High-throughput synthesis of HepDirect prodrugs of nucleoside monophosphates

A high-throughput phosphoramidite method for HepDirect prodrug synthesis was optimized on seven representative nucleosides, adenosine, inosine, guanosine, uridine, cytidine, AICA-riboside, and thymidine, each on a 5 mg scale. The variables optimized included (1) reaction time, (2) reaction temperature, (3) activating agent, (4) solvent, (5) purification method, and (6) stoichiometry. Preparative HPLC with mass-based fraction collection and yield determination from an ELSD standard curve enabled high-throughput. The optimized conditions for the representative nucleosides required 6 mol equiv of phosphoramidite to nucleoside and resulted in an average HPLC determined yield of 31 +/- 14% and HPLC purity of 93 +/- 3%.     

Synthesis and optical properties of a poly(2′,5′-dioctyloxy-4,4′,4″- terphenylenevinylene) with high content of (Z) vinylene units

Poly(2′,5′-dioctyloxy-4,4′,4″-terphenylenevinylene) with (E) configuration of the vinylene double bonds was prepared by Suzuki-Miyaura polymerization of (E)-4,4′-dibromostilbene and 2,5-dioctyloxy-1,4-benzenediboronic acid. Attempts to extend this simple procedure to the synthesis of the polymer with (Z) configuration, starting from (Z)-4,4′-dibromostilbene, were unsuccessful. However, the use of (Z)-4,4′-diiodostilbene and a careful choice of Pd catalyst and experimental conditions, lead to a material with a >95/<5 (Z)/(E) ratio of vinylene units. The investigation of optical properties of both the (E) and (Z) polymers evidenced that (Z) linkages act as defects which reduce the effective conjugation length in the polymer backbone.     

Do computed crystal structures of nonpolar molecules depend on the electrostatic interactions? The case of tetracene

We present a strategy for comparing the global properties of competing potential models. By systematically sampling the potential energy surface of crystalline tetracene, we assess how the number, energy and structure of its minima are modified by switching on (or off) the Coulombic interactions. The increased complexity of the Coulombic potential leads to a more "rugged" potential energy surface with a larger number of minima, but the effect is not large. In fact, we find a subset of minima stable only in presence of the Coulombic interactions, a smaller subset stable only in their absence, and a large majority stable in both cases. Among these, there is a very good, but not perfect, correlation between the energies and the structures computed with and without the electrostatic interactions. Although electrostatic interactions play a role even in a rigid nonpolar molecule such as tetracene, they are not as crucial as often believed, because altering the electrostatic model (or switching it off completely) leads, in most cases, to equivalent results.     

Unraveling the dynamics of the C(3P,1D) + C2H2 reactions by the crossed molecular beam scattering technique

A detailed investigation of the dynamics of the reactions of ground- and excited-state carbon atoms, C(3P) and C(1D), with acetylene is reported over a wide collision energy range (3.6-49.1 kJ mol-1) using the crossed molecular beam (CMB) scattering technique with electron ionization mass spectrometric detection and time-of-flight (TOF) analysis. We have exploited the capability of (a) generating continuous intense supersonic beams of C(3P, 1D), (b) crossing the two reactant beams at different intersection angles (45, 90, and 135 degrees ) to attain a wide range of collision energies, and (c) tuning the energy of the ionizing electrons to low values (soft ionization) to suppress interferences from dissociative ionization processes. From angular and TOF distribution measurements of products at m/z=37 and 36, the primary reaction products of the C(3P) and C(1D) reactions with C2H2 have been identified to be cyclic (c)-C3H + H, linear (l)-C3H + H, and C3 + H2. From the data analysis, product angular and translational energy distributions in the center-of-mass (CM) system for both the linear and cyclic C3H isomers as well as the C3 product from C(3P) and for l/c-C3H and C3 from C(1D) have been derived as a function of collision energy from 3.6 to 49.1 kJ mol-1. The cyclic/linear C3H ratio and the C3/(C3 + c/l-C3H) branching ratios for the C(3P) reaction have been determined as a function of collision energy. The present findings have been compared with those from previous CMB studies using pulsed beams; here, a marked contrast is noted in the CM angular distributions for both C3H- and C3-forming channels from C(3P) and their trend with collision energy. Consequently, the interpretation of the reaction dynamics derived in the present work contradicts that previously proposed from the pulsed CMB studies. The results have been discussed in the light of the available theoretical information on the relevant triplet and singlet C3H2 ab initio potential energy surfaces (PESs). In particular, the branching ratios for the C(3P) + C2H2 reaction have been compared with the available theoretical predictions (approximate quantum scattering calculations and quasiclassical trajectory calculations on ab initio triplet PESs and, very recent, statistical calculations on ab initio triplet PESs as well as on ab initio triplet/singlet PESs including nonadiabatic effects, that is, intersystem crossing). While the experimental branching ratios have been corroborated by the statistical predictions, strong disagreement has been found with the results of the dynamical calculations. The astrophysical implications of the present results have been noted.     

Car-Parrinello MD simulations for the Na+ -phenylalanine complex in aqueous solution

Car-Parrinello molecular dynamics (CPMD) calculations are presented for a Na (+)(Phe) complex in aqueous solution and for various stable Na (+)(Phe) complexes and Na (+)(H 2O) n clusters in the gas phase (with up to six water molecules). The CPMD results are compared to available experimental and ab initio reference data, to DFT results obtained with various combinations of density functionals and basis sets, and to previous classical mechanics MD simulations. The agreement with the reference data in the gas phase validates the CPMD method, showing that it is a valid approach for studying these systems and that it describes correctly the competing Na (+)-Phe and Na (+)-H 2O interactions. Analysis of MD trajectories reveals that the Na (+)(Phe) complex in aqueous solution maintains a stable configuration in which the Na (+) cation hovers above the phenyl ring, at an average distance of 3.85 A from the ring center, while remaining strongly bound to one of the carboxylic oxygens of Phe. Constrained MD simulations indicate that the free energy barrier opposing dissociation of the complex exceeds 5.5 kcal/mol. We thus confirm that "cation- pi" interactions between alcali cations and the pi ring, combined with other kinds of interactions, may allow aromatic amino acids to overcome the competition with water in binding a cation.     

A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data

Microarrays offer unprecedented possibilities for the so-called omic, e.g., genomic and proteomic, research. However, they are also quite challenging data to analyze. The aim of this paper is to provide a short tutorial on the most common approaches used for pattern discovery and cluster analysis as they are currently used for microarrays, in the hope to bring the attention of the Algorithmic Community on novel aspects of classification and data analysis that deserve attention and have potential for high reward. R. Giancarlo is partially supported by Italian MIUR grants PRIN “Metodi Combinatori ed Algoritmici per la Scoperta di Patterns in Biosequenze” and FIRB “Bioinformatica per la Genomica e la Proteomica” and Italy-Israel FIRB Project “Pattern Discovery Algorithms in Discrete Structures, with Applications to Bioinformatics”. D. Scaturro is supported by a MIUR Fellowship in the Italy-Israel FIRB Project “Pattern Discovery Algorithms in Discrete Structures, with Applications to Bioinformatics”.     

On stable cutsets in claw-free graphs and planar graphs

A stable cutset in a connected graph is a stable set whose deletion disconnects the graph. Let $K_4$ and $K_{1,3}$ (claw) denote the complete (bipartite) graph on 4 and $1+3$ vertices. It is NP-complete to decide whether a line graph (hence a claw-free graph) with maximum degree five or a $K_4$-free graph admits a stable cutset. Here we describe algorithms deciding in polynomial time whether a claw-free graph with maximum degree at most four or whether a (claw, $K_4$)-free graph admits a stable cutset. As a by-product we obtain that the stable cutset problem is polynomially solvable for claw-free planar graphs, and also for planar line graphs.Thus, the computational complexity of the stable cutset problem is completely determined for claw-free graphs with respect to degree constraint, and for claw-free planar graphs. Moreover, we prove that the stable cutset problem remains NP-complete for $K_4$-free planar graphs with maximum degree five.     

Perturbative calculation of Franck-Condon integrals: new hints for a rational implementation

Perturbative approaches to the mode mixing effects in the calculation of Franck-Condon integrals are analyzed and discussed. The zero order multidimensional Franck-Condon integrals are factorized into products of one-dimensional ones, so that recurrence relations can be used without need of storing a huge number of data. Calculations on model systems show that at the second order of perturbation, the method gives results in very good agreement with the exact ones, even in the case of significantly large Duschinsky effect. The accuracy of the results can be substantially improved by grouping together all those modes which are strongly mixed with each other, usually a few ones, for which Franck-Condon integrals can be computed exactly, and using the perturbative approach for treating the smaller mixing between all the other modes.     

Blue-LED Synthesis of Pummerer's Ketones by Peroxidase-Lignin-Catalyzed Oxidative Coupling of Substituted Phenols

Pummerer's ketones resembling the tricyclic scaffold of bioactive natural substances were synthesized by blue-LED driven Horseradish Peroxidase oxidative coupling of substituted phenols in 2-methyltetrahydrofuran by using meso-tetraphenylporphyrin as photosensitizer and dioxygen as primary oxidant. The application of functionalized lignin nanoparticles as a renewable and efficient platform for the immobilization of the enzyme extended the effectiveness of the overall process to heterogeneous catalysis under buffer limiting conditions.