Classical limit of relativistic quantal system with attractive Coulomb interaction

Using the appropriate harmonic oscillator states and reasonable approximations, we construct coherent wavepackets corresponding to the solutions of the Klein-Gordon equation for the attractive potentialV(r)=−k/r, k>0, in two and three space dimensions. We deduce the corresponding classical limit in two dimension by requiring that the expectation value 〈r〉 of the radial variable is large. In the case of three dimensions, besides the condition of large 〈r〉, we make the uncertainty Δr=[〈r ²〉 − 〈r〉²]^1/2 a minimum with respect to certain parameter of the wavepacket. We then investigate the trajectory traversed by the wavepacket in the classical limit. We find that the classical limit of this relativistic quantal problem gives, in the leading order, the same expression for the rate of motion of the perihelion as that given by the solution of the corresponding special relativistic classical dynamical problem. We also briefly discuss some of the subtle aspects of the classical limit of the relativistic quantal system, in general.     

Selective lighting up of segments around Gly,Ala and Ser/Thr in proteins

Direct detection of ¹³C nucleus can be used as a valuable alternative where ¹H detection poses a challenge due to relaxation effects, chemical exchange and poor chemical shift dispersion. In this context, we have designed a suite of 2D ¹³C^α‐detected hNCA experiments that provide sequential correlations of ¹³C^α with ¹⁵N on one hand and efficient spectroscopic labeling of certain groups of residues, namely, Gly, Ala, Ser and Thr, on the other. These residues act as checkpoints in the sequential walk, which in turn offer new possibilities of backbone assignment of small proteins from a set of 2D experiments, thereby providing great economy in terms of spectrometer time. The direct identification of peptide segments around Gly, Ala, Ser and Thr residues along a protein chain will be highly valuable for deriving important information on sites of ligand binding, phosphorylation, inhibitor/substrate binding, understanding protein folding pathways, comprehending local conformational dynamics etc. without having to obtain complete sequence‐specific assignments, which can be time consuming and at times formidable, especially in large proteins. We have illustratively demonstrated the multifaceted applications of these variants of 2D experiments on ubiquitin and M‐crystallin. We foresee that these 2D hNCA experiments will provide economic and efficient strategies for studying the structure and function of proteins. Copyright © 2012 John Wiley & Sons, Ltd.     

A facile microwave assisted synthesis of spiro-1,3-oxazines from N-(2-(cyclohex-1-en-1-yl)ethyl)amides

A mild and efficient methodology has been developed for the synthesis of spiro-1,3-oxazine derivatives by the microwave assisted cyclization of N-2-(1′-cyclohexenyl)ethyl-acetamides/benzamides. The reaction was catalyzed by in situ generated trimethylsilyl iodide and featured by its very short reaction time. The starting materials were easily obtained by the condensation of substituted acetic/benzoic acids with 2-(1′-cyclohexenyl)ethyl amine.     

pH‐Dependent Nitrotyrosine Formation in Ribonuclease A is Enhanced in the Presence of Polyethylene Glycol (PEG)

Protein nitration can occur as a result of peroxynitrite‐mediated oxidative stress. Excess production of peroxynitrite (PN) within the cellular medium can cause oxidative damage to biomolecules. The in vitro nitration of Ribonuclease A (RNase A) results in nitrotyrosine (NT) formation with a strong dependence on the pH of the medium. In order to mimic the cellular environment in this study, PN‐mediated RNase A nitration has been carried out in a crowded medium. The degree of nitration is higher at pH 7.4 (physiological pH) compared to pH 6.0 (tumor cell pH). The extent of nitration increases significantly when PN is added to RNase A in the presence of crowding agents PEG 400 and PEG 6000. PEG has been found to stabilize PN over a prolonged period, thereby increasing the degree of nitration. NT formation in RNase A also results in a significant loss in enzymatic activity.     

Dinucleosides with non-natural backbones: a new class of ribonuclease A and angiogenin inhibitors

Ribonuclease?A (RNase A) serves as a convenient model enzyme in the identification and development of inhibitors of proteins that are members of the ribonuclease superfamily. This is principally because the biological activity of these proteins, such as angiogenin, is linked to their catalytic ribonucleolytic activity. In an attempt to inhibit the biological activity of angiogenin, which involves new blood vessel formation, we employed different dinucleosides with varied non-natural backbones. These compounds were synthesized by coupling aminonucleosides with dicarboxylic acids and amino- and carboxynucleosides with an amino acid. These molecules show competitive inhibition with inhibition constant (K(i)) values of (59±3) and (155±5) μM for RNase A. The compounds were also found to inhibit angiogenin in a competitive fashion with corresponding K(i) values in the micromolar range. The presence of an additional polar group attached to the backbone of dinucleosides was found to be responsible for the tight binding with both proteins. The specificity of different ribonucleolytic subsites were found to be altered because of the incorporation of a non-natural backbone in between the two nucleosidic moieties. In spite of the replacement of the phosphate group by non-natural linkers, these molecules were found to selectively interact with the ribonucleolytic site residues of angiogenin, whereas the cell binding site and nuclear translocation site residues remain unperturbed. Docked conformations of the synthesized compounds with RNase A and angiogenin suggest a binding preference for the thymine-adenine pair over the thymine-thymine pair.     

Analysis of the local structure of phosphorus-substituted LAMOX oxide ion conductors

The effect of partial substitution of molybdenum by phosphorus on the global and local structural arrangement of the fast oxide-ion conductor La(2)Mo(2)O(9) (LAMOX) has been studied by X-ray powder diffraction as well as (139)La and (31)P solid state NMR. The diffraction patterns show that La(2)Mo(2-y)P(y)O(9-y/2) forms a solid solution at low phosphorus concentrations, and that there is a structural phase transition upon increasing phosphorus concentration. This phase transition is also reflected in (139)La and (31)P NMR spectra. The possibility to excite (31)P multiple-quantum coherences of one of the (31)P NMR signals gives evidence of an accumulation of phosphorus atoms on neighbouring Mo-type sites already before formation of three-dimensional precipitates. On the basis of our X-ray and NMR results we propose a possible structural arrangement of the compound La(2)Mo(2-y)P(y)O(9-y/2) that explains the experimental observations by crystal twinning.     

Mimicking transition metals in borrowing hydrogen from alcohols

Borrowing hydrogen from alcohols, storing it on a catalyst and subsequent transfer of the hydrogen from the catalyst to an in situ generated imine is the hallmark of a transition metal mediated catalytic N-alkylation of amines. However, such a borrowing hydrogen mechanism with a transition metal free catalytic system which stores hydrogen molecules in the catalyst backbone is yet to be established. Herein, we demonstrate that a phenalenyl ligand can imitate the role of transition metals in storing and transferring hydrogen molecules leading to borrowing hydrogen mediated alkylation of anilines by alcohols including a wide range of substrate scope. A close inspection of the mechanistic pathway by characterizing several intermediates through various spectroscopic techniques, deuterium labelling experiments, and DFT study concluded that the phenalenyl radical based backbone sequentially adds H⁺, H˙ and an electron through a dearomatization process which are subsequently used as reducing equivalents to the C–N double bond in a catalytic fashion.

An efficient method is developed for harvesting hydrogen, its storage and catalytic transfer by an odd alternant hydrocarbon. The strategy is reminiscent of transition metals in borrowing hydrogen mediated processes.     

Dinucleosides with Non‐Natural Backbones: A New Class of Ribonuclease A and Angiogenin Inhibitors

Ribonuclease A (RNase A) serves as a convenient model enzyme in the identification and development of inhibitors of proteins that are members of the ribonuclease superfamily. This is principally because the biological activity of these proteins, such as angiogenin, is linked to their catalytic ribonucleolytic activity. In an attempt to inhibit the biological activity of angiogenin, which involves new blood vessel formation, we employed different dinucleosides with varied non‐natural backbones. These compounds were synthesized by coupling aminonucleosides with dicarboxylic acids and amino‐ and carboxynucleosides with an amino acid. These molecules show competitive inhibition with inhibition constant (K_i) values of (59±3) and (155±5) μM for RNase A. The compounds were also found to inhibit angiogenin in a competitive fashion with corresponding K_i values in the micromolar range. The presence of an additional polar group attached to the backbone of dinucleosides was found to be responsible for the tight binding with both proteins. The specificity of different ribonucleolytic subsites were found to be altered because of the incorporation of a non‐natural backbone in between the two nucleosidic moieties. In spite of the replacement of the phosphate group by non‐natural linkers, these molecules were found to selectively interact with the ribonucleolytic site residues of angiogenin, whereas the cell binding site and nuclear translocation site residues remain unperturbed. Docked conformations of the synthesized compounds with RNase A and angiogenin suggest a binding preference for the thymine–adenine pair over the thymine–thymine pair.