Chemistry

<p>Shiv Nadar University is a comprehensive, multidisciplinary, research-focused, and student-centric University offering a full range of academic programs at the undergraduate, postgraduate and doctoral level. With state-of-the-art infrastructure, the University comprises of academic wings, sophisticated labs, international standard sports facilities, amphitheaters, auditorium, conference rooms and smart classrooms. The University&rsquo;s goal is to become internationally recognized for the quality of its research and creative endeavors and their applicability to improving quality of life, generating new insights and expanding the boundaries of human knowledge creativity. Committed to excellence in teaching, research and service, the University aims to serve the higher education needs of India and the world beyond.</p>

Shiv Nadar University

Due to the prevalent use of polycarbonate plastics and epoxy resins in packaging materials and paints for ships, there has been a widespread global contamination of environmental water sources with bisphenol A (BPA). BPA, an endocrine disruptor, has been found to cause tremendous health problems. Therefore, there is an urgent need for detecting BPA in a convenient and sensitive manner to ensure water safety. Herein, we develop a fluorescent turn-on BPA probe, named Bisphenol Orange (BPO), which could conveniently detect BPA in a wide variety of real water samples including sea water, drain water and drinking water. BPO shows superior selectivity toward BPA and up to 70-fold increase in fluorescence emission at 580. nm when mixed with BPA in water. Mechanistic studies suggest a plausible water-dependent formation of hydrophobic BPA clusters which favorably trap and restrict the rotation of BPO and recover its inherent fluorescence. © 2014 Elsevier B.V.

World University root node

(SoNS) School of Natural Sciences

Analytica Chimica Acta

"Orange alert": A fluorescent detector for bisphenol A in water environments

The Raman signal enhancement depends mainly on four critical factors. These factors are localized surface plasmon resonance (LSPR) of gold substrates along with shape and electronic absorbance of Raman reporters along with laser sources. Hence, the effects of all these four parameters were systematically studied by changing either the different geometries/shapes of the gold substrates having a wide range of SPR or electronic absorbance of Raman reporters under a fixed laser excitation of 633 nm or 785 nm. Enhancement factor (EF) values were evaluated for each individual substrate with respect to five different Raman reporters which cover the maximum absorbance from 530 nm to 800 nm. The EF values suggest that the signal intensity has been increased by at least ten times compared to previous reports. Among the five different shapes of the gold nanoparticles, the substrate of gold nanostars (GNSt) was found to be the most suitable substrate for the highest signal enhancement under both excitation laser sources. The substrate of gold nanosphere (GNSp) is the second best at 633 nm laser excitation; however it is the modest substrate for SERS enhancement at 785 nm laser excitation. After finding the key tools for the development of ultrasensitive SERS nanoprobes, we selected the best Raman reporter (Cy7LA) for the development of biocompatible SERS nanotags in three different SERS substrates for the effective detection of cancer cells under 785 nm laser source. © 2014 The Royal Society of Chemistry.

Fulltext

RSC Advances

Wavelength and shape dependent SERS study to develop ultrasensitive nanotags for imaging of cancer cells

Chemistry - An Asian Journal

Erratum: Synthesis of privileged scaffolds by using diversity-oriented synthesis (Chemistry - An Asian Journal (2013) 8 DOI: 10.1002/asia.201201203)

Exploration of sustainable alternatives to chemicals derived from petro-based industries is the current challenge for maintaining the balance between the needs of a changing world while preserving nature. The major source for sustainable chemicals is either the natural existing plant sources or waste generated from agro-based industries. The utility of such resources will supplement new processed materials with different sets of properties and environmental friendliness due to their biodegradability and low toxicity during preparation, usage and disposal. Amongst other polymers used on a day-to-day basis, phenolic resins account for vast usage. Replacement of petro-based monomers such as phenol and its derivatives either partly or completely utilized for the synthesis of such resins is ongoing. Extraction of natural phenolic components from cashew nut shell liquid, lignin, tannin, palm oil, coconut shell tar or from agricultural and industrial waste, and their utilization as synthons for the preparation of bio-based polymers and properties obtained are reviewed in this paper. This review article is designed to acknowledge efforts of researchers towards the "3C" motto-not only trying to create but also adapting the principles to conserve and care for a sustainable environment. This review paper describes how extraction, separation and recovery of desired phenolic compounds have occurred recently; how substituted phenol compounds, unmodified and modified, act as monomers for polymerization; and how the presence of sustainable phenolic material affects the properties of polymers. There are about 600 references cited and still there is a lot to uncover in this research area. This journal is © the Partner Organisations 2014.

Naturally occurring phenolic sources: Monomers and polymers

Catalytic signal amplification was used for the colorimetric detection of CN− in aqueous media by using the enzyme catalase in tandem with mesoporous silica nanoparticle based synthetic HRP enzyme mimic Fe-MSNs. Signal amplification up to a maximum of eight fold was observed for the reporter “oxidized TMB” with respect to the added CN− ion. © 2013 The Royal Society of Chemistry.

Chemical Communications

Catalytic signal amplification using [FeIII(biuret-amide)]-mesoporous silica nanoparticles: Visual cyanide detection

Change in pH plays a crucial role in the stability and function of the dengue envelope (DENV) protein during conformational transition from dimeric (pre-fusion state) to trimeric form (post-fusion state). In the present study we have performed various molecular dynamics (MD) simulations of the trimeric DENV protein at different pH and ionic concentrations. We have used total binding energy to justify the stability of the complex using the MMPBSA method. We found a remarkable increase in the stability of the complex at neutral pH (pH ∼ 7) due to the increment of sodium ions. However, at very low pH (pH ∼ 4), the total energy of the complex becomes high enough to destabilize the complex. At a specific pH, almost at a range of 6, the stability of the complex is significantly better than the stability of the trimer at neutral pH, which connotes that the trimer is most stable at this pH (pH ∼ 6). © 2012 Elsevier B.V. All rights reserved.

Biochimica et Biophysica Acta - Proteins and Proteomics

Stability of trimeric DENV envelope protein at low and neutral pH: An insight from MD study

Temperature dependent steady state and time resolved fluorescence measurements have been performed to explore the interaction and dynamics in polymer-electrolyte composite of the following general formula: 0.85 PEG 0.15{f KNO3 (1-f) LiNO3}, with f denoting fraction of potassium ion in the 0.15 mol electrolyte present in the medium. Poly(ethylene glycol) with number-averaged molecular weight of 300 (PEG300) has been employed as polymer and C153 as the fluorescent probe. Substantial excitation wavelength dependence of probe fluorescence emission in presence of electrolyte suggests presence of spatial heterogeneity which vanishes either upon raising temperature or removing the electrolyte. This has been interpreted as arising from the cation-induced arrest of polymer segmental motion. Temporal heterogeneity in these composites is manifested via fractional viscosity dependence of average solvation and rotation rates of the dissolved probe. Viscosity decoupling of these rates in composites is found to depend on cation identity and is also reflected via the corresponding activation energies. The degree of decoupling differs between solvation and rotation, inducing an analogy to the observations made in deeply supercooled liquids. In addition, conformity to hydrodynamic predictions is recovered by measuring f dependent solute rotation at higher temperatures. Several complimentary but different experiments are suggested to re-examine the mechanism proposed here, based on the fluorescence results, for the emergence of spatio-temporal heterogeneity in these composites and its disappearance either in the absence of any electrolyte or at higher temperatures. © 2013 American Institute of Physics.

Journal of Chemical Physics

Ionic arrest of segmental motion and emergence of spatio-temporal heterogeneity: A fluorescence investigation of (polyethylene glycol electrolyte) composites

Computational techniques are one of the most emerging topics in structural and molecular biology. Molecular dynamics (MD) simulations are used not only to explore the conformational aspects of biological systems but also to have significant scope in protein-ligand interactions. Then the binding free energy calculations are readily applied to the simulated systems in order to predict the binding affinities. The thermodynamic properties are directly related to protein-ligand interactions which are dependent upon a few specific parameters. In the present review, we highlight some facts related to protein-ligand complexes, by starting with a survey of MD simulations and binding free energy calculations and ending with some successful implementations of these computational techniques. © 2013 Bentham Science Publishers.

Current Computer-Aided Drug Design

Recent advances in protein-ligand interactions: Molecular dynamics simulations and binding free energy

Background: Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. Results: A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. Conclusions: The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands. © 2013 Munshi et al.; licensee BioMed Central Ltd.

BMC Structural Biology

Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein

Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements. © 2013 American Chemical Society.

Journal of Physical Chemistry B

Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: A combined dynamic fluorescence and all-atom molecular dynamics simulation study