A graph-theoretic approach to quantitative structure—activity/reactivity studies

Characterization of molecular species based on the use of suitable graph invariants (graph paths, in particular) can provide a quantitative means of encoding structure; the technique is complementary to commoner approaches to studies of quantitative structure— activity relationships. Graph path encoding is here applied to quantitative studies of relationships between molecular structures and biological activity; the examples are the rates of various substrate reactions with hexoldnase, and the potential opiate-like activity of enkephalin analogs.     

Bis(PheOH) maleic acid amide-fumaric acid amide photoizomerization induces microsphere-to-gel fiber morphological transition: the photoinduced gelation system

The photoinduced gelation system based on 1 (non-gelling) to 2 (gelling) molecular photoisomerization in water results by microspheres (1) to gel fibers (2) transformation at the supramolecular level.     

Oscillating autoxidation reaction of p-xylene in the liquid phase, catalyzed by metal oxides

Oscillatory reaction was observed during liquid-phase oxidation of p-xylene in the presence of certain transition metal oxides as catalysts. Experimental conditions under which oscillations occur and parameters influencing this behavior are described.

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Hybridization in some macrocyclic polyacetylenes

The hybridization in several cyclic polyacetylene compounds has been calculated by the maximum overlap method, assuming planar and non-planar geometries of the molecules. In the planar configuration the hybrids describing the molecular skeleton deviate from the corresponding bond directions. We have a few “bent” bonds, but in contrast to the situation in small rings, here the deviation angles are negative, i.e., the hybrids point toward the inside of the ring. Non-planar structures in which acetylene groups are kept in a plane and CCH₂ or CH₂ groups are displaced out of the plane show less deviation from the bond directions of bent bonds. Furthermore, the deviation angles decrease with an increase in the out-of-plane displacement of methylene groups. Finally, when the angle of bending of the molecules approaches 50°, the deviation vanishes, predicting a puckered conformation for the molecules. Correlation between CC stretching vibration frequencies and the corresponding CC bond overlap is discussed.     

Generalized bond orders

We introduce generalized bond orders defined in terms of weighted Kekule valence structures. The weights were determined by the contributions of linearly independent and minimal conjugated circuits in individual Kekule valence structure. When special values for the contributions of conjugated circuits of different size are assumed, one obtains quantities that show considerable similarity to the Pauling and the Clar's bond orders. Pauling bond orders are obtained when one assumes that all conjugated circuits make equal contribution to bond orders. © 1994 John Wiley & Sons, Inc.     

Graph-theoretical analysis of molecular properties. Isomeric variations in nonanes

Paths of length two and three appear to dominate variations in isomers of alkanes when various physical and chemical molecular properties are compared. The regularities previously observed for octanes have been fully examined for the set of 35 nonane isomers C₉H₂₀. Such examinations are facilitated by construction of appropriate grid graphs with paths of length two and three, respectively, representing molecules and connecting such points along the grid axes. By ordering structures in the two-dimensional coordinate plane, various trends and regular changes in the relative magnitudes for the selected thermodynamic properties have been traced to molecular connectivity and topology.     

Survey of structural regularities in molecular properties. I. Carbon-13 chemical shifts in alkanes

Many regularities in properties among structurally related compounds are known but a systematic approach to investigate all such cases is rare. A plan is outlined for a systematic study of structural regularities that is based on use of selected graph invariants as prime auxiliary quantities. In this paper carbon-13 chemical shifts in alkanes are examined. Since NMR spectra of paraffins are well understood, the example provides a useful illustration of the approach, introduces basic concepts, and illustrates the kind of the results that the graph-theoretical scheme generates. Differences and similarities between graph-theoretical viewing of the problem of structural regularities and customary direct use of additivities are discussed in some detail.     

Selective additions of polyhalogenated compounds to chloro substituted ethenes catalyzed by a copper complex

The Cu complex Cu(L)_nCl (L=2-propylamine) has been found to be an advantageous catalyst for the addition of polyhalogenated compounds to chloro substituted ethenes; the 11 adducts were formed almost exclusively in up to 71% yield.

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, , Cu(L)_nCl (L=2-), ; 71% 11.

     

A photochemical method for patterning the immobilization of ligands and cells to self-assembled monolayers

This work describes a chemically well defined method for patterning ligands to self-assembled monolayers (SAMs) of alkanethiolates on gold. This method begins with monolayers presenting a nitroveratryloxycarbonyl (NVOC)-protected hydroquinone which is photochemically irradiated to reveal a hydroquinone group. The resulting hydroquinone is then oxidized to the corresponding benzoquinone, providing a site for the Diels-Alder mediated immobilization of ligands. The rate constant for the photochemical deprotection is 0.032 s(-1) (with an intensity of approximately 100 mW/cm(2) between 355 and 375 nm), corresponding to a half-life of 21 s. The hydroquinone is oxidized to the benzoquinone using either electrochemical or chemical oxidation and then functionalized by reaction with a cyclopentadiene-tagged ligand. Two methods for patterning the immobilization of ligands are described. In the first, the substrate is illuminated through a mask to generate a pattern of hydroquinone groups, which are elaborated with ligands. In the second method, an optical microscope fit with a programmable translational stage is used to write patterns of deprotection which are then again elaborated with ligands. This technique is characterized by the use of well-defined chemical reactions to control the regions and densities of ligand immobilization and will be important for a range of applications that require patterned ligands for biospecific interactions.