MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures

Identification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation-pi, pi-pi and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.

Au Nanoparticles for Applications in Analysis of Cellular and Biomolecular Recognitions

Au nanoparticles (AuNPs) have attracted a great interest in fabrication of various biosensor systems for analysis of cellular and biomolecular recognitions. In conjunction with vast conjugation chemistry available, the materials are easily coupled with biomolecules such as nucleic acids, antigens or antibodies in order to achieve their many potential applications as ligand carriers or transducing platforms for preparation, detection and quantification purposes. Furthermore, the nanoparticles possess easily tuned and unique optical/ physical/ chemical characteristics, and high surface areas, making them ideal candidates to this end. In this topic, sensing mechanisms based on localized surface plasmon resonance (LSPR), particle aggregation, catalytic property, and Fluorescence Resonance Energy Transfer (FRET) of AuNPs as well as barcoding technologies including DNA biobarcodes will be discussed.

Design of Cyclophanes: Synthesis and Study of Photophysical and Biomolecular Recognition Properties

Development of organic molecules that exhibit selective interactions with different biomolecules has immense significance in biochemical and medicinal applications. In this context, our main objective has been to design a few novel functionaIized molecules that can selectively bind and recognize nucleotides and DNA in the aqueous medium through non-covalent interactions. Our strategy was to design novel cycIophane receptor systems based on the anthracene chromophore linked through different bridging moieties and spacer groups. It was proposed that such systems would have a rigid structure with well defined cavity, wherein the aromatic chromophore can undergo pi-stacking interactions with the guest molecules. The viologen and imidazolium moieties have been chosen as bridging units, since such groups, can in principle, could enhance the solubility of these derivatives in the aqueous medium as well as stabilize the inclusion complexes through electrostatic interactions.We synthesized a series of water soluble novel functionalized cyclophanes and have investigated their interactions with nucleotides, DNA and oligonucIeotides through photophysical. chiroptical, electrochemical and NMR techniques. Results indicate that these systems have favorable photophysical properties and exhibit selective interactions with ATP, GTP and DNA involving electrostatic. hydrophobic and pi-stacking interactions inside the cavity and hence can have potential use as probes in biology.

'In the Room' and 'School Chemistry Class'

Two poems in journal Axon. 2013 Issue 4.

Colloidal semiconductor nanocrystals : controlled synthesis and surface chemistry in organic media

Colloidal semiconductor nanocrystals (CS-NCs) possess compelling benefits of low-cost, large-scale solution processing, and tunable optoelectronic properties through controlled synthesis and surface chemistry engineering. These merits make them promising candidates for a variety of applications. This review focuses on the general strategies and recent developments of the controlled synthesis of CS-NCs in terms of crystalline structure, particle size, dominant exposed facet, and their surface passivation. Highlighted are the organic-media based synthesis of metal chalcogenide (including cadmium, lead, and copper chalcogenide) and metal oxide (including titanium oxide and zinc oxide) nanocrystals. Current challenges and thus future opportunities are also pointed out in this review.

Tunable electric field enhancement and redox chemistry on TiO2 island films via covalent attachment to Ag or Au nanostructures

Abstract Ag-TiO2 and Au-TiO2 hybrid electrodes were designed by covalent attachment of TiO2 nanoparticles to Ag or Au electrodes via an organic linker. The optical and electronic properties of these systems were investigated using the cytochrome b5 (Cyt b5) domain of sulfite oxidase, exclusively attached to the TiO2 surface, as a Raman marker and model redox enzyme. Very strong SERR signals of Cyt b 5 were obtained for Ag-supported systems due to plasmonic field enhancement of Ag. Time-resolved surface-enhanced resonance Raman spectroscopic measurements yielded a remarkably fast electron transfer kinetic (k = 60 s -1) of Cyt b5 to Ag. A much lower Raman intensity was observed for Au-supported systems with undefined and slow redox behavior. We explain this phenomenon on the basis of the different potential of zero charge of the two metals that largely influence the electronic properties of the TiO2 island film. © 2013 American Chemical Society.

Reactivity of Cationic Terminal Borylene Complexes: Novel Mechanisms for Insertion and Metathesis Chemistry Involving Strongly Lewis Acidic Ligand Systems

The reactions of terminal borylene complexes of the type [CpFe(CO)(2)(BNR2)](+) (R = `Pr, Cy) with heteroallenes have been investigated by quantum-chemical methods, in an attempt to explain the experimentally observed product distributions. Reaction with dicyclohexylcarbodiimide (CyNCNCy) gives a bis-insertion product, in which 1 equiv of carbodiimide is assimilated into each of the Fe=B and B=N double bonds to form a spirocyclic boronium system. In contrast, isocyanates (R'NCO, R' = Ph, 2,6-wXy1, CY; XYl = C6H3Me2) react to give isonitrile complexes of the type [CpFe(CO)(2)(CNR')]+, via a net oxygen abstraction (or formal metathesis) process. Both carbodiimide and socyanate substrates are shown to prefer initial attack at the Fe=B bond rather than the B=N bond of the borylene complex. Further mechanistic studies reveal that the carbodiimide reaction ultimately leads to the bis-insertion compounds [CpFe(CO)(2)C(NCy)(2)B(NCY)(2)CNR2](+), rather than to the isonitrile system [CpFe(CO)(2)(CNCy)](+), on the basis of both thermodynamic (product stability) and kinetic considerations (barrier heights). The mechanism of the initial carbodiimide insertion process is unusual in that it involves coordination of the substrate at the (borylene) ligand followed by migration of the metal fragment, rather than a more conventional process: i.e., coordination of the unsaturated substrate at the metal followed by ligand migration. In the case of isocyanate substrates, metathesis products are competitive with those from the insertion pathway. Direct, single-step metathesis reactivity to give products containing a coordinated isonitrile ligand (i.e. [CpFe(CO)(2)(CNR')](+)) is facile if initial coordination of the isocyanate at boron occurs via the oxygen donor (which is kinetically favored); insertion chemistry is feasible when the isocyanate attacks initially via the nitrogen atom. However, even in the latter case, further reaction of the monoinsertion product so formed with excess isocyanate offers a number of facile (low energetic barrier) routes which also generate ['CpFe(CO)(2)(CNR')](+), rather than the bis-insertion product [CpFe(CO)(2)C(NR')(O)B(NR')(O)CNR2](+) (i.e., the direct analogue of the observed products in the carbodiimide reaction).

Structural Crystallography and Crystal Chemistry

Abstract is not available.

Structural Crystallography and Crystal Chemistry

CaH406P-.K +, M r = 206.10, is orthorhombic, space group Pbca (from systematic absences), a = 14.538(4), b = 13.364(5), c = 6.880 (6)A, U = 1383.9 A 3, D x = 2.07 Mg m -a, Z = 8, ~.(Mo Ka) = 0.7107/~, p(MO Ka) = 1.015 mm -1. The final R value is 0.042 for a total of 1397 reflections. The high energy P-O(13) and the enolic C(1)-O(13) bonds are 1.612 and 1.374 A respectively. The enolpyruvate moiety is essentially planar. The orientation of the phosphate with respect to the pyruvate group in PEP.K is distinctly different from that in the PEP-cyclohexylammonium salt, the torsion angle C (2)-C (1)-O(13)- P being -209.1 in the former and -90 ° in the latter. The K + ion binds simultaneously to both the phosphate and carboxyl ends of the same PEP molecule. The ester O(13) is also a binding site for the cation. The K + ion is coplanar with the pyruvate moiety and binds to 0(22) and O(13) almost along their lone-pair directions. The carbonyl 0(22) prefers to bind to the K + ion rather than take part in the formation of hydrogen bonds usually observed in carboxylic acid structures.

Thiol cofactors for selenoenzymes and their synthetic mimics

The importance of selenium as an essential trace element is now well recognized. In proteins, the redox-active selenium moiety is incorporated as selenocysteine (Sec), the 21st amino acid. In mammals, selenium exerts its redox activities through several selenocysteine-containing enzymes, which include glutathione peroxidase (GPx), iodothyronine deiodinase (ID), and thioredoxin reductase (TrxR). Although these enzymes have Sec in their active sites, they catalyze completely different reactions and their substrate specificity and cofactor or co-substrate systems are significantly different. The antioxidant enzyme GPx uses the tripeptide glutathione (GSH) for the catalytic reduction of hydrogen peroxide and organic peroxides, whereas the larger and more advanced mammalian TrxRs have cysteine moieties in different subunits and prefer to utilize these internal cysteines as thiol cofactors for their catalytic activity. On the other hand, the nature of in vivo cofactor for the deiodinating enzyme ID is not known, although the use of thiols as reducing agents has been well-documented. Recent studies suggest that molecular recognition and effective binding of the thiol cofactors at the active site of the selenoenzymes and their mimics play crucial roles in the catalytic activity. The aim of this perspective is to present an overview of the thiol cofactor systems used by different selenoenzymes and their mimics.

The many ways to delimit species: hairs, genes and surface chemistry

Species identification forms the basis for understanding the diversity of the living world, but it is also a prerequisite for understanding many evolutionary patterns and processes. The most promising approach for correctly delimiting and identifying species is to integrate many types of information in the same study. Our aim was to test how cuticular hydro- carbons, traditional morphometrics, genetic polymorphisms in nuclear markers (allozymes and DNA microsatellites) and DNA barcoding (partial mitochondrial COI gene) perform in delimiting species. As an example, we used two closely related Formica ants, F. fusca and F. lemani, sampled from a sympatric population in the northern part of their distribu- tion. Morphological characters vary and overlap in different parts of their distribution areas, but cuticular hydrocarbons include a strong taxonomic signal and our aim is to test the degree to which morphological and genetic data correspond to the chemical data. In the morphological analysis, species were best separated by the combined number of hairs on pro- notum and mesonotum, but individual workers overlapped in hair numbers, as previously noted by several authors. Nests of the two species were separated but not clustered according to species in a Principal Component Analysis made on nuclear genetic data. However, model-based Bayesian clustering resulted in perfect separation of the species and gave no indication of hybridization. Furthermore, F. lemani and F. fusca did not share any mitochondrial haplotypes, and the species were perfectly separated in a phylogenetic tree. We conclude that F. fusca and F. lemani are valid species that can be separated in our study area relatively well with all methods employed. However, the unusually small genetic differen- tiation in nuclear markers (FST = 0.12) shows that they are closely related, and occasional hybridization between F. fusca and F. lemani cannot be ruled out.

Synthesis of substituted 8-aminoquinolines and phenanthrolines through a Povarov approach

The synthesis of 8-aminoquinolines and 1,10-phenanthrolines with substituents in alpha of the nitrogen has been performed through an inverse-demanding aza-Diels-Alder (Povarov reaction) in the fluoroalcohols TFE or HFIP. This path involves simple starting materials: 1,2-phenylenediamines, enol ethers and aldehydes.

Synthesis, characterization and antioxidant activity of angiotensin converting enzyme inhibitors

Angiotensin converting enzyme (ACE) catalyzes the conversion of angiotensin I (Ang I) to angiotensin II (Ang II). ACE also cleaves the terminal dipeptide of vasodilating hormone bradykinin (a nonapeptide) to inactivate this hormone. Therefore, inhibition of ACE is generally used as one of the methods for the treatment of hypertension. `Oxidative stress' is another disease state caused by an imbalance in the production of oxidants and antioxidants. A number of studies suggest that hypertension and oxidative stress are interdependent. Therefore, ACE inhibitors having antioxidant property are considered beneficial for the treatment of hypertension. As selenium compounds are known to exhibit better antioxidant behavior than their sulfur analogues, we have synthesized a number of selenium analogues of captopril, an ACE inhibitor used as an antihypertensive drug. The selenium analogues of captopril not only inhibit ACE activity but also effectively scavenge peroxynitrite, a strong oxidant found in vivo.

Synthesis and esterolytic chemistry of some (dialkylamino) pyridine-functionalized micellar aggregates. Evidence of catalytic turnover

Four new (dialkylamino)pyridine-functionalized surfactants have been synthesized. Micelles were generated either from the surfactant alone in aqueous buffer (pH 8.5 or 9.0) or by comicellization in 1 x 10(-3)-1 x 10(-4) M aqueous micellar cetyltrimethylammonium bromide (CTABr) solution at pH 8.5 or 9.0. Such aggregates were used to cleave p-nitrophenyl alkanoates or p-nitrophenyl diphenylphosphate. The nucleophilic reagents and the second-order ''catalytic'' rate constants toward esterolysis of the substrate p-nitrophenyl octanoate (at 25 degrees C, pH 9.0) were [cat.] = 1 x 10(-4) M, [CTABr] = 1 x 10(-3) M, and k(cat.) = 440.13 M(-1) s(-1) for 1b, [cat.] = 5 x 10(-4) M, [CTABr] = 5 x 10(-4) M, and k(cat.) = 30.8 M(-1) s(-1) for 1c, [cat.] = 5 x 10(-4) M, [CTABr] = 5 x 10(-3) M, and k(cat.) = 183.64 M(-1) s(-1) for 2a, and [cat.] = 3 x 10(-4) M and k(cat.) = 54.1 M(-1) s(-1) for 2b. The catalytic systems, especially 1b/CTABr and 2a/CTABr, also conferred significantly greater reactivity toward the esters derived from alkanoic acids of moderate chain length (C-6-C-10) during hydrolytic cleavages relative to their shorter and longer counterparts. Importantly, the catalytic systems comprising the coaggregates of either neutral 1b and CTABr (1:10) or anionic 2a and CTABr (1:10) conformed to the Michaelis-Menten kinetic scheme and demonstrated turnover behavior in the presence of excess substrate.