Amino Acid Based MOFs: Synthesis, Structure, Single Crystal to Single Crystal Transformation, Magnetic and Related Studies in a Family of Cobalt and Nickel Aminoisophthales

Four new 5-aminoisophthalates of cobalt and nickel have been prepared employing hydro/solvothermal methods: [Co2(C8H5NO4)2(C4H4N2)(H2O)2]·3H2O (I), [Ni2(C8H5NO4)2(C4H4N2)(H2O)2]·3H2O (II), [Co2(H2O)(μ3-OH)2(C8H5NO4)] (III), and [Ni2(H2O)(μ3-OH)2(C8H5NO4)] (IV). Compounds I and II are isostructural, having anion-deficient CdCl2 related layers bridged by a pyrazine ligand, giving rise to a bilayer arrangement. Compounds III and IV have one-dimensional M−O(H)−M chains connected by the 5-aminoisophthalate units forming a three-dimensional structure. The coordinated as well as the lattice water molecules of I and II could be removed and inserted by simple heating−cooling cycles under the atmospheric conditions. The removal of the coordinated water molecule is accompanied by changes in the coordination environment around the M2+ (M = Co, Ni) and color of the samples (purple to blue, Co; green to dark yellow, Ni). This change has been examined by a variety of techniques that include in situ single crystal to single crystal transformation studies and in situ IR and UV−vis spectroscopic studies. Magnetic studies indicate antiferromagnetic behavior in I and II, a field-induced magnetism in III, and a canted antiferromagnetic behavior in IV.

Influence of roughness parameters and surface texture on friction during sliding of pure lead over 080 M40 steel

In the present investigation, tests were conducted on a tribological couple made of cylindrical lead pin with spherical tip against 080 M40 steel plates of different textures with varying roughness under both dry and lubricated conditions using an inclined pin-on-plate sliding tester. Surface roughness parameters of the steel plates were measured using optical profilometer. The morphologies of the worn surfaces of the pins and the formation of transfer layer on the counter surfaces were observed using a scanning electron microscope. It was observed that the coefficient of friction and the formation of transfer layer depend primarily on the surface texture of hard surfaces. A newly formulated non-dimensional hybrid roughness parameter called 'xi' (a product of number of peaks and maximum profile peak height) of the tool surface plays an important role in determining the frictional behaviour of the surfaces studied. The effect of surfaces texture on coefficient of friction was attributed to the variation of plowing component of friction, which in turn depends on the roughness parameter 'xi'.

Cl-35 NQR study of cation polarizability in metal salts of monochloro acetic acid

Various metal salts (Na, K, Rb, and NH4) of monochloro acetic acid were prepared and the Cl-35 nuclear quadrupole resonance frequencies were measured at room temperature. A comparative study of nuclear quadrupole resonance frequencies of monochloro acetic acid and its metal salts is carried out. The frequency shifts obtained in the respective metal chloroacetates are used to estimate the changes in the ionicity of C-Cl bond. Further, the changes in the ionicity of C-Cl bond were used to estimate the percentage of intra-molecular charge transfer between respective cation-anion of the metal salts of chloro acetic acid. The nuclear quadrupole resonance frequency is found to decrease with increasing ionicity of the alkali metal ion.

Prospecting for alternate sources of shikimic acid, a precursor of Tamiflu, a bird-flu drug

Shikimic acid, more commonly known by its anionic form, shikimate, is an important intermediate compound of the ‘shikimate pathway’ in plants and microorganisms1. It is the principal precursor for the synthesis of aromatic amino acids, phenylalanine, tryptophan and tyrosine and other compounds such as alkaloids, phenolics and phenyl propanoids2. It is used extensively as a chiral building block for the synthesis of a number of compounds in both pharmaceutical and cosmetic industries3. In the recent past, the focus on shikimic acid has increased since it is the key precursor for the synthesis of Tamiflu, the only drug against avian flu caused by the H5N1 virus4,5. Shikimic acid is converted to a diethyl ketal intermediate, which is then reduced in two steps to an epoxide that is finally transformed to Tamiflu6.

Differential Mechanisms of Binding of Anti-Sigma Factors Escherichia coli Rsd and Bacteriophage T4 AsiA to E. coli RNA Polymerase Lead to Diverse Physiological Consequences

Anti-sigma factors Escherichia coli Rsd and bacteriophage T4 AsiA bind to the essential housekeeping sigma factor, sigma(70), of E. coli. Though both factors are known to interact with the C-terminal region of sigma(70), the physiological consequences of these interactions are very different. This study was undertaken for the purpose of deciphering the mechanisms by which E. coli Rsd and bacteriophage T4 AsiA inhibit or modulate the activity of E. coli RNA polymerase, which leads to the inhibition of E. coli cell growth to different amounts. It was found that AsiA is the more potent inhibitor of in vivo transcription and thus causes higher inhibition of E. coli cell growth. Measurements of affinity constants by surface plasmon resonance experiments showed that Rsd and AsiA bind to or 70 with similar affinity. Data obtained from in vivo and in vitro binding experiments clearly demonstrated that the major difference between AsiA and Rsd is the ability of AsiA to form a stable ternary complex with RNA polymerase. The binding patterns of AsiA and Rsd with sigma(70) studied by using the yeast two-hybrid system revealed that region 4 of sigma(70) is involved in binding to both of these anti-sigma factors; however, Rsd interacts with other regions of sigma(70) as well. Taken together, these results suggest that the higher inhibition of E. coli growth by AsiA expression is probably due to the ability of the AsiA protein to trap the holoenzyme RNA polymerase rather than its higher binding affinity to sigma(70).

Structural Insights into the acyl-intermediates of plasmodium falciparum fatty acid synthesis pathway; the mechanism of expansion of acyl carrier protein core

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.

High energy oxygen ion induced modifications in lead based perovskite thin films

The lead based ferroelectric PbZr0.53Ti0.47O3 (PZT), (Pb0.90La0.10)TiO3 (PLT10) and (Pb0.80La0.20)TiO3 (PLT20) thin films, prepared by pulsed laser ablation technique, were studied for their response to the 70 MeV oxygen ion irradiation. The dielectric analysis, capacitance-voltage (C- V) and DC leakage current measurements were performed before and after the irradiation to high-energy oxygen ions. The irradiation produced considerable changes in the dielectric, C-V, leakage characteristics and induced some amount of amorphization. The PZT films showed partial recrystallization after a thermal annealing at 400 degrees C for 10 min. The phase transition temperature [T-c] of PLT20 increased from 115 degrees C to 120 degrees C. The DC conductivity measurements showed a shift in the onset of non-linear conduction region. The current density decreased by two orders of magnitude after irradiation. After annealing the irradiated films at a temperature of 400 degrees C for 10 min, the films partially regained the dielectric and electrical properties. The results are discussed in terms of the irradiation-induced amorphization, the pinning of the ferroelectric domains by trapped charges and the thermal annealing of the defects generated during the irradiation. (C) 2007 Elsevier B.V. All rights reserved.

Hybrid peptide design. Hydrogen bonded conformations in peptides containing the stereochemically constrained gamma-amino acid residue, gabapentin

he crystal structure of 12 peptides containing the conformationally constrained 1-(aminomethyl)cyclohexaneacetic acid, gabapentin (Gpn), are reported. In all the 39 Gpn residues conformationally characterized so far, the torsion angles about the C-alpha-C-beta and C-beta-C-gamma bonds are restricted to the gauche conformation (+/- 60 degrees). The Gpn residue is constrained to adopt folded conformations resulting in the formation of intramolecularly hydrogen-bonded structures even in short peptides. The peptides Boc-Ac(6)c-Gpn-OMe 1 and Boc-Gpn-Aib-Gpn-Aib-OMe 2 provide examples of C-7 conformation; peptides Boc-Gpn-Aib-OH 3, Boc-Ac(6)c-Gpn-OH 4, Boc-Val-Pro-Gpn-OH 5, Piv-Pro-Gpn-Val-OMe 6, and Boc-Gpn-Gpn-Leu-OMe 7 provide examples of C-9 conformation; peptide Boc-Ala-Aib-Gpn-Aib-Ala-OMe 8 provides an example of C-12 conformation and peptides Boc-beta Leu-Gpn-Val-OMe 9 and Boc-beta Phe-Gpn-Phe-OMe 10 provide examples of C-13 conformation. Gpn peptides provide examples of backbone expanded mimetics for canonical alpha-peptide turns like the gamma (C-7) and the beta (C-10) turns. The hybrid beta gamma sequences provide an example of a mimetic of the C-13 alpha-turn formed by three contiguous alpha-amino acid residues. Two examples of folded tripeptide structures, Boc-Gpn-beta Phe-Leu-OMe 11 and Boc-Aib-Gpn-beta Phg-NHMe 12, lacking internal hydrogen bonds are also presented. An analysis of available Gpn residue conformations provides the basis for future design of folded hybrid peptides.

Amino acid interaction preferences in proteins

Understanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge-based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 x 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure.

Functional characterization of lysophosphatidic acid phosphatase from Arabidopsis thaliana

Lysophosphatidic acid (LPA) acts as a signaling molecule that regulates diverse cellular processes and it can rapidly be metabolized by phosphatase and acyltransferase LPA phosphatase gene has not been identified and characterized in plants so far The BLAST search revealed that the At3g03520 is similar to phospholipase family. and distantly related to bacterial phosphatases The conserved motif. (J)4XXXNXSFD, was identified in both At3g03520 like phospholipases and acid phosphatases In silico expression analysis of At3g03520 revealed a high expression during phosphate starvation and abiotic stresses. This gene was overexpressed in Escherichia coli and shown to posses LPA specific phosphatase activity These results Suggest that this gene possibly plays a role in signal transduction and storage lipid synthesis.

Self-acylation properties of type II fatty acid biosynthesis acyl carrier protein

Acyl carrier protein (ACIP) plays a central role in many metabolic processes inside the cell, and almost 4% of the total enzymes inside the cell require it as a cofactor. Here, we report self-acylation properties in ACPs from Plasmodium falciparum and Brassica napus that are essential components of type II fatty acid biosynthesis (FAS II), disproving the existing notion that this phenomenon is restricted only to ACPs involved in polyketide biosynthesis. We also provide strong evidence to suggest that catalytic self-acylation is intrinsic to the individual ACP. Mutational analysis of these ACPs revealed the key residue(s) involved in this phenomenon. We also demonstrate that these FAS 11 ACPs exhibit a high degree of selectivity for self-acylation employing only dicarboxylic acids as substrates. A plausible mechanism for the self-acylation reaction is also proposed.

Rationalizing the effects of amino acid side chain, pyridine, and imidazole on the assembly and reversible disassembly of a octanuclear Cu(III) complex

This paper reports the observation of a reversible disassembly process for a previously reported octanuclear Cu(II) complex with imidazole. To identify the factors responsible for the process, five Cu(II) complexes of different nuclearity with different amino acid-derived tetradentate ligands were structurally characterized. The results show that the coordination geometry preference of Cu(II), the tendency of imidazole to act as in-plane ligand, and H-bonding played important role in the formation and disassembly of the octanuclear complex. A general scheme describing the effect of different amino acid side arms, solvents, and exogenous ligands on the nuclearity of the Cu(II) complexes has been presented. The crystals of the complexes also showed formation of multifaceted networks in the resulting complexes.

Modeling of formation of gold nanoparticles by citrate method

Properties of nanoparticles are size dependent, and a model to predict particle size is of importance. Gold nanoparticles are commonly synthesized by reducing tetrachloroauric acid with trisodium citrate, a method pioneered by Turkevich et al (Discuss. Faraday Soc. 1951, 11, 55). Data from several investigators that used this method show that when the ratio of initial concentrations of citrate to gold is varied from 0.4 to similar to 2, the final mean size of the particles formed varies by a factor of 7, while subsequent increases in the ratio hardly have any effect on the size. In this paper, a model is developed to explain this widely varying dependence. The steps that lead to the formation of particles are as follows: reduction of Au3+ in solution, disproportionation of Au+ to gold atoms and their nucleation, growth by disproportionation on particle surface, and coagulation. Oxidation of citrate results in the formation of dicarboxy acetone, which aids nucleation but also decomposes into side products. A detailed kinetic model is developed on the basis of these steps and is combined with population balance to predict particle-size distribution. The model shows that, unlike the usual balance between nucleation and growth that determines the particle size, it is the balance between rate of nucleation and degradation of dicarboxy acetone that determines the particle size in the citrate process. It is this feature that is able to explain the unusual dependence of the mean particle size on the ratio of citrate to gold salt concentration. It is also found that coagulation plays an important role in determining the particle size at high concentrations of citrate.