Conformational landscape of l-threonine in neutral,acid and basic solutions from vibrational circular dichroism spectroscopy and quantum chemical calculations

The biological relevance of amino acids is well known. They can be used as zwitterionic, cationic or anionic forms according to the pH of the medium where they are. Thus, our aim herein was to study the conformational preference of the polar amino acid l-threonine [C₄H₉NO₃, (2S,3R)-2-amino-3-hydroxybutyric acid] under different pH conditions. A conformational study in an aqueous solution of the dissociation equilibrium of the amino acid l-threonine was carried out for this purpose. We recorded, at room temperature, the Mid-IR, Far-IR, Raman and VCD spectra of l-threonine from the aqueous solutions at pH values 5.70 (zwitterionic species), 1.00 (protonated species) and 13.00 (deprotonated species). The number of conformers found with the conformational search was 9 zwitterions, 27 anions and 52 cations. Both the study of the conformational landscape and the theoretical analysis of the vibrational features were accomplished by using DFT and ab initio calculations, that is, B3LYP/6-311++G(d,p) level of theory for all the conformers obtained from the conformational search, M062X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory for the most stable conformers. The presence of water was included with the IEF-PCM implicit hydration model. With regard to the zwitterion, the importance of the analysis of the low frequency region (700–30 cm^–1) in the Far-IR spectra should be noted, because it provides relevant information that can be used to determine the presence of the most stable structures.     

Validation of a novel very large eddy simulation method for simulation of turbulent separated flow

The paper describes the validation of a newly developed very LES (VLES) method for the simulation of turbulent separated flow. The new VLES method is a unified simulation approach that can change seamlessly from Reynolds‐averaged Navier–Stokes to DNS depending on the numerical resolution. Four complex test cases are selected to validate the performance of the new method, that is, the flow past a square cylinder at Re = 3000 confined in a channel (with a blockage ratio of 20%), the turbulent flow over a circular cylinder at Re = 3900 as well as Re = 140,000, and a turbulent backward‐facing step flow with a thick incoming boundary layer at Re = 40,000. The simulation results are compared with available experimental, LES, and detached eddy simulation‐type results. The new VLES model performs well overall, and the predictions are satisfactory compared with previous experimental and numerical results. It is observed that the new VLES method is quite efficient for the turbulent flow simulations; that is, good predictions can be obtained using a quite coarse mesh compared with the previous LES method. Discussions of the implementation of the present VLES modeling are also conducted on the basis of the simulations of turbulent channel flow up to high Reynolds number of Re_τ = 4000. The efficiency of the present VLES modeling is also observed in the channel flow simulation. From a practical point of view, this new method has considerable potential for more complex turbulent flow simulations at relative high Reynolds numbers. Copyright © 2013 John Wiley & Sons, Ltd.     

Kadomtsev–Petviashvili equation in relativistic fluid dynamics

The Kadomtsev–Petviashvili (KP) nonlinear wave equation is the three dimensional generalization of the Korteveg-de Vries (KdV) equation. We show how to obtain the cylindrical KP (cKP) and cartesian KP in relativistic fluid dynamics. The obtained KP equations describe the evolution of perturbations in the baryon density in a strongly interacting quark gluon plasma (sQGP) at zero temperature. We also show the analytical solitary wave solution of the KP equations in both cases.     

Concise synthesis of orthogonally diprotected l-glyceraldehyde

Orthogonally diprotected l-glyceraldehyde was efficiently prepared from readily available starting materials, allowing to obtain a highly stable and synthetically versatile chiral building block compared to known symmetrically protected derivatives.     

A DFT Study on Estrone – TNT Interaction

Trinitrotoluene, known as TNT, is a widely used powerful explosive. It is a poisonous material, which injures almost all cells, especially those of liver, bone marrow, and kidney. Estrone is a sex hormone having an electron rich aromatic (phenolic) ring that is capable of forming a π complex with molecules containing an electron deficient π system. This study has focused on investigating the tendency of the complex formation of TNT with estrone. It has been thought that the formation of estrone‐TNT π complex might take place in a human body exposed to acute or prolong period of this hazardous chemical and consequently estrone activities might be impaired. The complex formation reaction was investigated mainly using DFT method with B3LYP/6‐31G(d, p) basis set in gas phase. The existence of π interaction between estrone and TNT was demonstrated by computational spectroscopic analyses (UV/Vis, IR, and ¹H NMR techniques). The frontier molecular orbital (HOMO and LUMO) analyses have shown that the considered π complex is very resistant to oxidation with respect to its components, estrone and TNT.     

Variation Operators for Semigroups and Riesz Transforms on BMO in the Schrödinger Setting

In this paper we prove that the variation operators of the heat semigroup and the truncations of Riesz transforms associated to the Schrödinger operator are bounded on a suitable BMO type space.     

Hiv-1 Specific Reverse Transcriptase Inhibitors: why are Tsao-Nucleosides so Unique?

1. INTRODUCTION

AIDS will still be one of the most important challenges for the Scientific Community in the approaching new century. Since the identification, in 1983-84,^1,2 of human immunodeficiency virus (HIV) as the etiological agent of AIDS, significant progress has been made in the treatment of HIV-infected patients. This has been in part due to the discovery and clinical use of an increasing number of anti-HIV drugs. However, while highly active antiretroviral therapy (HAART)³ approaches have reduced the morbidity and mortality, the intertwined problems of drug induced viral resistance, poor compliance with complex regimens and therapy failure continue. Therefore, there remains a pressing need for the development of new antiviral agents that can be used not only as first line therapeutic candidates, but also in the antiretroviral-experienced patient population.     

Enzymatic Synthesis of Fructosyl Glycerol

ABSTRACT

The enzymatic synthesis of ß2-2' and ß2-1'-D- fructopyranosyl glycerol was carried out with levansucrase from Bacillus circulans or B.subtilis, using sucrose as fructosyl donor and glycerol. The specificity and efficiency of the enzyme was modified by controlling both the water and the total substrate concentrations. The products were purified by HPLC and analyzed by ¹H, ¹³C NMR and GC-MS.