Sharif Digital Repository

Coupling of side chain dynamics over long distances is an important component of allostery. Methionine side chains show the largest intrinsic flexibility among methyl-containing residues but the actual degree of conformational averaging depends on the proximity and mobility of neighboring residues. The 13C NMR chemical shifts of the methyl groups of methionine residues located at long distances in the same protein show a similar scaling with respect to the values predicted from the static X-ray structure by quantum methods. This results in a good linear correlation between calculated and observed chemical shifts. The slope is protein dependent and ranges from zero for the highly flexible... 

The heterobinuclear platinum(0)-gold(I) complex [(t-Bu3P)2PtAu(PPh3)] BF4, 5, was synthesized by the reaction of trinuclear cluster complex f[(PPh3)Au]3(μ-O)gBF4, 4, with one equiv of [(t-Bu3P)2Pt] at room temperature. The heterobinuclear complex 5 was characterized using multinuclear NMR spectroscopy and elemental microanalysis and was further identified by single crystal X-ray structure determination. Crystal structure of 5 shows a T-shaped geometry with an unsupported short distance Pt-Au dative bond  

The structural and conformational behavior of gemcitabine (20; 20-diuoro cytidine) was investigated by advanced NMR experiments and a computational quantum mechanical method (DFT) using Potential Energy Scanning (PES) in gas and solution phases in the Polarizable Continuum Model (PCM). Three stable conformers (G1, G2, and G3) were predicted from minimum points in a potential energy diagram. In order to measure coupling constant values, a set of 2D spectra (H-H COSY, H-C HMQC, and H-C HMBC) was analyzed. Optimized structures and spin-spin coupling constant calculations in gas and solution phases were performed by B3LYP/6-311++G(d,p) method. Both energy and NMR parameters showed that G1-form... 

The concentration and temperature behaviors of the self-diffusion coefficient were analyzed in glycerol-water and methanol-water solutions using Diffusion-Ordered Spectroscopy (DOSY) experiment. Our results indicate that the self-diffusion coefficient dips with increasing concentration and decreasing temperature. The concentration behavior shows that there is hydrogen bond interaction between water and alcohol, which declines the self-diffusion coefficients of both in the aqueous binary mixtures. The self-diffusion activation energies were estimated 13.6, 29.4, and 32.8 (kJ/mol) for methanol and 24.8, 25.5, and 27.6 (kJ/mol) for water in the methanol-water solutions with 0.03, 0.10, and 0.20... 

A mixture of the platinum(0) complex [Pt(PtBu3)2] and tetrakis(acetonitrile)copper(i) hexafluorophosphate in acetone activated a water molecule and gave the hydride platinum(ii) complex [PtH(CH3CN)(PtBu3)2]PF6, 1, and the hydroxide Cu(i) species. The crystal structure of complex 1 was determined by X-ray crystallography, indicating a distorted square planar geometry around the platinum center. Although three possible mechanisms are proposed for this transformation, monitoring of the reaction using NMR spectroscopy at low temperature reveals that a cooperative pathway involving formation of a Pt0-CuI dative bond complex is the most probable pathway. The hydride platinum complex 1 is stable in... 

Objective(s): This study aims to evaluate combined proton nuclear magnetic resonance (1H NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS) metabolic profiling approaches, for discriminating between mustard airway diseases (MADs) and healthy controls and for providing biochemical information on this disease. Materials and Methods: In the present study, analysis of serum samples collected from 17 MAD subjects and 12 healthy controls was performed using NMR. Of these subjects, 14 (8 patients and 6 controls) were analyzed by GC-MS. Then, their spectral profiles were subjected to principal component analysis (PCA) and orthogonal partial least squares regression discriminant... 

Objective(s): Hepatitis B virus infection causes chronic disease such as cirrhosis and hepatocellular carcinoma. The metabolomics investigations have been demonstrated to be related to pathophysiologic mechanisms in many disorders such as hepatitis B infection. The aim of this study was to investigate the saliva metabolic profile of patients with chronic hepatitis B infection and to identify underlying mechanisms as well as potential biomarkers associated with the disease. Materials and Methods: Saliva from 16 healthy subjects and 20 patients with chronic hepatitis B virus were analyzed by nuclear magnetic resonance (NMR). Then, multivariate statistical analysis was performed to identify... 

Objective(s): The molecular basis of “metabolically healthy obese” and “metabolically unhealthy non-obese” phenotypes is not fully understood. Our objective was to identify metabolite patterns differing in obese (metabolically healthy vs unhealthy (MHO vs MUHO)) and non-obese (metabolically healthy vs unhealthy (MHNO vs MUHNO)) individuals. Materials and Methods: This case-control study was performed on 86 subjects stratified into four groups using anthropometric and clinical measurements: MHO (21), MUHO (21), MHNO (22), and MUHNO (22). Serum metabolites were profiled using nuclear magnetic resonance (NMR). Multivariate analysis was applied to uncover discriminant metabolites, and enrichment... 

The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of... 

Multicore platforms are becoming the dominant trend in designing Mixed-Criticality Systems (MCSs), which integrate applications of different levels of criticality into the same platform. A well-known MCS is the dual-criticality system that is composed of low-criticality and high-criticality tasks. The availability of multiple cores on a single chip provides opportunities to employ fault-Tolerant techniques, such as N-Modular Redundancy (NMR), to ensure the reliability of MCSs. However, applying fault-Tolerant techniques will increase the power consumption on the chip, and thereby on-chip temperatures might increase beyond safe limits. To prevent thermal emergencies, urgent countermeasures,... 

Cementation factor greatly affects water saturation estimation. Factors such as depositional environment, diagenesis and depositional architecture make the estimation of water saturation a big challenge in carbonate reservoirs. The current study is introduced a method for calculating cementation factor in Archie formula. First, (MRGC) technique was applied on the (NMR) logging parameters along with (NDS) data to obtain the optimum number of clustering. After that, fuzzy logic method was applied on conventional log parameters obtained from the wells without any NMR log data. In the third part of the study, a novel crossplot introduced including compressional to shear-wave velocity ratio... 

Salep phosphate modified biopolymers with different phosphate contents were prepared via reacting salep (a multi-component polysaccharide obtained from dried tubers of certain natural terrestrial orchids) with a solution of primary and secondary sodium phosphates under basic conditions in a semidry process. Structural characterization of salep phosphates were carried out by 31P NMR, FT-IR spectra and TGA curves. Determination of the phosphate content in samples was done by a standard spectrophotometric method. Then, novel (salep phosphate)-based hydrogels were synthesized by graft copolymerization of acrylic acid (AA) monomer onto salep phosphate backbones. Effect of the phosphate contents... 

Calcineurin is an essential calcium-activated serine/threonine phosphatase. The six NMR-observable methionine methyl groups in the catalytic domain of human calcineurin Aα (CNA) were assigned and used as reporters of the presence of potential cis-trans isomers in solution. Proline 84 is found in the cis conformation in most calcineurin X-ray structures, and proline 309, which is part of a highly conserved motif in phosphoprotein phosphatases, was modeled with a cis peptide bond in one of the two molecules present in the asymmetric unit of CNA. We mutated each of the two prolines to alanine to force the trans conformation. Solution NMR shows that the P84A CNA mutant exists in two forms,... 

The six-coordinated silver(I) complex [Au2Ag(μ-(PPh2)2py)2(OTf)2](OTf), 4 (py = pyridine, OTf = CF3SO3), and the five-coordinated silver(I) complex [Au2Ag(acetone)(μ-(PPh2)2py)2](PF6)3, 6, were prepared by the reaction of the precursor complexes 1(OTf)2 and 1(PF6)2, in which 1 = [Au2(μ-(PPh2)2py)2]2+, with 1 equiv of Ag(OTf) in dichloromethane and excess of Ag(PF6) in a mixture of dichloromethane/acetone, respectively. Also, the five-coordinated silver(I) complex [Au2Ag(μ-(PPh2)2py)2(py)(OTf)](OTf)2, 5, was obtained by the reaction of 4 with pyridine. The clusters 4-6 were characterized using multinuclear NMR spectroscopy and elemental microanalysis. The single-crystal X-ray diffraction... 

Treated waste water (TWW) quality varies due to the occurrence of polycyclic aromatic hydrocarbons (PAHs) up to low μg L−1. In this study, a non-targeted metabolomic analysis was performed on lettuce (Lactuca sativa L) exposed to 4 PAHs by irrigation. The plants were watered with different concentrations of contaminants (0–100 μg L−1) for 39 days under controlled conditions and then harvested, extracted and analyzed by nuclear magnetic resonance (NMR). Different chemometric tools based on principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are proposed for the analysis of the complex data sets generated in the different exposure experiments.... 

Compound 3-benzyl-2H-pyrano[3,2-c]chromene-2,5(6H)-dione(3), was prepared and fully characterized. The vibrational modes (FT-IR) and NMR data ( 1H and 13C chemical shifts) were compared with the results of Density Functional Theory (DFT) method at the B3LYP/cc-PVTZ level. The calculated vibrational frequencies and NMR chemical shifts are in good agreement with the experimental results. The electronic (UV-Vis) spectrum was calculated using the TD-DFT method in CH2Cl2 with the Polarizable Continuum Model using the integral equation formalism variant (IEFPCM) and was correlated to the experimental spectra. The assignment and analysis of the frontier HOMO and LUMO orbitals indicate that... 

To investigate the factors influencing the luminescent properties of polymetallic cycloplatinated complexes a detailed study of the photophysical and structural properties of the heteronuclear complexes [Pt2Me 2(bhq)2(μ-dppy)2Ag2(μ-acetone) ](BF4)2, 2, [PtMe(bhq)(dppy)Tl]PF6, 3, and [Pt2Me2(bhq)2(dppy)2Tl]PF 6, 4, [bhq = benzo[h]quinoline, dppy = 2-(diphenylphosphino)pyridine] was conducted. Complexes 3 and 4 synthesized by the reaction of [PtMe(bhq)(dppy)], 1, with TlPF6 (1 or 1/2 equiv.) and stabilized by unsupported Pt-Tl bonds as revealed by multinuclear NMR spectroscopy and confirmed by X-ray crystallography for 3. DFT calculations for the previously reported butterfly Pt2Ag2 cluster 2... 

Metabonomics and other "omic" fields are essential science in analytical chemistry. Modern analytical instruments such as proton nuclear magnetic resonance (1H-NMR) can provide the great quantity of analytical information. In order to assign unknown samples, chemometric methods recognition build classification model based on experimental data. Firstly, some current strategies regarding disease diagnosis are exhibited in metabonomic studies. Some diseases such as crohn's disease can be difficult to diagnose since its signs and symptoms may be similar to other medical problems or often mimic other symptoms. Applications of NMR and supervised pattern recognition in the field of metabonomics are... 

Aim: The aim of this study was to search for metabolic biomarkers of Crohn's disease (CD). Background: Crohn's disease (CD) is a type of inflammatory bowel disease that causes a wide variety of symptoms. CD can influence any part of the gastrointestinal tract from mouth to anus. CD is not easily diagnosed because monitoring tools are currently insufficient. Thus, the discovery of proper methods is needed for early diagnosis of CD. Patients and methods: We utilized metabolic profiling using proton nuclear magnetic resonance spectroscopy (1HNMR) to find the metabolites in serum. Classification of CD and healthy subject was done using partial least squares discriminant analysis (PLS-DA)....