Studies of the representation of interatomic distances in molecules and crystal as sum of atomic radii

The electron diffraction investigation of the following compounds has been carried out: sulfur, sulfur nitride, realgar, arsenic trisulfide, spiropentane, dimethyltrisulfide, cis and trans lewisite, methylal, and ethylene glycol.

The crystal structures of the following salts have been determined by x-ray diffraction: silver molybdateand hydrazinium dichloride.

Suggested revisions of the covalent radii for B, Si, P, Ge, As, Sn, Sb, and Pb have been made, and values for the covalent radii of Al, Ga, In, Ti, and Bi have been proposed.

The Schomaker-Stevenson revision of the additivity rule for single covalent bond distances has been used in conjunction with the revised radii. Agreement with experiment is in general better with the revised radii than with the former radii and additivity.

The principle of ionic bond character in addition to that present in a normal covalent bond has been applied to the observed structures of numerous molecules. It leads to a method of interpretation which is at least as consistent as the theory of multiple bond formation.

The revision of the additivity rule has been extended to double bonds. An encouraging beginning along these lines has been made, but additional experimental data are needed for clarification.

Bombinakinin M gene associated peptide, a novel bioactive peptide from skin secretions of the toad Bombina maxima

A novel 28-amino acid peptide, termed bombinakinin-GAP, was purified and characterized from skin secretions of the toad Bombina maxima. Its primary structure was established as DMYEIKQYKTAHGRPPICAPGEQCPIWV-NH2, in which two cysteines form a disulfide bond. A FASTA search of SWISS-PROT databank detected a 32% sequence identity between the sequences of the peptide and a segment of rat cocaine- and amphetamine-regulated transcript (CART). Intracerebroventricular (i.c.v.) administration of the peptide induced a significant decrease in food intake in rats, suggesting that it played a role in the control of feeding by brain. Analysis of its cDNA structure revealed that this peptide is coexpressed with bombinakinin M, a bradykinin-related peptide from the same toad. Bombinakinin-GAP appears to be the first example of a novel class of bioactive peptides from amphibian skin, which may be implicated in feeding behavior. (C) 2003 Elsevier Science Inc. All rights reserved.

Cloning of novel bombesin precursor cDNAs from skin of Bombina maxima

Amphibian skin is a rich resource of bioactive peptides like proline-rich bombesin from frog Bombina maxima. A novel cDNA clone encoding a precursor protein that comprises proline-rich bombesin and a novel peptide, designated as bombestatin, was isolated from a skin cDNA library of B. maxima. The predicted primary structure of the novel peptide is WEVLLNVALIRLELLSCRSSKDQDQKESCGMHSW, in which two cysteines form a disulfide bond. A BLAST search of databases did not detect sequences with significant similarity. Bombestatin possesses dose-dependent contractile activity on rat stomach strips. The differences between cDNAs encoding PR-bombesin plus bombestatin and PR-bombesin alone are due to fragment insertions located in 3'-coding region and 3'-untranslational region, respectively. (c) 2005 Elsevier B.V. All rights reserved.

Frog albumin is expressed in skin and characterized as a novel potent trypsin inhibitor

A novel potent trypsin inhibitor was purified and characterized from frog Bombina maxima skin. A full-length cDNA encoding the protein was obtained from a cDNA library constructed from the skin. Sequence analysis established that the protein actually comprises three conserved albumin domains. B. maxima serum albumin was subsequently purified, and its coding cDNA was further obtained by PCR-based cloning from the frog liver. Only two amino acid variations were found in the albumin sequences from the skin and the serum. However, the skin protein is distinct from the serum protein by binding of a haem b (0.95 mol/mol protein). Different from bovine serum albumin, B. maxima albumin potently inhibited trypsin. It bound tightly with trypsin in a 1: 1 molar ratio. The equilibrium dissociation constants (K-D) obtained for the skin and the serum proteins were 1.92 x 10(-9) M and 1.55 x 10(-9) M, respectively. B. maxima albumin formed a noncovalent complex with trypsin through an exposed loop formed by a disulfide bond (Cys(53)-Cys(62)), which comprises the scissile bond Arg(58)(P-1)-His(59)(P-1'). No inhibitory effects on thrombin, chymotrypsin, elastase, and subtilisin were observed under the assay conditions. Immunohistochemical study showed that B. maxima albumin is widely distributed around the membranes of epithelial layer cells and within the stratum spongiosum of dermis in the skin, suggesting that it plays important roles in skin physiological functions, such as water economy, metabolite exchange, and osmoregulation.

A new protein structure of P-II class snake venom metalloproteinases: it comprises metalloproteinase and disintegrin domains

A new metalloproteinase-disintegrin, named Jerdonitin, was purified from Trimeresurus jerdonii venom with a molecular weight of 36 kDa on SDS-PAGE. It dose-dependently inhibited ADP-induced human platelet aggregation with IC50 of 120 nM. cDNA cloning and sequencing revealed that Jerdonitin belonged to the class II of snake venom metalloproteinases (SVMPs) (P-II class). Different from other P-II class SVMPs, metalloproteinase and disintegrin domains of its natural protein were not separated, confirmed by internal peptide sequencing. Compared to other P-II class SVMPs, Jerdonitin has two additional cysteines (Cys219 and Cys238) located in the spacer domain and disintegrin domain, respectively. They probably form a disulfide bond and therefore the metalloproteinase and disintegrin domains cannot be separated by posttranslationally processing. In summary, comparison of the amino acid sequences of Jerdonitin with those of other P-II class SVMPs by sequence alignment and phylogenetic analysis, in conjunction with natural protein structure data, suggested that it was a new type of P-II class SVMPs. (C) 2003 Elsevier Inc. All rights reserved.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Chiral synthesis on catalysts immobilized in microporous and mesoporous materials

This paper reviews the recent progress made in the asymmetric synthesis on chiral catalysts in porous materials and discusses the effects of surface and pores on enantio-selectivity (confinement effect). This paper also summarizes various approaches of immobilization of the chiral catalysts onto surfaces and into pores of solid inorganic supports such as microporous and mesoporous materials. The most important reactions surveyed for the chiral synthesis in porous materials include epoxidation. hydrogenation, hydroformylation, Aldol and Diels-Alder reactions, etc. The confinement effect originated from the surfaces and the pores turns out to be a general phenomenon. which may make the enantioselectivity increase (positive effect) or decrease (negative effect). The confinement effect becomes more pronounced particularly when the bonding between the catalyst and the surface is more rigid and the pore size is tuned to a suitable range. It is proposed that the confinement in chiral synthesis is essentially a consequence of subtle change in transition states induced by weak-interaction in pores or on surfaces. It is also anticipated that the enantioselectivity could be improved by tuning the confinement effect based on the molecular designing of the pore/surface and the immobilized catalysts according to the requirements of chiral reactions.

含二硫键多肽的基质辅助激光解析电离飞行时间质谱研究

The determination of disulfide bonds becomes an important aspect of obtaining a comprehensive understanding of the chemical structure of a protein. Numerous experimental methods have been developed for the determination of disulfide bonds in proteins. Modern mass spectrometry has developed as an important tool for the analysis of disulfide bond patterns due to its advantages of being simple, rapid and sensitive. The dissociations of the disulfide bonds were detected during the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis. These fragment ions were attributed to prompt fragmentation or “in-source decay” rather than “post-source decay”. For the double disulfide bonds, ions of plus sulfur and minus sulfur atoms corresponding to cleavages at different sites within the carbon-sulfur-sulfur-carbon disulfide bonds were also observed.

Regioselective Bis-Selenation of Allenes Catalyzed by Palladium Complexes: A Theoretical Study

The reaction mechanism of Pd(O)-catalyzed allene bis-selenation reactions is investigated by using density functional methods. The overall reaction mechanism has been examined. It is found that with the bulkier PMe3 ligand, the rate-determining step is the reductive elimination process, while allene insertion and reductive elimination processes are competitive for the rate-determining step with the PH3 ligand, indicating the importance of the ligand effect. For both cis and trans palladium complexes, allene insertion into the Pd-Se bond of the trans palladium complex using the internal carbon atom attached to the selenyl group is prefer-red among the four pathways of allene insertion processes. The formation of sigma-allyl and pi-allyl palladium complexes is favored over that of the sigma-vinyl palladium species. By using methylallene, the regioselectivity of monosubstituted allene insertion into the Pd-Se bond is analyzed.

PIFA-Mediated Oxidative Cyclization of 1-Carbamoyl-1-oximylcycloalkanes: Synthesis of Spiro-Fused Pyrazolin-5-one N-Oxides

convenient and efficient synthesis of spiro-fused pyrazolin-5-one N-oxides starting from readily available 1-carbamoyl-1-oximylcycloalkanes is developed. This general protocol features a novel and facile way for access to the five-membered azaheterocycles by formation of a new N-N single bond. The key cyclization step utilizes the formation of an N-oxonitrenium intermediate, mediated by the hypervalent iodine reagent PIFA, and its subsequent intramolecular trapping by the amide moiety under rather mild experimental conditions.

Efficient synthesis of highly substituted pyrrolin-4-ones via PIFA-mediated cyclization reactions of enaminones

A convenient and efficient synthesis of highly substituted pyrrolin-4-ones is developed via the PIFA-mediated cyclization reactions of readily available enaminones, and a mechanism involving sequential cleavage of N-C bond, formation of new N-C bond, intramolecular addition reaction, and benzilic acid type rearrangement is proposed.

Silicon dioxide coating of CeO2 nanoparticles by solid state reaction at room temperature

The synthesis Of SiO2 coated CeO2 nanoparticles by humid solid state reaction at room. temperature is described. Transmission electron microscope results show that CeO2 Particles were coated with a layer Of SiO2. Binding energy of Ce 3d(5/2) was shifted from 883.8 to 882.8 eV after coating in the XPS Ce 3d spectra. This confirms the chemical bond formation between SiO32- and Ce4+. Because the surface photovoltage property of CeO2 nanoparticles that were used as core materials in the experiment approaches to that of CeO2 macroparticles, peak P2 (electron transition from 0 2p on surface to Ce 4f) disappeared in the surface photovoltage spectrum of CeO2 nanoparticles. Also, the effect Of SiO2 on the electron transition from 0 2p to Ce 4f results in the lowering of surface photovoltage response intensity of P1 peak (electron transition from 0 2p in bulk to Ce 4f).

The reactivity of lanthanide alkyl compounds with phenylacetylene: Synthesis and structure of [(Bu(t)Cp)(2)LnC CPh](2) (Ln=Nd, Gd)

[(Bu(t)Cp)(2)LnCH(3)](2) (Ln = Nd, Gd) react with PhC=CH to form the dimeric alkynide-bridged complexes [(Bu(t)Cp)(2)LnC=CPh](2) [Ln = Nd (I), Gd (II)]. Both compounds crystallized from toluene in the monoclinic space group C2/c. The two complexes are homologous, composed of asymmetric metal-alkynide bridges with Nd-C, Gd-C (alkynide) bond lengths of 2.602(4), 2.641(5) (I) and 2.532(6), 2.601(7) Angstrom (II), respectively. The average Nd-C (ring) and Gd-C (ring) distances are 2.746(13) and 2.703(19)Angstrom.

STUDIES OF ELECTROCHEMICAL CATALYTIC REDUCTION REACTIONS OF TETRAPHENYLPORPHINATOCOBALT 1,2-DIBROMOETHANE AND 1,2-DICHLOROETHANE SYSTEMS IN NONAQUEOUS MEDIA

Electrochemical catalytic reactions of tetraphenylporphinatocobalt were studied in DMF and EtCl2 solutions in the presence of 1,2-dibromoethane and 1, 2-dichloroethane utilizing cyclic voltammetry, thin-layer electrochemistry, in situ UV-visible spectroel

APPLICATION OF AN ULTRAMICROELECTRODE IN HOMOGENEOUS CATALYTIC REACTIONS .4. ELECTROCATALYTIC REDUCTION OF ORGANOHALIDES BY METALLOPORPHYRIN AT ULTRAMICROELECTRODE

The electrocatalytic reduction of 1,2-dibromoethane and tetrabromoethane with CoTPP in DMF solutions containing 0.1 M TBAP was investigated at a Pt ultramicroelectrode. The experimental results indicated that CoTPP obviously exhibited catalytic activity for 1,2-dibromoethane and tetrabromoethane. The rate constants of 1,2-dibromoethane and tetrabromoethane in this system were calculated to be 0.14 x 10(3) and 0.5 x 10(2) M-1 S-1, respectively. The reaction mechanism of 1,2-dibromoethane and tetrabromoethane reduction electrocatalysed by CoTPP in 0.1 M TBAP DMF solution is discussed.