Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system

A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given.     

Glucose-sensitive inverse opal hydrogels: analysis of optical diffraction response

A glucose-sensitive inverse opal hydrogel was synthesized through photopolymerization of 2-hydroxyethyl methacrylate and 3-acrylamidophenylboronic acid within the interstitial space of a dried poly(styrene) colloidal crystal template, followed by template removal. Charged complex formation between the phenylboronic acid functional group and the 1,2-cis-diol glucose resulted in reversible swelling of the inverse opal hydrogel, which was observed through shifts in the optical diffraction wavelength. The hydrogel was sensitive to glucose at physiological concentrations and ionic strength. The effects of phenylboronic acid concentration, ionic strength, and buffer pH on the equilibrium hydrogel swelling were also studied. The kinetics of hydrogel swelling was also examined, and it was found that the rate of diffraction shift matched well with diffusion-limited kinetics. Additionally, the diffraction response was compared with simulations using the scalar wave approximation and transfer matrix method.     

PHYTOCHROME EVOLUTION: A PHYLOGENETIC TREE WITH THE FIRST COMPLETE SEQUENCE OF PHYTOCHROME FROM A CRYPTOGAMIC PLANT: (Selaginella martensii SPRING)

We have sequenced cDNA and genomic clones coding for phytochrome of the fern Selaginella. On the amino acid level, this phytochrome shares sequence homologies with phytochromes of higher plants which range between 62 (phytochrome B of Arabidopsis) and 55 (56)% [phytochrome C of Arabidopsis (Avena)]. Introns in the Selaginella gene are short and occupy positions known from phytochrome sequences of higher plants. A rooted phylogenetic tree based on mutation distances puts Selaginella phytochrome closest to the hypothetical ancestor. A similar tree arises if the tree is constructed with partial sequences (about 200 amino acids) around the chromophore attachment site. An extension of this tree by sequences of other cryptogamic plants (Mougeotia, Ceratodon, Psilotum) shows all these sequences including those of the phytochromes B and C of Arabidopsis on a branch, well separated from the branch formed by phytochromes known to accumulate in etiolated plants. The rooted phytochrome phylogenetic tree, however, is difficult to reconcile with the fossil record.     

Efficient search for all low energy conformations of polypeptides by Monte Carlo methods

The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below ?10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below ?10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.     

High-performance liquid chromatographic separation and dual competitive binding assay of corrinoids in biological material

Corrinoids were extracted with hot ethanol from human plasma and faeces and separated by high-performance liquid chromatography. The corrinoids (cobalamin and cobalamin analogues) were quantified in the eluted fractions by a dual radioisotope assay using as binders intrinsic factor and haptocorrin to detect cobalamin and total corrinoids, respectively. Recoveries ranged from 37.7 +/- 5.1% for hydroxycobalamin to 75.0 +/- 9.1% for cyanocobalamin. In plasma, the main forms of cobalamin were the coenzymes methylcobalamin and 5'-deoxyadenosylcobalamin (32.1 +/- 13.4 and 28.4 +/- 12.3%, respectively, of total corrinoids). The cobalamin analogue fraction of plasma was eluted with a retention time close to that of cobinamide and of deoxyadenosylcobalamin. In the faeces, most of the corrinoids separated were detected better by the haptocorrin assay than by the intrinsic factor assay. One corrinoid peak was eluted with the same retention time as cobinamide. This peak was detected by haptocorrin assay but not by intrinsic factor assay. It could therefore correspond to cobinamide.     

Syntheses of sulfoxide derivatives in the benzodiazine series. Diazines. Part 37

Syntheses of new sulfinylcinnolines, quinoxalines, quinazolines and phtalazines have been investigated starting from the appropriate halogenobenzodiazine derivatives. The latter were converted in one step to the corresponding sulfanyl benzodiazines which upon oxidation with m-CPBA led to the corresponding sulfoxide derivatives of benzodiazines in moderate to good yields. In parallel to this study, an improved method for the synthesis of 2-methylsulfinylquinoxaline starting from 2-sulfanylquinoxaline is also described and in the quinazoline series a synthetic route has been developed to prepare 2-tert-butyl-5-phenylsulfinylquinazoline with satisfactory yield as well as 2-tert-butyl-5-tert-butylsulfinyl-4(3H)-quinazolinone and 2-tert-butyl-8-tert-butylsulfinyl-4(3H)-quinazolinone.     

Improved determination of sulpiride in plasma by ion-pair liquid chromatography with fluorescence detection

A specific and sensitive high-performance liquid chromatographic method for the measurement of sulpiride in plasma is described. The internal standard used was veralipride, a structurally related substituted benzamide. A fluorescence detector with maximum excitation at 300 nm and maximum emission at 365 nm was used for quantitation. After an alkaline extraction procedure, the benzamides were separated on a 5-micron ODS column using a large organic counter ion in the mobile phase. The detector response was linear from 10 to 1000 ng/ml and the detection limit was 10 ng/ml, which is sensitive enough for pharmacokinetic studies. The suitability of the method for the analysis of biological samples was tested by studying the variation with time of plasma concentrations of sulpiride in normal human volunteers after a single therapeutic 200-mg oral dose of three different formulations of sulpiride.     

Phosphides with Zr2Fe12P7-type structure

Twenty-six ternary phosphides Ln₂T₁₂P₇ (Ln = lanthanoid, T = Fe, Co, Ni) were prepared for the first time by reaction of the elemental components in liquid tin or by reaction of the components in evacuated silica tubes. The analysis of their powder patterns indicates their isotypism with Zr₂Fe₁₂P₇. Their lattice constants are reported. Gd₂Ni₁₂As₇ also crystallizes with that structure.     

Gatekeeping patterns in the publication of analytical chemistry research

An analysis has been made of the nationalities of the members of advisory and editorial boards of analytical chemistry journals. Correlations were sought between their number and citation rates and between their number and the number of analytical papers published by scientists from the country in question. A comparison is given for the gatekeepers of organic and inorganic chemistry journals.     

Non-covalent polyvalent ligands by self-assembly of small glycodendrimers: a novel concept for the inhibition of polyvalent carbohydrate-protein interactions in vitro and in vivo

Polyvalent carbohydrate-protein interactions occur frequently in biology, particularly in recognition events on cellular membranes. Collectively, they can be much stronger than corresponding monovalent interactions, rendering it difficult to control them with individual small molecules. Artificial macromolecules have been used as polyvalent ligands to inhibit polyvalent processes; however, both reproducible synthesis and appropriate characterization of such complex entities is demanding. Herein, we present an alternative concept avoiding conventional macromolecules. Small glycodendrimers which fulfill single molecule entity criteria self-assemble to form non-covalent nanoparticles. These particles-not the individual molecules-function as polyvalent ligands, efficiently inhibiting polyvalent processes both in vitro and in vivo. The synthesis and characterization of these glycodendrimers is described in detail. Furthermore, we report on the characterization of the non-covalent nanoparticles formed and on their biological evaluation.