Department of Chemistry

Indian Institute of Technology Palakkad&nbsp;(IIT Palakkad or IIT PKD) is a public autonomous&nbsp;engineering&nbsp;and&nbsp;research&nbsp;institute located in&nbsp;Palakkad,&nbsp;Kerala. It was&nbsp;one of the five new&nbsp;IITs&nbsp;proposed in the&nbsp;2014 Union budget of India. The campus was inaugurated on 3 August 2015. The institute has 94 faculty, 978 students, and 63 non-teaching staffs.

IT Palakkad currently offers four-year Bachelor of Technology (B.Tech) and two years MS programmes in 8 different engineering disciplines including&nbsp;Computer Science, Electrical, Mechanical, Civil among others.

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IIT Palakkad

The efficient photoinduced electron transfer from a stilbene derivative incarcerated within a negatively charged organic nanocapsule to positively charged acceptors (methyl viologen and a pyridinium salt) adsorbed outside and the back electron transfer were controlled by supramolecular effects. © 2012 Royal Society of Chemistry.

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Chemical Communications

Photoinduced electron transfer between a donor and an acceptor separated by a capsular wall

A new class of macrobicyclic dinickel(ii) complexes [Ni2L 1,2B](ClO4)4 (1-6), where L1,2 are polyaza macrobicyclic binucleating ligands, and B is a N,N-donor heterocyclic base (viz. 2,2′-bipyridine (bipy) and 1,10-phenanthroline (phen)) are synthesized and characterized. The redox, catalytic, DNA binding and DNA cleavage properties were studied. They exhibit two irreversible waves in the cathodic region around Epc = -0.95 V and Epa = -0.85 V vs. Ag/Ag+ in CH3CN-0.1 M TBAP, respectively. The first order rate constants for the hydrolysis of 4-nitrophenylphosphate to 4-nitrophenolate by the dinickel(ii) complexes 1-6 are in the range from 3.36 × 10 -5 to 10.83 × 10-5 Ms-1. The complexes 3 and 6 show good binding propensity to calf thymus DNA giving binding constant values (Kb) in the range from 3.08 × 105 to 5.37 × 105 M-1. The binding site sizes and viscosity data suggest the DNA intercalative and/or groove binding nature of the complexes. The complexes display significant hydrolytic cleavage of supercoiled pBR322DNA at pH 7.2 and 37 °C. The hydrolytic cleavage of DNA by the complexes is supported by the evidence from free radical quenching and T4 ligase ligation. The pseudo Michaelis-Menten kinetic parameters kcat = 5.44 × 10-2 h-1 and KM = 6.23 × 10-3 M for complex 3 were obtained. Complex 3 also shows an enormous enhancement of the cleavage rate, of 1.5 × 106, in comparison to the uncatalysed hydrolysis rate (k = 3.6 × 10-8 h-1) of ds-DNA. © 2012 The Royal Society of Chemistry.

Fulltext

RSC Advances

Electrochemical, phosphate hydrolysis, DNA binding and DNA cleavage properties of new polyaza macrobicyclic dinickel(ii) complexes

GHB (γ-hydroxybutyrate) is both a neurotransmitter and a drug of abuse (date-rape drug). We investigated the catabolism of this compound in perfused rat livers. Using a combination of metabolomics and mass isotopomer analysis, we showed that GHB is metabolized by multiple processes, in addition to its previously reported metabolism in the citric acid cycle via oxidation to succinate. A substrate cycle operates between GHB and γ-aminobutyrate via succinic semialdehyde. Also, GHB undergoes (i) β-oxidation to glycolyl-CoA+acetyl-CoA, (ii) two parallel processes which remove C-1 or C-4 of GHB and form 3-hydroxypropionate from C-2+C-3+C-4 or from C-1+C- 2+C-3 of GHB, and (iii) degradation to acetyl-CoA via 4- phosphobutyryl-CoA. The present study illustrates the potential of the combination of metabolomics and mass isotopomer analysis for pathway discovery. © The Authors Journal compilation © 2012 Biochemical Society.

Biochemical Journal

Metabolism of γ-hydroxybutyrate in perfused rat livers

The FASEB Journal

Cyclical C7‐CoA esters derived from calcium levulinate, a pro‐drug of abuse

At EB 2010, we reported that in perfused rat livers and in live rats (i) levulinate (4-ketopentanoate, LEV) is converted to gamma-hydroxypentanoate (GHP), a new drug of abuse, analog of gamma-hydroxybutyrate, (ii) the formation of GHP from LEV is enhanced by ethanol oxidation, and (iii) the metabolism of LEV and GHP result in substantial accumulation of LEV-CoA, GHP-CoA and 4-phospho-GHP-CoA in the liver leading to CoA trapping. We now report a similar accumulation of LEV-derived CoA esters in (i) the brains of rats gavaged with Ca-LEV and (ii) rat hearts perfused with LEV. We also report new fates of LEV metabolism in liver. First, LEV-CoA is elongated with acetyl-CoA to 3,6-gamma-diketo-heptanoyl-CoA, which is converted to two types of cyclic CoA esters with a cyclopentane ring and with a pyrrole ring. The latter is similar to pyrrole compounds formed in the brain by the binding of toxic gamma-diketones (such as 2,5-diketohexane) to lysine. Such compounds may contribute to the toxicity of GHP derived from LEV. Oral ingestion of Ca-LEV plus ethanol is a public health concern since Ca-LEV is freely available. Supported by NIDDK RoadMap and by NIEHS.

The Federation of American Societies for Experimental Biology (FASEB) Journal

Calcium Levulinate: Dietary Calcium Supplement and Pro-drug of Abuse

Thioxanthone and benzil derivatives were incarcerated into an octa acid nanocapsule. Photoexcitation of these ketones generated electronic triplet excited states, which become efficiently quenched by positively charged nitroxides adsorbed outside on the external surface of the negatively charged nanocapsule. Although the triplet excited ketone and quencher are separated by a molecular wall (nanocapsule), quenching occurs on the nanosecond time scale and generates spin-polarized nitroxides, which were observed by time-resolved EPR spectroscopy. Because opposite signs of spin polarization of nitroxides were observed for thioxanthone and benzil derivatives, it is proposed that the electron spin polarization transfer mechanism of spin-polarized triplet states to nitroxides is the major mechanism of generating nitroxide polarization. © 2011 American Chemical Society.

Journal of Physical Chemistry Letters

CIDEP from a polarized ketone triplet state incarcerated within a nanocapsule to a nitroxide in the bulk aqueous solution

The design and preparation of novel M3L2 trigonal cages via the coordination-driven self-assembly of preorganized metalloligands containing octahedral aluminum(III), gallium(III), or ruthenium(II) centers is described. When tritopic or dinuclear linear metalloligands and appropriate complementary subunits are employed, M3L2 trigonal-bipyramidal and trigonal-prismatic cages are self-assembled under mild conditions. These three-dimensional cages were characterized with multinuclear NMR spectroscopy (1H and 31P) and high-resolution electrospray ionization mass spectrometry. The structure of one such trigonal-prismatic cage, self-assembled from an arene ruthenium metalloligand, was confirmed via single-crystal X-ray crystallography. The fluorescent nature of these prisms, due to the presence of their electron-rich ethynyl functionalities, prompted photophysical studies, which revealed that electron-deficient nitroaromatics are effective quenchers of the cages? emission. Excited-state charge transfer from the prisms to the nitroaromatic substrates can be used as the basis for the development of selective and discriminatory turn-off fluorescent sensors for nitroaromatics. © 2011 American Chemical Society.

Inorganic Chemistry

Coordination-driven self-assembly of M3L2 trigonal cages from preorganized metalloligands incorporating octahedral metal centers and fluorescent detection of nitroaromatics

Four new perylene bisimides containing carbazolyl and triphenylamino electron-donor groups in the bay region have been designed, synthesized and characterized. The materials possess high thermal stability and form uniform films. They display a wide absorption window extending to the near infrared region of the spectrum and demonstrate efficient photoinduced intramolecular electron transfer. Ionization potential values of these perylene bisimide derivatives measured by photoelectron spectroscopy range from 5.8 eV to 6 eV. Charge-transporting properties were investigated by the xerographic time of flight (XTOF) technique. Complementary ambipolar charge-transport was observed in differently linked carbazolyl substituted perylene bisimides while the triphenylamino substituted material exhibited competent electron drift mobility (&gt;10-3 cm2 V-1 cm-1) under ambient conditions. Density functional theory (DFT) calculations were performed for carbazolyl bay substituted perylene bisimides in order to understand the complementary ambipolar charge transport as well as the difference in the optical properties. © 2011 The Royal Society of Chemistry.

Journal of Materials Chemistry

Air stable electron-transporting and ambipolar bay substituted perylene bisimides

Cargo transport through the nuclear pore complex continues to be a subject of considerable interest to experimentalists and theorists alike. Several recent studies have revealed details of the process that have still to be fully understood, among them the apparent nonlinearity between cargo size and the pore crossing time, the skewed, asymmetric nature of the distribution of such crossing times, and the non-exponentiality in the decay profile of the dynamic autocorrelation function of cargo positions. In this paper, we show that a model of pore transport based on subdiffusive particle motion is in qualitative agreement with many of these observations. The model corresponds to a process of stochastic binding and release of the particle as it moves through the channel. It suggests that the phenylalanine-glycine repeat units that form an entangled polymer mesh across the channel may be involved in translocation, since these units have the potential to intermittently bind to hydrophobic receptor sites on the transporter protein. © 2011 American Institute of Physics.

Journal of Chemical Physics

Subdiffusion as a model of transport through the nuclear pore complex

Static disorder has recently been implicated in the non-exponential kinetics of the unfolding of single molecules of poly-ubiquitin under a constant force Kuo, Garcia-Manyes, Li, Barel, Lu, Berne, Urbakh, Klafter, and Fernndez, Proc. Natl. Acad. Sci. U.S.A. 107, 11336 (2010)10.1073/pnas.1006517107. In the present paper, it is suggested that dynamic disorder may provide a plausible, alternative description of the experimental observations. This suggestion is made on the basis of a model in which the barrier to chain unfolding is assumed to be modulated by a control parameter r that evolves in a parabolic potential under the action of fractional Gaussian noise according to a generalized Langevin equation. The treatment of dynamic disorder within this model is pursued using Zwanzigs indirect approach to noise averaging Acc. Chem. Res. 23, 148 (1990). In conjunction with a self-consistent closure scheme developed by Wilemski and Fixman J. Chem. Phys. 58, 4009 (1973)10.1063/1.1679757; ibid. 60, 866 (1974)10.1063/1.1681162, this approach eventually leads to an expression for the chain unfolding probability that can be made to fit the corresponding experimental data very closely. © 2011 American Institute of Physics.