Photochemical substitution reactions of 4-Pyridinecarbonitrile with aliphatic alcohols in neutral and acidified medium

Chemical evidence is given that the title photo-reactions proceed via hydrogen abstraction by the photo-excited base from the alcohol in neutral medium and via electron-transfer process between the photo-excited base and the alcohol in hydrochloric acid acidified medium.     

The topology of two-dimensional real algebraic varieties

Sunto È noto che ogni spazio analitico reale è localmente omeomorfo al cono su un poliedro con caratteristica di Eulero-Poincaré pari. Si dimostra che questa condizione è anche sufficiente affinchè un poliedro (compatto) di dimensione due P sia omeomorfo ad una varietà algebrica reale affine P. Segue inoltre dalla costruzione che la P ottenuta ha, in un certo senso, un insieme di singolarità algebriche minimale, compatibilmente con la topologia di P.

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The authors are members of the G.N.S.A.G.A.     

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k

Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.     

Measurement of harmonic phase differences by interference of attosecond light pulses

By using a self-referencing technique, we have experimentally measured the influence of the carrier-envelope phase of femtosecond light pulses on the phase of the electric field of the radiation produced by high-order harmonic generation. We show that, in particular experimental conditions, the temporal evolution of the electric field of the attosecond pulses, is directly controlled by the carrier-envelope phase of the driving pulses.     

Oxidative dissolution of chalcopyrite by Acidithiobacillus ferrooxidans analyzed by electrochemical impedance spectroscopy and atomic force microscopy

The microbiological leaching of chalcopyrite (CuFeS(2)) is of great interest because of its potential application to many CuFeS(2)-rich ore materials. However, the efficiency of the microbiological process is very limited because this mineral is one of the most refractory to bacterial attack. Knowledge of bacterial role during chalcopyrite oxidation is very important in order to improve the efficiency of bioleaching operation. The oxidative dissolution of a massive chalcopyrite electrode by Acidithiobacillus ferrooxidans was evaluated by electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM). A massive chalcopyrite electrode was utilized in a Tait-type electrochemical cell in acid medium for different immersion times in the presence or absence of bacterium. The differences observed in the impedance diagrams were correlated with the adhesion process of bacteria on the mineral surface.     

Molecular dynamics simulations of the ligand-induced chemical information transfer in the 5-HT(1A) receptor

Comparative molecular dynamics simulations of the 5-HT(1A) receptor in its empty as well as agonist- (i.e. active) and antagonist-bound (i.e. nonactive) forms have been carried out. The agonists 5-HT and (R)-8-OH-DPAT as well as the antagonist WAY100635 have been employed. The results of this study strengthen the hypothesis that the receptor portions close to the E/DRY/W motif, with prominence to the cytosolic extensions of helices 3 and 6, are particularly susceptible to undergo structural modification in response to agonist binding. Despite the differences in the structural/dynamics behavior of the two agonists when docked into the 5-HT(1A) receptor, they both exert a destabilization of the intrahelical and interhelical interactions found in the empty and antagonist-bound receptor forms between the arginine of the E/DRY sequence and both D133(3.49) and E340(6.30). For both agonists, the chemical information transfer from the extracellular to the cytosolic domains is mediated by a cluster of aromatic amino acids in helix 6, following the ligand interaction with selected amino acids in the extracellular half of the receptor, such as D116(3.32), S199(5.42), Y195(5.38), and F361(6.51). A significant reduction in the bend at P360(6.50), as compared to the empty and the antagonist-bound receptor forms, is one of the features of the agonist-bound forms that is related to the breakage of the interhelical salt bridge between the E/DRY arginine and E340(6.30). Another structural feature, shared by the agonist-bound receptor forms and not by the empty and antagonist-bound forms, is the detachment of helices 2 and 4, as marked by the movement of W161(4.50) away from helix 2, toward the membrane space.     

Physiological aspects involved in production of xylanolytic enzymes by deep-sea hyperthermophilic archaeon Pyrodictium abyssi

Xylanases (EC3.2.1.8) catalyze the hydrolysis of xylan, the major constituent of hemicellulose. The use of these enzymes could greatly improve the overall economics of processing lignocellulosic materials for the generation of liquid fuels and chemicals. The hyperthermophilic archaeon Pyrodictium abyssi, which was originally isolated from marine hot abyssal sites, grows optimally at 97°C and is a prospective source of highly thermostable xylanase. Its endoxylanase was shown to be highly thermostable (over 100 m in at 105°C) and active even at 110°C. The growth of the deep-sea archaeon P. abyssi was investigated using different culture techniques. Among the carbohydrates used, beech wood xylan, birch wood glucuronoxylan and the arabinoxylan from oats pelt appeared to be good inducers for endoxylanase and β-xylosidase production. The highest production of arabinofuranosidase, however, was detected in the cell extracts after growth on xylose and pyruvate, indicating that the intermediate of the tricarboxylic acid cycle acted as a nonrepressing carbon source for the production of thi enzyme. Electron microscopic studies did not show a significant difference in the cell surface (e.g., xylanosomes) when P. abyssi cells were grown on different carbohydrates. The main kinetic parameters of the organism have been determined. The cell yield was shown to be very low owing to incomplete substrate utilization, but a very high maximal specific growth rate was determined (μ_max=0.0195) at 90°C and pH 6.0. We also give information on the problems that arise during the fermentation of this hyperthermophilic archaeon at elevated temperatures.     

Close-loop three-laser scheme for chaos-encrypted message transmission

In this paper, we numerically evaluate private data transmission using a three-laser scheme, consisting of a pair of twin semiconductor lasers, driven to chaos by delayed optical feedback in a short cavity, and optically injected by a third chaotic laser which forces them to synchronize. This laser is selected with different internal parameters with respect to the twin pair, so that the emissions of the synchronized, matched lasers, are highly correlated, whereas their correlation with the driver is low. The digital message modulates the emission of the transmitter, as in a standard Chaos Modulation scheme. Message recovery is then obtained by subtracting, from the transmitted chaos-masked message, the chaos, locally generated by the synchronized receiver laser. Simulations have been performed with the Lang-Kobayashi model, and, in view of application to private transmission, we have investigated the effect of the parameter mismatch, between transmitter and receiver, on message recovery. A preliminary experimental evaluation has been also performed using specially designed InP integrated modules.     

Branched spines and contact structures on 3-manifolds

We introduce and analyze the characteristic foliation induced by a contact structure on a branched surface, in particular a branched standard spine of a 3-manifold. We extend to (fairly general) singular foliations of branched surfaces the local existence and uniqueness results which hold for genuine surfaces. Moreover we show that global uniqueness holds when restricting to tight structures. We establish branched versions of the elimination lemma. We prove a smooth version of the Gillman-Rolfsen PL-embedding theorem, deducing that branched spines can be used to construct contact structures in a given homotopy class of plane fields. Entrata in Redazione il 6 novembre 1998.     

Cooperativity in multiple unusual weak bonds

This review covers two aspects concerning cooperativity in multiple weak bonds: a summary of literature results and a theoretical study of a complete series of model complexes. All the 15 combination of five weak bonds were explored: hydrogen bonds, hydric bonds, dihydrogen bonds, halogen bonds and ion–π interactions. Since in several cases there were no examples reported, a systematic exploration has been carried out on simple models at the MP2/aug-cc-pVTZ level. The results thus obtained have been analyzed using the atoms in molecules methodology.