Department of Chemistry

&ldquo;IIT Jodhpur is committed to impart quality education to facilitate the creation of qualified, competent and responsible human resources to meet the emerging technological challenges of the world. It is working towards creating an equitable learning platform that is positive, accessible and effective in the face of the modern societal and scientific advancements.

Flexibility in curriculum, in all its academic programs, encompassing elements of teaching, research, creativity, innovation and entrepreneurship is the most unique feature of IIT Jodhpur. The Department of Science and Technology (DST), under the National Mission on Cyber Physical Systems, has identified IIT Jodhpur as a Technology &amp; Innovation Hub in the area of Augmented Reality and Virtual Reality. The institute has also been nominated as the coordinator for the Jodhpur City and Knowledge Cluster by the Office of Principal Scientific Adviser, Government of India.

The sprawling 852-acre IIT Jodhpur campus is a majestic tribute to the deep-rooted diverse cultural heritage of the region. The campus is an architectural masterpiece, which is slated to become an international exemplar of sustainability with net-zero energy, and advanced water and waste management strategies.&rdquo;

IIT Jodhpur

Spectroelectrochemicalinvestigation of racemic alanine on poly crystalline metal surfaces was studied in 1M LiClO4 medium, to achieve cost effective separation of biologically important molecules from the racemic mixture. Analysis of the FTIR spectrum of racemic alanine in 1M LiClO4 indicated degradation of the same. Upon prolonged exposure in LiClO4, byproducts from degradation of alanine increasedin concentration as also observed from UV-Vis spectroscopy. Cyclic Voltammetry studies unraveled different adsorption behaviors on different metal surfaces for the racemic and the enantiomeric solution of alanine. Further FTIR analysis of the alanine solution after Cyclic Voltammetry revealed possible presence of cyanide (-C=N) and terminal alkyne as byproducts. As predicted by Monte Carlo simulations earlier, Circular Dichroism implied the dextro rotation of the racemic alanine solution after Cyclic Voltammetry. These results support the preferential adsorption of L-alanine over D-alanine from racemic mixture that could be attributed to the umbrella inversion of the molecule after adsorption on the metal surface in presence of applied electric field in the LiClO4 environment. A plausible mechanism for the formation of terminal alkyne and - C=N byproducts had also been attempted. © The Electrochemical Society.

World University root node

ECS Transactions

Separation of enantiomers of alanine from racemic mixture by polycrystalline metal surfaces - A spectroelectrochemical approach

Abstract: Empirical stochastic multi-variable models for prediction of treatment efficiency of wetlands are presented in this article. Wetlands of seven different shapes are visualized using tracer studies. Two different variants of experiments are carried out. Numerous flow rate variations are performed keeping surface area of the wetland constant. The experiment is also carried out with a variation in volume of the wetland which helps to study the effect of flow height on the hydrodynamics within the wetland. A multi-variable model for treatment efficiency in terms of change in tracer concentration as a function of shape, volumetric height of water within the wetland, time, and mass flow rate is considered. Further, another set of experiments is performed studying the treatment efficiency in terms of electro-kinetic parameters. This involves measuring the pH, turbidity, temperature, electrical conductivity, total dissolved salts at inlet and outlet and residence time with varying flow rate, and height of water for the seven different wetland models under study. The electro-kinetic parameters changes due to difference in concentration of the tracer dye which simulates impurities. In this case, treatment efficiency is expressed as a function of the above-discussed electro-kinetic variables, time variation, water height, as well as variation in the mass flow rate. The stochastic multi-parameter models, thus, empirically derived in the above two cases have high coefficient of determination. The models thus derived may be used as a tool for quick analysis of treatment efficiency of any shape and size of a three-dimensional wetland. © 2014 Balaban Desalination Publications. All rights reserved.

Department of Mechanical Engineering

Department of Computer Science & Engineering

Desalination and Water Treatment

Multi-variable approach to determine treatment efficiency of wetland: size effect and electro-kinetic effects

Achieving high Raman enhancement (SERS) that is relatively uniform over a large substrate area has been a major challenge in nanomanufacturing, as enhancement is localized around a plasmonic hotspot and hotspots are not usually spread uniformly over a substrate. Herein, we demonstrate a single-step, scalable method for the fabrication of Ag nanohole-based SERS substrates exhibiting ∼108 enhancement factors. The SERS enhancement of these substrates could be further augmented by approximately 4 times through interference effects involving an underlying SiO2 spacer of controlled thickness on the Si substrate, in agreement with FDTD simulations. Electrical activation by applying a short DC pulse across the Ag film and Si substrate resulted in ∼12% additional increase in the enhancement factor, while importantly the standard deviation of the signal across the 1 cm2 substrate decreased from 9.5% to 3.1%. Both these effects could be attributed to electromigration of the metal producing protrusions on the nanoparticle surfaces thus populating with the hotspots for high performance SERS. These relatively uniform and reproducible SERS-chips with high enhancement factors can potentially be used as highly sensitive multi-functional platforms for point-of-care diagnostics. © 2015 The Royal Society of Chemistry.

RSC Advances

Solution processed nanomanufacturing of SERS substrates with random Ag nanoholes exhibiting uniformly high enhancement factors

Capsaicin is a versatile plant product which has been ascribed several health benefits and anti-inflammatory and analgesic properties. We have investigated the effect of capsaicin on the molecular stability, self-assembly, and fibril stability of type-I collagen. It was found that capsaicin suppresses collagen fibril formation, increases the stability of collagen fibers in tendons, and has no effect on the molecular stability of collagen. Turbidity assay data show that capsaicin does not promote disassembly of collagen fibrils. However, capsaicin moderately protects collagen fibrils from enzymatic degradation. Computational studies revealed the functions of the aromatic group and amide region of capsaicin in the collagen-capsaicin interaction. The results may have significant implications for capsaicin-based therapeutics that target excess collagen accumulation-linked pathology, for example thrombosis, fibrosis, and sclerosis.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Capsaicin inhibits collagen fibril formation and increases the stability of collagen fibers

Department of Bioscience & Bioengineering

Hypervalent iodine(III) reagents have been widely exploited in a diverse array of synthetic transformations. This chapter focuses on the general application of hypervalent iodine(III) reagents in the de novo synthesis and in the late stage functionalization of heterocyclic compounds. © Springer International Publishing Switzerland 2015.

Topics in Current Chemistry

Oxidative heterocycle formation using hypervalent iodine(III) reagents

(Graphical Abstract) The reaction of Ph3Bi with a sterically hindered phosphinic acid, 1,1,2,3,3-pentamethyltrimethylene phosphinic acid, {cycP(O)OH·2H2O}, at two different temperatures, one at refluxing conditions and another at room temperature, in tetrahydrofuran has been investigated. At refluxing conditions, cleavage of two Bi-C bonds (of BiPh3) leads to the formation of a 16-member macrocycle [(PhBi)4(cycPO2)8] (1). On the other hand, the reaction at room temperature leads to the cleavage of one Bi-C bond only, affording a 1D polymer [(Ph2Bi)(cycPO2)]n, ((1,1,2,3,3-pentamethyltrimethylene phosphinate is denoted as cycPO2) (2). Both the complexes were characterized by single crystal X-ray diffraction. In both complexes the phosphinate ligands are present in an anisobidentate (bridging) coordination mode. Copyright © Taylor & Francis Group, LLC.

Phosphorus, Sulfur and Silicon and the Related Elements

Bismuth Phosphinates: Temperature-dependent formation of a macrocycle and 1D coordination polymer

A highly efficient stereoselective method for the synthesis of functionalized spirooxindole derivatives with four contiguous stereogenic centers, including two adjacent quaternary stereogenic centers, was realized through an organocatalytic tandem Michael-Michael reaction. By employing a quinidine-derived thiourea organocatalyst, the reaction between (E)-2-cyano-2-(2-oxo-1-tritylindolin-3-ylidene)acetates and (E)-1-alkyl-6-nitro-hex-2-en-1-ones yields the desired spirooxindole products in good yields (up to 90%) and with excellent stereoselectivities (up to 95:5 dr and 98% ee). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced Synthesis and Catalysis

Organocatalytic Enantioselective Synthesis of Polysubstituted Spirooxindoles using a Tandem Michael-Michael Reaction

The correct interplay of interactions between protein, pigment and lipid molecules is highly relevant for our understanding of the association behavior of the light harvesting complex (LHCII) of green plants. To cover the relevant time and length scales in this multicomponent system, a multi-scale simulation ansatz is employed that subsequently uses a classical all atomistic (AA) model to derive a suitable coarse grained (CG) model which can be backmapped into the AA resolution, aiming for a seamless conversion between two scales. Such an approach requires a faithful description of not only the protein and lipid components, but also the interaction functions for the indispensable pigment molecules, chlorophyll b and chlorophyll a (referred to as chl b/chl a). In this paper we develop a CG model for chl b and chl a in a dipalmitoylphosphatidyl choline (DPPC) bilayer system. The structural properties and the distribution behavior of chl within the lipid bilayer in the CG simulations are consistent with those of AA reference simulations. The non-bonded potentials are parameterized such that they fit to the thermodynamics based MARTINI force-field for the lipid bilayer and the protein. The CG simulation shows chl aggregation in the lipid bilayer which is supported by fluorescence quenching experiments. It is shown that the derived chl model is well suited for CG simulations of stable, structurally consistent, trimeric LHCII and can in the future be used to study their large scale aggregation behavior. © the Owner Societies 2015.

Fulltext

Physical Chemistry Chemical Physics

Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems

We investigated structural and dynamical properties of nanodiscs comprising dimyristoylphosphatidylcholine (DMPC) lipids and major scaffold protein MSP1Δ(1-22) from human apolipoprotein A-1 using combined all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. The computational efficiency of the Martini-CG force field enables the spontaneous self-assembly of lipids and scaffold proteins into stable nanodisc structures on time scales up to tens of microseconds. Subsequent all-atom and CG-MD simulations reveal that the lipids in the nanodisc have lower configurational entropy and higher acyl tail order than in a lamellar bilayer phase. These altered average properties arise from rather differential behavior of lipids, depending on their location in the nanodisc. Since the scaffold proteins exert constrictive forces from the outer rim of the disc toward its center, lipids at the center of the nanodisc are highly ordered, whereas annular lipids that are in contact with the MSP proteins are remarkably disordered due to perturbed packing. Although specific differences between all-atom and CG simulations are also evident, the results obtained at both levels of resolution are in overall good agreement with each other and provide atomic level interpretations of recent experiments. Thus, the present study highlights the applicability of multiscale simulation approaches for nanodisc systems and opens the way for future applications, including the study of nanodisc-embedded membrane proteins. (Graph Presented). © 2015 American Chemical Society.