Ab initio calculation of inner-sphere reorganization energies of arenediazonium ion couples.

The geometries of a series of substituted arenediazonium cations (p-NO2, p-CN, p-Cl, p-F, p-H, m-CH3, p-CH3, p-OH, p-OCH3, p-NH2) and the corresponding diazenyl radicals were optimized at the HF/6-31G, MP2/6-31G, B3LYP/6-31G, B3LYP/TZP, B3PW91/TZP, and CASSCF/6-31G levels of theory. Inner-sphere reorganization energies for the single electron-transfer reaction between the species were computed from the optimized geometries according to the NCG method and compared to experimental values determined by Doyle et al. All levels of theory predicted a CNN bond angle of 180 degrees in the cation. A bent neutral diazenyl radical was predicted at all levels of theory excepting B3LYP/TZP and B3PW91/TZP for the p-Cl-substituted compound. Inner-sphere reorganization energies determined at the HF, MP2, and CASSCF levels of theory correlated poorly with both experimental results and calculated geometries. Density functional methods correlated best with the experimental values, with B3LYP/6-31G yielding the most promising results, although the ROHF/6-31G survey also showed some promise. B3LYP/6-31G calculations correctly predicted the order of the inner-sphere reorganization energies for the series, excluding the halogen-substituted compounds, with values ranging from 42.8 kcal x mol(-1) for the p-NO2-substituted species to 55.1 kcal x mol(-1) for NH2. The magnitudes of these energies were lower than the experimental by a factor of 2. For the specific cases examined, the closed-shell cation geometries showed the expected geometry about the CNN bond, with variations in the CN and NN bond lengths correlating with the electron-donating/withdrawing capacity of the substituent. As predicted by Doyle et al., a large geometry change was observed upon reduction. The neutral diazenyl radicals showed a nominal CNN bond angle of 120 degrees and variations in the CN and NN bond lengths also correlated with the electron-donating/withdrawing capacity of the substituent. Changes in theta(CNN) and r(CN) both correlated well with calculated lambda(inner). The key parameters influencing inner-sphere reorganization energy were the CN and NN bond lengths and the CNN bond angle. This influence is explained qualitatively via resonance models produced from NRT analysis and is related to the amount of CN double bond character. Based on these observations, B3LYP/6-31G calculations are clearly the most amenable for calculating inner-sphere reorganization energies for the single electron-transfer reaction between cation/neutral arenediazonium ion couples.

The mild cleavage of 2-amino-2-deoxy-D-glucoside methoxycarbonyl derivatives.

The conversion of methyl carbamate to the corresponding free amine is described for a series of 2-amino-2-deoxy-D-glucosamine derivatives. Cleavage of methoxycarbonyl moiety with MeSiCl(3) and triethylamine in dry THF at 60 degrees C and subsequent aqueous hydrolysis yields the free amine in 54 to 93% yields. The selective cleavage of methyl carbamates with MeSiCl(3) in the presence of a 2,2,2-trichloroethoxycarbonyl group or 2-azido glycosides affords selectively, orthogonal N-deprotected carbohydrates.

Synthesis of allophanate-derived branched glycoforms from alcohols and p-nitrophenyl carbamates.

[reaction: see text] The formation of saccharide-derived carbamates and alkyl 2, 4-dialkylallophanates from alcohols and p-nitrophenyl carbamates is described. Optimization of allophanate formation has led to the synthesis of branched glycoforms with inter-saccharide allophanate linkages that are rigidified by intramolecular hydrogen bonds.

Synthesis of carbamate-containing cyclodextrin analogues.

[formula: see text] The one-pot cyclooligomerization of a saccharide-derived p-nitrophenyl carbamate monomer was developed to generate a series of novel carbamate-containing cyclodextrin analogues. The "transcarbamoylation" occurs by initial base-induced activation to the isocyanate, followed by polycondensation/cyclization of the isocyanato alcohol. In the presence of NaH, only cyclized oligomers were observed, suggesting the importance of Na+ in promoting the efficiency of the cyclization process. The facile deprotection of the oligomers was achieved.

Towards a molecular understanding of arthritis.

Several different agents including free radicals, oxidizing compounds and proteases are believed to play a role in the onset of arthritis. The evidence and underlying chemistry presently available for each destructive agent are presented.

Construction and characterization of a manganese-binding site in cytochrome c peroxidase: towards a novel manganese peroxidase.

BACKGROUND: Manganese-binding sites are found in several heme peroxidases, namely manganese peroxidase (MnP), chloroperoxidase, and the cationic isozyme of peanut peroxidase. The Mn-binding site in MnP is of particular interest. Oxidation of Mn(II) to Mn(III) is a key step in the biodegradation of lignin, a complex phenylpropanoid polymer, as well as many aromatic pollutants. Cytochrome c peroxidase (CcP), which is structurally homologous to MnP despite a poor sequence homology, does not bind manganese. Thus, engineering a Mn-binding site into CcP will allow us to elucidate principles behind designing metal-binding sites in proteins, to understand the structure and function of this class of Mn-binding centers, and to prepare novel enzymes that can degrade both lignin and other xenobiotic compounds. RESULTS: Based on a comparison of the crystal structures of CcP and MnP, a site-directed triple mutant (Gly41-->Glu, Val45-->Glu, His181-->Asp) of residues near the putative Mn-binding site in CcP was prepared and purified to homogeneity. Titrating MnSO4 into freshly prepared mutant CcP resulted in electronic absorption spectral changes similar to those observed in MnP. The calculated apparent dissociation constant and the stoichiometry of Mn-binding of CCP were also similar to MnP. Titration with MnSO4 resulted in the disappearance of specific paramagnetically shifted nuclear magnetic resonance spectroscopy signals assigned to residues close to the putative Mn-binding site in the mutant CcP. None of the spectral features were observed in wild-type CcP. In addition, the triple mutant was capable of oxidizing Mn(II) at least five times more efficiently than the native CcP. CONCLUSIONS: A Mn-binding site has been created in CcP and based on our spectroscopic studies the designed Mn-binding site is similar to the Mn-binding site in MnP. The results provide a basis for understanding the structure and function of the Mn-binding site and its role in different heme peroxidases.

The solution conformation of hyaluronan: a combined NMR and molecular dynamics study.

Hyaluronan (HA) is a negatively charged glycosaminoglycan that exhibits a wide variety of biological effects mediated by binding to cell-surface and extracellular matrix proteins (hyaladherins). Short HA oligosaccharides have been shown to retain the specific interactions and biological effects of high molecular weight HA. Although it has a simple disaccharide repeating unit, the aqueous solution conformation of HA has been very difficult to determine because of strong coupling and overlapping resonances. In this study, we propose aqueous solution conformations for an octasaccharide of HA, derived from proton-proton NOE data and restrained molecular dynamics. To overcome spectral overlap and strong coupling, alternate methods for extracting distance restraints were employed. Restrained molecular dynamics calculations yielded one set of interglycosidic angle values for the beta (1,3) linkage (phi 13 = 46 degrees, psi 13 = 24 degrees). In contrast, two sets of values for the beta (1,4) linkage were consistent with the NOE restraints (phi 14 = 24 degrees, psi 14 = -53 degrees or phi 14 = 48 degrees, psi 14 = 8 degrees). The potential difference in flexibility for the two linkages is consistent with unrestrained as well as the restrained molecular dynamics trajectories described here. The conformational parameters obtained from restrained molecular dynamics are used to predict helical parameters of high molecular weight HA and will provide a basis for studies of HA binding to proteins.