Chiral methylbenzylammonium salts of aryldithiophosphonic acids containing glucofuranose,allofuranose, and galactopyranose diacetonide scaffolds

Abstract

New chiral methylbenzylammonium salts of aryldithiophosphonic acids containing glucofuranose, allofuranose, and galactopyranose diacetonide substituents were obtained using (S)-(–)-α-methylbenzylamine, (R)-(+)-α-methylbenzylamine, and (R,S)-(±)-α-methylbenzylamine. Salts obtained possess antimicrobial activity.     

Simple models for the diurnal cycle and convectively coupled waves

This paper presents a study of the diurnal cycle of tropical precipitation and its interaction with convectively coupled waves in the context of simple models with crude vertical resolution. One and two baroclinic mode models are tested in both the context of a one-column model and the context of a full spatial dependency that permits waves to propagate and interact with the diurnal cycle. It is found that a one baroclinic mode model is capable of reproducing a realistic diurnal cycle of tropical precipitation both over land and over the ocean provided an adequate switch function is used to mimic the congestus preconditioning mechanism that operates in the multicloud model of Khouider and Majda. However, a full two baroclinic mode multicloud model is needed to capture the interaction of convectively coupled tropical waves with the diurnal cycle. In a more conventional mass flux parameterization framework, both one and two baroclinic mode models fail to capture the diurnal cycle of tropical precipitation.     

Running coupling corrections to non-linear evolution for diffractive dissociation

We determine running coupling corrections to the kernel of the non-linear evolution equation for the cross section of single diffractive dissociation in high energy DIS. The running coupling kernel for diffractive evolution is found to be exactly the same as the kernel of the rcBK evolution equation.     

Multi-Particle Processes with Reinforcements

We consider a multi-particle generalization of linear edge-reinforced random walk (ERRW). We observe that in absence of exchangeability, new techniques are needed in order to study the multi-particle model. We describe an unusual coupling construction associated with the two-point edge-reinforced process on ℤ and prove a form of recurrence: the two particles meet infinitely often a.s. This research was supported in part by NSF VIGRE Grant DMS 9983726 at UCLA.     

Targeted analysis of glycomics liquid chromatography/mass spectrometry data

Hydrophilic interaction chromatography (HILIC) liquid chromatography/mass spectrometry (LC/MS) is appropriate for all native and reductively aminated glycan classes. HILIC carries the advantage that retention times vary predictably according to oligosaccharide composition. Chromatographic conditions are compatible with sensitive and reproducible glycomics analysis of large numbers of samples. The data are extremely useful for quantitative profiling of glycans expressed in biological tissues. With these analytical developments, the rate-limiting factor for widespread use of HILIC LC/MS in glycomics is the analysis of the data. In order to eliminate this problem, a Java-based open source software tool, Manatee, was developed for targeted analysis of HILIC LC/MS glycan datasets. This tool uses user-defined lists of compositions that specify the glycan chemical space in a given biological context. The program accepts high-resolution LC/MS data using the public mzXML format and is capable of processing a large data file in a few minutes on a standard desktop computer. The program allows mining of HILIC LC/MS data with an output compatible with multivariate statistical analysis. It is envisaged that the Manatee tool will complement more computationally intensive LC/MS processing tools based on deconvolution and deisotoping of LC/MS data. The capabilities of the tool were demonstrated using a set of HILIC LC/MS data on organ-specific heparan sulfates.     

Rare tautomer hypothesis supported by theoretical studies: ab initio investigations of prototropic tautomerism in the N-methyl-p base

Density functional theory calculations were applied to the prediction of the tautomeric properties of N-methyl-P (6-methyl-3,4-dihydro-8H-pyrimido[4,5-c][1,2]oxazin-7-one), a base of the nucleoside analogue dP (6-(2-deoxy-beta-D-ribofuranosyl)-3,4-dihydro-8H-pyrimido[4,5-c][1,2]oxazin-7-one), for which water-solution experimental data have become available recently. The calculations have been performed for three tautomers in the gas phase, with various numbers of water molecules, and within the polarizable continuum model (PCM) of solvation. The obtained results correctly predict the presence of two tautomers and reproduce accurately the experimentally obtained ratio of the two most stable tautomeric forms when using a combination of explicit water molecules and the PCM of solvation. This lends additional support to the rare tautomer hypothesis of substitution mutagenesis in DNA replication.     

A note on adiabatic theorem for Markov chains

We state and prove a version of an adiabatic theorem for Markov chains using well-known facts about mixing times. We extend the result to the case of continuous time Markov chains with bounded generators.     

Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study

The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization approach) followed by calculations of the interactions between the base pair and a water/sodium cation.