The chemistry of 2'' ,3''-seconucleosides II. Reactions and biological properties of 2'',3''-secopyrimidine ribonucleosides

Reaction of 2',3'-secouridine with acetone gave the 3',5'-$\text{O}$-isopropylidene derivative (1) which upon treatment with mesylchloride gave the 2'-$\text{O}$-mesyl compound (2). Replacement of the mesyl group of 2 with halide could be effected by reaction with a metal halide in DMF. The 3',5'-$\text{O}$-isopropylidene group was removed simultaneously to give a 2'-halogeno-2'-deoxy-2',3'-secouridine. 2',3'-Dichloro-2',3'-dideoxy-2',3'-secouridine upon treatment with base gave 6($\text{R}$)-chloromethyl-2($\text{R}$)-(uracil-1-yl)-1,4-dioxane in addition to O²,2'-anhydro-3'-chloro-3'-deoxy-2',3'-secouridine, as previously reported. 2',3'-Dichloro-2',3'-dideoxy-5'-0-trityl-2',3'-secouridine was converted to 2',3'-dichloro-2',3'-dideoxy-2',3'-secocytidine (16) $\text{via}$ a triazole derivative. Compound 16 was unstable and appeared to form O²,2'-anhydro-3'-chloro-3'-deoxy-2,3'-secocytidine upon standing at room temperature. 5-Vinyl- and 5-($\text{E}$) (2-bromovinyl) uridine dialdehydes have been made, as well as a number of other 5-substituted 2',3'-secouridine derivatives. None of the compounds obtained showed significant activity against a number of virus strains or tumor cell lines, except for 5-($\text{E}$)(2-bromovinyl) uridine dialdehyde, which was inhibitory to the growth of human lymphoblast (Raji, Namalva) cells at a concentration of 28 μ/ml.     

Consolidation behavior in sedimentation of TiO(2) suspensions in the presence of electrolytes

The consolidation of TiO(2) suspensions (anatase and rutile) due to gravity sedimentation in the presence of electrolytes has been investigated as a function of pH. Sodium and barium nitrate were used as flocculating electrolytes. The particle interaction was related to the zeta potential and the thickness of the electrical double layer, kappa(-1), by utilizing the repulsive barrier in the classical DLVO theory. The stability of the suspensions was represented as the average final solids content of the sediment cake, phi(fin). The batch sedimentation process was followed by scanning the sample cell with X-rays, from which the solids content and the particle size were calculated. Generally, dense sediments, with phi(fin) up to volume fractions of 0.5, were found for stable suspensions. Flocculated suspensions produced sediments with low phi(fin). The phi(fin) was observed to increase linearly with increasing repulsive barrier. However, at pH values only slightly higher than the isoelectric point (pH(iep)) the phi(fin) remained low until it returned to linearity at a pH much higher than pH(iep). This was attributed to the stronger affinity of sodium than of nitrate for the particle surface, which may be explained by the higher negative hydration energy of sodium. The stronger affinity of sodium was also shown as unsymmetrical distribution of phi(fin) around pH(iep), with stronger flocculation at pH>pH(iep). The interpretation of phi(fin) as a function of the repulsive barrier (or kappa(-1)) also made it possible to distinguish between the adsorption mechanisms of ions from solution. Addition of electrolyte at a fixed low and high pH (surface positively and negatively charged, respectively) clearly showed the specificity in adsorption and consequent flocculation of the barium ion from the indifferent nitrate. Sodium was, however, again observed to flocculate the TiO(2) suspensions slightly more strongly than nitrate.     

Bimodal proton transfer in acid-base reactions in water

We investigate one of the fundamental reactions in solutions, the neutralization of an acid by a base. We use a photoacid, 8-hydroxy-1,3,6-trisulfonate-pyrene (HPTS; pyranine), which upon photoexcitation reacts with acetate under transfer of a deuteron (solvent: deuterated water). We analyze in detail the resulting bimodal reaction dynamics between the photoacid and the base, the first report on which was recently published. We have ascribed the bimodal proton-transfer dynamics to contributions from preformed hydrogen bonding complexes and from initially uncomplexed acid and base. We report on the observation of an additional (6 ps)(-1) contribution to the reaction rate constant. As before, we analyze the slower part of the reaction within the framework of the diffusion model and the fastest part by a static, sub-150 fs reaction rate. Adding the second static term considerably improves the overall modeling of the experimental results. It also allows to connect experimentally the diffusion controlled bimolecular reaction models as defined by Eigen-Weller and by Collins-Kimball. Our findings are in agreement with a three-stage mechanism for liquid phase intermolecular proton transfer: mutual diffusion of acid and base to form a "loose" encounter complex, followed by reorganization of the solvent shells and by "tightening" of the acid-base encounter complex. These rearrangements last a few picoseconds and enable a prompt proton transfer along the reaction coordinate, which occurs faster than our time resolution of 150 fs. Alternative models for the explanation of the slower "on-contact" reaction time of the loose encounter complex in terms of proton transmission through a von Grotthuss mechanism are also discussed.     

Synthesis and modification of terrylenediimides as high-performance fluorescent dyes

Two new synthetic approaches to terrylenediimides, highly photostable fluorescent dyes, are described. For the first time terrylenediimide has been synthesised in a straightforward procedure that makes large quantities available. The second route includes an efficient cross-coupling reaction followed by a cyclodehydrogenation. Monofunctionalisation of the imide structure allows terrylenediimides now to be coupled with a variety of compounds, for example, by Suzuki cross-coupling, which can lead to an array of terrylenediimides with new functional groups such as hydroxy, amino, or carboxy groups needed to link up with other molecules. The functionalisation in the bay region is used to tune the properties of terrylenediimides and extend the range of applications, for example, by introducing water solubility. These tetrasubstituted terrylenediimides offer, depending on the substituents used, exciting features such as good solubility in common organic solvents, water solubility, or NIR absorption.     

Asymmetric radical additions of trialkylboranes to 2H-azirine-3-carboxylates

Asymmetric additions of alkyl radicals, generated from R3B, to chiral 2H-azirine-3-carboxylates offer a new entry to enantio-enriched aziridines, and proceed with high diastereoselectivity when using 8-phenylmenthol as chiral auxiliary.     

The synthesis of unsymmetrically N-substituted chiral 1,4,7-triazacyclononanes

A number of chiral unsymmetrically N-substituted 1,4,7-triazacyclononane ligands have been prepared by modular methods. The key step in the synthesis centres on the macrocyclisation of three tertiary amide precursors under standard Richman-Atkins conditions which allows for subsequent N-functionalisation.     

Synthesis of α-2′-deoxynucleosides

α-Thymidine (4) was synthesized from thymidine (1) in 3 steps in 36% overall yield without using chro-matography and with the possibility of increasing the yield to 85% by reusing the remaining α,β-mixture. 1-(2-Deoxy-3,5-di-O-p-toluoyl-α-D-erythro-pentofuranosyl)thymine (3) was further converted to 1-(2-deoxy-α-D-erythro-pentofuranosyl)-5-methylcytosine (5) .     

Carbocyclic analogues of nucleosides from bis-(Hydroxymethyl)-cyclopentane: synthesis,antiviral and cytostatic activities of adenosine,inosine and uridine analogues

Six new carbocyclic nucleosides were prepared by constructing a purine base (in compounds 9-11) or pyrimidine base (in 6-8) on the amino groups of (+/-)-(1 beta,2 alpha,4 beta)-4-amino-1,2-cyclopentanedimethanol (4) and (+/-)-(1 beta,3 alpha,4 beta)-4-amino-1,3-cyclopentanedimethanol (5), and their activities against a variety of viruses and tumour cell lines were determined.     

Synthesis of 2′-Deoxy-5-(isothiazol-5-yl)uridine and Its Interaction with the HSV-1 Thymidine Kinase

2′-Deoxy-5-(isothiazol-5-yl)uridine ( 12 ) was synthesized starting from 2′-deoxy-5-iodouridine using a Pd-catalysed cross-coupling reaction with propiolaldehyde diethyl acetal followed by deprotection and ring closure using thiosulfate. 2′-Deoxyuridine 12 has a particular place among the 5-heteroaryl-substituted 2′-deoxyuridines in that it has a high affinity for herpes simplex virus type 1 (HSV-1)-encoded thymidine kinase (TK) without antiviral activity. Biochemical studies revealed that 12 is a substrate for viral TK. We further investigated the interaction of 12 with the HSV-1 thymidine kinase. The conformation of 12 in solution was established by NMR spectroscopy. The most stable conformer 12A has the S-atom of the isothiazole ring placed in the neighbourhood of the C(4)?O group of the pyrimidine moiety. The compound was docked in its most stable conformation in the active site of HSV-1 TK and subjected to energy minimization. This demonstrated that the isothiazole moiety binds in a cavity lined by the side chains of Tyr-132, Arg-163, Ala-167, and Ala-168 and that the C(3) atom of the isothiazole moiety is located in close proximity of the phenolic O-atom of Tyr-132 and the aliphatic part of the Arg-163 side chain.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.