Approximating the maximum 2- and 3-edge-colorable subgraph problems

For a fixed value of a parameter k≥2, the Maximum k-Edge-Colorable Subgraph Problem consists in finding k edge-disjoint matchings in a simple graph, with the goal of maximising the total number of edges used. The problem is known to be -hard for all k, but there exist polynomial time approximation algorithms with approximation ratios tending to 1 as k tends to infinity. Herein we propose improved approximation algorithms for the cases of k=2 and k=3, having approximation ratios of 5/6 and 4/5, respectively.     

Radical–anion coupling through reagent design: hydroxylation of aryl halides

The design and development of an oxime-based hydroxylation reagent, which can chemoselectively convert aryl halides (X = F, Cl, Br, I) into phenols under operationally simple, transition-metal-free conditions is described. Key to the success of this approach was the identification of a reducing oxime anion which can interact and couple with open-shell aryl radicals. Experimental and computational studies support the proposed radical-nucleophilic substitution chain mechanism.

The design and development of an oxime-based hydroxylation reagent, which can chemoselectively convert aryl halides (X = F, Cl, Br, I) into phenols under operationally simple, transition-metal-free conditions is described.     

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch

The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.     

Exchange frequency in replica exchange molecular dynamics

The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.     

Theoretical study of the isomerization mechanism of azobenzene and disubstituted azobenzene derivatives

A series of azobenzenes was studied using ab initio methods to determine the substituent effects on the isomerization pathways. Energy barriers were determined from three-dimensional potential energy surfaces of the ground and electronically excited states. In the ground state (S(0)), the inversion pathway was found to be preferred. Our results show that electron donating substituents increase the isomerization barrier along the inversion pathway, whereas electron withdrawing substituents decrease it. The inversion pathway of the first excited state (S(1)) showed trans --> cis barriers with no curve crossing between S(0) and S(1). In contrast, a conical intersection was found between the ground and first excited states along the rotation pathway for each of the azobenzenes studied. No barriers were found in this pathway, and we therefore postulate that after n --> pi (S(1) <-- S(0)) excitation, the rotation mechanism dominates. Upon pi --> pi (S(2) <-- S(0)) excitation, there may be sufficient energy to open an additional pathway (concerted-inversion) as proposed by Diau. Our potential energy surface explains the experimentally observed difference in trans-to-cis quantum yields between S(1) and S(2) excitations. The concerted inversion channel is not available to the remaining azobenzenes, and so they must employ the rotation pathway for both n --> pi and pi --> pi excitations.     

Photoelectron spectroscopy of S1 toluene: II. Intramolecular dynamics of selected vibrational levels in S1 toluene studied by nanosecond and picosecond time-resolved photoelectron spectroscopies

We present results which suggest that the photophysics of S(1) toluene is significantly more complicated than that of the related molecules p-fluorotoluene or p-difluorobenzene. We have measured a range of photoelectron spectra for a number of S(1) internal energies, on different time scales and at different temperatures, in an attempt to unravel the competing processes, but the final conclusion remains outstanding.     

Gas-phase fragmentation of long-lived cysteine radical cations formed via no loss from protonated S-nitrosocysteine

In this work, we describe two different methods for generating protonated S-nitrosocysteine in the gas phase. The first method involves a gas-phase reaction of protonated cysteine with t-butylnitrite, while the second method uses a solution-based transnitrosylation reaction of cysteine with S-nitrosoglutathione followed by transfer of the resulting S-nitrosocysteine into the gas phase by electrospray ionization mass spectrometry (ESI-MS). Independent of the way it was formed, protonated S-nitrosocysteine readily fragments via bond homolysis to form a long-lived radical cation of cysteine (Cys^•+), which fragments under collision-induced dissociation (CID) conditions via losses in the following relative abundance order: •COOH ≫ CH₂S > •CH₂SH-H₂S. Deuterium labeling experiments were performed to study the mechanisms leading to these pathways. DFT calculations were also used to probe aspects of the fragmentation of protonated S-nitrosocysteine and the radical cation of cysteine. NO loss is found to be the lowest energy channel for the former ion, while the initially formed distonic Cys^•+ with a sulfur radical site undergoes proton and/or H atom transfer reactions that precede the losses of CH₂S, •COOH, •CH₂SH, and H₂S.     

Hydroboration of an alkene by amine-boranes catalysed by a [Rh(PR3)2]+ fragment. Mechanistic insight and tandem hydroboration/dehydrogenation

The catalytic hydroboration of tert-butylethene using H(3)B·NMe(3) gives RH(2)B·NMe(3). With H(3)B·NMe(2)H tandem hydroboration under mild conditions/dehydrocoupling occurs that produces R(2)B=NMe(2) (R = H, CH(2)CH(2)(t)Bu).     

Characterization of β-cyclodextrin inclusion complex with procaine hydrochloride by 1H NMR and ITC

The inclusion of local anesthetic drug procaine hydrochloride by β-cyclodextrin was investigated by 1D and 2D proton NMR spectroscopy and isothermal titration calorimetry (ITC) at 298 K. The stoichiometry of the complex was determinate by the method of continuous variation, using the chemical induced shift of both host and guest protons. The association constant K, of the obtained complex was calculated and found to be 293.17 M^?1. Rotating frame NOE spectroscopy, was used to ascertain the solution geometry of the host–guest complex. The result reveals that the procaine molecule penetrates into the β-cyclodextrin cavity with the aromatic ring. The energetics of complexation process is investigated by ITC technique. The analysis indicates that the complexation of procaine by β-CD is an exothermic process and show that both enthalpy and entropy contribute to the binding process. The obtained value for the association constant is in good agreement with that obtained from NMR.