Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). I. Algorithms for finding graph orbits and canonical numbering of atoms

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.     

Scan-rate-dependent melting transitions of interleukin-1 receptor (type II): elucidation of meaningful thermodynamic and kinetic parameters of aggregation acquired from DSC simulations

The role of thermal unfolding as it pertains to thermodynamic properties of proteins and their stability has been the subject of study for more than 50 years. Moreover, exactly how the unfolding properties of a given protein system may influence the kinetics of aggregation has not been fully characterized. In the study of recombinant human Interleukin-1 receptor type II (rhuIL-1R(II)) aggregation, data obtained from size exclusion chromatography and differential scanning calorimetry (DSC) were used to model the thermodynamic and kinetic properties of irreversible denaturation. A break from linearity in the initial aggregation rates as a function of 1/T was observed in the vicinity of the melting transition temperature (T(m) approximately 53.5 degrees C), suggesting significant involvement of protein unfolding in the reaction pathway. A scan-rate dependence in the DSC experiment testifies to the nonequilibrium influences of the aggregation process. A mechanistic model was developed to extract meaningful thermodynamic and kinetic parameters from an irreversibly denatured process. The model was used to simulate how unfolding properties could be used to predict aggregation rates at different temperatures above and below the T(m) and to account for concentration dependence of reaction rates. The model was shown to uniquely identify the thermodynamic parameters DeltaC(P) (1.3 +/- 0.7 kcal/mol-K), DeltaH(m) (74.3 +/- 6.8 kcal/mol), and T(m) with reasonable variances.     

2-Aminopyrimidine directed self-assembly of zinc porphyrins containing bulky 3,5-di-tert-butylphenyl groups

The 2-aminopyrimidin-5-yl ligand is revealed to be a promising candidate for the construction of supramolecular porphyrin arrays with broad absorption bands for efficient light-harvesting. 10-Mono- and 10,20-di(2-aminopyrimidin-5-yl) derivatives of 5,15-bis(3,5-di-tert-butylphenyl)porphyrin have been synthesized in high yield. Their Zn(II) salts show variable concentration and temperature-dependent UV/vis spectra in solution, consistent with supramolecular aggregation. Whereas the FAB mass spectra of the monosubsituted derivative in toluene suggest the formation of a tetramer at high concentrations and low temperatures (estimated association free enthalpy Delta H = 220 +/- 10 kJ/mol), the larger splitting of the Sorret band (ca. 40 nm) in the variable temperature UV/vis spectra of the disubstituted bis(3,5-di-tert-butylphenyl)porphyrin is indicative of yet higher aggregates involving both 2-aminopyrimidin-5-yl groups. The tetrameric nature of the monosubsituted derivative is confirmed by X-ray analysis, which reveals that two of the 2-aminopyrimidin-5-yl groups are encapsulated by the aggregate and consequently are prevented from undergoing hydrogen bonding. NMR studies show there is no exchange of the 2-aminopyrimidin-5-yl groups, so the tetramer is rigid, which is confirmed by molecular modeling calculations. The tetramer formation is governed by pi-pi interactions, metal coordination, and hydrogen bonding. The di(2-aminopyrimidin-5-yl) derivative forms strongly scattering solutions, which upon standing form green flocculate precipitates, reminiscent of shaken suspensions of bacteriochlorophyll c.     

Electron impact mass spectra of 3,5,7-triaryl-and -trialkyl-4H-1,2-diazepines

Electron impact mass spectra of 3,5,7-trisubstituted 4H-1,2-diazepines indicate that aryl substituents lead to N₂ expulsion while alkyl substitutents do not. A common fragmentation pattern is observed and discussed for all alkyldiazepines, most of which are newly reported compounds. Assignments are based on electron impact mass spectra of deuteriated substrates and high resolution mass spectra. A previous interpretation of N₂ expulsion is corrected.     

Mass spectrometry in structural and stereochemical problems—CC A study of the fragmentation processes of some pyrilium salts

The principal mode of fragmentation, at both 70 and 15 eV, of pyrilium iodides (I to V) which are substituted by at least one methyl group is the elimination of hydrogen iodide from the non-detectable molecular ion. In contrast the mass spectrum (Fig. 6) of 2,4,6-triphenyl pyrilium iodide (VI) shows its dominant fragmentation to be due to the loss of an iodine atom from the molecular ion. The mass spectra (for example Figs. 6 and 7) of 2,4,6-triphenyl pyrilium iodide, bromide and tetrafluoroborate (VI, VII and VIII) are virtually identical except for the peaks corresponding to a molecule of iodine (m/e 254), hydrogen iodide (m/e 128) and iodine (m/e 127) in the mass spectrum (Fig. 6) of the iodide. Other fragmentation routes common to these pyrilium salts are described.     

Propagators and renormalization transformations for lattice gauge theories. I

Lattice gauge theories may be looked at as perturbations of the theory of a vector field with a Gaussian action. We study this theory here and in following papers obtaining crucial results for understanding the renormalization group method in more complicated non-Abelian gauge field theories.Research supported in part by the National Science Foundation under Grant PHY-82-03669