Cosmic dust and our origins

The small solid particles in the space between the stars provide the surfaces for the production of many simple and complex molecules. Processes involving the effects of ultraviolet irradiation of the thin (hundredth micron) mantles are shown to produce a wide range of molecules and ions also seen in comets. Some of the more complex ones inferred from laboratory experiments are expected to play an important role in the origin of life. An outline of the chemical evolution of interstellar dust as observed and as studied in the laboratory is presented. Observations of comets are shown to provide substantial evidence for their being fluffy aggregates of interstellar dust as it was in the protosolar nebula, i.e. the interstellar cloud which collapsed to form the solar system. The theory that comets may have brought the progenitors of life to the earth is summarized.     

Benzo[d]-1,2-oxaphospholes as precursors of stabilized C-centered radicals

[reaction: see text] Several benzo[d]-1,2-oxaphosphole 2-oxides were examined as potential precursors of stabilized C-centered radicals. The transient absorption spectra obtained after laser flash photolysis in the presence of di-tert-butyl peroxide showed the features of benzylic radicals with formation and decay kinetics not significantly influenced by the presence of oxygen. In the case of compounds with two possible diastereomeric forms, the C-H bond of the trans-isomers [corrected] is more reactive toward hydrogen abstraction.     

On the convergence of isolated neutral oxygen vacancy and divacancy properties in metal oxides using supercell models

The properties of isolated neutral oxygen vacancies and divacancies of metal oxides of increasing complexity (MgO, CaO, alpha-Al2O3, and ZnO) have been studied by means of density-functional theory within a supercell periodic approach. Vacancy formation energies, vacancy-vacancy interactions, and geometry rearrangements around these point defects have been investigated in detail. The characterization of the electronic structure of these point defects has been established by analysis of the density of states and of the topology of the electron density and of electron localization function. It is found that the chemical character of the oxide determines the properties of the oxygen vacancies. For the covalent ZnO oxide, a more complex scheme arises in which the relaxation around the oxygen vacancy is much larger leading to the formation of Zn4-like almost metallic particles in the crystal. The relationship of these structures with the crystal shear planes is discussed. The present study shows that supercells containing approximately 200-300 atoms provide converged values for the geometric and electronic structure of oxygen vacancies of these metal oxides in the point defect low concentration limit.     

Liquid chromatography with ultraviolet absorbance detection for the analysis of tetracycline residues in honey

The separation of tetracyclines (TCs) using reversed-phase liquid chromatography (LC) is proposed. The use of an amide-based stationary phase prevents the interaction of tetracyclines with the residual silanol groups and thus avoids the appearance of tailed peaks. Detection was based on using an UV spectrophotometer and gradient elution with acetonitrile-oxalic acid as mobile phase permitted good separation of all the peaks. Specificity was demonstrated by the retention characteristics, UV spectra and peak purity index. Linearity, precision, recovery and sensitivity were satisfactory. The procedure was applied to the analysis of tetracycline residues (tetracycline, oxytetracycline (OTC), chlortetracycline (CTC), doxycycline (DC), minocycline (MINO) and methacycline (MTC)) in honey of different types. Extraction involved using a mild acidic solvent containing EDTA to release protein-bound or sugar-bound tetracyclines. For the clean-up step, solid phase extraction using phenyl cartridges was applied. Detection limits in the honey using the proposed procedure are between 15 and 30 ng g(-1), depending on the tetracycline.     

Development and validation of an analytical methodology for the determination of p,p′-DDT, p,p′-DDE and p,p′-DDD in fish oil pills

An analytical methodology was proposed and validated to be applied to the determination of p,p′-DDT and its metabolites p,p′-DDE and p,p′-DDD in fish oil. The analytical procedure presented in this paper involves a single-step clean up process prior to the analysis. A solution of 1,2,3,4-tetrachloronaphtalene was used as internal standard.The analytical technique used was gas chromatography coupled to an electron capture detector. Details on the validation process are provided.The limits of detection ranged from 2.6 to 4.7 pg μL^− 1. The BCR 598 standard reference material (cod liver oil) was used to evaluate the performance of the methodology with satisfactory recoveries for all the compounds.The analytes were determined in three different fish oil pills sold in Spain as a supplementary vitamin support. The sum of p,p′-DDT and metabolites was from 13.2 to 51.3 ng g^− 1, the dominant compound being p,p′-DDE.     

Solid-phase synthesis of the cyclic lipononadepsipeptide [N-Mst(Ser1), d-Ser4, L-Thr6, L-Asp8, L-Thr9]syringotoxin

An optimized solid-phase strategy for the preparation of the cyclic lipononadepsipeptide [N-Mst(L-Ser1), D-Ser4, L-Thr6, L-Asp8, L-Thr9]syringotoxin is reported. The strategy is based on the use of a mild orthogonal protection scheme and the incorporation of the nonproteinogenic amino acid (Z)-Dhb into the peptide chain as the dipeptide Fmoc-Thr(tBu)-(Z)-Dhb-OH. The didehydrodipeptide was synthesized by a water-soluble carbodiimide-induced beta-elimination of a protected dipeptide containing a residue of Thr with its free hydroxy side chain unprotected.     

Stereoselective synthesis of trans-2,3-disubstituted pyrrolidines via addition to N-acyliminium ions

An efficient and stereoselective synthesis of trans-2,3-disubstituted pyrrolidines is described. The intermolecular alkylation of racemic N-acyliminium ions generated in situ from the corresponding 3-substituted lactams proceeds stereoselectively and in high yield.     

Design and synthesis of push-pull chromophores for second-order nonlinear optics derived from rigidified thiophene-based pi-conjugating spacers.

Two series of push-pull chromophores built around thiophene-based pi-conjugating spacers rigidified either by covalent bonds or by noncovalent intramolecular interactions have been synthesized and characterized by UV-vis spectroscopy, electric field induced second harmonic generation (EFISH) and differential scanning calorimetry. Comparison of the linear and second-order nonlinear optical properties of chromophores based on a covalently bridged dithienylethylene (DTE) spacer with those of their analogues based on open chain DTE shows that the rigidification of the spacer produces a considerable bathochromic shift of the absorption maximum together with a dramatic enhancement of the molecular quadratic hyperpolarizability (mu beta) which reaches values among the highest reported so far. A second series of NLO-phores has been derived from a 2,2'-bi(3,4-ethylenedioxythiophene) (BEDOT) pi-conjugating spacer. As indicated by X-ray and UV-vis data, rigidification of the spacer originates in that case, from noncovalent intramolecular interactions between sulfur and oxygen atoms. Again, comparison with the parent compounds based on an unsubstituted bithiophene spacer reveals a marked red shift of the absorption maximum and a large enhancement of mu beta. In an attempt to distinguish the contribution of the electronic and geometrical effects of the ethylenedioxy group, a third series of NLO-phores based on 3,4-ethylenedioxythiophene (EDOT) and 3,4-dihexyloxythiophene spacers has been synthesized. Comparison with compounds based on unsubstituted thiophene shows that, despite a red shift of lambda(max), introduction of alkoxy groups leads to a decrease of mu beta. Theoretical calculations indicate that this effect results from a decrease of the dipole moment (mu) caused by the auxiliary electron-donor alkoxy groups on the thiophene ring. In contrast, replacement of BT by BEDOT produces an increase of mu, which associated with the noncovalent rigidification of the BT system accounts for the observed enhancement of mu beta.     

Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.