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

A new PtII 2 organometallic building block with 90° geometry, 3,6-bis[trans-platinum(triethylphosphine)2(nitrate) (ethynyl)]carbazole (5), containing an ethynyl functionality is synthesized in reasonable yield by employing a Sonagashira coupling reaction. Multinuclear NMR and electrospray ionization mass spectrometry (ESI-MS) including a single-crystal X-ray diffraction study characterized this 90° building unit. The self-assembly of 5 with three flexible ditopic donors (La-L c) afforded [2 + 2] metallamacrocycles (6a-c) [where La = 1,3-bis(4-pyridyl)isophthalamide; Lb = 1,3-bis(3-pyridyl) isophthalamide, and Lc = 1,2-di(4-pyridyl)ethane]. All three [2 + 2] self-assembled macrocycles were characterized by various spectroscopic techniques, and the molecular structure of 6a was determined by the single-crystal X-ray diffraction method. The square-type macrocycle 6a was designed using amide-based ligand La to make it a suitable system composed of a fluorophorereceptor combination. The amide functional group is the receptor site for the anions, which can bind through hydrogen-bonding interaction, whereas the carbazole-based 90° building unit is the fluorophore unit. Macrocycle 6a was found to be fluorescent in nature and showed dramatic fluorescence enhancement in a DMF/H2O solvent mixture upon titration with P2O74-, which plays important roles in various biological functions such as energy transduction in organisms and controls metabolic processes by participating in various enzymatic reactions. Interestingly, the nonresponsive nature of the fluorescence intensity of 6a upon addition of the anions F-, ClO4-, and H2PO4- makes it a suitable fluorescent sensor for pyrophosphate anion (P2O74-). © 2010 American Chemical Society.

World University root node

Organometallics

Coordination-driven self-assembly of metallamacrocycles via a new Pt II2 organometallic building block with 90° geometry and optical sensing of anions

(Figure Presented) 4-Hydroxyacids are ubiquitous in human physiology. They are derived from the drugs of abuse γ-hydroxybutyrate (GHB), γ-hydroxypentanoate(GHP), in addition to the omnipresent lipid peroxidation product 4-hydroxy-2-(E)-nonenal (4-HNE). Previously we reported that 4-hydroxyacids are catabolized through two parallel pathways. In this report we detail two isotopic tools that have allowed the dissection of this catabolic process and illustrate how these tools can be used to quantify the relative flux down each pathway. We found that 4-hydroxynonanoate (4-hydroxyacid derived from 4-HNE) is primarly catabolized through a pathway that phosphorylates the C-4 hydroxyl and isomerizes it to a C-3 hydroxy compound, which is catabolized through β-oxidation. © 2010 American Chemical Society.

Journal of the American Chemical Society

Using isotopic tools to dissect and quantitate parallel metabolic pathways

A drug library of 17200 compounds was screened to select small molecules that inhibit the secretion of amyloid β peptide (Aβ), the major component of Alzheimer disease senile plaques, from a human neuronal cell line. Twenty-nine hits were validated that decreased Aβ secretion by >40% at 10 μM, for a 0.17% hit rate. A lead hit was selected for further study based on its activity and low cytotoxicity, and it was found to inhibit Aβ secretion through activation of the α-secretase pathway. Twenty-four commercially available and 53 synthesized analogues were analyzed for activity. Selected analogues were evaluated for biological stability by incubation with hepatoma cells and for transcellular permeability using Caco-2 cell monolayers. The analogue with the best permeability was evaluated in 2-month old amyloid precursor protein transgenic mice and found to acutely reduce cerebral Aβ levels by 40% after a single iv administration. © 2010 American Chemical Society.

Journal of Medicinal Chemistry

Synthesis and biological evaluation of analogues of a novel inhibitor of β-amyloid secretion

The conformational behaviour of polymer chains has been examined using Langevin dynamics simulation techniques. Polymer chains were modelled as "beads" undergoing Brownian motion in a defined potential that accounted for stretching, bending and solvation energies. As expected, the competition between chain stiffness and solvent interactions was found to yield standard swollen or collapsed configurations in good or poor solvents, respectively. However, when a torsional term was introduced into the model, additional biologically relevant conformations such as helices, sheets, turns and hairpins naturally arose. © 2010 Elsevier Ltd.

Journal of Theoretical Biology

Langevin dynamics simulations reveal biologically relevant folds arising from the incorporation of a torsional potential

Using path integrals, we derive an exact expression-valid at all times t -for the distribution P (Q,t) of the heat fluctuations Q of a Brownian particle trapped in a stationary harmonic well. We find that P (Q,t) can be expressed in terms of a modified Bessel function of zeroth order that in the limit t→∞ exactly recovers the heat distribution function obtained recently by Imparato [Phys. Rev. E 76, 050101(R) (2007)]10.1103/PhysRevE.76.050101 from the approximate solution to a Fokker-Planck equation. This long-time result is in very good agreement with experimental measurements carried out by the same group on the heat effects produced by single micron-sized polystyrene beads in a stationary optical trap. An earlier exact calculation of the heat distribution function of a trapped particle moving at a constant speed v was carried out by van Zon and Cohen [Phys. Rev. E 69, 056121 (2004)]10.1103/PhysRevE.69.056121; however, this calculation does not provide an expression for P (Q,t) itself, but only its Fourier transform (which cannot be analytically inverted), nor can it be used to obtain P (Q,t) for the case v=0. © 2010 The American Physical Society.

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Exact path-integral evaluation of the heat distribution function of a trapped Brownian oscillator

With the help of 1H NMR and EPR techniques, we have probed the dynamics of guest molecules included within a water-soluble deep cavity cavitand known by the trivial name octa acid. All guest molecules investigated here form 2:1 (host/guest) complexes in water, and two host molecules encapsulate the guest molecule by forming a closed capsule. We have probed the dynamics of the guest molecule within this closed container through 1H NMR and EPR techniques. The timescales offered by these two techniques are quite different, millisecond and nanosecond, respectively. For EPR studies, paramagnetic nitroxide guest molecules and for 1H NMR studies, a wide variety of structurally diverse neutral organic guest molecules were employed. The guest molecules freely rotate along their x axis (long molecular axis and magnetic axis) on the NMR timescale; however, their rotation is slowed with respect to that in water on the EPR timescale. Rotation along the x axis is dependent on the length of the alkyl chain attached to the nitroxide probe. Overall rotation along the y or z axis was very much dependent on the structure of the guest molecule. The guests investigated could be classified into three groups: (a) those that do not rotate along the y or z axis both at room and elevated (55 °C) temperatures, (b) those that rotate freely at room temperature, and (c) those that do not rotate at room temperature but do so at higher temperatures. One should note that rotation here refers to the NMR timescale and it is quite possible that all molecules may rotate at much longer timescales than the one probed here. A slight variation in structure alters the rotational mobility of the guest molecules. © 2010 American Chemical Society.

Langmuir

Guest rotations within a capsuleplex probed by NMR and EPR techniques

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY

Metabolism of 4-hydroxy acids and 4-hydroxynonenal using a selective isotope labeling strategy

We show that a model of target location involving n noninteracting particles moving subdiffusively along a line segment (a generalization of a model introduced by Sokolov et al. [Biophys. J. 2005, 89, 895.]) provides a basis for understanding recent experiments by Pelta et al. [Phys. Rev. Lett. 2007, 98, 228302.] on the kinetics of diffusion-limited gel degradation. These experiments find that the time tc taken by the enzyme thermolysin to completely hydrolyze a gel varies inversely as roughly the 3/2 power of the initial enzyme concentration [E]. In general, however, this time would be expected to vary either as [E]-1or as[E]-2, depending on whether the Brownian diffusion of the enzyme to the site of cleavage took place along the network chains (1-d diffusion) or through the pore spaces (3-d diffusion). In our model, the unusual dependence of tc on [E] is explained in terms of a reaction-diffusion equation that is formulated in terms of fractional rather than ordinary time derivatives. © 2010 American Chemical Society.

Journal of Physical Chemistry B

A model of anomalous enzyme-catalyzed gel degradation kinetics

The FASEB Journal

Partial beta‐oxidation and bilateral alpha‐oxidation of gamma‐hydroxybutyrate (GHB) in perfused rat livers

We report a single-step approach to producing small and stable bubbles functionalized with nanoparticles. The strategy includes the following events occurring in sequence: (i) a microfluidic generation of bubbles from a mixture of CO2 and a minute amount of gases with low solubility in water, in an aqueous solution of a protein, a polysaccharide, and anionic nanoparticles; (ii) rapid dissolution of CO2 leading to the shrinkage of bubbles and an increase in acidity of the medium in the vicinity of the bubbles; and (iii) co-deposition of the biopolymers and nanoparticles at the bubble-liquid interface. The proposed approach yielded microbubbles with a narrow size distribution, long-term stability, and multiple functions originating from the attachment of metal oxide, metal, or semiconductor nanoparticles onto the bubble surface. We show the potential applications of these bubbles in ultrasound and magnetic resonance imaging. © 2010 American Chemical Society.