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.

&nbsp;

IIT Palakkad

Biological systems have long recognized the importance of macromolecular diversity and have evolved efficient processes for the rapid synthesis of sequence-defined biopolymers. However, achieving sequence control via synthetic methods has proven to be a difficult challenge. Herein we describe efforts to circumvent this difficulty via the use of orthogonal allyl acrylamide building blocks and a liquid-phase fluorous support for the de novo design and synthesis of sequence-specific polymers. We demonstrate proof-of-concept via synthesis and characterization of two sequence-isomeric 10-mer polymers. 1H NMR and LCMS were used to confirm their chemical structure while tandem MS was used to confirm sequence identity. Further validation of this methodology was provided via the successful synthesis of a sequence-specific 16-mer polymer incorporating nine different monomers. This strategy thus shows promise as an efficient approach for the assembly of sequence-specific functional polymers. © 2014 American Chemical Society.

World University root node

Journal of the American Chemical Society

Sequence-defined polymers via orthogonal allyl acrylamide building blocks

A low cost optical fiber pH sensor has been proposed. The sensor is configured by coating a pH sensitive film of hydrogel synthesized by Poly (Vinyl Alcohol)/Poly (Acrylic Acid) blend coated on an etched single mode fiber. The pH response of the gel coated fiber is studied. © OSA 2014.

Proceedings 12th International Conference on Fiber Optics and Photonics, Photonics 2014

Study on polymer coated etched optical fiber for pH sensing

The reaction of metal carbonyl compounds with group 6 and 8 metallaboranes led us to report the synthesis and structural characterization of several novel mixed-metal chalcogenide tetrahedral clusters. Thermolysis of arachno-[(Cp∗RuCO)2B2H6], 1 and [Os3(CO)12] in the presence of 2-methylthiophene yielded [Cp∗Ru(CO)2(μ-H){Os3(CO)9}S], 3 and [Cp∗Ru(μ-H){Os3(CO)11}], 4. In a similar fashion, the reaction of [(Cp∗Mo)2B5H9], 2, with [Ru3(CO)12] and 2-methylthiophene yielded [Cp∗Ru(CO)2(μ-H){Ru3(CO)9}S], 5 and conjuncto-[(Cp∗Mo)2B5H8(μ-H){Ru3(CO)9}S], 6. Both compounds 3 and 5 can be described as 50-cve (cluster valence electron) mixed-metal chalcogenide clusters, in which a sulfur atom replaces one of the vertices of the tetrahedral core. Compounds 3 and 5 possess a [M3S] tetrahedral core, in which the sulfur is attached to an exo-metal fragment, unique in the [M3S] metal chalcogenide tetrahedral arrangements. All the compounds have been characterized by mass spectrometry, IR and 1H, 11B and 13C NMR spectroscopy in solution and the solid state structures were unequivocally established by crystallographic analysis of compounds 3, 5 and 6. © 2014 the Partner Organisations.

Dalton Transactions

Mixed-metal chalcogenide tetrahedral clusters with an exo-polyhedral metal fragment

Self-assembly of a chloro-bridged half-sandwich p-cymene ruthenium(II) complex [Ru2 (l-Cl2)(g6-pcymene) 2Cl2] 1 with linear ditopic donor [L; trans-1,2-bis(4- pyridyl)ethylene] in presence of 2 eq. AgNO3 in CH3CN yielded a chloro-bridged molecular rectangle 2. The rectangle 2 was isolated as nitrate salt in high yield (90 %) and characterized by infra-red, 1H NMR spectroscopy including ESI-MS analyses. Molecular structure of 2 was determined by single crystal X-ray diffraction study The diffraction analysis shows that 2 adopts a tetranuclear rectangular geometry with the dimensions of 5.51 Å 9 13.29 Å and forming an infinite supramolecular chain with large internal porosity arising through multiple p-p and CH-p interactions between the adjacent rectangles. Furthermore, rectangle 2 is used as selective receptor for phenolic-nitroaromatic compounds such as picric acid, dinitrophenol and nitrophenol. © The National Academy of Sciences, India 2014.

Proceedings of the National Academy of Sciences India Section A - Physical Sciences

Self-assembly of chloro-bridged arene-ruthenium based rectangle: Synthesis, structural characterization and sensing study

Herein we report a study combining metabolomics and mass isotopomer analysis used for investigation of the biochemical fate of γ- hydroxybutyric acid (GHB). Using various 13C incorporation labeling patterns into GHB, we have discovered that GHB is catabolized by previously unknown processes that include (i) direct β-oxidation to acetyl-CoA and glycolate, (ii) α-oxidation to 3-hydroxypropionyl-CoA and formate, and (iii) cleavage of C-4 to yield 3-hydroxypropionate and CO2. We further utilized the unique attributes of our labeling patterns and the resultant isotopomers to quantitate relative flux down the identified pathways. © 2014 American Chemical Society.

Fulltext

ACS Chemical Biology

Modular isotopomer synthesis of γ-hydroxybutyric acid for a quantitative analysis of metabolic fates

International Conference on Fibre Optics and Photonics, 2014

The oxazole homodimer YOYO-1 has served as a valuable tool for the detection and quantification of nucleic acids. While the base specificity and selectivity of binding of YOYO-1 has been researched to some extent, the effect of unorthodox nucleic acid conformations on dye binding has received relatively less attention. In this work, we attempt to correlate the quadruplex-forming ability of G-rich sequences with binding of YOYO-1. Oligonucleotides differing in the number of tandem G repeats, total length, and length of loop sequence were evaluated for their ability to form quadruplexes in presence of sodium (Na+) or potassium (K+) ions. The fluorescence behavior of YOYO-1 upon binding such G-rich sequences was also ascertained. A distinct correlation was observed between the strength and propensity of quadruplex formation, and the affinity of YOYO-1 to bind such sequences. Specifically, as exemplified by the oligonucleotides 5′-G4T2G4-3′ and 5′-G3TG3TG3-3′, sequences possessing longer G-rich regions and shorter loop sequences formed stronger quadruplexes in presence of K+ which translated to weaker binding of YOYO-1. The dependence of binding of YOYO-1 on sequence and structural features of G-rich DNA has not been explored previously and such studies are expected to aid in more effective interpretation of applications involving the fluorophore. © 2013 © 2013 Taylor &amp; Francis.

Journal of Biomolecular Structure and Dynamics

Interaction of YOYO-1 with guanine-rich DNA

The encapsulation of odorants by the synthetic receptor cucurbit[7]uril (CB[7]) reduces the response of olfactory receptors in Mozambique tilapia (Oreochromis mossambicus) in vivo. For example, the olfactory receptor response to the odorant adamantan-1-amine, as measured by electro-olfactography, was suppressed by 92% in the presence of CB[7]. A reduction in olfactory response of 88% was observed for pentane-1,5-diamine (cadaverine), an odorant associated with carrion avoidance in some fish. The results reveal how the association constants and the concentrations of natural and synthetic receptors play a determinant role and show that synthetic receptors can be used to remove bioactive molecules from fish olfaction. © 2014 American Chemical Society.

Synthetic versus natural receptors: Supramolecular control of chemical sensing in fish

The phototransformation of benzimidazole (BZ) and of the benzimidazole pesticide thiabendazole (TBZ) was investigated in aqueous solution in the absence and presence of the supramolecular host cucurbit[8]uril (CB8). ESI-MS and NMR reveal that both compounds form stable 1:2 host-guest complexes with CB8 (BZ2@CB8, TBZ2@CB8). The phototransformation of free BZ leads to dehydrodimerization, while for TBZ the photoreactivity leads to BZ, benzimidazole-2-carboximide and 2-acetylbenzimidazole. Inside CB8, BZ undergoes photohydrolysis to form 2-aminoformanilide, while for TBZ2@CB8 additional photoproducts were observed which are pH dependent. At pH 1.2 photolysis of TBZ2@CB8 leads to new red-shifted photoproducts with extended π conjugation. © The Royal Society of Chemistry and Owner Societies.

Photochemical and Photobiological Sciences

Phototransformation of benzimidazole and thiabendazole inside cucurbit[8]uril

Oxidative stress triggers the peroxidation ofω-6-polyunsaturated fatty acids to reactive lipid fragments, including (2E)-4-hydroxy-2-nonenal (HNE). We previously reported two parallel catabolic pathways of HNE. In this study, we report a novel metabolite that accumulates in rat liver perfused with HNE or 4-hydroxynonanoic acid (HNA), identified as 3-(5-oxotetrahydro-2-furanyl)propanoyl-CoA. In experiments using a combination of isotopic analysis and metabolomics studies, three catabolic pathways of HNE were delineated following HNE conversion to HNA. (i) HNA is ω-hydroxylated to 4,9-dihydroxynonanoic acid, which is subsequently oxidized to 4-hydroxynonanedioic acid. This is followed by the degradation of 4-hydroxynonanedioic acid via β-oxidation originating from C-9 of HNA breaking down to 4-hydroxynonanedioyl-CoA, 4-hydroxyheptanedioyl-CoA, or its lactone, 2-hydroxyglutaryl-CoA, and 2-ketoglutaric acid entering the citric acid cycle. (ii) ω-1-hydroxylation of HNA leads to 4,8-dihydroxynonanoic acid (4,8-DHNA), which is subsequently catabolized via two parallel pathways we previously reported. In catabolic pathway A, 4,8-DHNA is catabolized to 4-phospho-8-hydroxynonanoyl-CoA, 3,8-dihydroxynonanoyl-CoA, 6-hydroxyheptanoyl-CoA, 4-hydroxypentanoyl-CoA, propionyl-CoA, and acetyl-CoA. (iii) The catabolic pathway B of 4,8-DHNA leads to 2,6-dihydroxyheptanoyl-CoA, 5-hydroxyhexanoyl-CoA, 3-hydroxybutyryl-CoA, and acetyl-CoA. Both in vivo and in vitro experiments showed that HNE can be catabolically disposed viaω- and ω-1-oxidation in rat liver and kidney, with little activity in brain and heart. Dietary experiments showed thatω- and ω-1-hydroxylation of HNA in rat liver were dramatically up-regulated by a ketogenic diet, which lowered HNE basal level. HET0016 inhibition and mRNA expression level suggested that the cytochrome P450 4A are main enzymes responsible for the NADPH dependent ω- and ω-1-hydroxylation of HNA/HNE. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.