radial distribution functions ; available volume ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Analysis of the convergence of the general coupling operator method for one-configuration-type wave functions (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 368-376 
    Details
    ISSN: 0192-8651
    Keywords: general coupling operator ; coupling operator ; wave functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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    Monte-Carlo model for the hydrogenation of alkenes on metal catalyst (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 396-403 
    Details
    ISSN: 0192-8651
    Keywords: Monte-Carlo simulation ; catalytic processes ; stochastic kinetic model ; solid surfaces ; graphic representation ; catalysis by metal ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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
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  • 100
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    Asymmetrization effects on structures and populations of the ground state of dipolar donor-acceptor-substituted molecular organic NLO materials (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1130-1140 
    Details
    ISSN: 0192-8651
    Keywords: asymmetrization effects ; electron donor-acceptor ; materials for nonlinear optics ; population analysis ; dipole alignment ; structural effects of conjugation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Asymmetric donor-acceptor-substituted π-conjugated systems with low dipole moments and structural components that favor parallel alignment of neighboring molecules are potential molecular organic materials with nonlinear optical properties for which near prefect dipole parallel alignment is possible. The asymmetrical 4-methoxysubstituted acetophenone azines with the substituents fluorine (1), chlorine (2), bromine (3), cyano (4), and nitro (5) in the 4′-position have been studied in this context, and for 2 and 3 the dipole parallel alignment has indeed been accomplished in crystals of the pure material. In the present study, the effects of asymmetrization on the structure and the electronic structures of the ground states of 1-5 have been explored at the RHF/6-31G* level. The properties of the optimized structures of the azines 1-5, a comparative analysis of asymmetrical and symmetrical azines, and natural population analyses, all show no significant evidence for conjugation over the azine bridge. The concept of azine spacers as “conjugation stoppers” is useful and the dipole moments of asymmetrical azines are relatively small. The analysis suggests that the charge transfer between the donor and acceptor contributes to the dipole moment much less than is generally assumed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1130-1140, 1998
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