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  • 1985-1989  (1,204)
  • 1955-1959  (4)
  • 1940-1944
  • Atomic, Molecular and Optical Physics  (1,119)
  • gene expression
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Years
Year
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Cellular and molecular life sciences 45 (1989), S. 526-535 
    ISSN: 1420-9071
    Keywords: Interferon ; cytokines ; interleukins ; gene expression ; transcription ; autoimmune ; disease
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Specific interferon genes are transcribed at low levels in the spleen, liver, and peripheral blood leukocytes of normal individuals in the apparent absence of virus infection while other interferon genes remain unexpressed in the same tissues. In contrast, the genes of cytokines such as IL-1, IL-6 and TNF are expressed at relatively high levels in the organs of normal individuals. The level of expression of the IL-1, IL-6 and TNF genes is markedly reduced in the livers of patients with autoimmune liver disease compared to the level of expression in the liver of normal individuals, whereas the expression of interferon genes is similar in both normal and diseased liver, suggesting that a defect in the expression of specific cytokines is associated with severe liver disease.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1572-994X
    Keywords: BAL31 nuclease ; CAT assay ; gene expression ; HTLV-I ; R region ; 5′ untranslated sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We previously demonstrated the activity of the R fragment in the long terminal repeat of human T-cell leukemia virus type I for elevation of the level of gene expression. In this study, the fragment was deleted with BAL31 nuclease to determine its functional domain. Series of the shortened R fragments were linked to the simian virus 40 promoter unit, which regulated expression of a reporter gene. Examination with the R fragments deleted from the 5′ and 3′ ends showed that borders of the functional domain were mapped within nucleotide positions 458 to 473 for the 5′ end and nucleotide positions 559 to 594 for the 3′ end, respectively. Thus we conclude that a 136-base-pair fragment corresponding to the second half of the R region was sufficient to allow elevation of the level of gene expression.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Bulletin of experimental biology and medicine 108 (1989), S. 999-1001 
    ISSN: 1573-8221
    Keywords: brain ; gene expression ; mRNA ; transplantable hepatomas
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1573-4927
    Keywords: mouse ; salivary protein ; lacrimal protein ; gene expression ; Spt locus ; multigene family
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The murine submandibular gland (SMG) produces a novel class of highly acidic salivary proteins encoded by one or more highly abundant mRNA transcripts. In inbred mice, these transcripts are encoded by members of a multigene family comprising approximately 8–12 homologues. Most, and probably all, of these homologues are clustered at a new locus near belted (bt) on chromosome 15, which we designateSpt (salivary protein). Although physically closely linked,Spt genes differ in their patterns of expression both in strains of mice and in their tissues. One gene,Spt-1, is expressed at high levels in the SMG of all inbred strains examined. This gene is also expressed at significant levels in the lacrimal gland. A second gene,Spt-2, appears to be present as a single copy in some strains and as two copies in others. This gene is expressed at high levels only in the SMG of those strains carrying two copies, andSpt-2 mRNA is not detectable in the SMG of strains carrying only one copy. In contrast toSpt-1, theSpt-2 gene is not expressed at detectable levels in the lacrimal gland.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1573-4927
    Keywords: mouse ; salivary protein ; lacrimal protein ; gene expression ; Spt locus ; multigene family
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The murine submandibular gland (SMG) produces a novel class of highly acidic salivary proteins encoded by one or more highly abundant mRNA transcripts. In inbred mice, these transcripts are encoded by members of a multigene family comprising approximately 8–12 homologues. Most, and probably all, of these homologues are clustered at a new locus near belted (bt) on chromosome 15, which we designateSpt (salivary protein). Although physically closely linked,Spt genes differ in their patterns of expression both in strains of mice and in their tissues. One gene,Spt-1, is expressed at high levels in the SMG of all inbred strains examined. This gene is also expressed at significant levels in the lacrimal gland. A second gene,Spt-2, appears to be present as a single copy in some strains and as two copies in others. This gene is expressed at high levels only in the SMG of those strains carrying two copies, andSpt-2 mRNA is not detectable in the SMG of strains carrying only one copy. In contrast toSpt-1, theSpt-2 gene is not expressed at detectable levels in the lacrimal gland.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Cellular and molecular neurobiology 9 (1989), S. 281-294 
    ISSN: 1573-6830
    Keywords: cholecystokinin ; mammillary region ; development ; gene expression ; hybridization histochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary 1. The ontogeny and adult distribution of neurons containing cholecystokinin (CCK) mRNA in the premammillary and mammillary nuclei and supramammillary region of the rat brain were studied using hybridization histochemistry. 2. The earliest detection of CCK mRNA in the mammillary region was on E14, followed by a marked increase in transcript levels during the next 4 days, a time during which neurons in this region still divide. During the first 2 weeks of life, few changes in the levels of CCK transcripts were seen, and an adult-like pattern of expression was seen on the twenty-first day of life. 3. Low levels of transcripts were present in numerous neurons located in all divisions of the medial nucleus and in the posterior nucleus known to project ipsilaterally to the anteroventral and anteromedial thalamic nuclei. In contrast, none of the neurons in the lateral nucleus (projecting bilaterally to the anterodorsal thalamic nucleus) had detectable transcripts. 4. Many neurons in the supramammillary nucleus had low, moderate, or high levels of transcripts. Some nearby nuclei (such as the dorsal premammillary nucleus) had smaller numbers of neurons with low levels of CCK mRNA, whereas others (such as the ventral premammillary nucleus) had none.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 12 (1989), S. 295-299 
    ISSN: 1573-5028
    Keywords: gene expression ; multiple transcripts ; phytochrome ; Pisum sativum ; red/far-red reversible effect
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The reversible effect of red and far-red light on the level of two RNA transcripts of the single-copy phytochrome gene in pea was investigated using the primer extension assay. In dark-grown seedlings, a brief irradiation with red light markedly reduced the level of one of the phytochrome transcripts, RNA1. This red light effect was reversed by subsequent irradiation with far-red light. The other phytochrome transcript, RNA2, was only slightly influenced by light. In light-grown seedlings, a brief irradiation with far-red light increased the content of both RNA1 and RNA2 when the seedlings were transferred from light to darkness. This far-red light effect was reversible by subsequent red light irradiation.
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  • 8
    ISSN: 1573-5028
    Keywords: antisense RNA ; β-glucuronidase ; tobacco ; transgenic plants ; gene expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Antisense RNA was used to specifically inhibit the expression of a GUS gene introduced in a transgenic plant. A tobacco transformant containing a single intact copy of the GUS gene and showing relatively high constitutive levels of GUS activity (GUS+) was re-transformed with an Agrobacterium Ti-derived binary vector containing an antisense version of this reporter gene. The sense and antisense GUS genes were each under the regulation of the CaMV 35S promoter. Re-transformed plants contained 1–5 copies of the antisense construct and all showed a greater than 90% reduction in GUS activity relative to the original GUS+ plant. This reduction in GUS activity correlated closely with the levels of GUS enzyme and steady state GUS mRNA observed in these plants. The relatively low levels of sense and antisense GUS transcripts found in the re-transformed plants may indicate a rapid degradation of the RNA:RNA duplex in the cell.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1573-4919
    Keywords: complement ; factor B ; gene expression ; interferon-ψ ; interleukin-1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract The serine protease complement factor B (Bf), an acute phase plasma protein, is a component of the alternative pathway of complement activation. Previous studies revealed that several cytokines including IFN-γ and IL-1 are involved in mediating acute phase Bf expression. To determine the molecular details of Bf expression we isolated, sequenced and characterized the 5′ flanking regions of the human and murine Bf genes. In both species the Bf transcriptional start site in liver was located 〈400 by 3′ to the polyadenylation site of the upstream C2 gene. This upstream intergenic region contained 〉65% nucleotide homology between species. Within this region, an IRS and three heat shock consensus elements were found in the murine sequence in an identical position to that of the human. To examine the functional details of Bf expression, a series of mouse and human Bf promoter - chloramphenicol acetyltransferase (CAT) chimeric gene constructs were transfected into mouse L or human HepG2 cells. Analysis of expression of these fusion gene constructs revealed that 1) cis-acting DNA sequences identified, at least in part, in the 3′ untranslated region of the C2 gene (within the 400 by upstream of the Bf cap site) mediate responsiveness to IL-1 and IFN-γ, 2) the responsiveness to each mediator appears to be conferred by separate upstream regions similar in position and homologous in man and mouse, and 3) the IL-1 responsive region in both species appears to have the characteristics of an enhancer element. The results of this analysis suggest a selective pressure to conserve the intergenic sequence between C2 and Bf genes and that further studies of these sequences will be useful in elucidating mechanisms controlling the acute phase response.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Bioscience reports 9 (1989), S. 157-188 
    ISSN: 1573-4935
    Keywords: matrix hypothesis ; morphogenesis ; protodynamics ; growth control ; DNA ; genome organisation ; gene expression ; gene regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract A theoretical concept is proposed, in order to explain some enigmatic aspects of cellular and molecular biology of eukaryotic organisms. Among these are the C-value paradox of DNA redundancy, the correlation of DNA content and cell size, the disruption of genes at DNA level, the “Chromosome field” data of Lima de Faria (Hereditas 93∶1, 1980), the “quantal mitosis” proposition of Holtzeret al. (Curr. Top. Dev. Biol. 7∶229 1972), the inheritance of morphological patterns, the relations of DNA and chromosome organisation to cellular structure and function, the molecular basis of speciation, etc. The basic proposition of the “Unified Matrix Hypothesis” is that the nuclear DNA has a direct morphogenic function, in addition to its coding function in protein synthesis. This additional genetic information is thought to be largely contained in the non-protein coding transcribed DNA, and in the untranscribed part of the genome.
    Type of Medium: Electronic Resource
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  • 11
    ISSN: 1573-5028
    Keywords: cadmium ; Datura innoxia ; gene expression ; heat shock ; tolerance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The effect of Cd on gene expression in suspension cultures of twoDatura innoxia cell lines with differing Cd tolerance was studied.In vivo labeling experiments using [3H] leucine showed that Cd induced the synthesis of a similar range of proteins in both cell lines at a concentration which will kill the sensitive but not the tolerant cells. Corresponding changes in levels of translatable mRNA were also observed. The induction of the synthesis of proteins by Cd was transient since Cd-tolerant cells growing continuously in 250 μM CdCl2 contained a similar set ofin vitro translation products to cells growing in the absence of Cd. Although Cd had a similar effect on gene expression in both cell lines, Cd-tolerant cells possess two abundant mRNAs which are constitutively produced. These mRNAs encode proteins of low molecular weight (about 11 kDa) and are either absent or present at a low level in Cd-sensitive cells. The functions of these proteins are not known but they may be involved in the tolerance mechanism. Two-dimensional gel electrophoresis ofin vitro translation products showed that many of the Cd-induced proteins are also induced by heat shock. A 42°C heat shock resulted in agreater range and more intense induction of translatable mRNAs than 4 h exposure to 250 μM CdCl2. However a subset of mRNAs were induced specifically by Cd while other mRNAs were heat shock-specific. There was no difference in the ability of the two cell lines to tolerate heat shock. This was also reflected by the same pattern of major proteins induced by heat shock in the two cell lines.
    Type of Medium: Electronic Resource
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 12 (1989), S. 667-672 
    ISSN: 1573-5028
    Keywords: ferredoxin ; gene expression ; heterocyst ; Anabaena 7120 ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genes for ferredoxin from heterocysts (fdx H) and vegetative cells (pet F) of Anabaena sp. strain 7120 were subcloned into plasmid pUC 18/19. Both genes were expressed in Escherichia coli at high levels (≈10% of total protein). Pet F could be expressed from its own promoter. The ferredoxins were correctly assembled to the holoprotein. Heterocyst ferredoxin was purified from E. coli extracts on a large scale. Its biochemical and biophysical properties were identical to those of the authentic ferredoxin, isolated from Anabaena heterocysts.
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  • 13
    ISSN: 1573-5028
    Keywords: acyl carrier protein ; fatty acid synthesis ; gene expression ; gene fusion ; protein A ; spinach
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A synthetic gene encoding spinach acyl carrier protein I (ACP-I) was fused to a gene encoding the Fc-binding portion of staphylococcal protein A. This gene fusion, under the control of the λPR promoter, was expressed at high levels in Escherichia coli producing a 42 kDa fusion protein. This fusion protein was phosphopantethenylated in E. coli. In vitro the ACP portion of the fusion protein was able to participate in acyl ACP synthetase reactions, plant malonyl-CoA:ACP transacylase (MCT) reactions, and plant fatty acid synthetase (FAS) reactions. Inhibitory effects of high ACP concentrations on in vitro plant FAS were observed with the unfused ACP-1 but not with the fusion protein. As with unfused ACP-I, the fusion protein was a poor substrate for E. coli FAS reactions. When injected into rabbits, the fusion protein was also able to generate antiserum to spinach ACP-I.
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  • 14
    ISSN: 1573-5028
    Keywords: cDNA sequence ; gene expression ; glutamine synthetase ; legume-Rhizobium symbiosis ; nitrogen metabolism ; Phaseolus vulgaris L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report the sequence of an essentially full-length glutamine synthetase (GS) cDNA clone (pcGS-γ1) isolated from a root nodule library ofPhaseolus vulgaris L. The polypeptide encoded by this cDNA has been producedin vitro by transcription/translation and shown to co-migrate on two-dimensional gels with the previously identified major cytosolic GS polypeptide (γ) of nodules. Two previously identified GS cDNA clones, pR-2 and pR-1 (see Gebhardtet al., EMBO J 5: 1429–1435, 1986) have similarly been shown to encode the α and β cytosolic GS polypeptides respectively. An RNase protection technique has been used to analyse specifically and quantitatively the abundance of mRNA related to these three GS cDNAs and to the cDNA (pcGS-δ1) encoding the chloroplast-located GS, during nodulation. Differences in the abundances of these mRNAs at different times suggest that they are not coordinately regulated. Moreover, using this technique mRNA specifically related to pcGS-γ1 was found at high levels in nodules but not in roots or leaves. Surprisingly the expression of this gene is not nodule-specific as previously suggested, as its mRNA was also detected, but at lower levels, in stems, petioles and in green cotyledons. By comparison, mRNA related to a leghaemoglobin gene was detected only in nodules. Comparisons of the relative abundances of the pcGS-γ1 mRNA and the γ polypeptide in different organs and at different stages during nodulation, suggest that the appearance of the γ polypeptide is largely under transcriptional control.
    Type of Medium: Electronic Resource
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  • 15
    ISSN: 1573-5028
    Keywords: differential cDNA screening ; gene expression ; hybrid-select in vitro translation ; nuclear run-off transcription ; RNA blot hybridization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA library from cultured parsley (Petroselinum crispum) cells was differentially screened using labeled run-off transcripts derived from nucleic of elicitor-treated and untreated cells. This resulted in the isolation of 18 independent cDNA families representing putative defense-related genes. All genes are rapidly and transiently activated after elicitor application, but the time courses of transcriptional activity exhibit considerable variations, indicating differences in the mechanisms of gene regulation.
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  • 16
    ISSN: 1573-5028
    Keywords: deformation factor ; gene expression ; pea ; Rhizobium leguminosarum ; root hairs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The mRNA population in pea root hairs was characterized by means of in vitro translation of total root hair RNA followed by 2-dimensional gel electrophoresis of the translation products. Root hairs contain several mRNAs not detectable in total RNA preparations from roots. Most of these root hair-specific mRNAs occur in elongating root hairs at higher levels than in mature root hairs. The expression of some genes in pea root hairs is typically affected by inoculation with Rhizobium leguminosarum. One gene, encoding RH-42, is specifically induced while the expression of another gene, encoding RH-44, is markedly enhanced. Using R. leguminosarum mutants it was shown that the nodC gene is required for the induction and enhancement of expression of the RH-42 and RH-44 genes, respectively, while the Rhizobium chromosomal gene pss1, involved in exopolysaccharide synthesis, is not essential. After induction of the nod genes with apigenin the bacteria excrete into the culture medium a factor that causes root hair deformation. This deformation factor stimulates the expression of the RH-44 gene but does not induce the expression of the gene encoding RH-42.
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  • 17
    ISSN: 1573-5028
    Keywords: C4 photosynthesis ; gene structure ; gene expression ; genetic variation ; silent substitution ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have determined the structure of the maize (Zea mays L. subsp.mays line B73) nuclear gene encoding the phosphoenolpyruvate (PEP) carboxylase isozyme involved in C4 photosynthesis. The gene is 5.3 kb long and has ten exons that range in size from 85 to 999 bp. The nine introns vary from 97 to 872 bp. The sequence of 663 bp of 5′-flanking and 205 bp of 3′-flanking DNA is reported along with the entire gene sequence. Several short repetitive sequences were found in the 5′-flanking DNA that have characteristics similar to elements important in the light regulation of pea genes encoding the small subunit of ribulose 1,5-bisphosphate carboxylase. In addition, some 5′-flanking sequence similarities were found in a comparison with other light-regulated genes from maize and wheat. The level of DNA sequence variation among different PEP carboxylase alleles is similar to the allelic variation observed for several other maize nuclear genes. The data suggest modern maize variaties have retained much of the genetic variation present in their ancestral forms. Finally, accumulation of transcripts encoding the PEP carboxylase isozyme involved in C4 photosynthesis is quite high in several structures besides leaves, including inner leaf sheaths, tassels and husks. This indicates that expression of this gene is not leaf-specific and may not necessarily be coupled to the development of Kranz anatomy.
    Type of Medium: Electronic Resource
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 12 (1989), S. 673-682 
    ISSN: 1573-5028
    Keywords: amylase inhibitor ; barley ; cDNA sequence ; gene expression ; hormonal regulation ; protease inhibitor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have cloned and sequenced a full-length cDNA from barley (Hordeum vulgare L.) seeds encoding the bifunctional α-amylase/subtilisin inhibitor (BASI). The nucleotide sequence predicts an open reading frame coding for a protein of 203 amino acids. The first 22 amino acids exhibit the sequence characteristic of a signal peptide, as found in several other plant protease inhibitors. Northern blot hybridization experiments indicate that BASI mRNA accumulation is strictly tissue-specific and is developmentally programmed. BASI mRNA transcripts were only identified in 1) developing starchy endosperm tissue from 14 days after flowering and 2) aleurone tissue of germinating seeds. In this latter tissue, BASI mRNA accumulation is enhanced by abscisic acid and abolished by gibberellic acid. Expression of BASI mRNA was also studied in the lys 3a high-lysine barley mutants Risø No. 1508 and Piggy. These high-lysine barleys show 2–4-fold higher levels as well as prolonged accumulation of BASI mRNA compared to the normal motherline Bomi. This correlates with the increased deposition of BASI protein in lys 3a barley mutants. Genomic blot analysis of barley DNA suggests that there are one or two BASI structural genes per haploid genome. Possible roles of BASI as part of a defence mechanism against precocious germination and pathogens are discussed.
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  • 19
    ISSN: 1573-5028
    Keywords: cDNA ; gene expression ; hydroxypyruvate reductase ; light regulation ; peroxisomal enzyme
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A full-length cDNA encoding NADH-dependent hydroxypyruvate reductase (HPR), a photorespiratory enzyme localized in leaf peroxisomes, was isolated from a λgt11 cDNA library made by reverse transcription of poly(A)+ RNA from cucumber cotyledons. In vitro transcription and translation of this clone yielded a major polypeptide which was identical in size, 43 kDA, to the product of in vitro translation of cotyledonary poly(A)+ RNA and subsequent immunoprecipitation with HPR antiserum. Escherichia coli cultures transformed with a plasmid construct containing the cDNA insert were induced to express HPR enzyme activity. RNA blot analysis showed that HPR transcript levels rise significantly in the first eight days of light-grown seedling development. This closely resembles the pattern seen for HPR-specific translatable mRNA. DNA blot analysis indicated that a single HPR gene is likely present per haploid genome. Nucleotide sequence analysis revealed an open reading frame of 1146 bases which encodes a polypeptide with a calculated molecular weight of 41.7 kDa. The derived amino acid sequence from this open reading frame is 26% identical and 50% similar to the amino acid sequence of the E. coli enzyme phosphoglycerate dehydrogenase, which catalyzes a similar reaction and functions in a related pathway. Statistical analyses show that this similarity is significant (z〉10). The derived amino acid sequence for HPR also contains the characteristics of an NAD-binding domain.
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  • 20
    Electronic Resource
    Electronic Resource
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 41 (1989), S. 179-188 
    ISSN: 0730-2312
    Keywords: protein kinase C ; TPA ; cell transformation ; gene expression ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: We have used a previously described retroviral expression vector pMV7-PKCβ1 to develop derivatives of two rat liver epithelial cell lines, K16 and K22, that stably express about tenfold-higher PKC activity than control cells. Despite these high levels of PKC, these cells did not exhibit gross morphologic changes, anchorage-independent growth, or tumorigenicity. K16PKC-4 and K22PKC-2, two lines with the highest PKC enzyme activity, were studied further in terms of several responses to the phorbol ester tumor promoter TPA. When treated with 100 ng/ml of TPA, the control K16MV7 and K22MV7 cells displayed a slight change in morphology, whereas the K16PKC-4 and K22PKC-2 cells displayed a marked change in morphology. Northern blot analyses demonstrated that TPA induced increased levels of fos, myc, phorbin, and ODC RNAs in control K16MV7 and K22MV7 cells, with maximum induction occurring at about 0.5, 1, 8, and 8 h, respectively. In K16PKC-4 and K22PKC-2 cells, TPA induction of phorbin and ODC RNAs was markedly enhanced, but this was not the case for myc and fos RNAs. In addition, the levels of myc RNA were constitutively higher in both K16PKC-4 and K22PKC-2 cells than in the control cells. Taken together, these results provide direct evidence that PKC plays a critical role in modulating the expression of myc, phorbin, and ODC RNAs. On the other hand, overexpression of PKCβ1 is not itself sufficient to cause cell transformation.
    Additional Material: 3 Ill.
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  • 21
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 167-180 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: There are significant differences between the conditions for chemical and biochemical reactivity. There-fore, models for treating chemical reactions are mostly not suitable for investigating interactions and transformations of bio(macro)molecules. Common features of numerous processes occurring in vivo and in vitro (such as the role of water, ions, and colloids and the significance of Helmholtz energy surfaces) are outlined. Some characteristics of a model suitable for studying van der Waals interactions between biomacromolecules, based on Brownian dynamics and the Lifshitz theory, are described.
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  • 22
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 181-191 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quantum chemical studies (INDO-RHF-SCF) have been made for the resting state active sites of three closely related heme proteins, cytochrome c peroxidase (CCP), metmyoglobin (MMB), and catalase (CAT). The relative energies of the germane sextet, quartet, and doublet spin-states of each active site were calculated. Both CCP and MMB have similar heme units, consisting of an Fe(III)-protoporphyrin-IX with an imidazole and water as axial ligands. Our calculations show that the larger doming of the porphyrin, greater out-of-planarity of the iron, and the shorter iron-water distance in MMB leads to a sextet ground state with a low-lying quartet state. By contrast, the order of these two states is reversed in CCP, when a neutral imidazole is used as the endogenous axial ligand. An imidazolate ligand, on the other hand, which is an extreme representation of the H-bonding believed to occur in CCP with a nearby aspartate residue, leads to a sextet ground state with a low-lying quartet state. Assuming at least a partially anionic ligand in the intact protein, it follows that the quartet contribution to the ground state properties will be larger in CCP than in MMB. These predictions are consistent with the observed differences in the temperature-dependent magnetic susceptibility for these two proteins. The present results suggest that the experimentally observed Mössbauer resonance spectra of CCP should be reinterpreted in terms of sextet and quartet state contributions to the electric field gradient. Calculations for catalase, which has a single phenolate ligand, result in a sextet ground state with a low-lying quartet state consistent with available Mössbauer and magnetic susceptibility data. Our calculations of the Im- form of CCP show that it more closely resembles CAT. Thus, the effect of proton transfer in CCP can account at least in part for the similarities between CCP and CAT function. Minor differences in ground spin-state and electronic properties calculated for CCP and MMB, however, cannot explain why MMB does not have significant peroxidase activity. The different functions of MMB and CCP must then be due in part to other known differences in their protein environment such as polar residues around the distal ligand binding pocket of CCP, which are absent in MMB, and could help its transformation to an active oxidizing state.
    Additional Material: 5 Tab.
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  • 23
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 223-239 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recent studies performed in our group on a classical problem of quantum chemistry, with strong implications for theoretical biochemistry and pharmacology, are here summarized. Ab initio descriptions of noncovalent interactions, and in particular H bonds and acid-base couples, have been reexamined using as novel tools the decomposition of ΔE with the inclusion of CP corrections and a further decomposition of the ΔE components into group contributions. Some results of systematic analyses performed over H-bonded dimers are reported, supplemented by a successful application of this approach to a problem of noticeable economic importance (the identification of catalysts for the industrial synthesis of tensioactives). A new feature, presented here for the first time, is the extension of the CP-corrected decomposition of ΔE to bimolecular interactions in solution.
    Additional Material: 8 Ill.
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  • 24
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 297-303 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two new numerical methods for solving the Schrödinger equation for an N-well periodic potential are presented. One is a diagonalization method based on Floquet-Bloch formalism, and the other is a renormalized Numerov-Cooley method with periodic boundary conditions. The numerical superiority of these methods over the standard diagonalization technique is demonstrated. The methods are illustrated by applications to internal rotation.
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  • 25
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    International Journal of Quantum Chemistry 35 (1989), S. 325-330 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown that configuration interaction calculations, with inclusion of the relativistic corrections, constitute an appropriate approach for the prediction of atomic energy levels and that results of experimental accuracy are possible given the availability of large-scale, fast computers. The results obtained for He through F emphasize both the practical difficulties to be encountered and the possibility of predictions with less than 1% error.
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  • 26
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    International Journal of Quantum Chemistry 35 (1989), S. 331-337 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Through a formalism developed in formr papers, some problems, set by the determination, from experimental data of the evolution equation of an n-states quantum system are considered.
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  • 27
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    International Journal of Quantum Chemistry 35 (1989), S. 361-372 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An “apparatus” operator approach is presented for the extension of the density functional theory of Hohenberg, Kohn, and Mermin. Using the Mermin entropy principle, a one-to-one correspondence is established between the density matrix for the system and the electron charge density for a finite-temperature system in the presence of an apparatus. In the zero-temperature limit in the absence of an apparatus, the Hohenberg-Kohn theory is recovered. The central aspect of this new density functional theory is that the principle of maximum entropy is applied to the system plus its surroundings under the additional constraint that the electron charge density is given. The system is treated as a subsystem of a composite system and is not necessarily in the equilibrium state as in the Mermin theory. As an example, it is shown how, in principle, excited states are encompassed by the theory.
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  • 28
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    International Journal of Quantum Chemistry 35 (1989), S. 577-580 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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  • 29
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    International Journal of Quantum Chemistry 35 (1989) 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 30
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    International Journal of Quantum Chemistry 35 (1989), S. 581-581 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 31
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    International Journal of Quantum Chemistry 35 (1989), S. 593-612 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A practical method for generating irreducible matrix reps of point groups and a concise formula about projection operators are proposed. By using this formula as well as versatile classification schemes, the symmetry adaptation of a many-electron system is simplified. A unified algorithm and program of symmetry adaptation of spin-free space have been developed.
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  • 32
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    International Journal of Quantum Chemistry 35 (1989), S. 679-685 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The self-consistent multiple scattering Xα (MSXα) method is used to arrive at the electronic structure of a helium-trapped vacancy in aluminum using a cluster model. The calculated orbital energies, electron density, and charge distributions are compared with the available theoretical results. It is shown that helium trapping causes the reshuffling and upward movement of the cluster levels (with vacancy).
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  • 33
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    International Journal of Quantum Chemistry 35 (1989), S. 779-791 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light positive particles can be introduced in metallic lattices where they take up interstitial positions. The motion of particles between these sites is usually described as a phonon-assisted tunneling process, which at high temperatures approaches a classical over-barrier jump motion.The present paper reviews briefly the study of such phenomena at very low temperatures where phonon assistance is no longer effective. Experiments on proton transfer between certain sites in niobium metal and on positive muons which diffuse in copper or aluminium lattices show unusual temperature dependencies, which have been explained quantitatively with recent tunneling theories. These approaches take into account the simultaneous dissipation of energy to the electron bath, a phenomenon which was shown by J. Kondo to be determined by the screening electrons following the particle. The temperature dependence is essentially an effect of the Fermi distribution of the conduction electrons. The interaction of the particle with the itinerant electrons will also determine whether the particle wavefunction will be localized or form an extended (Bloch-like) state.
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  • 34
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    International Journal of Quantum Chemistry 35 (1989), S. 827-838 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reflected and transmitted electric fields generated by s- and p-polarized incident radiation are discussed using a microscopic approach that matches the solution of Maxwell's equation (obtained by integration over the surface region) to the incident and the reflected fields in the vacuum and to the transmitted fields in the bulk. At positions where the dielectric response is varying rapidly, the parallel components of the oscillating polarization are the sources of reflected as well as transmitted fields, and the corresponding perpendicular components (which exist only for p-polarized incident radiation) lead to charge oscillations that are the source of both longitudinal and transverse fields. The presence of the surface makes possible the generation of transverse and longitudinal excitations with large normal components of the wave vector, whose propagation directions are given by the conservation of the parallel component of the wave vector. This formulation does not make use of additional surface boundary conditions (ABC) but requires an explicit model for the nonlocal dielectric function in the surface region. Besides discussing the fields, we discuss the choice of electromagnetic potentials. We also discuss nonlinear properties with applications to second harmonic generation.
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  • 35
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    International Journal of Quantum Chemistry 36 (1989), S. 1-3 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 36
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    International Journal of Quantum Chemistry 36 (1989), S. 19-33 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A set of 18 aryltriazenes and the antitumor drug DTIC, whose mutagenicity has been determined in the Ames test, has been studied using octanol-water partition coefficients (P) as a measure of relative hydrophobicity and MNDO molecular orbital energies and electron distributions to account for variation in their electronic characteristics. A good structure-activity relationship was found using log P in combination with either εHOMO, or qHOMO, where the latter is defined as the HOMO electron density on N1 of the triazene. The dependence of mutagenicity on hydrophobicity is similar to what had been found earlier by Venger, Hansch, Hatheway, and Amrein [4] for the aryltriazenes alone using σ+ as a descriptor of electronic characteristics. A consistent role for electronic factors is found using σ+, εHOMO and qHOMO, namely, increased mutagenicity is associated with structural variations that increase the electron donating ability of the triazenes.
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  • 37
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    International Journal of Quantum Chemistry 36 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 38
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    International Journal of Quantum Chemistry 36 (1989), S. 119-125 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Static longitudinal polarizabilities αzz and cubic hyperpolarizabilities γzzzz are obtained by the FPT-INDO method for finite chain C4N+2H2N+4 (N = 1-15) models of polydiacetylene and polybutatriene. For the acetylenic structure the onset of saturation first becomes evident at about C14—C18 for the linear polarizability and C22—C26 for the cubic term. The values per C4H2 unit are accurately extrapolated to the infinite chain limit. In the case of the butatrienic structure, no saturation is observed through C54.
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  • 39
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    International Journal of Quantum Chemistry 36 (1989), S. 187-188 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 40
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    International Journal of Quantum Chemistry 36 (1989), S. 225-240 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Analytical and numerical studies are performed concerning the exclusion of the basis set superposition error (BSSE) from the SCF calculations of intermolecular interactions. Based on these studies a new procedure is proposed, which consists of the following steps: (1) determine the orbitals by the SCF scheme based on the recent “chemical Hamiltonian approach” (CHA-SCF method), i.e., excluding the delocalization effects caused by BSSE, and then (2) calculate the usual energy expectation value. (This gives results superior to those obtained by the previous nonsymmetric CHA energy formula.) The actual numerical calculations performed for different simple systems (He2, water dimer) by using various basis sets indicate that the CHA/CE (CHA with “conventional energy” formula) potential curves are well-balanced and are close to those obtained by the Boys-Bernardi (BB) method and usually (but not necessarily) go slightly beyond the latter. So our method gives results better than (or close to) those given by the BB method by performing only a single ∼N4 calculation at each geometrical arrangement of the system.
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  • 41
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    International Journal of Quantum Chemistry 36 (1989), S. 127-140 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A explicit expression for the unitary group Clebsch-Gordan coefficients, which couple two fully antisymmetric single-column states into the two-column Gel'fand-Tsetlin states, is given in terms of isoscalar factors for the canonical subgroup chain U(n) ⊃ U(n - 1) ⊃ … ⊃ U(1). The isoscalar factors are expressed through the step numbers labeling canonical basis states and enable a straightforward construction of Gel'fand-Tsetlin states in the Clifford algebra unitary group approach, without the use of the tables for the symmetric group outer-product reduction coefficients.
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  • 42
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    International Journal of Quantum Chemistry 36 (1989), S. 379-389 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this article, the Hamiltonian for the scattering of the He + H2 system is given by using the interaction potential V(X, Y, Θ) determined by experiments and the semiclassical method. From this Hamiltonian we find a dynamical algebra h6. The statistical expectation of the energy and the transition probability of H2, Pn→m, are derived; therefore, selection rules have been found easily.
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  • 43
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    International Journal of Quantum Chemistry 36 (1989), S. 427-427 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 44
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    International Journal of Quantum Chemistry 36 (1989), S. 241-253 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio molecular orbital methods are employed to study the low-lying states of C3H+, SiC2H+, Si2CH+, and Si3H+. Special attention is paid to a comparative study between C3H+ and Si3H+. In both cases a 3B2 state is found to lie the lowest at the HF level, although inclusion of correlation effects favor a linear structure (1Σ+ state) for C3H+, which lies 25 kcal/mol below the 3B2 state at the MP4 level, and a bent structure (1A′ state) for Si3H+, which lies just 2 kcal/mol below the 3B2 state. The proton affinities of C3, SiC2, Si2C, and Si3 are estimated at different levels of theory. Both protonation at carbon and silicon atoms are considered for SiC2 and Si2C. It is found that C3 comparatively has a low proton affinity. On the other hand, Si3 has a relatively high proton affinity compared with the protonation at silicon atom for both SiC2 and Si2C. These results are discussed on the basis of electronic structure arguments.
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  • 45
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    International Journal of Quantum Chemistry 36 (1989), S. 341-351 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An alternative scheme for ab initio polymer band structure calculations based on a Filon-type quadrature is proposed. This scheme avoids the explicit calculation and the storage of the “troublesome” Fourier transforms of the LCAO density matrix elements and is a first step towards a better control of the convergence of the different lattice sums appearing in the configuration space LCAO-SCF-CO method. The potential of the proposed technique is illustrated by a minimal basis set calculations on an infinite chain of H atoms.
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  • 46
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently we extended our strategy for MRD-CI (multireference double excitation-configuration interaction) calculations based on localized/local orbitals and an “effective” CI Hamiltonian for molecular decompositions of large molecules to breaking a chemical bond in a molecule in a crystal or other solid environment. Our technique involves solving a quantum chemical ab-initio SCF explicitly for a system of a reference molecule surrounded by a number of other molecules in the multipole environment of more distant neighbors. The resulting canonical molecular orbitals are then localized and the localized occupied and virtual orbitals in the region of interest are included explicitly in the MRD-CI with the remainder of the occupied localized orbitals being folded into an “effective” CI Hamiltonian. The MRD-CI calculations are carried out for breaking a bond in the reference molecule. This method is completely general. The space treated explicitly quantum chemically and the surrounding space can have voids, defects, deformations, dislocations, impurities, dopants, edges and surfaces, boundaries, etc. We previously applied this procedure successfully to the H3C—NO2 bond dissociation of nitromethane in a nitromethane crystal with extensive testing of the number of molecules that have to be included explicitly in the SCF and how many molecules have to be represented by more distant multipoles. The results indicated that it took more energy to dissociate the H3C—NO2 bond when the nitromethane molecule was in the crystal than it did to dissociate that bond in the free nitromethane molecule. In this present study we have investigated the effect of voids (both in the nitromethane molecules treated explicitly in the SCF and those in the environment represented by multipoles) on the calculated H3C—NO2 bond dissociation energies.
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  • 47
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    International Journal of Quantum Chemistry 36 (1989), S. 417-425 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetooptical properties (B terms) vibronically induced have been calculated for a series of carbonyl compounds in the region of the first absorption band. The rules deduced experimentally for the signs and sizes of the B terms induced by vibrations of different symmetry are generally confirmed by these calculations.
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  • 48
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    International Journal of Quantum Chemistry 36 (1989), S. 429-453 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A particularly compact form of the orthogonally spin-adapted coupled-cluster equations involving all singly and doubly excited clusters is derived for the general case of a non-Hartree-Fock closed-shell reference determinant. The diagrammatic approach based on the graphical methods of spin algebras is applied. The relationship of different diagrammatic procedures for spin-adaptation, employing both bare and spin-adapted two-electron interaction vertices, is discussed. A comparison with the results obtained with algebraic spin-adaption approaches is also given.
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  • 49
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    International Journal of Quantum Chemistry 36 (1989), S. 533-533 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 50
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    International Journal of Quantum Chemistry 36 (1989), S. 503-524 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A graphical approach to the configuration interaction in the basis of pure Slater determinants is presented. The formulation based on the spin-separated two-slope graph (SSTSG), enabling the selection of determinants with the fixed Ms value, has a direct relation to the well-known concept of the group-function product. The commonly used excitation criterion and the spatial (Abelian) symmetry properties are analyzed in terms of the graph's internal structure. The Slater formulae for the Hamiltonian matrix elements between determinants, in the particle-hole formalism and in the spin-separated form, are related to different classes of loops within graphs. Some aspects of implementation within both the matrix-element-driven (ME) and integral driven (ID, direct) CI algorithms are discussed. The presented formulation, of a general complete active space (CAS) CI type, is a basis of the Graphical Determinantal Configuration Interaction (GDCI) computer program.
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  • 51
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    International Journal of Quantum Chemistry 36 (1989), S. 541-541 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 52
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    International Journal of Quantum Chemistry 35 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 53
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We start by pointing out relationships between production of information, global simulation, and supercomputing, thus placing our research activities in today's society context. Then we detail the evolution in hardware and software for 1CAP, our experimental supercomputer, which we claim to be especially well suited for supercomputing in science and engineering. A preliminary discussion of 1CAP/3090 (our latest experimental effort) is included. Many examples from different disciplines are provided to verify our assertions. We “prove” our point by presenting an example of global supercomputing. Starting with 3 nuclei and 10 electrons, building up to a single water molecule, then to a few hundred, we learn, for example, about Raman, infrared, and neutron scattering; we then move up to a few hundred thousand molecules to analyze particle flow and obstructions; finally we experiment, but only preliminarily, with a few million particles to learn more on nonequilibrium dynamics as in the Rayleigh-Benard systems. In this way, quantum mechanics is overlapped with statistical mechanics and expanded into microdynamics. The entire paper is finally reanalyzed from a different perspective, presenting rather systematically, even if most briefly, our ideas on “modern” computational chemistry, where quantum mechanics is as much needed as fluid dynamics and graphics. In this section the main computational techniques are analyzed in terms of computer programs and their associated flow diagrams to solve the basic equations using parallel supercomputers.
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  • 54
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    International Journal of Quantum Chemistry 35 (1989), S. 153-165 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of a proximate condensed environment as the solvent and cellular structured patterns (biopolymers, membranes, etc.) play an important role in determination of the courses of molecular processes in biology. We present here the background of methods developed for such an environmental effects estimation combining the continuum and discrete models. Their applications within theoretical studies into the mechanisms of carcinogenic action of alkylating N-nitrosocompounds are shown. The results given cover four different areas, namely the quantitative structure-activity relationship, mechanistic studies into their metabolic activation reactions, interactions of the ultimate carcinogens with DNA, and finally their genetic consequences.
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  • 55
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    International Journal of Quantum Chemistry 35 (1989), S. 255-255 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 56
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    International Journal of Quantum Chemistry 35 (1989), S. 277-282 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The idea of a Franck-Condon (FC) operator is introduced, and its normally ordered form is obtained through the newly developed technique of “integration within an ordered product of operators (IWOP).” It is shown that the FC operator leads to a new approach for the calculation of FC factors. The results of existing theories are viewed, and the connection between the FC operator and the “squeeze-operator” is pointed out.
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  • 57
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    International Journal of Quantum Chemistry 35 (1989), S. 305-313 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown that infinite long polyacene chains may have three energetically close but structurally distinct isomers (a symmetrical, sym, form and two lower symmetry forms: one with double bonds in a trans and another isomer with double bonds in a cis pattern). The energetics is based on solid state MNDO theory. We discuss that the symmetrical form has a substantial energy gap Eg in the Hartree-Fock approach owing to exact exchange terms, which are nonlocal. Broken symmetry Hartree-Fock (HF) solutions for polyacene are also described. An angularly distorted structure suggested earlier on Jahn-Teller grounds is found to be energetically not favorable.
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  • 58
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extensive theoretical calculation of the tetraphenyldithiapyranylidene DIPSφ4 molecule by means of the MSXα method is presented. The results obtained permit one to interpret the optical spectrum and the XPS spectrum as well as the charge transfer between DIPSφ4 and planar molecular semiconductor compounds such as TCNQ. To our knowledge, this is the first theoretical determination to date of such a charge transfer ratio from separate parameter-free calculations on large-size molecules.
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  • 59
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    International Journal of Quantum Chemistry 35 (1989), S. 813-825 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ground (N) state and the 1B1u(V) excited state of planar ethylene have been studied at the CPF and MR-SDCI levels of theory, using an extended CGTO basis set of the ANO type. The investigation especially addresses the near-degeneracy problem in the ground state and the coupling between the diffuse character of the π* orbital and the amount of correlation included in the wave function of the V state. The MR-SDCI results yield a vertical excitation energy in the range 7.8-8.0 eV, whereas the CPF result is 7.9 eV. The best MR-SDCI result for 〈1π*‖z2‖1π*〉 is 7.8, whereas CPF calculations based on MR-SDCI INOS give the value 6.7. It is clear from the results that these numbers have not converged and that more extended calculations than was possible in the present work would yield an even more compact wave function.
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  • 60
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    International Journal of Quantum Chemistry 36 (1989), S. 169-178 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of a new time-dependent ket, variationally determined as a linear combination of Slater determinants associated with an electric field variant factor, provides an efficient technique for the calculation of dynamic polarizability tensors. Including electron correlation, the method is applied to the evaluation of the frequency-dependent polarizability of H2O and N2 and can be used even when the photon energy is near the excitation energy. With relatively small basis sets, calculated polarizabilities and resonance frequencies are in good agreement with experimental values for H2O but have to be improved for N2.
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  • 61
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    International Journal of Quantum Chemistry 35 (1989), S. 103-112 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Results of a Monte Carlo simulation of the hydration of caffeine (1,3,7-trimethyl-2,6-dioxipurine) and three different configurations of its stacked dimer are presented. Simulations were performed in a cluster approximation; the system contained 200 water molecules. The nature of the stabilization of caffeine stacking associates in water was considered. A hydrophobic behavior of methyl groups during association of caffeine molecules in water is shown. Results of the simulation of caffeine hydration are compared with experimental data from the study of the system of caffeine-water.
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  • 62
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    International Journal of Quantum Chemistry 35 (1989), S. 125-139 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A close scrutiny of the relationship between geometric constraints and motion in a system of water molecules allows the prediction of a role of solvent dynamics in the solvent-mediated interaction between two solutes and between different parts of one solute. The predicted mechanism is cooperative, and its operation is widely supported by experiments (not only by our group) in which solvent dynamics were modulated by isotopic or cosolvent perturbations. More recent experimental work by our group and simulation work of MCY water by Fornili et al, strengthens this evidence and visualizes how an immobilized water molecule can “seed” or “pin” a high-connectivity patch of H bonds. Involvement of the mechanism in pattern-specific, solvent-mediated driving forces of significant size (additional to those due to electrostatic recognition determinants) and in functional proton-transfer is inferred from available evidence.
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  • 63
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    International Journal of Quantum Chemistry 35 (1989) 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 64
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    International Journal of Quantum Chemistry 35 (1989), S. 495-512 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A many-body diagrammatic perturbation theory of rotation-vibration spectra is elaborated. The present approach is based on two many-body techniques, namely on the second quantization formalism (a rotating-vibrating molecule is formally treated here as a system of interacting vibrons, obeying the Bose-Einstein statistics) and the many-body diagrammatic theory of a model Hamiltonian, initially suggested in the microscopic theory of nuclei and in the last decade very frequently exploited in the accounting for the correlation effects in many electron systems. In the framework of this theory, the rotation-vibration energies are determined as the eigenvalues of a finite-dimensional model eigenproblem.
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  • 65
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    International Journal of Quantum Chemistry 35 (1989), S. 519-549 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The contributions of the triple and quadruple excitations to the fifth-order perturbation energy for the perturbation configuration interaction using localized orbitals (PCILO) method are derived. This completes the development of a fifth-order constant denominator perturbation theory initiated in a previous paper [5] with the single and double excitations. This theory is tested on molecules containing strained ring geometries, stretched bonds, strongly polarized bonds, and delocalized pi systems: cases where the starting zero order reference wave function poorly describes the system. Although the perturbation expansions turn out to be slowly convergent, the Padé approximant taken from an energy series which itself is constructed from Padé approximants provides results accurate to within a few kilocalories/mole of benchmark calculations. Computational times as in the original PCILO procedure remain proportional to N3, where N is the number of bonds.
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  • 66
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    International Journal of Quantum Chemistry 35 (1989), S. 257-266 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Wave function tails are analyzed quantitatively by investigating the dependence of exterior electron density (EED) on basis sets; the EED is defined as the integrated electron density outside the repulsive molecular surface. Ab initio MO calculations with large scale basis sets were performed to establish the benchmark order of EED values for valence orbitals of some simple molecules. It is found that very popular basis sets, such as 4-31G, which are determined by energy optimization, are inferior in describing the wave function tails to some similar size basis sets, such as MIDI-4, which are obtained by least-squares fit to near Hartree-Fock atomic functions. Further the EED values for atomic 2s functions are shown to be unfavorably smaller than those for atomic 2p functions when the same value is used for the exponent α in the GTO basis sets. This indicates that the frequently used constraint αs = αp is not appropriate for describing wave function tails with medium-size basis sets. Deficiencies in the energy-optimized basis sets are found to become more serious for molecules including heavier atoms.
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  • 67
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    International Journal of Quantum Chemistry 35 (1989), S. 267-275 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a simple model for calculating the interatomic interaction energies in the electron gas approximation. We use a generalization of the supermolecular electronic density which includes a density overlap term. We present numerical calculations for the He-He interaction as an illustration of the method.
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  • 68
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    International Journal of Quantum Chemistry 35 (1989), S. 665-677 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: N-Nitrosamines are believed to act as carcinogens by alkylating DNA in their ultimate carcinogenic forms which are produced by metabolic activation. Alkylation at certain oxygen sites in DNA, described as “promutagenic,” appears to be of particular significance for mutagenesis and cancer, as indicated by experimental findings. This theoretical study deals with two factors involved in the alkylation of these promutagenic oxygen sites by N-nitrosamine ultimate carcinogens. The first is the competition between alkylation at the promutagenic O6-guanine and O4-thymine sites and that at the nonmutagenic N7-guanine site, which is here related to the degree of participation of cationic ultimate carcinogens as compared with neutral ultimate carcinogens. Parent dialkylnitrosamines are classified structurally according to their degree of cationic ultimate carcinogen participation and preference for promutagenic alkylation. The second factor is the thermodynamic facileness of alkylation at the O6-guanine and O4-thymine sites. Heats of alkylation by candidate ultimate carcinogens are calculated here for numerous parent dialkylnitrosamines. Finally, these two factors are jointly considered in an attempt to correlate them with experimental carcinogenic potency of the parent nitrosamines. Out of the patterns of correlation observed, light is shed on mechanistic factors likely to be involved in the modulation of parent carcinogenic potency.
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  • 69
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    International Journal of Quantum Chemistry 35 (1989), S. 717-719 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 70
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    International Journal of Quantum Chemistry 35 (1989), S. 751-760 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Formulas for the energies and widths of shape resonances, i.e., quasi-stationary levels for a quantal particle moving in a spherically symmetric potential, valid also close to the top of the potential barrier, have been published by Drukarev, Fröman, and Fröman. On the basis of these formulas, in the present paper the potential is explicitly expressed in terms of experimental data on the energies and widths of the quasi-stationary states. The treatment is related to previous treatments by Wheeler and by Cole and Good, Jr., which are in turn related to the Rydberg-Klein-Rees method.
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  • 71
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Structural parameters of a set of five thiocarbonyl molecules in the lowest nπ* states are calculated by using a generalized orbital optimization algorithm (a variant of the orthogonal gradient method) in an INDO MCSCF framework. Transition energies, singlet-triplet splittings, planar inversion barriers, and dipole moments in nπ* states of different spin multiplicities are reported. Predicted structural features agree reasonably well with available experimental or theoretical data. Some interesting trends are noted in the computed inversion barrier heights, singlet-triplet splittings, and dipole moments in nπ* states.
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  • 72
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    International Journal of Quantum Chemistry 35 (1989), S. 687-700 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We consider the Hückel approximation to the π-electron spectrum of molecules which are built by linking a number of identical fragments to a central atom in an identical manner. The Hückel matrix H of the composite molecule (or equivalently the adjacency matrix of the molecular graph) is simply related to the Hückel matrix h of the fragment and a vector \documentclass{article}\pagestyle{empty}\begin{document}$ vec{f} $\end{document} which encodes the bonding of a fragment to the central atom. The eigenvalues and eigenvectors of H are obtained from those of h. The orbitals of the composite molecule are of three types: (1) a molecular orbital of the fragment localized on one of the fragments, (2) a molecular orbital of the fragment spread over more than one fragment, and (3) orbitals spread over the entire molecule including the central atom. The orbital energies Λ of the first two types of orbitals are same as the orbital energies λ of the fragment. Energies of the third type of orbitals separate a subset of orbital energies of the fragment and, barring accidental degeneracy, they are distinct from all orbital energies of the fragment. It is only through the third type of orbitals that the composite molecule manifests itself as a new entity rather than an aggregate of noninteracting fragments. It is shown that the graph group of H fails to explain its degeneracy if any eigenvector of the subgraph, not orthogonal to the connection vector \documentclass{article}\pagestyle{empty}\begin{document}$ vec{f} $\end{document}, belongs to a degenerate manifold of h. This solves a long-standing puzzle regarding degeneracy in the Hückel spectrum of triphenylmethyl.
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  • 73
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    International Journal of Quantum Chemistry 35 (1989), S. 711-715 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A personal and partially anecdotal account is given of the role of the Debye-Waller factor in protein crystallography and protein dynamics.
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    International Journal of Quantum Chemistry 35 (1989), S. 745-749 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quantum system is repeatedly prepared in the same way and then observed in measurement processes. The following problem is stated and solved: Given the results of a series of observations, what is the best guess for a density matrix describing the ensemble of prepared systems? The corresponding classical problem and its solution are obtained as a special case.
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  • 75
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    International Journal of Quantum Chemistry 35 (1989), S. 887-893 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: New solutions for reaction-diffusion equations, called singletons and polytons, are found to be of fundamental significance. They exhibit properties of self-formation. In the presence of nonlinear saturation effects their evolutions in time have pronounced maxima. Information about details of an initial spatial distribution is found to be carried along in time with the dynamic process of forming a growing singleton and to be restored at a later stage.
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  • 76
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    International Journal of Quantum Chemistry 36 (1989), S. 277-285 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of electron correlation on the results of pseudopotential calculations was examined using a simple analytical semiempirical pseudopotential and a correlated floating-type one-center wave function. Investigations were performed for the XH alkali metal hydride molecules (X = Na, K, Rb, Cs). The inclusion of the electron correlation in the ground state proved important for the calculation of the dissociation and ionization energies, but it is less significant for the determination of the equilibrium nuclear distances. The ground state potential energy curves are also determined.
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  • 77
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  • 78
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    International Journal of Quantum Chemistry 36 (1989), S. 473-486 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown that doubly excited states play an important role in calculations of the optical activity of molecules with well-conjugated electron systems, such as the DNA bases. In some significant cases it is necessary to include a large number of excited states in the configuration interaction (CI) to obtain a reliable, converging result. A new version of the CNDO/OPTIC method, which includes doubly excited states in the CI, is proposed. As an application, the electric transition moments in different pyrimidines are considered. The calculated results agree with experimental data and results obtained from ab initio calculations and INDO calculations using doubly excited states in the CI.
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  • 79
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    International Journal of Quantum Chemistry 36 (1989), S. 157-167 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The simple semiquantitative approach to the calculation of the energy of surface states, proposed recently by the authors, is applied to high-symmetry surfaces of selected transition metal carbides, nitrides, and oxides. The results are compared with recent experimental and theoretical data. The necessity to include the changes in the potential at the crystal surface is indicated.
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  • 80
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    International Journal of Quantum Chemistry 36 (1989), S. 201-211 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper a general method for the evaluation of the matrix elements of spin-dependent operators is proposed to improve the treatment primitively suggesteed by Cooper and Musher. This approach is largely based on the recent results which the present authors have achieved in the representation theory for the inner- and outer-product reduction of the symmetric group. It is shown that the so-called outer-product coupling coefficients (OPCC) can be used to generalize the method for constructing the irreducible tensor operators of group Sn. Together with the use of inner-product coupling coefficients (IPCC), an expression for the matrix elements of spin-dependent operators is presented as the product of a Racah coefficient for Sn and a reduced matrix element which can be expressed in terms of IPCC, OPCC, and the related integrals. The treatment for one- and two-electron spin-dependent operators is discussed in detail.
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  • 81
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    International Journal of Quantum Chemistry 36 (1989), S. 599-632 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A spin-free symmetry-adapted valence bond (VB) state, named bonded tableau (BT), is deduced from the classical bonded function and labeled by an at most two-column Weyl tableau. The complete set, which is composed of the BT basis or canonical bonded tableau (CBT), can be constructed from an overcomplete set of BT states. CI CBT and VB CBT are two kinds of complete sets that are constructed in this paper. They can be used, respectively, in the CI and VB theory. It is shown that there is a one-to-one correspondence between the labeling scheme for CI CBT and the Gelfand-Tsetlin (GT) basis. This relationship enables an efficient generation and compact representation of the BT basis if one desires to use the known global representation scheme for the GT basis. Effective algorithms for the matrix element evaluation of unitary group generators and products of generators between BT states are presented. In the formulation, the action of a generator on a BT state yields another BT state times a coefficient, so that the matrix elements of an arbitrary multiple product of generators are reduced to a calculation of the overlaps between BT states. The evaluation of the overlaps leads to a simple factorization into cycle contributions, whose values are given explicitly and only depend on the length parameters of the cycles. It is hoped that the presented formalism can facilitate the procedures for handling of the many-electron correlation problem.
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    International Journal of Quantum Chemistry 36 (1989), S. 647-657 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A well-known model of two coupled Morse oscillators is studied within the context of box quantization. Two variants are considered: analysis of stabilization graphs or addition of an optical potential. These methods are shown to give efficient alternatives for the determination of unimolecular dissociation rates.
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    International Journal of Quantum Chemistry 36 (1989) 
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 84
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    International Journal of Quantum Chemistry 36 (1989), S. 705-726 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Linkage properties of the diagrammatic representation of the energies obtained in the multireference many-body perturbation calculations with respect to the incompleteness or completeness of the model space are discussed. The case of not completely degenerate model space is considered for which a comparison with the standard single-reference many-body perturbation expansion is possible. The Hose-Kaldor type of graphical representation of the perturbation expansion for the effective Hamiltonian is used in this comparison. It is shown that for an incomplete model space the perturbation expansion is not size-extensive. In this case, for a truncated expansion of the effective Hamiltonian, the energies obtained by diagonalization of the effective Hamiltonian matrix are represented by both linked and unlinked irreducible contributions. The unlinked ones do not appear when the complete model space is used.
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    International Journal of Quantum Chemistry 36 (1989), S. 791-791 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 86
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    International Journal of Quantum Chemistry 36 (1989), S. 553-561 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic properties of a one-dimensional diatomic crystal have been analyzed by using the MO-LCAO method in the tight binding approximation, with mathematical techniques involved in setting up and solving difference equations. The approach gives the exact sets of analytic solutions for both localized and nonlocalized states. The theory of surface states is developed as a characteristic value problem. To illustrate the method the surface states for a semiinfinite crystal which contains a local imperfection at the surface were examined. It appears that this method has advantages over previous methods developed to solve surface problems in crystalline lattices.
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    International Journal of Quantum Chemistry 36 (1989), S. 633-646 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Energy levels of I2 ⃛ X van der Waals (VDW) molecules, where X is a rare gas atom (X = He, Ne) are obtained in an approximate way by using cofocal elliptic coordinates and taking the I2 internuclear axis as a quantization axis. This is the starting point to study vibrational predissociation (VP) of larger I2 ⃛ Xn (n ≥ 2) clusters, where a good energetic description may provide accurate initial conditions from which trajectory calculations can be carried out.
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  • 88
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    International Journal of Quantum Chemistry 36 (1989), S. 669-670 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 89
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    International Journal of Quantum Chemistry 36 (1989), S. 765-771 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational and vibration-rotational energy levels of ozone and its isotopic substitutes have been calculated variationally by the ladder operator method. Thirty vibrational band origins and rotational energies of vibrational ground states for these molecules have been given. The good agreement between the calculated results and the observed values shows that the calculation method is a promising one for variational studies of vibrational and vibration-rotational properties of nonlinear polyatomic molecules.
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    International Journal of Quantum Chemistry 36 (1989), S. 741-748 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Earlier work on the Pauli potential VPauli, which allows the square root of the electron density to be calculated directly from a Schrödinger equation, is generalized from two-level (radial) systems such as the Be atom to the n-level case in one dimension. This is achieved using hyperspherical functions, in terms of which the first- and second-order density matrices are expressed. It is confirmed that VPauli can be constructed from the ground-state density ρ (x) and its first two derivatives, plus the functional derivative of the single-particle kinetic energy with respect to ρ. Finally, contact is made with the Harriman construction, but now using approximate one-body orbitals.
    Type of Medium: Electronic Resource
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  • 91
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 373-383 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Herndon-Simpson model for a particular catacondensed polyphene chain is considered as a nontrivial many-body Hamiltonian, defined on a space with a basis of orthonormal Kekulé structures. An Explicitly correlated cluster expanded resonance-theoretic wave function is described for this model, and its quality is judged by calculation of the standard deviation for the energy expectation. The quality is found to be high. Indeed, for a particular parameter ratio within the range of experimental interest, the wave function ansatz is found to be exact. This very accurate solution is then used to gauge the quality of the common ansatz with equally weighted Kekulé structures, and it is found to be reasonably good.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 92
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 433-439 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We show that even when the nuclear motion is quantum mechanically described, the energy of a molecular state can be exactly expressed as a sum of terms, each one related to a nuclei of the molecule. This is a generalization of a similar result obtained by Politzer and Parr for the case in which the nuclei are in fixed positions. In fact, the nuclear motion is exactly taken into account through a modified screening function derivative evaluated on each nucleus of the molecule. We discuss how the screening function derivatives corresponding to the fixed nuclei case relate to those which take into account the nuclear motion. A simple relation between these two arises in the so-called crude Börn-Oppenheimer approximation.
    Type of Medium: Electronic Resource
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  • 93
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 461-470 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A combinatorial derivation of the product of the class of three cycles, [(1)N-3(3)]N with an arbitrary class operator of the symmetric group SN is presented. The form of this result suggests a conjecture concerning the expression of the general class operator product in terms of a relatively small number of reduced class coefficients. The conjecture is applied to the determination of the products of [(1)N-4(4)]N, [(1)N-4(2)2]N, and [(1)N-5(5)]N with arbitrary class operators. General expressions for the reduced class coefficients of the simplest type are obtained.
    Type of Medium: Electronic Resource
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  • 94
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 513-518 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The local energy is examined as an indicator of the accuracy of approximate wave functions for the ground state of helium. It is observed that at a given point (1) an inaccurate local energy may or may not correspond to an inaccurate value of the wave function or probability density, but (2) a value of the local energy within 0.1 a.u. of the ground-state energy corresponds to a value of the approximate wave function or probability density within about 10% of that for the ground-state wave function.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
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  • 95
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 567-575 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A configuration-averaged Fock (CAHF) operator is developed within the restricted open-shell formulation (ROHF) for the case of any number of open-shell orbitals containing any number of electrons. The resulting orbitals and energies should be useful for those cases where there is a great degeneracy of states, either preventing self-consistent field convergence, or negating the value of a pure state description itself. This procedure is compared with the hyper-Hartree-Fock method of Slater and the grand canonical Hartree-Fock ansatz of Abdulnar, Linderberg, Öhrn, and Thulstrup.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 585-592 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new unitary operator U, which can transform the Fock space of a three-dimensional isotropic harmonic oscillator into the space in which the Hamiltion of three coupled oscillators is diagonized, is found. The coordinate representation of U is presented and is used to directly derive the wave function of the energy eigenstate of the coupled oscillators.
    Type of Medium: Electronic Resource
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 649-663 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An explicit relation is derived between the one-body potential energy and the electron density for the ground state of the Be atom in a nonrelativistic framework. This same relation applies to any four-electron atomic ion (or to Be itself) in a state where the electrons occupy two doubly filled orbitals. The relation is interpreted as an exact Hartree-like model of the Hohenberg-Kohn theorem within the general context of N electrons and a potential that is not necessarily spherically symmetrical.
    Type of Medium: Electronic Resource
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 701-701 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 769-778 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: After a brief review of the historical development of the concept “antiparticle,” some recent theoretical results on CP violation are reviewed.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 36 (1989), S. 35-48 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A spin-free polynomial representation of antisymmetrized geminal products is presented for several cases. In particular, products of identical geminals, which possess different spin multiplicity, are considered. The cases of singlet geminals, singlet geminals with one or two triplet geminals coupled to the lowest possible spin multiplet, and triplet geminals coupled to an arbitrary multiplet are considered in detail, and explicit polynomial representation is given.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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