GEOMETRY OF INTERCALATION OF PSORALENS IN DNA APPROACHED BY MOLECULAR MECHANICS*

The results of molecular mechanical calculations on intercalation complexes of 3-carbethoxypsoralen, 5-methoxypsoralen, 8-methoxypsoralen, 7-methylpyrido[3,4-c]psoralen (MepyPs) and 7-methylpyrido[4,3-c]psoralen (2N-MePyPs) with the double stranded duodecanucleotide d(CGCGATATCGCG)2 are presented. In the energy-minimized structures, the psoralens are intercalated with their plane orthogonal to the helix axis. Stacking interactions between the furan ring of the psoralen and the adjacent bases are maximized in most derivatives studied, whereas the effect of the various substituents of the psoralen ring is to specifically push part of the molecule towards either the minor or the major groove, preventing a symmetrical intercalation (with respect to the two strands of the DNA). The relative position of the psoralen ring and of the adjacent thymine foreshadows the formation of furan-side monoadducts in 3-CPs, MePyPs and 2N-MePyPs, whereas the formation of a pyrone-side monoadduct appears as geometrically more favourable in 5-MOP and both furan- and pyrone-side monoadducts can be geometrically envisaged in 8-MOP. A good correlation therefore exists between the more or less favourable equilibrium geometries and the experimentally observed photoreactions. The present study is the first attempt to characterize the geometrical parameters as part of a complex set of geometrical, dynamical and excited state parameters governing the overall DNA-psoralen photoreaction.     

Application of recombinant phage display antibody system in study of Codakia orbicularis gill proteins

We used the recombinant phage display antibody system (RPAS) to obtain chimeric single-chain fragment variable (ScFv) antibodies to gill proteins of the white clam Codakia orbicularis (Linné, 1758). After three rounds of selection on immunotubes loaded with total gill protein extract, recombinant phages exhibiting antibodies to gill proteins were isolated and tested by enzyme-linked immunosorbent assay (ELISA). Clones exhibiting a high affinity for the mollusk proteins were selected for production of soluble ScFv antibodies, which were purified for subsequent analysis. ScFv antibodies exhibited a reaction specific for a protein whose molecular mass was about 15,000 Daltons and that was detected by the antigen capture technique followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blotting.     

Synthesis of a new polyfluorinated vinylogue of tetrathiafulvalene through 1,3-dipolar cycloaddition of ethyl beta-bromoperfluorodithiocrotonate with dimethyl acetylenedicarboxylate

The ethyl ester of beta-bromoperfluorodithiocrotonic acid reacts with dimethyl acetylenedicarboxylate to give 1,4-difluoro-2,3-bis(trifluoromethyl)-but-2-ene-1,4-diylidene-2,2'-bis(4',5'-dicarbomethoxy-1',3'-dithiole) (4), a new type of vinylogue of tetrathiafulvalene. The thermal transformations of this compound lead, depending on the temperature, to the formation of the cyclization products: 11,14-difluoro-2,3,8,9-tetra(carbomethoxy)-12,13-bis(trifluoromethyl)-1,4,7,10-tetrathiadispiro[4.0.4.4]tetradeca-2,8,11,13-tetraene (8) or 5,8-difluoro-6,7-bis(trifluoromethyl)-2,3-bis(carboxymethyl)-1,4-benzodithiine (11).     

Computation of Smooth Manifolds Via Rigorous Multi-parameter Continuation in Infinite Dimensions

In this paper, we introduce a constructive rigorous numerical method to compute smooth manifolds implicitly defined by infinite-dimensional nonlinear operators. We compute a simplicial triangulation of the manifold using a multi-parameter continuation method on a finite-dimensional projection. The triangulation is then used to construct local charts and an atlas of the manifold in the infinite-dimensional domain of the operator. The idea behind the construction of the smooth charts is to use the radii polynomial approach to verify the hypotheses of the uniform contraction principle over a simplex. The construction of the manifold is globalized by proving smoothness along the edge of adjacent simplices. We apply the method to compute portions of a two-dimensional manifold of equilibria of the Cahn–Hilliard equation.     

gem-Heteroatom-Substituted Fluoroalkenes as Mimics of Amide Derivatives or Phosphates: A Comprehensive Review

gem-Heteroatom-substituted fluoroalkenes have received little attention despite their great potential in medicinal chemistry or in fine chemistry. Indeed, due to the electronic and steric similarity between the fluoroalkene moiety and the amide bond as well as the high strength of the carbon-fluorine bond, these gem-heteroatom-substituted fluoroalkenes could be envisioned as stable mimics of various important organic functions, such as phosphates, carbamates, S-thiocarbamates and ureas. We present herein an overview describing the syntheses over the last decade of heteroatom-substituted fluoroalkenes in geminal position. This review will be divided into several sections covering each the common following heteroatom: oxygen-, nitrogen-, sulfur-, phosphorus-, boron- and silicon-substituted fluoroalkenes.     

Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.     

Narrow-line phase-locked quantum cascade laser in the 9.2 microm range

We report the operation of a 50 mW continuous-wave quantum cascade laser (QCL) in the 9.2 microm range, phase locked to a single-mode CO(2) laser with a tunable frequency offset. The wide free-running emission spectrum of the QCL (3-5 MHz) is strongly narrowed down to the kilohertz range, making it suitable for high-resolution molecular spectroscopy.     

A two-mass expanding exact space-time solution

In order to understand how locally static configurations around gravitationally bound bodies can be embedded in an expanding universe, we investigate the solutions of general relativity describing a space–time whose spatial sections have the topology of a 3-sphere with two identical masses at the poles. We show that Israel junction conditions imply that two spherically symmetric static regions around the masses cannot be glued together. If one is interested in an exterior solution, this prevents the geometry around the masses to be of the Schwarzschild type and leads to the introduction of a cosmological constant. The study of the extension of the Kottler space–time shows that there exists a non-static solution consisting of two static regions surrounding the masses that match a Kantowski–Sachs expanding region on the cosmological horizon. The comparison with a Swiss-Cheese construction is also discussed.