TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

July 13, 2015 at 4.00 pm in AG-69

Title :

Purpose-built Molecules & Molecular Assemblies for Predictive Optical Responses

Abstract :

Designing molecules or molecular assemblies that are capable of functioning in predictive manner in presence of a certain external stimulation is an area that has fascinated most chemists since long. The rich database on various synthons for non-bonding interactions as well as synthetic intricacies in making organic/inorganic molecules has provided means for achieving molecular assembly or function in a desired fashion. Our research interests include harnessing both coordinative interactions as well as various non-bonding interactions for realizing desired functions of a molecule or molecular assembly.

 

Over the recent years, dye-sensitized solar cells (DSSC) have emerged as the major cost effective alternative for efficient harvesting of solar power. However, conversion efficiency of these DSSCs is still lower than that of the silicon-based photovoltaic cells. Among various factors, nature of the anchoring group and thus the synthesis of purpose-built sensitizer molecule contribute significantly in designing an efficient dye. Our sustained efforts on this aspect shall be discussed to reveal the relationship between the design aspects, dynamics of the photoinduced processes and the mechanistic elucidation for explaining the possible efficiency of the DSSC.  

  

We could also demonstrate that changes in molecular conformation or motions in a supramolecular assembly could actually be probed by monitoring changes in optical responses in an appropriately designed host-guest assembly and such examples are scanty in contemporary literature. Some of our recent efforts on this issue shall also be discussed in the presentation.

 

 

July 6, 2015 at 4.00 pm in AG-69

Title :

Small Molecule Tools for Studying Cellular Redox Homeostasis

Abstract :

It has long been recognized that maintenance of redox homeostasis is crucial for cellular survival and growth. However, precise cellular responses to redox stress, where cells loses capacity to counteract excess of reducing or oxidizing equivalents, remain poorly characterized. An important sub-set of various cellular components useful for maintenance of redox homeostasis is gaseous reactive species of nitrogen, oxygen and sulfur. Altered levels of these gases are associated with various pathophysiological conditions and disease states underscoring the importance of regulating intracellular levels of these species. Owing to their high reactivity and diffusible nature, the use of chemical tools for this purpose has become indispensable. Our laboratory has developed several small molecule tools to reliably enhance gaseous redox-active reactive species including superoxide (O2·), nitric oxide (NO), sulfur dioxide (SO2) and hydrogen sulfide (H2S). Our design strategy offers both scope for spatiotemporal control as well as cell-type specificity. Here, we present examples of tools developed in our laboratory that can reliably enhance reactive oxygen, nitrogen and sulfur species and the progress towards studying cellular responses. For example, we have developed bis(4-nitrobenzyl)sulfane, a class of organic sources of H2S, that is specifically activated by the bacterial enzyme nitroreductase to generate H2S. We provide evidence for the suitability of (4-nitrobenzyl)sulfanes for enhancement of intracellular H2S levels in a range of bacteria including mycobacteria. Next, we have developed HyPR-1, a small molecule containing a superoxide generator, strategically linked to a diazeniumdiolate-based nitric oxide donor. HyPR-1 produces nearly temporally concurrent fluxes of superoxide and NO in physiological pH when triggered by DT-diaphorase (DT-D), an enzyme that is commonly found in mammalian cells. We provide unequivocal evidence for HyPR-1’s ability to generate ONOO in cell-free systems in the presence of DT-D as well as reliably enhance ONOO within cells. Using HyPR-1 in colorectal cancer cells as a case study, we present evidence that ONOO mediates epithelial-mesenchymal transition (EMT), which is a key process in metastasis and tumour progression. Together, these studies lay the foundation for understanding mechanisms of antibiotic resistance and cancer progression and metastasis.

June 29, 2015 at 4.00 pm in AG-69

Title :

Protein Conformation, Dynamics and Aggregation: One Molecule at a time

Abstract :

Our laboratory has been investigating the mechanistic details of how a protein attains its functional three dimensional structure. We are also studying the conformational and other factors which contribute to the alteration of folding pathways leading to aggregation. The problems of protein mis-folding and aggregation, which have serious implications in a number of neurodegenerative diseases, are difficult to study.  This is because; the folding and aggregation landscape is inherently heterogeneous, consisting of multiple pathways. Since the traditional biochemical and biophysical techniques require an optimum concentration of aggregated molecules for their detection, monitoring the early stages is difficult. Our lab has been using sensitive fluorescence methods, which can provide single molecule resolution, to address these problems. In this talk, we would discuss some of these data, which have been obtained using a number of relevant model proteins.

 

June 25, 2015 at 2.30 pm in AG-80

Title :

Glucose Clusters : Unravelling the Interactions in Gas Phase

June 22, 2015 at 4.00 pm in AG-69

Title :

Elucidating Structure and Dynamics under Optically and Thermally manipulated conditions: Perspectives of a Femtosecond Spectroscopist

Abstract :

Matter under the influence of optical and/or thermal perturbation can behave quite differently, more so when such perturbations are abrupt and extreme. Using femtosecond lasers that are tailored to our needs, we can generate either of the conditions.  Such light-matter interaction can be of large benefit in unravelling many hitherto unseen phenomena, of which I present a few examples from our recent work that encompass optical microscopy, nanomaterial manipulation under optical field, coherent oscillations from micro-heterogeneity as well as demonstrating the molecular nature of thermal lens spectroscopy.  Each of the examples would demonstrate the uniqueness of the femtosecond laser pulses in their study.

 

June 15, 2015 at 11.30 am in AG-80

Title : 

Physics and Chemistry at the Single-Molecule Level

Abstract :

Understanding and controlling electron transfer across metal/organic interfaces is of critical importance to the field of organic electronics and photovoltaics. Single molecule devices offer an ideal test bed for probing charge transfer and mechanics at these interfaces, allowing us to understand fundamental physics and chemistry at the single-molecule level. The ability to fabricate single molecule devices and probe their electronic characteristics reliably and reproducibly has enabled us to study and model their physical, electronic and chemical properties. In this talk, I will review the scanning tunneling microscope break-junction technique we use to measure conductance through single molecule junctions.1 I will discusshow we use this platform to measure secondary characteristics of such junctions such as thermopower2 and force,3 and present new results on our ability to create single-molecule rectifiers.

 

[1]          L. Venkataraman, J. E. Klare, C. Nuckolls, M. S. Hybertsen, and M. L. Steigerwald, "Dependence of single-molecule junction conductance on molecular conformation", Nature442, 904-907 (2006).

[2]          E. J. Dell, B. Capozzi, J. Xia, L. Venkataraman, and L. M. Campos, "Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes", Nat. Chem.7, 209-214 (2015).

[3]          S. V. Aradhya, M. Frei, M. S. Hybertsen, and L. Venkataraman, "Van der Waals Interactions at Metal/Organic Interfaces at the Single-Molecule Level", Nat. Mat.11, 872-876 (2012).

 

 

June 8, 2015 at 4.00 pm in AG-69

Title

Chemical reactivity hotspots on protein landscape

Abstract :

The surface of protein offers a rich landscape of functional groups. Chemical tools for site-specific labeling of these functionalities is desired for their wide range of applications in understanding biological interactions, ligand discovery, disease diagnosis, and biophysical investigations. Typically, these diagnostic tools can be accessed by the derivatization of nucleophilic side chains in the case of unmodified proteins.

Our research group is investing efforts to develop chemo- and site-selective chemical methodologies for labeling of proteins. Here, the first step involves the development of transformations that would be efficient in controlled reaction conditions such as aqueous buffer, neutral pH and room temperature. The most critical challenge relates to the identification of principles that would allow us to generate reactivity biases at specific sites of the protein. Our ongoing efforts in this direction will be discussed in the presentation. 

June 1, 2015 at 4.00 pm in AG-69

Title :

UV Photoelectron Spectroscopy (UVPES) at Near Ambient Pressure : A Necessary Tool to Explore Materials and Catalysis under in-situ/operando conditions

Abstract :

Conventional photoelectron spectrometer (PES) works at ultra-high vacuum (10 -9 Torr or lower) to minimize the inelastic scattering. Recent advances in electronics and mechanical design allowed PES to operate at 1 mbar and significantly high pressures. Near-ambient pressure photoelectron spectroscopy (NAPPES) is becoming increasingly popular to explore the materials and catalysis aspects at near ambient pressure (around 1 mbar) and high temperature conditions. NAPPES works fine with x-ray photons, or rather high kinetic energy (KE) electrons, mainly due to relatively lower inelastic scattering and hence good S/N is maintained. However, when the KE of photoelectrons are <100 eV, there are serious problems in observing the spectra with decent S/N ratio under NAPPES conditions. In the recently installed laboratory-based NAPPES system at NCL, Pune, 1 we are able to observe the ultraviolet PES (UVPES) with He-I and He-II excitation sources under near ambient conditions. As a test case we explored the oxidation of copper surfaces (Cu to CuO through Cu 2 O) under molecular O 2 at different partial pressures and temperatures to explore the change in
electronic structure. 2,3 Surface modification of Pd-metal surfaces, by oxygen diffusion into the subsurfaces, and its influence in heterogeneous catalysis was explored through CO oxidation. The most important point is the observation of UVPES under high pressure conditions, which demonstrate the direct evolution of electronic structure. Reasons for the observation of UVPES at NAPPES conditions will be presented along with important features of APPES unit in detail


References:
1. K. Roy, C. P. Vinod, C. S. Gopinath, J. Phys. Chem. C 117, 4717 (2013).
2. K. Roy C. S. Gopinath, Anal. Chem. 86, 3683 (2014).
3. K. Roy, R. Jain, C. S. Gopinath, ACS Catal. 4, 1801 (2014); K. Roy and C. S. Gopinath, ChemCatChem 6, 531 (2014).
4. C. S. Gopinath, K. Roy and S. Nagarajan, ChemCatChem 7, 588 (2015).

May 27, 2015 at 2.30 pm in AG-80

Title :

A tale of prolycopene isomerization reaction:  "Ultrafast triplet generation and redox triggered activation

May 25, 2015 at 4.00 pm in AG-69

Title :

Detecting the mononuclear intermediate and minimal entity required for the formation of CuA center in cytochrome c oxidase

May 21, 2015 at 2.30 pm in AG-80

Title :

What makes amyloidogenic peptides sticky: The case of Alzheimer’s  amyloid beta (Aβ) and human islet amyloid polypeptide (hIAPP)

May 20, 2015 at 2.30 pm in AG-80

Title :

Ultra-Small Gold Nanoclusters in Efficient Biofuel Cell Design

Abstract :

Energy security is one of the most pressing challenges in the world that need to be addressed through fundamental scientific research. With sources of fossil fuels dwindling, there is an urgent need to find cheap and renewable forms of energy using naturally abundant resources such as sunlight, air, and water. Nanostructured materials and enzymatic fuel cells are showing great promise in alternative energy conversion. 1 The cathodic oxygen reduction reaction (ORR) is a technologically important reaction in the process of energy production. One of the limiting factors that dictate the performance of enzymatic electrodes towards ORR is the slow rate of electron transfer (ET) at the enzyme-electrode interface. 2 Therefore, efficient ET is needed to lift this critical methodological barrier in biofuel cells design. Few atom ultra-small metal nanoclusters (<2nm in diameter) possess many interesting properties compared to bulk metals owing to their discrete electronic states distribution. In this talk I will discuss synthesis and characterization of a new DNA-templated gold nanocluster (AuNC) of ~1 nm in diameter and possessing ~7 Au atoms. When integrated with bilirubin oxidase (BOD), an enzyme used for cathodic ORR in biofuel cells, and carbon nanotubes (CNTs) as a support material, the AuNCs act as remarkable enhancer of ET for ORR by lowering the overpotential for the electrocatalytic ORR by ~15 mV compared to BOD alone. This unique property of AuNCs as ET enhancer at the enzyme-electrode interface makes them potential candidates for development of cathodes in enzymatic fuel cells and removes a critical technological barrier in biofuel cell design. 3


(1) a) Cosnier, S.; Le Goff, A.et al. In Nanobioelectrochemistry; Springer: 2013, p 49; b) Meredith, M. T.; Minteer, S. D. Annu. Rev. Anal. Chem. 2012, 5, 157.
(2) Liu, J.; Chakraborty, S.et al. Chem. Rev. 2014, 114, 4366.
(3) Chakraborty, S.; Babanova, S. et al. submitted 2015.

May 19, 2015 at 2.30 pm in AG-80

Title :

Grafting High Affinity Metal Coordination to Design Artificial Metalloproteins

Abstract :

Metalloproteins represent some of the best-known inorganic catalysts in nature, catalyzing difficult and important reactions with exceptional efficiency. 1 Design of artificial metalloproteins allows us to understand the critical features required for their structure and function. Equipped with this knowledge it is possible to engineer novel structures and functions not found in nature. In the first part of this talk I will focus on our efforts in de novo metalloprotein design to build self-assembling polypeptide systems capable of sequestering toxic heavy metals (Cd, Pb, Hg) with exceptionally high affinity and site-selective molecular recognition properties, and highlight the factors that control these properties. 2 In the second part I will describe a biosynthetic metalloprotein design approach to successfully engineer artificial biocatalysts mimicking a complex metalloenzyme involved in biological denitrification (nitric oxide reductases that reduce NO to N 2 ). 3 I will discuss how these model systems help us delineate the likely mechanisms by which this enzyme catalyzes this
environmentally important reaction.

(1) a)Chakraborty, S.; Hosseinzadeh, P.et al. In Encyclopedia of Inorganic and Bioinorganic Chemistry; John Wiley & SonsLtd: 2011; b)Liu, J.; Chakraborty, S.et al. Chem. Rev. 2014, 114, 4366; c) Lu, Y.; Chakraborty, S.et al. In Comprehensive Inorganic Chemistry II (Second Edition); Reedijk, J., Poeppelmeier, K., Eds.; Elsevier: Amsterdam, 2013; Vol. 3, p 565.
(2) a)Chakraborty, S.; Iranzo, O.et al. J. Am. Chem. Soc. 2012, 134, 6191; b) Chakraborty, S.; Kravitz, J. Y.et al. Angew. Chem. Int. Ed. 2011, 50, 2049; c) Chakraborty, S.; Touw, D. S.et al. J Am. Chem. Soc. 2010, 132, 13240; d) Iranzo, O.; Chakraborty, S.et al. J. Am. Chem. Soc. 2011, 133, 239.
(3) a) Chakraborty, S.; Reed, J.et al. Angew. Chem. Int. Ed. 2014, 53, 2417; b) Matsumura, H.; Hayashi, T. et al. J. Am. Chem. Soc. 2014, 136, 2420

May 18, 2015 at 4.00 pm in AG-69

Title :

Designing Nanostructures in Reaction Flask

Abstract :

How to architect different nanosutuctures in solution?  From the literature survey, one can understand that all the reaction processes in designing different kinds of nanostructures are simple and handy. Just add precursors along with few specific stabilizing ligands dissolved in appropriate solvent in the reaction flask, set the reaction temperature as per their reactivity and timely harvest; this remains the main theme of the reaction for almost all nanostructures synthesis. However, on the other side, chemists always think differently and the main goal remains on understanding the crystal growth and to induce new functional properties in the designed materials. Hence, apart from the injections of the precursors and cooking in a reaction flask, the physics and chemistry involved in the nanomaterials synthesis puzzle the chemists. However, it is really exciting to find peculiar kinds of nanostructures under the microscope, and that again boosts up when the shape evolution is tagged with the reaction chemistry followed in the reaction flask. In last thirty years, the field has improved tremendously and a wide variety of nanomaterials are already designed and reported. But, while functional materials are concerned, as per the development of new technology, developments of new materials with improved materials properties are always in demand. Keeping this view in mind, this talk would present the state of art in development of chemical synthesis of one of the most demanding functional materials, Heterostructured nanomaterials. A detail study on the physics and chemistry of designing such materials with semiconductor-semiconductor and semiconductor-noble metal hetero-junctions would be discussed. In addition, the formation mechanism in bringing two dissimilar materials with different physical/chemical properties together and the tuning of materials properties through hetero-structure formation would be presented.

May 14, 2015 at 2.30 pm in AG-80

Title :

Probing Excited State Redox Reactions Inside Molecular Containers