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 reduction of disulfides has a broad importance in chemistry, biochemistry and materials science, particularly those methods that use mechanochemical activation. Here we show, using isotensional simulations, that strikingly different mechanisms govern disulfide cleavage depending on the external force. Desolvation and resolvation processes are found to be crucial, as they have a direct impact on activation free energies. The preferred pathway at moderate forces, a bimolecular SN2 attack of OH- at sulfur, competes with unimolecular C-S bond rupture at about 2 nN, and the latter even becomes barrierless at greater applied forces. Moreover, our study unveils a surprisingly rich reactivity scenario that also includes the transformation of concerted SN2 reactions into pure bond-breaking processes at specific forces. Given that these forces are easily reached in experiments, these insights will fundamentally change our understanding of mechanochemical activation in general, which is now expected to be considerably more intricate than previously thought. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

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Nature Chemistry

Unexpected mechanochemical complexity in the mechanistic scenarios of disulfide bond reduction in alkaline solution

Oligothioetheramides: A novel strategy for the assembly of sequence-defined macromolecules

Significant progress has been observed in recent years in the synthesis of allylic amines, which are important building blocks in synthetic chemistry. Most of these processes are effective toward the preparation of allylic amines, with limited potential to introduce three or four different substituents on the olefinic unit in a stereocontrolled fashion. Therefore, the discovery of a mild and operationally simple protocol allowing such challenging stereoselective synthesis of multisubstituted allylic amines remains an inspiring target. Herein, we report the first general and practical methodology for the stereoselective synthesis of tri- and tetrasubstituted allylic amines based on Pd-catalyzed conversion of allyl surrogates readily obtained from cyclic vinyl carbonates. These rare conversions are characterized by excellent stereoselectivity, operational simplicity, mild reaction conditions, and wide scope in reaction partners. DFT studies were performed to rationalize the stereocontrol in these allylic amine formation reactions, and evidence is provided that the formation of a six-membered palladacyclic intermediate leads toward the formation of (Z)-configured allylic amine products. © 2016 American Chemical Society.

Fulltext

Journal of the American Chemical Society

Stereoselective and Versatile Preparation of Tri- and Tetrasubstituted Allylic Amine Scaffolds under Mild Conditions

We describe the design and characterization of a DNA polymerase-nanopore protein construct on an integrated chip. This system is able to incorporate all four DNA bases and distinguish single tagged nucleotide addition in real-time. Coupling protein catalysis and nanopore-based detection to an electrode array could provide the foundation of a highly-scalable, single-molecule, electronic DNA sequencing platform.

20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016

Design and characterization of a nanopore-coupled polymerase for single molecule DNA sequencing by synthesis on an integrated electronic array

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an a-hemolysin (aHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin-polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.

Proceedings of the National Academy of Sciences of the United States of America

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a singlemolecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotidebased polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time singlemolecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

We demonstrate for the first time the use of Fe-based nanoparticles on N-doped graphene as spacer and cavity materials and study their plasmonic effect on the spontaneous emission of a radiating dipole. Fe-C-MF was produced by pyrolizing FeOOH and melamine formaldehyde precursor on graphene, while Fe-C-PH was produced by pyrolizing the Fe-phenanthroline complex on graphene. The use of the Fe-C-MF composite consisting of Fe-rich crystalline phases supported on N-doped graphene presented a spacer material with 116-fold fluorescence enhancements. On the other hand, the Fe-C-PH/Ag based cavity resulted in an 82-fold enhancement in Surface Plasmon-Coupled Emission (SPCE), with high directionality and polarization of Rhodamine 6G (Rh6G) emission owing to Casimir and Purcell effects. The use of a mobile phone as a cost-effective fluorescence detection device in the present work opens up a flexible perspective for the study of different nanomaterials as tunable substrates in cavity mode and spacer applications. © 2016 American Chemical Society.

ACS Applied Materials and Interfaces

Earth Abundant Iron-Rich N-Doped Graphene Based Spacer and Cavity Materials for Surface Plasmon-Coupled Emission Enhancements

Mammalian sirtuins (SIRT1-7) are members of a highly conserved family of nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylases that regulate many biological processes including metabolism, genome stability, and transcription. Among the seven human sirtuins, SIRT7 is the least understood, to a large extent due to the lack of enzymatic activity in vitro. Here, we reported that SIRT7 can be activated by DNA to hydrolyze the acetyl group from lysine residues in vitro on histone peptides and histones in the chromatin context. Both N- and C- termini of SIRT7 are important for the DNA-activated deacetylase activity. The regulatory mechanism of SIRT7 is different from that of SIRT6, which also showed increased activity on chromatin substrates, but the deacetylase activity of SIRT6 on a peptide substrate cannot be activated by DNA. This finding provides an improved enzymatic activity assay of SIRT7 that will promote the development of SIRT7 modulators. Further investigation into the activation mechanism of SIRT7 by DNA could provide new insights into its biological function and help the development of sirtuin activators. © 2016 American Chemical Society.

ACS Chemical Biology

SIRT7 Is Activated by DNA and Deacetylates Histone H3 in the Chromatin Context

The syntheses and structural characterization of the CS2–metal complexes [(η5-C5Me5M)(η2-S2CH2)(η3-S2CH)] (1: M = Mo; 2: M = W), which feature partially and fully reduced CS2, are reported. In addition, the cis and trans isomers of the dimetallic (sulfido)molybdenum complexes [(η5-C5Me5Mo)2(µ-S2CH2S)2] (3-cis and 4-trans) are described. The [Mo2S4] cores of 3-cis and 4-trans represent paddlewheel-like arrays. All the new compounds were characterized in solution by mass spectrometry, IR spectroscopy and1H and13C NMR spectroscopy. Their structural architectures were established by X-ray crystallographic analysis. Quantum-chemical calculations by DFT methods on the model compounds 1′–4′-trans showed good agreement with the experimentally observed structural parameters. The large HOMO–LUMO (HOMO = highest occupied molecular orbital, LUMO = lowest unoccupied molecular orbital) gaps are consistent with the high thermodynamic stabilities of these complexes. Further, the presence of short metal–metal cross-cluster bonds in the X-ray structures of 3-cis and 4-trans is supported by natural bond order (NBO) calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

European Journal of Inorganic Chemistry

Reactivity of CS2 – Syntheses and Structures of Transition‐Metal Species with Dithioformate and Methanedithiolate Ligands

Chloro-rhodaboratrane [(Cp∗Rh)(L2)BCl] 4 has been synthesized from rhodium N,S-heterocyclic carbene complex [(Cp∗Rh)(L2)(1-benzothiazol-2-ylidene)], 1, (L = C7H4NS2) and borane reagent BHCl2.SMe2. The Rh-B bond in 4 is buttressed between two benzothiazolyl units in [3.3.0] fashion. The presence of B-Cl bond allowed us to explore the chemistry of boratrane 4 at the boron centre. The reaction of ethynylmagnesium bromide with 4 yielded η1-vinyl complex [Cp∗RhBr(C2H2)L] 5, containing a five membered metallaheterocycle. In an objective to abstract the chloride, alike borylene synthesis from haloboryl, we performed the reaction of 4 with NaBArF4 that resulted the thiolato bridged bimetallic compound [Cp∗Rh(μ-L)3RhCp∗][BArF4] 6 (ArF: C6H3(CF3)2-3,5). © 2016 Elsevier B.V. All rights reserved.