General base catalysis in the decomposition of N-Cl-Valine in aqueous solution

This article analyzes the kinetics of the decomposition of N-Cl-Valine in aqueous solution, which is formed rapidly by chlorination of Valine with sodium hypochlorite. A general-base catalyzed process not yet described is reported. The experimental evidence shows two competitive decomposition paths: an unimolecular concerted fragmentation process (k = (1.8 ± 0.1) · 10^?4 s^?1 at 298 K) and the other one is an E2 elimination process whose importance increases with pH and depends on the nature and the concentration of the bases present in the medium. © 1994 John Wiley & Sons, Inc.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Equilibrium of the reaction between dissolved sodium sulfide and biologically produced sulfur

The equilibrium of the heterogeneous reaction between dissolved sodium sulfide and biologically produced sulfur particles has been studied. Biologically produced sulfur was obtained from a bioreactor of a hydrogen sulfide removal process in which the dominating organism is Thiobacillus sp. W5. Detailed knowledge of this reaction is essential to understand its effect on the process. The results were compared with the equilibrium of the reaction of sulfide with ‘inorganic’ elemental sulfur. The equilibrium between dissolved sodium sulfide and biologically produced sulfur particles can be described by an equilibrium constant, K_x, which consists of a weighted sum of constants for polysulfide ions of different chain length, rather than a true single equilibrium constant. For biologically produced sulfur pK_x = 9.10 ± 0.08 (21 °C) and 9.17 ± 0.09 (35 °C) with an average polysulfide chain length x = 4.91 ± 0.32 (21 °C) and 4.59 ± 0.31 (35 °C). The pK_x value for biologically produced sulfur is significantly higher than for reaction of dissolved sodium sulfide with inorganic sulfur (pK_x = 8.82; 21 °C). This difference is probably caused by the negatively charged polymeric organic layer, which is present on biologically produced sulfur but absent with “inorganic” sulfur. Specific binding of polysulfide ions to the organic layer results in a higher polysulfide concentration at the reaction site compared to the bulk concentration. This results in an apparent decrease of the measured equilibrium constant, K_x.     

Preparation of quinoxalines, dihydropyrazines, pyrazines and piperazines using tandem oxidation processes

Alpha-hydroxyketones undergo MnO2-mediated oxidation followed by in situ trapping with aromatic or aliphatic 1,2-diamines to give quinoxalines or dihydropyrazines, respectively, in a one pot procedure which avoids the need to isolate the highly reactive 1,2-dicarbonyl intermediates. Modifications of the procedure allow the formation of pyrazines and piperazines.     

Chiroptical properties of 2-substituted pyrrolidines

The CD spectra of L-2-methylpyrrolidine, L-prolinol, and their N-methylated derivatives have been determined. As in the 2-substituted piperidines, N-methylation results in an inversion of the sign of the Cotton effects (CE). However, the sign of the long-wavelength CE does not follow the simple helicity rule found for 2-substituted piperidines, since the pyrrolidine ring is itself chiral and makes its own contributions to the observed CE's. The rotational contribution due to pyrrolidine ring chirality appears to be opposite in sign to and larger in magnitude than that due to the 2-substituent in both the secondary and the tertiary amines.     

Estimating entropies from molecular dynamics simulations

While the determination of free-energy differences by MD simulation has become a standard procedure for which many techniques have been developed, total entropies and entropy differences are still hardly ever computed. An overview of techniques to determine entropy differences is given, and the accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated using liquid water as a test system. Reasonably accurate entropy differences are obtained through thermodynamic integration in which many copies of a solute are desolvated. When only one solute molecule is involved, only two methods seem to yield useful results, the calculation of solute-solvent entropy through thermodynamic integration, and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference. One-step perturbation methods seem unsuitable to obtain entropy estimates.     

Synthesis and binding affinities of novel SRIF-mimicking beta-D-glucosides satisfying the requirement for a pi-cloud at C1

[reaction: see text] The synthesis of four bioactive analogues of the somatostatin (SRIF-14) mimetic, beta-d-glucoside (+)-2, in which the C1 indole side chain is replaced with indole surrogates, has been achieved. These congeners, possessing the naphthyl, benzothiophene, benzyl, and benzofuran substituents, were predicted to satisfy the electrostatic requirements of the tryptophan binding pocket of SRIF. Unlike the previously described C4 picolyl and pyrazinyl congeners, these ligands bind the hSST4 receptor.     

Theoretical investigations into the intermediacy of chlorinated vinylcobalamins in the reductive dehalogenation of chlorinated ethylenes

The reductive dehalogenation of perchloroethylene and trichloroethylene by vitamin B(12) produces approximately 95% (Z)-dichloroethylene (DCE) and small amounts of (E)-DCE and 1,1-DCE, which are further reduced to ethylene and ethane. Chloroacetylene and acetylene have been detected as intermediates, but not dichloroacetylene. Organocobalamins (RCbls) have been proposed to be intermediates in this process. Density functional theory based approaches were employed to investigate the properties of chlorinated vinylcobalamins and chlorinated vinyl radicals. They reveal that all vinyl radicals studied have reduction potentials more positive (E degrees >or= -0.49) than that of the Co(II)/Co(I) couple of B(12) (E degrees = -0.61 V), indicating that any (chlorinated) vinyl radicals formed in the reductive dehalogenation process should be reduced to the corresponding anions by cob(I)alamin in competition with their combination with Co(II) to yield the corresponding vinylcobalamins. The computed Co-C homolytic bond dissociation enthalpies (BDEs) of the latter complexes range from 33.4 to 45.8 kcal/mol. The substituent effects on the BDEs are affected by the stabilities of the vinyl radicals as well as steric interactions between (Z)-chloro substituents and the corrin ring. The calculated E degrees values of the cobalamin models were within approximately 200 mV of one another since electron attachment is to a corrin ring pi-orbital, whose energy is relatively unaffected by chloride substitution of the vinyl ligand, and all were >500 mV more negative than that of the Co(II)/Co(I) couple of B(12). Reduction of the base-off forms of vinyl- and chlorovinylcobalamin models also involves the corrin pi* orbital, but reduction of the base-off dichlorovinyl- and trichlorovinylcobalamin models occurs with electron attachment to the sigma(Co)(-)(C*) orbital, yielding calculated E degrees values more positive than that of the calculated Co(II)/Co(I) couple of B(12). Thus, cob(I)alamin is expected to reduce these base-off vinyl-Cbls. Heterolytic cleavage of the Co-C bonds is much more favorable than homolysis (>21 kcal/mol) and is significantly more exergonic when coupled to chloride elimination.     

Enzymatic hydrogen atom abstraction from polyunsaturated fatty acids

The oxidation of polyunsaturated fatty acids such as arachidonic and linoleic acid initiates a plethora of cell signaling pathways in animals and plants. The chemistry of the enzymatic oxidation has been investigated for several enzymes, most notably prostaglandin synthase and the lipoxygenases, revealing many surprises and impressive examples of enzymatic control of hydrogen atom abstraction and subsequent oxygenation.