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  • 1985-1989  (201)
  • 1905-1909
  • 1820-1829
  • 1985  (201)
  • Ultrastructure  (112)
  • Biochemistry  (89)
  • 101
    ISSN: 1615-6102
    Keywords: First pollen mitosis ; Gasteria verrucosa ; Male plastid inheritance ; Pollen development ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary This paper describes the development of pollen grains ofGasteria verrucosa from the late microspore to the mature two-cellular pollen grain. Ultrastructural changes and the distribution of plastids as a result of the first pollen mitosis have been investigated using light and electron microscopy. The microspores as well as the generative and the vegetative cell contain mitochondria and other cytoplasmic organelles during all of the observed developmental stages. In contrast, the generative cell and the vegetative cell show a different plastid content. Plastids are randomly distributed within the microspores before pollen mitosis. During the prophase of the first pollen mitosis the plastids become clustered at the proximal pole of the microspore. The dividing nucleus of the microspore is located at the distal pole of the microspore. Therefore, the plastids are not equally distributed into both the generative and the vegetative cell. The possible reasons for the polarization of plastids within the microspore are briefly discussed. The lack of plastids in the generative cell causes a maternal inheritance of plastids inGasteria verrucosa.
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  • 102
    Electronic Resource
    Electronic Resource
    Springer
    Protoplasma 126 (1985), S. 1-18 
    ISSN: 1615-6102
    Keywords: Mitosis ; Ultrastructure ; Phylogeny ; Basidiomycotina ; Tulasnella araneosa
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary This is a report of a light and electron microscopic study of mitosis in the basidiomycetous fungusTulasnella araneosa. The study employs serial section analyses of nuclei preselected with fluorescence microscopy. It is the first such study of nuclear division in theTulasnellaceae and the first of conjugately dividing nuclei in basidiomycetous hyphal segments lacking clamp connections. Mitosis inT. araneosa is unusual in that the spindle pole body (SPB) develops asymmetrically; the SPB middle piece is large and transversely curved; and the nuclear envelopes of adjacent late anaphase nuclei fuse. Analyses of mitotic characteristics used for phylogenetic purposes indicate that, of the many characters available, only SPB characteristics are presently valuable. Available evidence indicates that the SPB ofT. araneosa is more different from that ofUredinales than it is from representatives of the other four orders ofBasidiomycotina that have been thoroughly studied.
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  • 103
    Electronic Resource
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    Springer
    Protoplasma 127 (1985), S. 204-211 
    ISSN: 1615-6102
    Keywords: Biogenesis ; Cytochemistry ; Ribonucleoprotein bodies ; Ribosomes ; Timmiella barbuloides (Musci) ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Vegetative cells of the gametophyte phase of the mossTimmiella barbuloides (Pottiales) are characterized by large cytoplasmic bodies of spherical shape (SBs) whose ribonucleoprotein composition is cytochemically demonstrated. SBs seem to be derived from massive aggregation of cytoplasmic ribosomes, with possible participation by rough endoplasmic reticulum elements. SBs have been found in stereids, parenchymatous cells and young hydroids of the gametophyte stem, and in euricysts of the leaf nerve. The SBs develop early in the course of cell differentiation and, once formed, persist until advanced stages of cell senescence.
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  • 104
    ISSN: 1615-6102
    Keywords: Plasmodesmata ; Ultrastructure ; Freeze-fracture ; Salt glands
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Numerous plasmodesmata occur in the walls between the secretory cells ofTamarix salt glands. The plasmalemma bounds the plasmodesmata and is continuous from cell to cell. In freeze-fracture, the e-face of the plasmalemma within the plasmodesmata is virtually devoid of intramembranous particles while, in contrast, the p-face is decidedly enriched with particles. The axial components appear to be a tightly curved membrane bilayer, as judged from measurements and their appearance in freeze-fracture, and the e-face of this membrane is also devoid of particles. Observations from both thin sections and freeze-fracture replicas indicate the presence of a circular cluster of six particles around the axial component near the cytoplasmic termini of the plasmodesmata. These particles extend from the p-face of the axial component to the p-face of the plasmalemma. These observations are summarized in a model.
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  • 105
    ISSN: 1615-6102
    Keywords: Acacia terminalis ; Extrafloral nectary ; Histochemistry ; Secretion ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The extrafloral nectary ofAcacia terminalis is of the flat type and is located on the adaxial surface of the petiole of the bipinnate leaf. The secretory area is restricted to the base of the trough and no gaps or pores were detected by staining with vital dyes. Between the vascular bundles beneath the nectary and the surface cuticle there were three cell types. The cells of the flanking zone adjacent to the vascular bundles did not appear to be producing secretion whereas the cells of the glandular and secretory zones were secreting. The cells of the glandular zone were elongated whereas those of the surface secretory zone were spherical. Both had endoplasmic reticulum and Golgi bodies with secretory vesicles which were observed in close association with the plasmalemma. Secretion accumulated in the intercellular spaces of the glandular zone cells and forced the cells of the secretory zone apart. Symplastic contact was maintained in all cell types by plasmodesmata which were often associated with endoplasmic reticulum. Secretion accumulated beneath the cuticle which was distended but remained intact on the surface of the secretion.
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  • 106
    ISSN: 1615-6102
    Keywords: Azolla ; Anabaena ; Symbiosis ; Nitrogen fixation ; Trichome ; Transfer cell ; Ontogeny ; Ultrastructure ; Gland ; Metabolite exchange
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Anabaena azollae is associated with two types of multicellular epidermal trichomes inAzolla leaf cavities, the simple and branched hairs. The observation of transfer cell ultrastructure in some hair cells led to speculation that the cavity hairs might participate in metabolite exchange between the symbionts. The developmental ontogeny of cavity trichomes is described here, using transmission electron microscopy, with a goal of improving our understanding of possible functions of these structures in the symbiosis. The observations have established that all cells of simple and branched hairs develop the structural characteristics of transfer cells, but not simultaneously. Rather, there is an acropetal succession of transfer cell ultrastructure beginning in terminal cells, moving to body cells where present, and ending in stalk cells. The transfer cell stage is followed immediately by senescence in all hair cells. The timing of transfer cell differentiation, considered together with information from other studies, suggests that branched hairs may be involved in exchange of fixed nitrogen between the symbionts, while simple hairs may participate in exchange of fixed carbon fromAzolla toAnabaena.
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  • 107
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    Protoplasma 128 (1985), S. 107-119 
    ISSN: 1615-6102
    Keywords: Actinorhizal root nodules ; Development ; N2 fixation ; Elaeagnus ; Frankia ; Symbiosis ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A correlated light and electron microscopic study was undertaken of the initiation and development of root nodules of the actinorhizal tree species,Elaeagnus angustifolia L. (Elaeagnaceae). Two pure culturedFrankia strains were used for inoculation of plants in either standing water culture or axenic tube cultures. Unlike the well known root hair infection of other actinorhizal genera such asAlnus orMyrica the mode of infection ofElaeagnus in all cases was by direct intercellular penetration of the epidermis and apoplastic colonization of the root cortex. Root hairs were not involved in this process and were not observed to be deformed or curled in the presence of the actinomyceteFrankia. In response to the invasion of the root, host cells secreted a darkly staining material into the intercellular spaces. The colonizingFrankia grew through this material probably by enzymatic digestion as suggested by clear dissolution zones around the hyphal strands. A nodule primordium was initiated from the root pericycle, well in advance of the colonizingFrankia. No random division of root cortical cells, indicative of prenodule formation was observed inElaeagnus. As the nodule primordium grew in size it was surrounded by tanninised cells of a protoperiderm. The endophyte easily traversed this protoperiderm, and once inside the nodule primordium cortex ramified within the intercellular spaces at multiple cell junctions. Invasion of the nodule cortical cells occurred when a hyphal branch of the endophyte was initiated and grew through the plant cell wall, again by apparent enzymatic digestion. The plant cell plasmalemma of invaded cells always remained intact and numerous secretory vesicles fused with it to encapsulate the advancingFrankia within a fibrous cell wall-like material. Once within the host cell some endophyte cells began to differentiate into characteristic vesicles which are the presumed site of nitrogen fixation. This study clearly demonstrates that alternative developmental pathways exist for the development of actinorhizal nitrogen-fixing root symbioses.
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  • 108
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    Protoplasma 125 (1985), S. 94-102 
    ISSN: 1615-6102
    Keywords: Biogenesis ; Plasma membrane ; Regeneration ; Ultrastructure ; Paramecium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Fragments ofParamecium caudatum cells obtained by merotomy were fixed in 1% OsO4 within 5 seconds after cutting. The ultrastructure of the damaged area of the fragment was studied in oriented ultrathin sections and by scanning electron microscopy. The cytoplasm exposed by merotomy was covered during a few seconds with a new membrane. This was a typical trilaminar membrane continuous with the plasma membrane covering the undamaged surface of the cell. The surface over the wound was wrinkled into irregular grooves and ridges. The cytoplasm, mitochondria and trichocysts in the injured region were electron translucent. The cytoplasm under the new membrane contained an unusually high amount of small membrane vesicles, 20–90 nm in diameter. These were probably the remnants of subpellicular alveoli and the plasma membrane destroyed by microsectioning. The possibility that the exposed cytoplasm would be covered by mere shifting of the existing plasma membrane can be excluded. The complex structure of the cortex with its subpellicular alveoli and regularly distributed cilia provide a strong argument against this notion. It seems probable that the new membrane was built up from the available molecular material,e.g., phospholipids and proteins present in the cytoplasm. Fragments of the membrane and alveolar membranes in the form of small vesicles may have also been included into the new membrane.
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  • 109
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    Protoplasma 125 (1985), S. 140-151 
    ISSN: 1615-6102
    Keywords: Mitosis ; Cytokinesis ; Alga ; Isochrysis ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mitosis and cytokinesis have been studied in the flagellate algaIsochrysis galbana Parke (Prymnesiophyceae). Nuclear division is preceded by replication of the flagella and haptonema, the Golgi body and the chloroplast; fission in the chloroplast occurs in the region of the pyrenoid. During prophase, spindle microtubules radiating from two ill-defined poles are formed. The nuclear envelope breaks down and the chromatin condenses. At metaphase the spindle is fully developed, some pole-to-pole microtubules passing through the well-defined chromatin plate, others terminating at it. No kinetochores or individual chromosomes were observed. By late metaphase, many Golgi-derived vesicles may be seen against the two poleward faces of the metaphase plate. During anaphase, the two daughter masses of chromatin move towards the poles. In early telophase, the nuclear envelope of each daughter nucleus is complete only on the side towards the adjacent chloroplast, remaining open on the interzonal side. However, during telophase each nucleus becomes reorientated so that it lies lateral to the long axis of the spindle and with its open side towards the chloroplasts. By late telophase, each new nuclear envelope is complete and confluence with the adjacent chloroplast ER established. Cytokinesis and subsequent segregation of the daughter cells are effected by the dilation of Golgi- and ER-derived vesicles in the interzonal region. No microtubular structures are involved. Comparisons with the results from other studies of mitosis in members of thePrymnesiophyceae show that they all have a number of features in common, but that there are differences in detail between species.
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  • 110
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    Langenbeck's archives of surgery 366 (1985), S. 703-703 
    ISSN: 1435-2451
    Keywords: Ultrastructure ; Peritoneum ; Bacterial peritonitis ; Ultrastruktur ; Peritoneum ; Bakterielle Peritonitis ; Rasterelektronenmikroskopie
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Zusammenfassung Studienergebnisse über eine dreijährige rasterelektronenmikroskopische and transmissionselektronenmikroskopische Untersuchung des Peritoneums ergaben, daß bei Patienten mit bakterieller Peritonitis die Mesothelzellen abgerundet sind, keine langen Mikrovilli im Peritoneum parietale ausgebildet werden, jedoch auf der Oberfläche Fibrinablagerungen, Epithelaufbrüche und Kollagenfasern feststellbar sind. Die Abwehrmechanismen bei Peritonitis beginnen mit Kontraktion der Mesothelzellen and Bildung von Intercellularspalten Bowie Stomata. Bei fortgeschrittener Peritonitis kommt es zur Destruktion des Mesothels mit Epithelaufbrüchen and Mobilisation von Epithelzellen zum Zwecke der Phagocytose.
    Notes: Summary The human peritoneum was studied by transmission and scanning electron microscopy, which demonstrated oval-shaped mesothelial cells, disappearance of the long microvilli at the parietal peritoneum, fibrinous membranes, collagenous fibrillae, and epithelial cracks in cases of bacterial peritonitis. The defense mechanism begins with mesothelial cell contractions and then formation of intercellular gaps and stomata. In advanced peritonitis, the mesothelial cells disintegrate with cracks and are finally mobilized for phagocytosis. After continuous peritoneal lavage, the cellular structures of the human peritoneum appear almost normal.
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  • 111
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 112
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    Journal of Computational Chemistry 6 (1985), S. 1-4 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is noticed that inclusion of an electrostatic term in the molecular-mechanical treatment of hydrocarbons would compel the nonbonding parameters of different force fields to become more alike than they are at present. Apart from removing the discontinuity in passing from the calculation of an unfunctionalized parent compound to the calculation of its functionalized derivatives, it is expected that the inclusion would improve results for the hydrocarbons themselves.
    Additional Material: 2 Ill.
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  • 113
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    Journal of Computational Chemistry 6 (1985), S. 5-8 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present energy component analysis calculations on alkali atom (Li,Na) hydride (H2O,NH3,H2S) interactions and compare these with corresponding (Li+ … NH3) cation … hydride interactions. In contrast to cation hydride interactions, the neutral atom-hydride interactions are shown to involve considerable contributions from all energy components.
    Additional Material: 1 Tab.
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  • 114
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    Journal of Computational Chemistry 6 (1985), S. 28-38 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The values of log10 P (partition coefficient, in octanol/water) were calculated for about 200 organic molecules of diverse structures and functionalities. The method involves a simple procedure and appears accurate enough for semiquantitative applications. Further, this method of calculating log10 P values was shown to be successful in providing a better quantitative structure activity relationship (QSAR) than the Hansch-type approach in the study of inhibitory activity of substituted phenols on Bacillus Subtilis spore germination.
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  • 115
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program SURVIB is described for calculating vibrational anharmonicity constants for polyatomic molecules. The program requires as input a grid of calculated energies in the vicinity of a stationary point. This grid is fit, in a least squares sense, to a polynomial function of the internal coordinates. This analytic representation of the energy surface is employed in a normal mode analysis, and the energy is reexpanded as a polynominal function of the normal mode coordinates (expressed as vectors in the mass-weighted atomic Cartesian coordinate space). The resulting coefficients are used in a second-order perturbation theory analysis to obtain the vibrational anharmonicity constants. Also reported is an application of this program to formaldehyde employing ab initio, RHF, MP2, MP3, and RHF-CI calculations. The spectroscopic constants obtained for H2CO are in good agreement with experimentally derived values recently reported by Reisner.
    Additional Material: 9 Tab.
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  • 116
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    Journal of Computational Chemistry 6 (1985), S. 56-60 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: α↑HF and α↓HF are derived for use in spin polarized Hartree-Fock-Slater programs. They are assumed to depend only on the number of up and down spin electrons in the atom. The calculated eigenvalues show a slight improvement only for carbon, nitrogen, and oxygen.
    Additional Material: 4 Ill.
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  • 117
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy profiles were calculated for τ1, the C—C—C=O torsion, and τ2, the C—C—C—C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ1, τ2) = (0, -60), (0, 180), (120, 180), (120, -60), and the maxima (0, 0), (180, 180), and (60, -60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C—H bond trans to a C—C bond (C—Hs) is consistently shorter than a C—H bond (C—Ha) trans to another C—H bond. Specifically, for X—C(α) (= O)—C(β)—C(γ)—C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)—Hs 〈 C(δ)—Ha in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C—H⃛O=C interaction. (2) In the most stable conformers, (0, 60), C(β)—Ha 〈 C(β)—Hs, and C(γ)—Ha 〈 C(γ)—Hs, regardless of X. (3) The average C—C bonds in the τ2 = 180° conformers are consistently shorter than those with τ2 = 60° (compared at τ1 constant). In the most stable conformations (τ1 = 0°, τ2 = 60° or 180°), the bonding sequence is consistently C(α)—C(β) 〈 C(β)—C(γ) 〈 C(γ)—C(δ); whereas, when τ1 = 120°, C(α)—C(β) 〈 C(β)—C(γ) 〉 C(γ)—C(δ).
    Additional Material: 5 Ill.
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  • 118
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    Journal of Computational Chemistry 6 (1985), S. 76-76 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 119
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    Journal of Computational Chemistry 6 (1985), S. 78-78 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 120
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    Journal of Computational Chemistry 6 (1985), S. 77-77 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 121
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    Journal of Computational Chemistry 6 (1985), S. 88-92 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: If numerical configuration selection procedures are used in MRDCI calculations, the full MRDCI energy may be estimated by adding energy corrections obtained by perturbation theory. Accurate results may then be obtained by including all selected CFs in the zero-order function instead of only the reference CFs.
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  • 122
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    Journal of Computational Chemistry 6 (1985), S. 93-107 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Repulsion and dispersion parameters for alkali-metal halide diatomic molecules were computed by ionic Rittner and truncated Rittner models with radial dependent repulsion terms. Experimental data on the bond energies, the equilibrium interionic distances, and the spectroscopic frequencies were employed for the purpose. The polarizabilities used were also computed from the experimental dipole moments of alkali-metal halides. The potential parameters obtained were compared with parameters from other sources and checked for consistency. The computed potential parameters of alkali-metal halide monomer molecules were used to predict the energetics and geometries for alkali-metal halide dimer molecules. The predicted values are in good agreement with experiment and other calculations indicating the consistency and reliability of the potential employed. Although the magnitude of repulsive and dispersive energy terms varies with potential functions employed, the difference between the two for a molecule is constant. The repulsive term is more sensitive than the attractive term. The uncertainty in the exponential repulsion results in an inaccurate representation of the attractive contribution. Introduction of the radial-dependent repulsion term changes the relative magnitudes of repulsive and dispersive parameters and hence the relative contribution to the total potential with monomers. But this has no significant effect on the energetics and geometries of the dimers.
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  • 123
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    Journal of Computational Chemistry 6 (1985), S. 142-147 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Localized molecular orbitals (LMOs) for several octahedral complexes are presented. Wavefunctions are calculated within the PRDDO approximations and localized by the Boys criterion. Complexes of general formula (NH3)x(CO)6-xM, M = Cr0 or Mn+ and x = 1, 2, or 3 illustrate the general trends for carbonyl complexes. Weak to moderate π-bonding results in three equivalent inner shell LMOs dominantly of metal 3s, 3p and 3d character but highly delocalized to the carbonyls. These three LMOs flank the M-CO bond axis. Other π back-bonding situations result in metal-ligand double bonds which are nonequivalent and have σ-π separability [(NH3)5(py)Mn+] and also equivalent double bonds [(NH3)5(NO)Cr+].
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  • 124
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    Journal of Computational Chemistry 6 (1985) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 125
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    Journal of Computational Chemistry 6 (1985), S. 157-167 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Sets of atom equivalents have been developed which permit the estimation of heats of formation, ΔH°f298(g), from ab initio total energies (3-21G and 6-31G* basis sets). This extends the isodesmic reaction scheme of Pople and the group equivalents of Wiberg. A variety of small inorganic and organic molecules, including fluorocarbons, free radicals, carbocations, and protonated species give excellent agreement with experiment; average errors are less than 1 kcal/mol with unstrained hydrocarbons (both basis sets), and are on the order of 2 kcal/mol for all molecules considered (6-31G*; the 3-21G basis errors, as expected, usually are somewhat higher). The results substantiate Pople's early conclusions that Hartree-Fock theory provides a generally satisfactory description of classical molecules.
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  • 126
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    Journal of Computational Chemistry 6 (1985), S. 173-181 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges obtained with a previously published charge scheme are given for amino acids and peptides. In order to do this, a method of handling charged species with the basic scheme2,3 has been developed. The charges obtained for alkylammonium ions and carboxylate ions with the scheme are presented and compared with CNDO and ab initio values. The calculated experimental dipole moments of the zwitterionic forms of glycine, alanine and β-alanine are then discussed. Finally, the atomic charges obtained for the naturally occurring amino acids are given, both in the form of the N-acetyl-N′-methyl amino acid amides, used as models for the amino acid residues in enzymes, and as the free zwitterionic amino acids. The charges obtained show a good correlation with n. m. r. chemical shifts of both carbon and hydrogen atoms.
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  • 127
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    Journal of Computational Chemistry 6 (1985), S. 189-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MO calculations have been performed for neutral and cationic C2H2F2 structures. Olefinic and carbene structures are investigated for the neutral isomers, while olefinic, carbene, and fluoronium-type cations are found. Stability orders and rotational barriers are discussed in terms of orbital and Coulomb interaction. Contrary to previous studies, the higher stability of the geminal isomers is interpreted to be caused by Coulomb attraction.
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  • 128
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method of graphically exhibiting detailed information about a three-dimensional electron distribution function f(x,y,z) is described. Contour lines f = constant are drawn on a set of equidistant parallel planes that intersect the distribution, and a perspective view of all contours on all planes is displayed. Representative examples are given.
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  • 129
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    Journal of Computational Chemistry 6 (1985), S. 216-228 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is described to analyze observed conformations for molecular fragments with more than three torsional degrees of freedom. The method is an adaption of statistical cluster analysis to multidimensional, symmetric, periodic distributions of data points. Application to the molecular fragment M(PPh3)2 with eight torsional degrees of freedom reveals a model of conformational interconversion. The model implies gearing motion of the two PC3 fragments alternating with stepwise inversions of the helicities of the PPh3-propellers.
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  • 130
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    Journal of Computational Chemistry 6 (1985) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 131
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    Journal of Computational Chemistry 6 (1985), S. 148-155 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have carried out a series of molecular mechanics calculations on the alkali ion complexes of valinomycin. For the ions Na+, K+, Rb+, and Cs+ we have found three-fold rotationally symmetric conformations as the lowest energy structures, while for Li+ a markedly asymmetric configuration is preferred. The relative free energies of the complexes show that Li+ is by far the poorest binding partner in solution, followed by Na+, which is in turn far poorer than any of the three larger ions. The binding selectivity derives from the slower variation of the complexation free energy with ionic size than the ionic solvation free energy, so that the ionophore is unable to compete with the solvent for the smaller ions. Our calculated strain energies suggest that valinomycin's failure to form complexes with the smaller ions in solution is due partially to the rigidity of the ionophore structure, which prevents the central cavity from contracting to accommodate them. Certain geometric criteria indicate that K+ provides the best fit to the binding site, although there is some inconsistency between the energetic and geometric criteria of binding ability.
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  • 132
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    Journal of Computational Chemistry 6 (1985), S. 168-172 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The protonation energies of alkylated derivatives of NH3 and OH2 are calculated at the Hartree-Fock level with the split-valence 4-31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (∼30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.
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  • 133
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    Journal of Computational Chemistry 6 (1985), S. 182-188 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The lowest potential energy surfaces of NO3 have been investigated using CASSCF and contracted CI methods, to determine if NO3 is an intermediate in the oxidation of nitric oxide. This reaction is observed to be termolecular where an intermediate is almost certainly formed. The calculations, which were performed in C2v symmetry, show that the form of NO3 which has a near D3h geometry should not be possible to reach from ground state NO and O2. The energy of this isomer of NO3 is calculated to be 25 kcal/mol higher in energy than separated NO and O2. Furthermore, NO + O2 is separated from NO3 by very high barriers. The C2v constrained barrier is as high as 145 kcal/mol, which makes it very unlikely that NO3 could be formed even along less symmetric pathways. The origin of the barriers are analyzed, and it is shown that a special type of mechanism is involved for the state with the lowest barrier. In this mechanism, which was observed recently also for NiH2, the occupation in each symmetry changes only by one unit in each step of the reaction. The only isomer of NO3 which could be formed is a weak van der Waals complex with a very long bond distance of 6.5 a.u. N2O2 does, however, in this respect seem to be a more likely intermediate with its shorter bond distance of 4.5 a.u. Calculations around the D3h equilibrium further show that 2B2 is the ground state of this isomer of NO3 with 2A2 and 2B1 slightly higher in energy.
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  • 134
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    Journal of Computational Chemistry 6 (1985), S. 200-208 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The CGTO integral evaluation, SCF, SCF-gradient, integral transformation, and MR-CI (SD) steps of the COLUMBUS system of programs have been adapted for the CYBER 205. A description is given of our efforts and the partly heavy modifications necessary to exploit the potential of this supercomputer and to avoid its shortcomings. Typical timings are reported, vector and scalar performance are compared.
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  • 135
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    Journal of Computational Chemistry 6 (1985), S. 229-236 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new instrument of exploration can be used to develop unrecognized connections among points in a variety of geometric designs. Operational methods are used to derive the relationships, and a new approach to extremum location is demonstrated. The technique is suitable for interpolation problems which arise in experimental design and the treatment of data.
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  • 136
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    Journal of Computational Chemistry 6 (1985), S. 249-255 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The direct interconversion of the two C3-symmetric enantiomeric conformations of triethylamine, via C—N bond rotation, has been studied by molecular mechanics (MM2) calculations. The MM2 calculations have been used to characterize the minima (equilibrium geometries) and first-order saddle points (transition states) for this process. For one interconversion, there are five saddle points and six minima. The highest energy saddle point results from the uncoupled rotation of one ethyl group to eclipse the lone pair. Two of the barriers result from coupled rotation of two ethyl groups in close passage.
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  • 137
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    Journal of Computational Chemistry 6 (1985), S. 237-248 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The new contracted Gaussian-type orbitals (CGTOs) for molecular calculations have been developed from Li to Ne. The CGTOs are minimal type, i.e. composed of two s-type CGTOs, s1, s2, and one p-type CGTO, p1. They are new family of CGTOs given by Tatewaki and Huzinaga, and others. In the previous works three primitive GTOs are used for s2, which is the main part of the 2s orbital, whereas four primitive GTOs are employed in the present work. The sets generated are [54/5], [64/5], [64/6], [74/6], and [74/7]. In almost all the cases the errors in the 2s and 2p orbital energies are smaller than those of DZ. The resulting 2s orbitals are close to the orbitals of the uncontracted GTO sets, (13/n) and (14/n) of Duijneveldt. It is found that the 2s and 2p orbitals given by [64/6], [74/6], and [74/7] are satisfactorily near to those of Hartree-Fock. The basis sets [54/5], [64/6], and [74/7] are applied to the N2 molecule in the split valence forms of [5211/311], [6211/3111], and [7211/4111]. Adding the d-type polarization functions from one through three, the quality of the basis sets has been examined. All of the three sets show good behavior and the sets augmented with three d-type polarization functions give almost entirely the same results as the very extended basis set.
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  • 138
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    Journal of Computational Chemistry 6 (1985), S. 282-286 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The orbital behavior of both the singlet and triplet Rydberg series for 1sns configurations of the He atom has been investigated using one- and two-configuration Hartree-Fock wave functions. The core orbital within the triplet series changes negligibly; however, a contract trend is noticeable as the Rydberg orbital penetrates more into the core region, which is in contrast to that found in the 1s2ns 2S Rydberg series of Li atom. Although some properties of the whole atom can be calculated, the core relaxation of the singlet series can not be drawn without ambiguity because a two-configuration correlated wave function has to be used, and thus the orbital picture is lost.
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  • 139
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    Journal of Computational Chemistry 6 (1985), S. 287-295 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Relativistic effective potentials (REP) are now widely used in molecular electronic structure calculations. Tests of these REP are needed to assess their accuracy. This can now be done for AgH and AuH since Lee and McLean have published Dirac-Fock calculations for these molecules. Comparative SCF calculations have been performed for two types of effective potential. Satisfactory agreement between the effective potential results and Dirac-Fock values is found for spectroscopic constants and dipole moments, which supports the use of these potentials for heavy atom containing molecules.
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  • 140
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    Journal of Computational Chemistry 6 (1985) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 141
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    Journal of Computational Chemistry 6 (1985), S. 302-311 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics calculations (MM2) are used to elucidate energies and structures of possible reaction products in olefin metathesis of 2,3-dimethylnorbornadiene. The comparison of experimental and calculational results concerning norbornadiene itself shows excellent agreement both in energy and structure. The predicted isomers of lowest energy in a series of three different reaction products seem highly reliable and will lead to a more precise interpretation of the olefin metathesis reaction and the resulting product distribution. Some sixty different isomers have been considered and structures and energies are given. Nonplanarity of double bonds and van der Waals repulsions of closely related hydrogen atoms in polycyclic cycloolefins are considered in some detail. In order to reduce computing time and efforts in obtaining starting coordinates, a computer program for some dimeric structures was devised, which can combine minimized structures stemming from MM2 calculations.
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  • 142
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    Journal of Computational Chemistry 6 (1985), S. 350-359 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A very efficient algorithm for determining the geometrically feasible binding modes of a flexible ligand molecule at the receptor site is presented. It is based on distance geometry but maintains the requirements of three dimensions. The distance geometry manipulation can superimpose two bodies without explicitly calculating the necessary rigid rotation and translation. The whole conformation space of a flexible molecule can be efficiently examined by considering only a finite number of conformational points. The method is suitable only when the criterion for superposition is some minimum distance limit. It cannot, however, give the exact distance between two points in two different bodies.
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  • 143
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    Journal of Computational Chemistry 6 (1985), S. 343-349 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General expressions for monocenter electron repulsion integrals in a basis of real atomic orbitals are derived in terms of the radial integrals Rabcdk. The final expressions for these integrals can be classified into five main classes which are characterized by the angular part of the real atomic orbitals. For a basis of real s, p, d, and f AO's the total number of monocenter repulsion integrals is 65536, from which 6652 are different from zero. The nonzero integrals can be classified into 430 groups which contain integrals of equal value.
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  • 144
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    Journal of Computational Chemistry 6 (1985), S. 514-519 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Reequilibration processes are often encountered within solids and they have long been described mathematically. However, computation of reequilibration data over entire processes is often difficult. An algorithm has been developed specifically for this purpose. It allows a fast and efficient computation of reequilibration parameters. Anisotropic diffusion can, moreover, be taken into account.
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  • 145
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    Journal of Computational Chemistry 6 (1985), S. 432-436 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a real-time docking method using molecular graphics and high-speed calculation of the energy of interaction between a drug and a receptor. A three-dimensional tabulation of the potential is computed prior to the docking experiment, and the total interaction energy is calculated and updated on the display screen in real-time to provide immediate visual feedback to the user as the drug molecule is moved inside the receptor pocket. The “Simplex” method is then used to minimize the energy of interactions after each docking. Using this real-time method, it is now possible to examine rapidly the interactions of a large number of drugs and their analogues with receptor molecules. As an application, the interaction of thyroid hormone and its analogues with prealbumin is considered. The final interaction energies of this very rapid method compare well with those calculated by more orthodox means, while also providing visual feedback on both molecular geometry and energy.
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  • 146
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    Journal of Computational Chemistry 6 (1985), S. 455-461 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The thermal limiting high-pressure unimolecular rate constant k∞ represents, operationally, the Laplace transform of the product of microcanonical rate constant for decomposition of molecules having specified energy E [k(E)] and the density of states [N(E)]. By inversion, it is possible to recover k(E)N(E), from which one can obtain the energy dependence of k(E) and the pressure dependence of kuni, the thermal general-pressure unimolecular rate constant. This article examines numerical aspects of three methods of inversion, their reliability and dependence on sampling, i.e., on the number of available experimental data points, by comparing exact k(E) and kuni with those obtained by inversion. It turns out that the method of steepest descents is the best all-round performer.
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  • 147
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    Journal of Computational Chemistry 6 (1985), S. 478-480 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular mechanics (MMP2) description of the torsion of a methyl group attached to a conjugated system has been improved by using bond order dependent torsional force constants.
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  • 148
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    Journal of Computational Chemistry 6 (1985), S. 481-485 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A corrected Born equation, which describes the solute-dipolar solvent interaction by placing the charges of the atoms of the solute at their position in space inside a spherical cavity of the solvent, is used to calculate the solvent effect on three systems: the hydrated OH- ion, the lithiated aziridine, and the lithiated oxirane. It is found that the solvent effect stabilizes the addition of a water molecule to the OH-(H2O)3 system with the additional water acting as a proton donor. It is also found that the lithiation energy of aziridine and oxirane which are found to be 47 and 43 kcal/mol in gas-phase, respectively, decrease to 32 and 23 kcal/mol in water solution.
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  • 149
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    Journal of Computational Chemistry 6 (1985), S. 492-506 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of chance correlations in studies of structure - activity relationships using multivariate linear regression techniques is addressed. Random correlations are simulated by scrambling real potency values in data bases consisting of molecules possessing various biological properties. The statistical parameters of these correlations are compared to those obtained using the actual potency/compound data pairs and it is noted that the most noticeable differences are in the magnitude of the F values for the overall regression. Cutoff points for this parameter are suggested, which, when implemented in the recently introduced CASE method that correlates biological activity with substructural descriptors, can serve to weed out effectively the majority of meaningless correlations.
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  • 150
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    Journal of Computational Chemistry 6 (1985), S. 507-513 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SINDO1 calculations were performed to study the reactivity of molecules with a valence number derived from the density matrix. A comparison of valence numbers was made for selected examples of rotation barriers, substituted strained molecules, radical gas phase reactions, and acid-base reactions. Relations between valence, geometry, and energy changes are discussed.
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  • 151
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    Journal of Computational Chemistry 6 (1985), S. 520-532 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for preparing compact orbital and auxiliary basis sets for LCAO-LSD calculations has been developed. The method has been applied to construct basis sets for first row transition metal atoms from Sc to Zn for the 3dn-14s1 and 3dn-24s2 configurations. The properties of different expansion patterns have been tested in atomic calculations for the chromium atom.
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  • 152
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An iterative algorithm is described for finding topological equivalence, ordering, and canonical numbering of vertexes (atoms) in molecular graphs. Like the Morgan algorithm, it is based on extended connectivities but: (i) the latter are used hierarchically, i. e., the discrimination in the next iteration is carried out only for the vertices having the same extended connectivities (ranks) at the previous iteration; (ii) at equal extended connectivities, additional discrimination is introduced by the ranks of adjacent vertices; (iii) there is no “best name” search; (iv) three levels of complexity of chemical structures are distinguished and handled by different procedures.Two schemes of application of HOC procedures are presented: one directed towards a fast canonical numbering for coding systems, and another one yielding levels of topological equivalence allowing a unique topological representation of the molecule with possible applications to similarity search, structure-activity correlations, etc.
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  • 153
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A topological code is devised on the basis of the unique topological representation of the molecule described in the preceding two parts of this series.1 By adding to the topological code additional chemical information on atoms and/or bonds, as well as stereochemical information, a chemical and respectively stereochemical code (SHOC) are also constructed. The advantages of the new linear codes are that they are convention-free codes, preserving the symmetry of molecular graph, and easily implemented either manually or by means of computer programs. By concentrating all topological, chemical, and stereochemical information, our code (SHOC) is more compact and more general than the codes based on several separate lists.
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  • 154
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    Journal of Computational Chemistry 6 (1985), S. 581-586 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different schemes are explored for the calculation of the proton transfer process in the hydrogen bonded cation [CH3OH · H · NH3]+. Results from ab-initio calculations with the STO-3G, 3-21G and 4-31G basis sets, are compared in search for an efficient reliable scheme to study the potential energy curves for the proton transfer. The curve constructed from the lowest energies calculated with the frozen optimized geometries of the two possible pairs of proton donor and acceptor fragments, (i.e., CH3OH2+/NH3 and CH3OH/NH4+) is in good agreement with that obtained when all the fragments of the hydrogen bonded complex are completely optimized simultaneously.
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  • 155
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The computer implementation of the HOC procedures presented in Parts I, II and III of this series is based on the module principle. It contains a main program and seventeen subroutines in Fortran IV. The system is able to provide unique atom numbering and code for all kinds of chemical compounds in their tremendous variety of structures.
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  • 156
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    Journal of Computational Chemistry 6 (1985), S. 598-609 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The many applications of the distance matrix, D(G), and the Wiener branching index, W(G), in chemistry are briefly outlined. W(G) is defined as one half the sum of all the entries in D(G). A recursion formula is developed enabling W(G) to be evaluated for any molecule whose graph G exists in the form of a tree. This formula, which represents the first general recursion formula for trees of any kind, is valid irrespective of the valence of the vertices of G or of the degree of branching in G. Several closed expressions giving W(G) for special classes of tree molecules are derived from the general formula. One illustrative worked example is also presented. Finally, it is shown how the presence of an arbitrary number of heteroatoms in tree-like molecules can readily be accommodated within our general formula by appropriately weighting the vertices and edges of G.
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  • 157
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    Journal of Computational Chemistry 6 (1985), S. 614-624 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The cellular species formed in the hydrolysis of cis-Pt(NH3)2Cl2 (DDP), namely, cis-[Pt(NH3)2XY]n+ (X, Y = Cl-, H2O, OH-; n = 0, 1, 2) have been investigated theoretically using the relativistic and nonrelativistic extended Huckel molecular orbital method. Molecular orbital (MO) results for trans-DDP and its hydrolysis products are also reported for comparison. Transition energies, molar absorption coefficients (∊), and B terms from magnetic circular dichroism (MCD) derived from theory are presented for each of the species studied. The electronic absorption and MCD spectra of all the complexes are predicted to exhibit ligand field transitions arising primarily from excitations between the occupied Pt 5d orbitals and the unoccupied Pt 5d and 6pz orbitals, respectively. The 5d → 6pz transitions are expected to yield intense absorptions in the UV spectral region. Some intensity is generated in the d → d transitions as a result of the low symmetry of these complexes. Correlation of available experimental data with theory allows spectral assignments to be made and predicted. Substituent effects in the cis- and trans-isomeric species are discussed. Finally, the applicability of the EHMO method to these systems is examined.
    Additional Material: 5 Ill.
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  • 158
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    Journal of Computational Chemistry 6 (1985), S. 634-646 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article presents a strategy to perform molecular dynamics simulations using parallel processing techniques on a parallel-distributed loosely coupled system consisting of IBM host computers (4341 and 4381) with attached scientific processors (FPS-164). This substantially enhances our ability to perform fast and more realistic large scale many-body trajectory simulations. A powerful extention of the computational range of molecular dynamics the parallel approach offers the opportunity to substantially reduce the simulation time to allow a longer simulation period to study more realistic models and larger systems. It is flexible and uses, for the most part, standard products and straightforward implementation with a broad range of applicability. The implementation of a simulation of water molecules with the inclusion of two- and three-body interactions is discussed. Some considerations in the design and implementation of parallel programs on a loosely coupled system are also presented.
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  • 159
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    Journal of Computational Chemistry 6 (1985), S. 652-655 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We compare calculated total energies for 150 open-chain molecules using ab initio methodology and the PRDDO approximations. The bulk of the errors implicit in the PRDDO approximations are apparently of a one-center nature, i.e., they are due to the number and type of atoms in the molecule, and not the details of the molecular geometry. Atomic correction factors are developed which reduce the errors in the calculated total energy of PRDDO wave functions by a factor of eight relative to the ab initio reference calculations. PRDDO calculations on ring and cage compounds are shown to have additional systematic errors in the total energy.
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  • 160
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    Journal of Computational Chemistry 6 (1985), S. 662-673 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Benzylic anions were studied with the semiempirical MNDO molecular orbital method. Structural changes were analyzed as metal counterions and solvents were allowed to interact with the benzylic carbon. Generally, benzylic carbanions were found to be trigonal planar but became pyramidal or bent when metals were included in the calculation.
    Additional Material: 8 Ill.
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  • 161
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    Journal of Computational Chemistry 6 (1985), S. 256-263 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using the previously reported ab initio interaction energies among K+, Na+, water, and Gramicidin A (GA), this report presents Monte Carlo simulations for the microscopic effect of an applied voltage (0.5 V/32 Å) on a solvated gramicidin. The reorientation of water molecules due to the applied voltage is found to be marginal for both cations. The energy contribution due to water dipoles was within 10% of the total energy contribution due to the applied voltage. Inside the channel the total energy contribution varied almost linearly along the channel axis; outside the channel the slope of the total energy contribution with respect to the channel axis decreased.
    Additional Material: 4 Ill.
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  • 162
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    Journal of Computational Chemistry 6 (1985), S. 265-273 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized monopole expansions for the peptide subunits of proteins are developed by a reparameterization of the Hückel-Del Re procedure designed to reproduce closely the electrostatic properties obtained with ab initio OMTP multipole expansions. It is shown that satisfactory values of both potential and field may be obtained for different conformations of the peptide backbone as well as for the common side chains. A comparison is presented for the pentadecapeptide Gramicidin A.
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  • 163
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    Journal of Computational Chemistry 6 (1985), S. 274-281 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures of α-X-cyclopropyl and α-X-isopropyl radicals (X = H, CH3, NH2, OH, F, CN, and NC) are reported at the RHF 3-21G level of theory. The isopropyl radicals are pyramidal with out-of-plane angles varying from 12° (X = CN) to 39° (X = NH2), and barriers to inversion ranging from 0.4 kcal/mol (X = H) to 4.0 kcal/mol (X = NH2). The cyclopropyl radicals have larger out-of-plane angles, from 39.9° (X = CN) to 49.4° (X = NH2), and their barriers to inversion, which increase with the inclusion of polarization functions, vary from 5.5 kcal/mol (X = H) to 16.7 kcal/mol (X = F). In both types of radicals the amino group is the most stabilizing substituent, while the α-fluoro has little effect. The β-fluoro group is weakly destabilizing in the cyclopropyl radical. The strain energies of the cyclopropyl radicals (36-43 kcal/mol) are compared with those of similarly substituted anions, cations, and cyclopropanes.
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  • 164
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    Journal of Computational Chemistry 6 (1985), S. 296-301 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis set expansion and correlation effects on the computed proton affinities of the oxygen and nitrogen bases CH3OH, H2CO, CO, CH3NH2, CH2NH, and HCN have been evaluated. Basis set enhancements lead to systematic changes in computed proton affinities. These effects appear to be additive, and are greater for correlated proton affinities than for Hartree-Fock energies. Inclusion of correlation decreases proton affinities, with fourth-order Møller-Plesset energies bracketed by second and third order energies.
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  • 165
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    Journal of Computational Chemistry 6 (1985), S. 312-315 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A basis set with bond functions (6-31G + BF) has been tested for its applicability to calculation of dissociation energies of single and multiple bonds by Moeller-Plesset perturbation theory at the second and third orders. Results have been compared with those calculated in the 6-31G* basis set. The 6-31G + BF basis at the MP2 and MP3 levels yields better results than 6-31G* basis and the time consumption is less as well. Consideration of the bond functions on the bonds neighboring the bond being broken has no significant influence on the dissociation energies either at the SCF or at the MP2 levels. If both reactants and products can be characterized by two-center bonds, the 6-31G + BF basis and UMP2 variant of perturbation theory can be recommended for practical calculation of De values, especially for the systems where the use of more exact bases is rather difficult.
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  • 166
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    Journal of Computational Chemistry 6 (1985), S. 316-329 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new approach is presented for identifying all possible cycles in graphs. Input data are the total numbers of vertices and edges, as well as the vertex adjacencies using arbitrary vertex numbering. A homeomorphically reduced graph (HRG) is constructed by ignoring vertices of degree less than three. The algorithm is based on successive generation of possible edge-combinations in the HRG. If a combination yields a cycle, it is either printed or stored and then finally printed in a list of all possible cycles arranged in the order of increasing ring size. A unique numbering of the cycle is used. The computer program is listed and exemplified. Computing times are given.
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  • 167
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    Journal of Computational Chemistry 6 (1985), S. 360-367 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Highly accurate vibration-rotation Franck-Condon factors qab, for a transition between two diatomic electronic states (a) and (b), are sought. When the potentials of states (a) and (b) are of the RKR type, the computation of qab is reduced to that of Franck-Condon integral Iab(i) = ∫riri+1 ψa(r)ψb(r) dr in an interval ri, ri+1. By using convenient interpolations for the potentials Ua and Ub in the considered interval, this integral becomes Iab(i) = ∑n=ON δnab (ri+1 - ri)n+1/(n + 1), where the “coupling constants” δnab depend uniquely on the eigenvalues Ea and Eb of the considered transition and on the potentials Ua and Ub (the number N of terms depends on the desired accuracy). The method used computes the Franck-Condon factors qab without the explicit use of the wave function and by replacing the integrals by simple summations. To test the values of qab obtained by this method, the orthogonality rule ∫0∞ ψv′ψv″ dr = 0 (for v′ ≠ v″) is used for one state or the other. This test, along with other tests, show that the Franck-Condon factors computed by the present method are accurate to nine significant figures for high and low levels.
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  • 168
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A series of ab initio calculations have been carried out, using the 4-21G basis set. Ethane and propane were first studied to obtain reference points. The effect of adding an electronegative atom (fluorine, or carbonyl oxygen) onto the framework was then studied as a function of the torsional angle about the single bond. Some pronounced trends in structural changes were observed, and these can in part be correlated with hyperconjugative effects. For example, fluoroethane has bond lengths which are shorter than those in ethane itself, by 0.024 Åin the C—C bond, and 0.003 Åin the α C—H bonds. These changes are essentially torsionally independent. On the other hand, in propionaldehyde, the C—C bond length of the methyl group and the C—H bond lengths of the hydrogens attached to the alpha carbon vary as a function of the torsion angle. If the methyl C—C bond in the carbonyl plane is taken as a reference, the bond stretches .016 Åwhen the torsion angle is increased to 90°, an α C—H bond similarly stretches up to .007 Å. Many of these geometric changes are large, well beyond the experimental errors in modern measurements.
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  • 169
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    Journal of Computational Chemistry 6 (1985), S. 429-431 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Timings are reported for 6-31G*/UMP2 calculations on planar allene, twisted ethylene, cyclopropenyl anion, allyl, ethyl, isopropyl and CF3 radicals performed by means of the programs GAUSSIAN 80 and HONDO UMP2. The comparison of the two programs is used for pointing out several factors affecting the speed of MP2 calculations.
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  • 170
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    Journal of Computational Chemistry 6 (1985), S. 437-440 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Hammett σ and Taft σ0 constants have been examined using the MNDO computational procedure. They are both best explained by using computed properties based upon the benzoate ion, especially the reciprocal of the energy of the highest occupied molecular orbital.
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  • 171
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational properties of the recently synthesized highly strained permethylcyclohexane molecule 2 have been studied by empirical force field calculations using three different potentials (CFF, MM2, MM2′) and second-derivative optimization methods. A comparison of the results with the conformational behavior of parent cyclohexane 1 leads to the following conclusions: The best conformation of 2 is a chair minimum whose six-membered ring is flatter than that of 1, due to the strong H…H repulsions introduced by the methyl groups. The twist minimum of 2 is energetically less favorable than the chair by an amount similar to 1. A potential energy barrier Δ V# for the chair inversion of 2 of 15.32 kcal/mol results with the CFF, only about three kcal/mol higher than for 1. The free energy of activation ΔG# for this process obtained with the CFF is 16.96 kcal/mol (at 333 K) and agrees well with the experimental value of 16.7(2) kcal/mol.1 MM2 and MM2′ give substantially lower and higher potential energy inversion barriers Δ V# of 9.03 and 20.29 kcal/mol, respectively, which is attributed to inappropriate torsional energy terms in these force fields. The characteristic difference in the conformational behavior of 2 and 1 concerns the boat forms which are substantially less favorable in the per-methyl compound than in 1. Expectedly, strong H…H repulsions between the 1,4 diaxial flagpole-bowsprit methyl groups in 2 are responsible for this difference. The particularly high strain of the boat forms of 2 leads to flexibility differences as compared to 1 which in turn affect the relative entropies of the various statiomers (stationary point conformations); e.g., the chair ring inversion activation entropies of 2 and 1 are predicted by the CFF calculations to have opposite signs (-4.82 and 3.41 cal/mol K, respectively, at 298 K). The twist and half-twist statiomers of 2 are much more rigid than those of 1, which is a consequence of the substantially larger boat barriers along their pseudorotational interconversion paths. The boat transition state separating two enantiomeric twist minima represents a barrier calculated to be more than tenfold higher for 2 than for 1 (CFF Δ V# values 11.14 and 0.92 kcal/mol, respectively); likewise the half-boat chair inversion barrier of 2 is calculated 5.07 kcal/mol less favorable than the respective half-twist barrier. These statiomers are practically equienergetic in the case of 1. Except for the axial flagpole-bowsprit CH3 substituents of the boat forms, the methyl groups of all the relevant calculated statiomers of 2 are more or less staggered. The rotational barrier of the equatorial methyl groups of the chair minimum of 2 is computationally predicted to be 5.78 kcal/mol (ΔG#), i.e., unusually high. Interesting vibrational effects are brought about by the strong H…H repulsions in 2; thus the chair minimum has a largest C—H stretching frequency estimated to be 3050 cm-1 and involves several particularly low frequencies which have a substantial influence on its entropy. CFF calculations for the lower homologue permethylcyclopentane 5 indicate that its pseudorotational properties are similar to those of cyclopentane 4, in contradistinction to the pair 2/1.
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  • 172
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    Journal of Computational Chemistry 6 (1985), S. 441-446 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular association between some substituted β-carbolines and a model flavin, lumiflavin, has been studied by means of a semiempirical approach proposed by Fraga based on a 1/R expansion of atom-atom pair potentials. Only stacked minima have been considered because of their possible biological interest. The calculations characterize 15 different minimum stacked conformations, most of them occurring in the complexes considered. The structural and energetic effects of 1-Me, 6-OH and 7-OH substituents of β-carboline are discussed. An equilibrium conformation involving geometric overlap between the pteridinic portion of flavin and the indole group of β-carboline is predicted to be the most characteristic structure of the complexes. The recognition of this feature can serve to check the effect of substituents and substitution sites of β-carboline in its association complexes.
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  • 173
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    Journal of Computational Chemistry 6 (1985), S. 447-454 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program is developed in Pascal for the generation of king and color polynomials of graphs. The king polynomial was defined by Motoyama and Hosoya and was shown to be useful in dimer statistics, enumeration of Kekulé structures, etc. We show that the king polynomial of a lattice is the same as the color polynomial of the associated dualist graph, where the color polynomial is defined here as the number of ways of coloring the vertices of a graph with one type of color (say, green) such that two adjacent vertices are not colored with the same color. Applications of these polynomials to exact finite method of lattice statistics are outlined.
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  • 174
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    Journal of Computational Chemistry 6 (1985), S. 469-477 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Local pseudopotential calculations have been performed for the ground state of disilane as well as for the lowest singlet and triplet states of disilene and silylsilylene. Comparison with all-electron calculations shows good agreement for geometries and relative stabilities.
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  • 175
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    Journal of Computational Chemistry 6 (1985), S. 462-468 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The maximization of the exchange interaction between the canonical Hartree-Fock virtual and occupied orbitals leads to a transformed set of virtual orbitals which are well suited as one-electron functions for CI calculations. The procedure, generally known for a long time is seldom applied, despite its simplicity and very low computational demand. However, it is found to be particularly useful in the case of multireference CI, since an improved energy is obtained with a considerable shortening of the CI expansion. Moreover, in the final CI wave function, several configurations appear with considerable weight, thus allowing an easy choice of additional configurations to be inserted in the definition of a new zero-order wave function. The efficiency of the computational procedure is discussed for the case of a Li6 cluster of D3h symmetry and for the NaCO and PdCO complexes. Results are reported for the relative stability of four different geometrical arrangements of the Li6 cluster.
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  • 176
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    Journal of Computational Chemistry 6 (1985) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 177
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    Journal of Computational Chemistry 6 (1985), S. 486-491 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The hydrogen atom transfer reaction between substituted methanes (substituents; H, F, CH3, OH, and CN) and methyl radicals was studied by 4-31G (UHF) calculations using the MINDO/3 geometries. The transition state structures and energy barriers were determined, and variations of the transition state and of the reactivity due to the change of substituent were analyzed based on the potential energy surface characteristics. It was concluded that the reaction is of the SH2 type with a backside attack, and transition state variations are controlled by the vector sum of the component parallel to (Hammond rule) and one perpendicular to the reaction coordinate (anti-Hammond rule). It was also concluded that the most important factor influencing the reactivity is bond dissociation energy effect directly related to the spin transfer of the radical species, and the polar effect need not be overemphasized.
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  • 178
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    Journal of Computational Chemistry 6 (1985), S. 647-651 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Inner projections of the polarization propagator (IPPP) are used to study several features of the throughspace transmission of 31P-31P coupling constants. Cis-1,2-diphosphinoethylene is chosen as a model compound. INDO ground state wave functions are used, including two different second-row parameterizations. Results obtained with a phosphorus spd basis set are also presented. It is found that the overlap of phosphorus lone-pairs constitute an efficient coupling pathway. Results are discussed in terms of experimental values for similar compounds taken from the literature. Theoretical predictions are in line with experimental trends.
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    Journal of Computational Chemistry 6 (1985), S. 656-661 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the Frame's method (also, Le Verrier-Faddeev's method) for characteristic polynomials of chemical graphs can be extended to periodic graphs and structures. The finite periodic structures are represented by cyclic structures in the Born-von Kárman boundary condition which leads to complex matrices. In this article we demonstrate that our earlier computer program (based on Frame's method) can be extended to these periodic networks. The characteristic polynomials of several lattices such as polydiacetylenes, one-dimensional triangular, square, and hexagonal lattices are obtained. These polynomials can be obtained with very little computer time using this method.
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  • 180
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    Journal of Computational Chemistry 6 (1985), S. 674-674 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 181
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    Journal of Computational Chemistry 6 (1985), S. 9-12 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Part of the reaction between 2H-pyran-2-ones and organomagnesium compounds has been investigated by means of MNDO and ab initio calculations. Criteria for the mechanism of reaction are provided by the stereoselectivity observed and calculations are consistent with this stereoselectivity. Conformations of the reaction intermediates are given.
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  • 182
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    Journal of Computational Chemistry 6 (1985), S. 39-45 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hartree-Fock computations of the potential surface of Ar—H2 have been carried out and supplemented with calculations of the dispersion energy, with use of the counterpoise method to remove the basis set superposition error. The collinear and perpendicular bisector geometries are considered. The resulting potentials agree quite well with the actual experimental data.
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  • 183
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    Journal of Computational Chemistry 6 (1985), S. 46-55 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Fully optimized geometries are computed at the Hartree-Fock level for formamide and methylamine with basis sets ranging up to ones that are triple-zeta plus two sets of polarization functions in the valence shell. The effect of very diffuse s and p functions is also examined. The relation of basis set size and composition to the computed amino group out-of-plane angle and to the related localized molecular orbitals is systematically investigated and compared with scattered results previously reported for other systems. It is concluded that the amino group angle is the result of a delicate balance between lone pair character of the nitrogen electrons and delocalization of these electrons into other portions of the molecule. Polarization functions in the nitrogen basis set are necessary to provide for proper description of the lone pair character, but even in methylamine the delocalization is not properly described without an extensive basis set, either polarization functions or very diffuse s and p functions, on the other heavy atoms. The effect is extreme for molecules such as formamide, aniline, and PF2NH2, where very large basis sets are required to obtain the correct out-of-plane angle.
    Additional Material: 2 Ill.
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  • 184
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    Journal of Computational Chemistry 6 (1985), S. 68-75 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The addition reactions of hydroxyl radical with imidazole and its protonated form to yield radical adducts have been investigated by ab initio SCF MO methods using STO-3G and 4-31G basis sets. Analogous radical species are of importance in radiation damage to biological systems. Of the possible radical products, the calculations indicate that the allylic species are generally favored energetically over the nonallylic forms. On an energetic basis, the results show that the allylic adducts formed by addition at the C2 and C5 positions are about equally favorable. Although the C5 species is generally identified as the experimentally observed product in aqueous media for both protonated and unprotonated imidazole, some experimental evidence exists indicating the presence of other forms. Our results suggest that this other form is the C2 adduct. The calculations also point to the protonated form of imidazole being less reactive than imidazole, which is in accord with experimental observations.
    Additional Material: 4 Ill.
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  • 185
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    Journal of Computational Chemistry 6 (1985), S. 76-77 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 186
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 187
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    Journal of Computational Chemistry 6 (1985), S. 79-87 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Transition states for the two probable pathways for the gas-phase hydrolysis of hydrogen isocyanate have been determined using the MINDO/3 method. Activation barriers obtained showed that the one-step mechanism is preferred to the two-step mechanism involving an intermediate. It was shown that the reaction of polymeric water has lower activation barrier than the reaction of monomeric water. Energy and charge decomposition analysis showed that in the former less energy is required in the deformation of molecules for the transition state (TS) formation due to the cyclic flow of electronic charges in the TS.
    Additional Material: 5 Ill.
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  • 188
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    Journal of Computational Chemistry 6 (1985), S. 108-115 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General definitions of valence, degree of bonding between pairs of atoms, and atomic anisotropy and reactivity are given. They can be applied to closed- or open-shell molecular wave functions (in the semiempirical, quasi or full ab initio SCF levels), as well as to GVB ones. The properties and usefulness of the definitions are discussed as well as their relation to former empirical notions. Examples of their application are also reported.
    Additional Material: 1 Ill.
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  • 189
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    Journal of Computational Chemistry 6 (1985), S. 116-121 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Third-order Møller-Plesset perturbation theory (MP3) with a 6-31G** basis set was applied to study the relative stabilities of H+(X)2 conformations (X = CO and N2) and their clustering energies. The effect of both basis set extensions and electron correlation is not negligible on the relative stabilities of the H+(CO)2 clusters. The most stable conformation of H+(CO)2 is found to be a C∞v structure in which a carbon atom of CO bonds to the proton of H+(CO), whereas that of H+(N2)2 is a symmetry D∞h structure. The second lowest energy conformations of H+(CO)2 and H+(N2)2 lie within 2 kcal/mol above the energies of the most stable structures. Clustering energies computed using MP3 method with the 6-31G** basis set are in good agreement with the experimental findings of Hiraoka, Saluja, and Kebarle. The low-lying singlet conformations of H+(X)3 (X = CO and N2) have been studied by the use of the Hartree-Fock MO method with the 6-31G** basis set and second-order Møller-Plesset perturbation theory with a 4-31G basis set. The most stable structure is a T-shaped structure in which a carbon atom of CO (or a nitrogen atom of N2) attacks the proton of the most stable conformation of H+(X)2 clusters.
    Additional Material: 1 Ill.
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  • 190
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    Journal of Computational Chemistry 6 (1985), S. 122-141 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program in Pascal is developed for computing the matching polynomials of graphs and lattices. This program is based on the recursive relation for matching polynomials outlined by Hosoya [Bull. Chem. Soc. Jpn., 44, 2332 (1971)], Gutman and Hosoya [Theor. Chim. Acta, 48, 279 (1978)], and others. The graph whose matching polynomial is of interest is reduced recursively until the graph reduces to several trees. The characteristic polynomial of a tree is the same as the matching polynomial. The characteristic polynomials of resulting trees are computed using the computer program based on Frame's method developed by Balasubramanian [Theor. Chim. Acta, 65, 49 (1984)]; J. Comput. Chem., 5, 387 (1984). The resulting polynomials are then assembled to compute the matching polynomial of the initial graph. The program is especially useful in generating the matching polynomials of graphs containing a large number of vertices. The matching polynomials thus generated are potentially useful in several applications such as lattice statistics (dimer covering problem), aromaticity, valence bond methods (enumeration of perfect matchings) in the calculation of grand canonical partition functions, in the computation of thermodynamic properties of saturated hydrocarbons, and in chemical documentation.
    Additional Material: 8 Ill.
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  • 191
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    Journal of Computational Chemistry 6 (1985), S. 368-376 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The complete molecular structure of biphenyl, characterized by 12 independent parameters, has been derived by ab initio gradient techniques using a STO-3G basis set for coplanar, perpendicular, and minimum energy conformations with the constraint of planar phenyl ring units and a C2 symmetry axis along the CC interring bond. The minimum torsional angle obtained was φ = 38.63° with torsional energy barriers of 8.59 and 10.04 kJ/mol for φ = 0° and φ = 90°, respectively.
    Additional Material: 5 Tab.
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  • 192
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    Journal of Computational Chemistry 6 (1985), S. 377-400 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with STO-3G and 3-21G basis sets are reported for approximately 85 pteridines of interest to the study of the reaction and inhibition mechanisms of dihydrofolate reductase. These include tautomeric, protonated, deprotonated, reduced and 6-substituted forms of the 2-amino-4-oxo- and 2,4-diamino-pteridines, many of which are not easily amenable to experimental investigation. Full geometry optimizations at the SCF/STO-3G level for 30 such pteridines have been performed. A step-wise computational protocol designed to identify the minimum level of theory necessary for reliable prediction of relative tautomer, reduction and ionization energies has been developed in an effort to minimize the cost of calculations for this reasonably large N-heterobicylic system. In general, SCF/STO-3G results were found to be inadequate while SCF/3-21G results obtained with STO-3G optimized geometries agreed with all available experimental evidence with the exception of the relative acidity of 6-methyl-7,8-dihydropterin. Correlation graphs relating experimental pKa's to the calculated ionization energies are presented: these are of potential predictive value. An analysis is given of the importance of resonance substructures, such as the guanidinium and extended-guanidinium groups, in stabilizing some preferred tautomeric and ionized forms, and in explaining the observed geometry changes.
    Additional Material: 11 Ill.
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  • 193
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    Journal of Computational Chemistry 6 (1985), S. 533-537 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The compact orbital and auxiliary basis sets for LCAO-LSD calculations introduced in Part I are tested in molecular calculations on Cr2 and Ni4. The present results for spectroscopic constants and valence orbital energies obtained using medium size orbital expansions with a double-zeta representation for valence orbitals are in very good agreement with those previously calculated with very extended sets. Since the computational time of the present calculations is reduced severalfold compared with the extended basis set calculations, the present basis sets allow increased efficiency of the LCAO-LSD calculations and allow the method to be extended to larger systems.
    Additional Material: 4 Tab.
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  • 194
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    Journal of Computational Chemistry 6 (1985), S. 552-561 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The basic notions and definitions, necessary for the better understanding of Part I of this series, are presented. The mathematical proof is given for sufficiency of the various HOC procedures for vertex canonical numbering and graph orbit finding.
    Additional Material: 1 Ill.
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  • 195
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    Journal of Computational Chemistry 6 (1985), S. 570-580 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometries of ten isomers of dimethyl cyclohexane were determined by ab initio gradient geometry refinement with the 4-21G basis set. It is found that many intramolecular interactions are clearly manifested by correlated structural trends, and that they are consistent with strain energies calculated by employing previously defined ab initio group equivalents. Specifically, non-bonded interactions are found between two adjacent methyl groups in some of the forms, and between axial methyl groups and adjacent axial C—H bonds in others. Unperturbed axial C—H and C—C bonds are consistently longer than equatorial bonds. In general, C—H bonds which are involved in non-bonded repulsive interactions are shortened, i.e., strengthened, and the corresponding H—C—C angles are large, compared to non-interacting parameters.
    Additional Material: 4 Ill.
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  • 196
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    Journal of Computational Chemistry 6 (1985), S. 592-597 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometrical parameters for benzene, fluorobenzene, and cyanobenzene have been calculated using the 6-31G*(5D) and 6-31G** basis sets, and, in addition, the 6-31 + G*(5D) basis set in the case of fluorobenzene. Compared to previous results obtained using the 6-31G basis set there are minor changes in the magnitude of the bond lengths and angles in the ring, but the relative values remain unaltered. The values for the ipso angles in fluorobenzene and cyanobenzene are again somewhat less than those reported from microwave and/or electron diffraction studies. The distortion of the ring is characterized as either an elongation or a flattening with respect to the F-C1⃛C4 and N≡C—C1≡C4 axes, and the shape is characterized as either a broadening or a narrowing across the ring just below the F and Cn group, i.e., an increase or a decrease in the C2⃛C6 internuclear distance, relative of the C3⃛C5 distance.
    Additional Material: 1 Ill.
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  • 197
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    Journal of Computational Chemistry 6 (1985), S. 610-613 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Within the model of anisotropic rotational diffusion, the quantitative treatment of dipolar and quadrupolar spin-lattice relaxation provides valuable information about molecular structures and molecular associations. When quadrupolar relaxation is involved, the title program calculates: (1) the electric field gradient tensor (EFGT) which is diagonalized; (2) the assymetry parameter, the components of the principal axes of the EFGT in the molecular frame of reference and the quadrupole coupling constant; and (3) the rotational diffusion constants which are iteratively determined from the experimental quadrupolar relaxation times. Analogously, for dipolar relaxation ISHTAR calculates the tensor of inertia, the diagonalization of which leads to diffusion constants and free rotor correlation times and the rotational diffusion constants from the experimental spectral densities.
    Additional Material: 3 Tab.
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  • 198
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    Journal of Computational Chemistry 6 (1985), S. 625-633 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Infrared spectra were obtained for the series of 2,X-dimethylheptanes (X = 2,3,4,5,6) and were interpreted with the aid of normal coordinate calculations. 2,2-DMH exists as two conformers, with the Cs conformer being the only one present in the crystalline solid. 2,3-DMH exists in at least three conformations, all of C1 symmetry. Ambiguities in spectral data indicate that more conformations are present. Two C1 conformations of 2,4-DMH were shown to be present, but an unassigned band may indicate the presence of a third conformer. The presence of at least four conformers, all of C1 symmetry, was shown to be necessary to explain the spectrum of 2,5-DMH. Finally, 2,6-DMH was shown to exist as three conformers, of symmetries Cs, C2, and C1. Vibrational assignments were made for all the probable conformers of all five compounds.
    Additional Material: 5 Tab.
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  • 199
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    Journal of Orthopaedic Research 3 (1985), S. 1-16 
    ISSN: 0736-0266
    Keywords: Cartilage ; Variation ; Proteoglycans ; Collagen ; Biochemistry ; Morphology ; Life and Medical Sciences
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Topographically, there are both morphological and biochemical differences in the articular cartilage of the tibial plateau of normal adult dogs when the cartilage covered by the meniscus is compared with that more centrally placed and not covered by meniscus. Histologically, differences are present in the surface morphology, in intra- and extracellular lipid content, and in the morphology of the mineralization front. Electron microscopy shows, in the covered cartilage, variability in collagen fiber size, with evenly spaced fibers apparently randomly distributed and an orderly relationship between the proteoglycans and collagen, whereas in the uncovered area, the collagen is aggregated into bundles and appears to be dissociated in large part from the proteoglycans. The most striking feature in the biochemistry of the two regions is an increased water content in the uncovered cartilage, as compared with the covered. In addition, there is an increased amount of proteoglycans that can be extracted in the uncovered cartilage. The heterogeneity of the cartilage on the tibial plateau should be taken into account when considering both the histologic and biochemical variations found in osteoarthritic cartilage; and when reflecting on the pathogenesis of osteoarthritis.
    Additional Material: 19 Ill.
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  • 200
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    Journal of Electron Microscopy Technique 2 (1985), S. 11-28 
    ISSN: 0741-0581
    Keywords: Ultrastructure ; Semithick sections ; Three-dimensional ; Serial sections ; Stereomicroscopy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Natural Sciences in General
    Notes: Many transmission electron microscopes are available which can be used to examine biological material in 0.25-0.50-μm-thick sections. When compared to the traditional thin section, these “semithick” sections possess a number of inherent advantages: They can be screened for content with the phase contrast light microscope, they facilitate many types of studies requiring an analysis of serial sections, and they are frequently the optimum thickness for stereomicroscopy. Structures such as microtubule-associated components, as well as structural relationships between cellular constituents, may also be clearly visible in semithick sections which are not visible, or go unnoticed, in thin sections. Together these advantages enable an investigator to obtain a more complete three-dimensional picture of a cell or cell component in a significantly (i.e., up to 90%) shorter period of time than would be required if thin sections were used. Semithick sections may, therefore, make a study feasible which is not approachable, or which is approachable only with great difficulty, by conventional thin sectioning techniques.
    Additional Material: 11 Ill.
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