Anomalous distance dependence of electron transfer across peptide bridges

The first investigation on the distance dependence of a dissociative electron transfer process across peptide bridges is reported. This study was carried out by using a series of donor-peptide-acceptor systems in which the donor is a phthalimido moiety, the peptide bridges are provided by alpha-aminoisobutyric acid (Aib) homooligomers, and the acceptor is a peroxide functional group. The intramolecular electron transfer from the electrogenerated phthalimido radical anion to the peroxide was studied in comparison with the thermodynamic and kinetic information obtained with models of the acceptor and the donor. The intramolecular rate constants were determined in N,N-dimethylformamide by taking into account the corresponding intermolecular values. The experimental results point to an unusual non-exponential dependence of the intramolecular electron transfer rate on the number of bridge units. The same trend could be verified also by taking into account the actual donor-acceptor edge-to-edge distance. The peculiar distance dependence that was observed for the intramolecular electron transfer rate is attributed to the mediating effect of the intramolecular C=O...H-N hydrogen bonds.     

Theoretical and electrochemical analysis of dissociative electron transfers proceeding through formation of loose radical anion species: reduction of symmetrical and unsymmetrical disulfides

The dissociative reduction of a series of symmetrical (RSSR, R = H, Me, t-Bu, Ph) and unsymmetrical disulfides (RSSR', R = H, R' = Me and R = Ph, R' = Me, t-Bu) was studied theoretically, by MO ab initio calculations and, for five of them, also experimentally, by convolution voltammetry in N,N-dimethylformamide. The reduction is dissociative but proceeds by a stepwise mechanism entailing the formation of the radical anion species. The electrochemical data led to estimated large intrinsic barriers, in agreement with an unusually large structural modification undergone by the disulfide molecules upon electron transfer. The theoretical results refer to MP2/3-21G*//MP2/3-21G*, MP2/3-21*G*//MP2/3-21G*, CBS-4M, and G2(MP2), the latter approach being used only for the molecules of small molecular complexity. A loose radical-anion intermediate was localized and the dissociation pattern for the relevant bonds analyzed. For all compounds, the best fragmentation pathway in solution is cleavage of the S-S bond. In addition, S-S bond elongation is the major structural modification undergone by the disulfide molecule on its way to the radical anion and eventually to the fragmentation products. The calculated energy of activation for the initial electron transfer was estimated from the crossing of the energy profiles of the neutral molecule and its radical anion (in the form of Morse-like potentials) as a function of the S-S bond length coordinate. The inner intrinsic barrier obtained in this way is in good agreement with that determined by convolution voltammetry, once the solvent effect is taken into account.     

Thermal and kinetic study of tyre waste pyrolysis via TG-FTIR-MS analysis

The world production of tyre waste amounts to 5·10⁶ ton year^–1, 2·10⁶ tons of which are produced in Europe, but the final destination of nearly 65–70% of them is the landfill, despite the high added value materials lost and the consequent environmental impact. Treatments alternative to landfilling take into account reconstruction and reuse of the tyres or the matter and/or energy recovery by means of thermal treatment processes (incineration, gasification and pyrolysis). Among these, pyrolysis seems to be a promising and realistic alternative to attain the conversion of tyre waste into valuable and reusable products. Present work relates to experimental tests and results obtained for the study of tyre waste pyrolysis, conducted by means of thermo-gravimetric analysis (TG) of the material and the simultaneous determination, through Fourier transform infrared (FTIR) and mass spectrometry (MS), of the decomposition products. The analysis of the volatile fraction allows to isolate, within the thermograms, the evolution of products referable to specific tyre components and therefore it suggests the application of a multi-component decomposition model. The kinetic model consequently developed agrees fairly well with the experimental data.     

Inclusion complex characterization between progesterone and hydroxypropyl-β-cyclodextrin in aqueous solution by NMR study

The aim of this work is the determination of the molecular association of progesterone (P) with hydroxypropyl-β-cyclodextrin (HPβCD) in aqueous solution. The stoichiometry and the binding constants of the inclusion complex were calculated using NMR techniques.     

Precipitation-free high-affinity multivalent binding by inline lectin ligands

Multivalent ligand–protein interactions are a key concept in biology mediating, for example, signalling and adhesion. Multivalent ligands often have tremendously increased binding affinities. However, they also can cause crosslinking of receptor molecules leading to precipitation of ligand–receptor complexes. Plaque formation due to precipitation is a known characteristic of numerous fatal diseases limiting a potential medical application of multivalent ligands with a precipitating binding mode. Here, we present a new design of high-potency multivalent ligands featuring an inline arrangement of ligand epitopes with exceptionally high binding affinities in the low nanomolar range. At the same time, we show with a multi-methodological approach that precipitation of the receptor is prevented. We distinguish distinct binding modes of the ligands, in particular we elucidate a unique chelating binding mode, where four receptor binding sites are simultaneously bridged by one multivalent ligand molecule. The new design concept of inline multivalent ligands, which we established for the well-investigated model lectin wheat germ agglutinin, has great potential for the development of high-potency multivalent inhibitors as future therapeutics.

Integration of sugar epitopes into a backbone structure generates multivalent lectin ligands with a defined binding mode and high affinity without precipitating the protein.     

Nitroxyl peptides as catalysts of enantioselective oxidations

The achiral, nitroxyl-containing alpha-amino acid TOAC (TOAC = 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid), in combination with the chiral alpha-amino acid C(alpha)-methyl valine [(alphaMe)Val], was used to prepare short peptides (from di- to hexa-) that induced the enantioselective oxidation of racemic 1-phenylethanol to acetophenone. The best catalyst was an N(alpha)-acylated dipeptide alkylamide with the -TOAC-(alphaMe)Val- sequence folded in a stable, intramolecularly hydrogen-bonded beta-turn conformation with large, lipophilic (hydrophobic) N- and C-terminal blocking groups. We rationalized our findings by proposing models for the diastereomeric intermediates between (R)-[and (S)]-1-phenylethanol and the catalyst Fmoc-TOAC-L-(alphaMe)Val-NHiPr, based on the X-ray diffraction structure of the latter.     

A catalytic antibody programmed for torsional activation of amide bond hydrolysis

Amidase antibody 312d6, obtained against the sulfonamide hapten 4 a that mimics the transition state for hydrolysis of a distorted amide, accelerates the hydrolysis of the corresponding amides 1 a-3 a by a factor of 10(3) at pH 8. The mechanisms of both the uncatalyzed and antibody-catalyzed reactions were studied. Between pH 8 and 12 the uncatalyzed hydrolysis of N-toluoylindoles 1 a and 3 a shows a simple first-order dependence on [OH(-)], while hydrolysis of 3 a is zeroth-order in [OH(-)] below pH 8. The pH profile for hydrolysis of the corresponding tryptophan amide 2 a is more complex due to the dissociation of the zwitterion into an anion with pK(a) 9.74; hydrolysis of the zwitterionic and the anionic form of 2 a both show simple first-order dependence on [OH(-)]. Absence of (18)O exchange between H(2) (18)O/(18)OH(-) and the substrate, a normal SKIE for both 1 a (k(H)/k(D)=1.12) and 3 a (k(H)/k(D)=1.24) and the value of the Hammett constant rho for hydrolysis of p-substituted amides 3 a-e are consistent with an ester-like mechanism in which formation of the tetrahedral intermediate is rate-determining and the amine departs as anion. The 312d6-catalyzed hydrolysis of 3 a was studied between pH 7.5 and 9, and its independence of pH in this range indicates that water is the reacting nucleophile. Hydrolysis of 3 a is only partially inhibited by the sulfonamide hapten, and this indicates that non-specific catalysis by the protein accompanies the specific process. Only the nonspecific process is observed in the hydrolysis of amides 3 with para substituents other than methyl. Binding studies on the corresponding series of p-substituted sulfonamides 5 a-e confirm the high specificity of antibody 312d6 for p-methyl substituted substrates.     

Sequential amination/annulation/aromatization reaction of carbonyl compounds and propargylamine: a new one-pot approach to functionalized pyridines

A general one-pot synthesis of pyridines 4a-t from the reaction of dialkyl acyclic/cyclic ketones 1a-i, methyl, aryl/heteroaryl ketones 1m-r, and aldehydes bearing alpha-hydrogens 1s,t with propargylamine 2 is described. Gold and copper salts are efficient catalysts for the reaction of ketones with 2. The formation of the pyridines 4 is suggested to proceed through the sequential amination of carbonyl compounds followed by regioselective 6-endo-dig cyclization of the N-propargylenamine (N-propargyldienamine) intermediate 3(5) and aromatization reaction. Whereas the preparation of linear polycyclic pyridine 4i can be carried out by reacting cholestan-3-one 1i with 2, the angular polycyclic pyridine 4j has been obtained starting from cholest-5-en-3-one 1j. Selectivity of the reaction of polycyclic dicarbonyls 1k,l with 2 has also been investigated.     

The Crystal Structure of the Macrocyclic Hexathioether 1,4,7,11,14,17-Hexathiacycloeicosane: Implications for Metal Complexation

Several metal complexes of the twenty-membered ring hexathioether macrocycle, 1,4,7,11,14,17-hexathiacycloeicosane (20S6), have now been prepared and crystallographically characterized. In order to examine structural changes in the ligand which may occur under complexation, we undertook an analysis of the structure of the 20S6 ligand by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group C₂/c with the unit cell dimensions: a = 22.481(1) Å, b = 5.433(2) Å, c = 17.9259(9) Å, and = 117.711(4)°. The conformation adopted by this ligand is such that four of the sulfur atoms are exodentate, but two sulfur atoms are syn endodentate, unusual for a macrocycle of this type. All twelve of the C—S—C—C torsional bond angles in 20S6 are gauche as expected, and the ligand conformation may account for the complexation properties observed for this hexathioether macrocycle.     

Mode of binding of camptothecins to double helix oligonucleotides

We report an NMR study on the interaction of topotecan (Tpt) and other camptothecins (Cpts) with several double helix and single strand oligonucleotides. The results obtained by (31)P NMR spectroscopy, nuclear Overhauser experiments (NOE) and molecular dynamics (MD) simulations show that Cpt drugs do not intercalate into the double helix, as suggested by many authors. Phosphorus NMR spectra indicated that no deformation occurs at any level of the phosphodiester backbone, while 2D NOESY experiments allowed the detection of several contacts between the aromatic protons of Cpts and those of the double helix. Models of the drug/oligonucleotide complexes, built on the basis of NOE data, show that the drug is located at the end of the double helix, by stacking the A and B rings with the guanine or cytidine of the terminal CG base pairs, with a preference for the 3[prime or minute]-terminal end sites. Cpts interact with double strand, as well as with single strand oligomers, as can be seen from the NMR shift variation observed on the drug protons; but this shielding effect cannot be an evidence of intercalation, as it is largely due to external non-specific interactions of the positively charged drug with the negatively charged ionic surface of the oligonucleotide. The molecular weight of one of the complexes was obtained from the correlation time value. The conformational behaviour of the DNA fragment d(CGTACG)(2) was studied by MD simulations on a ns time scale in the presence of water molecules and Na(+) ions. Different models were examined and the deformations induced on the phosphodiester backbone by molecules that are known to intercalate, were monitored by MD simulations.