TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

February 14, 2017 at 2.30 pm in AG-69

Title :

Inhibition of formation of alpha-synuclein amyloid fibrils by Triphala, a herbal preparation

February 13, 2017 at 4.00 pm in AG-69

Title :

EUV Laser Photoelectron Spectroscopy of Mass Selected Neutral Clusters and Molecules

Abstract :

Over the past 15 years our research interests have focused on four main and related areas: 1. properties, chemistry, catalytic, and photo-catalytic behavior of neutral, inorganic, isolated clusters, MmM’nXpHq (M,M’ = metals, X = O, S, C); 2. initial release of stored chemical energy from isolated energetic molecules (e.g., RDX, HMX, CL -20, high N- content species, …); 3. small molecule, neutral clusters (e.g., (NH3)n, (H2O)n, (NH3BH3)n, (SO2)n, …) and their ion chemistry; and 4. structure, energetics, ion fragmentation reactions of “simple” bio-related molecules (e.g., amino acids, saccharides, neurotransmitters, and DNA bases). These studies have evolved from characterization of energy levels and intermolecular interactions, to ultrafast kinetics and dynamics of molecular cluster reactions, to the study of inhomogeneous catalytic and photo-catalytic cluster reactions. Clusters and molecules are identified through mass spectrometry, UV/Vis electronic spectroscopy, and most recently photo-electron spectroscopy (PES) employing visible, UV, VUV, extreme ultraviolet (EUV, soft x-ray) lasers. Decomposition reactions for the initial release of molecular stored chemical energy have been time resolved at less than 100 fs. In order to acquire, analyze, and interpret the experimental data obtained on these systems, we have had to develop an essential theoretical/calculational component for our program. This seminar reviews our initial synthesis and reaction studies through mass spectrometry of neutral catalytic and photo-catalytic inorganic clusters, small molecule cluster ion reactions, and generation of new cluster species. These results serve as motivation for constructing a new PES apparatus employing visible, UV, VUV, and EUV photons for photo-detachment of anionic and neutral species in order to acquire spectroscopic data on the systems of interest. We will discuss these new results for FexSyHz clusters, energetic materials, and bio-related saccharides and DNA bases. The importance of the new spectroscopic (PES) data for these systems is that they enable the evaluation of theoretical techniques in order that proper algorithms and approaches may be employed to generate results that are not presently experimentally accessible, such as cluster and molecular structure, reaction mechanisms, and general electronic state specific potential energy surfaces. 

February 7, 2017 at 2.30 pm in AG-69

Title :

Modulation of the Electronic Structure and Phonon Transport of SnTe for High Thermoelectric Performance

Abstract :

Lead chalcogenides are the best performers for thermoelectric power generation at mid-high temperatures; however, environmental concern about Pb limits its use in large-scale thermoelectric applications. SnTe, a IV-VI narrow band gap semiconductor, can be an alternative of PbTe due to its similar crystal structure and valence band characteristics.1 The journey of SnTe, as a potential thermoelectric material begins with In doped SnTe where In creates resonance level. This has been further optimized via lattice thermal conductivity reduction in SnTe1-xSex.2 Another constraint of SnTe is the large energy separation between the light and heavy hole valence bands which restricts the contribution of heavy hole mass to the Seebeck coefficient. Doping of Mg and Ag in SnTe significantly tunes the electronic structure of SnTe, which decreases energy difference between the light hole and heavy hole valence bands, leading to enhanced Seebeck coefficient and thermoelectric efficiency.3,4 Co-doping of the In and Ag in SnTe yields synergistic enhancement in Seebeck coefficient and power factor over a broad temperature range because of the introduction of resonance state and convergence of valence bands.1 Moreover, pristine SnTe exhibits κlat of ~2.88 Wm-1K-1 at room temperature, while theoretical limit for minimum lattice thermal conductivity (κmin) is ~0.5 Wm-1K-1. We have successfully reduced lattice thermal conductivity of SnTe near to its theoretical minimum limit, κmin, via Sb alloying which spontaneous form nanodomains of Sb-rich layered intergrowth SnmSb2nTe3n+m compounds.5

1. Banik, A.; Shenoy, U. S.; Waghmare, U. V.; Biswas, K. J. Am. Chem. Soc. 2016, 138, 13068.

2. Banik, A.; Biswas, K. J. Mater. Chem. A 2014, 2, 9620-9625.

3. Banik, A.; Shenoy, U. S.; Anand, S.; Waghmare, U. V.; Biswas, K. Chem. Mater. 2015, 27, 581.

4. Banik, A.; Biswas, K. J. Solid State Chem. 2016, 242, 43.

5. Banik, A.; Vishal, B.; Perumal, S.; Datta, R.; Biswas, K. Energy Environ. Sci. 2016, 9, 2011-2019.

February 6, 2017 at 4.00 pm in AG-69

Title :

Fibrous Nanosilica: Tunable Synthesis, Its Applications in Catalysis, CO2 Capture and Novel Materials Design

February 3, 2017 at 2.30 pm in AG-69

Title :

Revealing the Nanoscale Order of Dynamic Molecules Within Microscale Assemblies (Part-II)

Abstract :

Living systems differ from inanimate ones by their ability to create and sustain ordered assemblies of molecules at the expense of chemical energy. The ‘parts list’ of biomolecular assemblies is being discovered at a rapid pace, but how these parts come together to form functional cellular mechanisms remains an outstanding question in many fields of biology. For example, the principal components of the cellular contractile machinery that shapes, divides, and moves cells have been known for a long time, viz., actomyosin network, plasma membrane, and adhesion complexes. But the dynamic architecture of this machinery remains challenging to measure, especially in three-dimensional (3D) (patho)physiological environments.

The architecture of the molecular assemblies within cells that adhere to 2D unphysiological substrates often does not provide predictive insights into the assemblies’ function in the 3D physiological environments. We have devised a confocal LC-PolScope, which employs liquid crystal (LC)-based tuning of polarization, to measure nanoscale alignment and orientation of filamentous assemblies in 3D environments. Our data provides new insights into the molecular architecture of the contractile machinery that drives cytokinesis and migration of cells in 3D environments. 

Building upon above advances, the future studies will reveal the molecular architectural basis of the directional forces generated by single cells and a collective of cells within 3D (patho)physiological environments.

 

February 2, 2017 at 2.30 pm in AG-80

Title :

Revealing the Nanoscale Order of Dynamic Molecules Within Microscale Assemblies (Part-I) 

Abstract :

Living systems differ from inanimate ones by their ability to create and sustain ordered assemblies of molecules at the expense of chemical energy. The ‘parts list’ of biomolecular assemblies is being discovered at a rapid pace, but how these parts come together to form functional cellular mechanisms remains an outstanding question in many fields of biology. For example, the principal components of the cellular contractile machinery that shapes, divides, and moves cells have been known for a long time, viz., actomyosin network, plasma membrane, and adhesion complexes. But the dynamic architecture of this machinery remains challenging to measure, especially in three-dimensional (3D) (patho)physiological environments.

Our recent work has led to fluorescence-based computational microscopy assays that reveal nanoscale architecture of molecules within the context of microscale assemblies. We exploit intrinsic polarization of fluorescence to measure sub-resolution orientation and alignment of molecules. We have developed an instantaneous fluorescence polarization microscope (instantaneous fluorescence PolScope) to analyze the dynamic changes in concentration, position, and orientation of molecules (Mehta et al., PNAS 2016). Instantaneous fluorescence PolScope acquires four polarization-resolved images of dynamic molecules with single molecule sensitivity. The image data is then computationally translated into orientation, concentration, and kinetics of the cytoskeletal networks. This computational microscopy approach revealed nanoscale orientation of actin filaments relative to the retrograde flow of the network at the leading edge of cells migrating on 2D surfaces. Analysis of actin filament orientation at the leading edge has been possible only in fixed cells with electron microscopy. Further, in a multi-institutional collaboration (Swaminathan et al., bioRxiv 2016 and Nordenfelt et al., bioRxiv 2016), synergistic use of fluorescence polarization microscopy and computational analysis revealed that integrin transmembrane receptors are ‘actively aligned’ by their engagement with retrograde flow and extracellular ligand. The active alignment of integrin receptors may be a general mechanism used by cells to sense directional cues within extracellular matrix and is uniquely accessible with fluorescence polarization microscopy in live cells. 

 

January 30, 2017 at 4.00 pm in AG-69

Title :

Towards a Novel Theoretical Approach to Characterize Biomolecular Flexibility

January 25, 2017 at 11.00 a.m. in AG-80

Title :

Allostery in Chaperonins: How and Why?

Abstract :

Chaperonins are large protein assemblies that assist protein folding in an atp-dependent fashion. I will discuss their allosteric mechanisms and how they impact their folding function.

January 24, 2017 at 2.30 pm in AG-80

Title :

Carbonaceous- and Layered-material based Hybrids for Drug Delivery and Catalysis

Abstract :

In this presentation, I will talk about synthesis and characterization of various hybrid materials and their applications in drug delivery and catalysis. Carbonaceous nanospheres derived from glucose show preferential accumulation into the mice brain. We have modified the surface of these spheres with magnetic (Prussian blue and its analogues) nanoparticles and luminescent (lanthanide) probes to make brain theranostic agents. These multifunctional hybrid spheres showed enhanced magnetic and luminescent behaviour. They were biocompatible, entered brain, and showed no toxicity to the mice. The method of fabrication was versatile and could be used to create a number of theranostic systems for brain. Hybrid nanoparticles were synthesized from glucose derived carbon and iron oxide in the form of different morphology. Depending on their shape, these nanoparticles could compartmentalize inside the brain cells in the in vivo conditions. Biconcave shape of nanoparticles showed preferential nuclear entry, whereas nanotube morphology was restricted to the cytoplasm. Also, shape dependent compartmentalized delivery of an activator of an epigenetic enzyme was demonstrated. Smart hybrid nanospheres were prepared using layered clay and polyelectrolytes in a layer-by-layer fashion. These hybrid spheres showed reversible size change (about 60%) in response to pH, in the range of physiologically relevant pH values. Hybrids were also demonstrated for their pH dependent drug release ability. Catalytic behaviour of layered boron nitride and boron nitride supported metals towards oxidative dehydrogenation of propane was studied. Boron nitride (a generally accepted inert material) catalysed the propane oxidative dehydrogenation reaction. The catalytic activity was found to improve with increasing surface area of the catalyst. The catalytic activity was stable for nearly 5 hours and could be regenerated easily by heating in dilute ammonia. Oxidation of surface B-N bonds in oxygen leads to the diminishing catalytic activity, which on heating in ammonia reduced back to their native form regaining the indigenous catalytic activity. Remarkably, the high propene selectivity and yields obtained for these metal free catalysts were comparable to the reported catalysts and could be further increased by using higher surface area boron nitride samples.

References:

1. P Chaturbedy et. al. Journal of Nanobiotechnology (2012), 10, 35.

2. P Chaturbedy et. al. J. Mater. Chem. B (2013), 1, 939-945.

3. P Chaturbedy et. al. Journal of Controlled Release (2015), 217, 151-159.

4. P Chaturbedy et. al. ACS Nano (2010), 4, 5921-5929.

5. P Chaturbedy et. al. Manuscript under preparation (2017).

 

January 23, 2017 at 4.00 pm in AG-69

Title :

Encoding Formation Mechanism of KCC-1

January 20, 2017 at 2.30 pm in AG-69

Title :

Strategy to Tune Equilibrium Dopant Composition in Semiconductor Nanocrystals

Abstract :

Intentional incorporation of dopants into the semiconductor nanocrystals can dramatically alter the electronic, optical, magnetic, and electrical properties. Understanding the fundamental chemical boundaries of nanocrystal composition control for new and challenging dopant/host combinations could yield unprecedented doped semiconductor nanomaterials for applications from spectral conversion in lighting and luminescent solar concentrators (LSCs), to optical nano-thermometry, bioimaging, plasmonics, or spinbased electronic/photonic information processing. Enormous efforts and many attempts have been made to dope semiconductor nanocrystals with transition metal ions by means of colloidal chemical synthesis. Despite these efforts, successful dopant incorporation into host nanocrystals remains a long-standing challenge. The primary challenges are associated with unfavorable impurity/host competition kinetics during nanocrystal growth. To overcome these challenges, a qualitatively new method of nanocrystal diffusion doping under thermodynamic control has recently been developed where dopants are introduced into preformed nanocrystals via stoichiometric addition of cations and anions, followed by diffusion of these impurities into the nanocrystal's internal volume while maintaining the nanocrystal size, shape, and structural uniformity. This talk focuses on broadening the scope of this powerful chemistry, in conjunction with cation exchange chemistries, to allow dopants to be incorporated into the host nanocrystal lattice, thereby providing a general methodology for controlling dopant composition under thermodynamic equilibrium. In addition, mechanistic understanding of the dopant ion diffusion in these nanocrystals will be discussed, which contributes to our fundamental understanding of this rich area of nanoscience and improves our ability to tailor the compositions of nanostructures for future advanced technological applications.

January 19, 2017 at 2.30 pm in AG-69

Title :

Variation of the Cooperativity and the Role of Ligand-field States in Spincrossover Compounds

Abstract :

The spin-crossover process involves the rearrangement of electrons within metal dorbitals from the high-spin (HS) to the low-spin (LS) configuration corresponding to the distribution that yields maximum and minimum number of unpaired electrons respectively. The relative population of the spin states is a function of various external perturbations such as temperature, magnetic fields, external pressure, and light irradiation. Therefore, these materials are of current interest in chemistry and materials science not only because of their intrinsic fundamental properties but also because of their potential applications as functional materials for the construction of sensors, as well as memory and display devices. In the present talk, the thermal and photo-induced spin switching dynamics and the variation of the cooperative effects in the spin-crossover coordination networks will be discussed. The aim is to understand the physics of cooperative effects and establish the limits of cooperativity. In addition, the role of ligand-field states in the ultrafast photophysics of the prototypical spin-crossover compound will be discussed. The involvement of ligand-field states in transition-metal photophysics is nevertheless crucial, and that they are by no means innocent is borne out by the discovery of photo-induced processes in spin-crossover compounds, which has no low-energy Metal-to-Ligand-Charge-Transfer (MLCT) states.

January 16, 2017 at 4.00 pm in AG-69

Title :

RNA Editing by Adenosine Deaminases

Abstract :

ADARs (adenosine deaminases acting on RNA) are editing enzymes that convert adenosine (A) to inosine (I) in duplex RNA, a modification that has wide-ranging consequences on RNA function including altering miRNA recognition sites, redirecting RNA splicing and changing the meaning of specific codons in mRNA. Recent work has demonstrated a causal link between altered RNA editing and human disease. However, our understanding of the ADAR reaction mechanism, origin of editing site selectivity and the effect of disease-causing mutations was limited by the lack of high-resolution structural data for complexes of ADARs bound to RNA. This presentation will describe the combined chemical biology/structural biology approach used to solve this problem wherein we used RNA bearing a nucleoside analog to trap the reaction intermediate allowing for crystallization of the complexes. Solving the structures of the complexes uncovered ADARs’ use of a unique base-flipping mechanism well-suited for modifying duplex RNA, revealed an ADAR-specific RNA-binding loop near the enzyme active site and explained flanking sequence preferences. In addition, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.

January 5, 2017 at 2.30 pm in AG-80

Title :

Design and Application of Sensors for Bioimaging

Abstract :

Over the last two decades, the development and applications of optical chemical sensors and bio-imaging agents have been pursued with great interest by many researchers. There is a tremendous potential for employing such methods in diverse areas, such as the determination of pollutants in the environment or that of bioactive small molecules in living systems. This talk attempts to address three key problems. Firstly, to detect the real time distribution of toxic heavy metals i.e. Hg2+; secondly, to design and synthesise carbon dot-based probes for toxic quinone derivatives; and finally to visualize and quantify monoamine neurotransmitter (MNT) like serotonin (5-HT) and dopamine (DA) in live cells and in living organisms  (e.g. zebrafish). I will talk about how tools of organic synthesis, fluorescence correlation spectroscopy (in solution) and optical imaging methods help us tease out the critical roles of the respective analytes in these model systems. 

January 3, 2017 at 2.30 pm in AG-69

Title :

Electron Transport in Molecular Circuits

Abstract :

The idea of building electronic devices using single molecule as active component was first proposed by Aviram and Ratner in the early seventies. Indeed, molecules are of great interest for application in electronic devices because of their small size, their recognition properties, their ability of self-organization and their possibility of chemical modification and customisation. Thus, the ability to measure and control charge transport across metal/molecule/metal junction is of considerable fundamental interest and represents a key step towards the development of molecular electronic devices.

 

In the first part of my presentation, I will introduce working principle our measurement techniques (i.e STM break junctions (STM-BJ), mechanically controllable break junction (MCBJ) and Conducting probe AFM (CP-AFM) technique).1,2 Using the results from several case studies, I will try to demonstrate a frame work for building a molecular circuit theory based on metal/molecule/metal junctions at single molecular level.2,3,4,5 In the later part of my presentation, I will discuss the results mainly focusing on bottom up fabrication of smart surfaces and exploiting the functionality of these smart surfaces for different applications ranging from molecular electronics to catalysis and energy storage/conversion.5,6 

 

References: 

1. Hong, W.J et al., Beilstein J. Nanotechnol. 2011. 2, 699-713. 

2. Kaliginedi et al., Journal of American chemical society. 2012, 134 (11), 5262–5275. 

3. Seth, C., Kaliginedi et al., Chemical Science. 2016, Accepted (DOI: 10.1039/C6SC03204D). 

4. Moreno-Garcia et al., Journal of American chemical society. 2013, 135(33), 12228−12240. 

5. Kaliginedi et al., Nanoscale. 2015, 7 (42), 17685-17692. 

6. Kaliginedi et al., Science Advances. 2016, under revision.