TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

February 2, 2015 at 4.00 pm in AG-69

Title :

Strategies to Reduce Rate of Charge Recombination

Abstract :

Modulating excitons generated as a result of photoinduced electron transfer in crowded environments is vital for the development of photo-functional materials.1 The hetero-junctions (HJs) in organic photovoltaics are termed as “transport highways” for the charge carriers to the respective electrodes.2Careful design and organization of molecular architectures at the HJs in organic solar cells dictates the fate of excitons generated. Molecular organization relies on interplay between various inter/intra molecular interactions such as multi-pole electrostatic interactions, dispersion and inductive effects, p-p interactions, hydrogen bonding etc. which determines electronic and optical properties associated with these materials. Myriads of models have been proposed in enhancing the survival times of the excitons generated at the HJs. Mullen and co-workers3 substantiated that compromise and dominance of various inter and intra molecular interactions operating in donor (D) - acceptor (A) self-assembled systems could generate segregated D-D/A-A stacks, D-A interdigitating alternate stacks etc. Aida and co-workers4 demonstrated the photochemical generation of spatially separated charge carriers through co-axial nanotubular arrangement of D and A. Wasielewski et al.5extended the survival time of charge separated states through self-assembled D-A tetramers, trefoils, dimers and hydrogen bonded foldamers.Recent report from our group6 demonstrated the importance of supramolecular vesicular scaffold in reducing the rate of charge recombination of the charge separated states.7Recently we are successful in synthesizing near-orthogonal D-A helical and columnar stacks wherein the latter undergo self-assembly in CHCl3 to form spherical aggregates which couldhelp in sustaining the charge transfer intermediates for longer timescales through D-A stacks. The following scheme represents the different models of D-A self-assembled systems reported and under investigation.

References:

1.   Engel, G. S.; Calhoun, T. R.; Read, E. L.; Ahn, T.-K.; Mancal, T.; Cheng, Y.-C.; Blankenship, R. E.; Fleming, G. R., Nature 2007,446 (7137), 782-786.

2.   Wang, M.; Wudl, F., J. Mater. Chem. 2012,22 (46), 24297-24314.

3.   (a) Dössel, L. F.; Kamm, V.; Howard, I. A.; Laquai, F.; Pisula, W.; Feng, X.; Li, C.; Takase, M.; Kudernac, T.; De Feyter, S.; Müllen, K., J. Am. Chem. Soc. 2012,134 (13), 5876-5886;(b) Samorì, P.; Fechtenkötter, A.; Reuther, E.; Watson, M. D.; Severin, N.; Müllen, K.; Rabe, J. P., Adv. Mater. 2006,18 (10), 1317-1321;(c) Mativetsky, J. M.; Kastler, M.; Savage, R. C.; Gentilini, D.; Palma, M.; Pisula, W.; Müllen, K.; Samorì, P., Adv. Funct. Mater. 2009,19 (15), 2486-2494.

4.   (a) Yamamoto, Y.; Fukushima, T.; Suna, Y.; Ishii, N.; Saeki, A.; Seki, S.; Tagawa, S.; Taniguchi, M.; Kawai, T.; Aida, T., Science 2006,314 (5806), 1761-1764;(b) Li, W.-S.; Saeki, A.; Yamamoto, Y.; Fukushima, T.; Seki, S.; Ishii, N.; Kato, K.; Takata, M.; Aida, T., Chem.-Asian J. 2010,5 (7), 1566-1572.

5.   (a) Gunderson, V. L.; Smeigh, A. L.; Kim, C. H.; Co, D. T.; Wasielewski, M. R., J. Am. Chem. Soc. 2012,134 (9), 4363-4372;(b) Lefler, K. M.; Kim, C. H.; Wu, Y.-L.; Wasielewski, M. R., J. Phys. Chem. Lett. 2014,5 (9), 1608-1615;(c) Lefler, K. M.; Co, D. T.; Wasielewski, M. R., J. Phys. Chem. Lett. 2012,3 (24), 3798-3805;(d) Wu, Y.-L.; Brown, K. E.; Wasielewski, M. R., J. Am. Chem. Soc. 2013,135 (36), 13322-13325.

6.   (a) Cheriya, R. T.; Joy, J.; Alex, A. P.; Shaji, A.; Hariharan, M., J. Phys. Chem. C. 2012,116 (23), 12489-12498;(b) Cheriya, R. T.; Nagarajan, K.; Hariharan, M., J. Phys. Chem. C. 2013,117 (7), 3240-3248.

7.             Cheriya, R. T.; Mallia, A. R.; Hariharan, M., Energy Environ. Sci. 2014,7 (5), 1661-1669.

 

January 27, 2015 at 2.30 pm in AG-69

Title :

Design and Development of Chemical Tools and Animal Models for Probing Mn (II) In Vivo

January 21, 2015 at 2.30 pm in AG-80

Title :

Probing the Molecular Basis of Photo-induced Charge Generation in π-Conjugated  Organic Materials for Photovoltaic Applications

January 19, 2015 at 2.30 pm in Guest House Conference Room

Title :

Bio-compatible Probes for Imaging Mn(II) in vivo

 

January 12, 2015 at 4.00 pm in AG-69

Title

Probing Dynamic Solvation of Water Soluble Molecular Cages through Host-Guest CT States

January 6, 2015 at 2.30 pm in AG-69

Title :

Diels-Alderase: Myth or Reality!

Abstract :

The Diels-Alder (DA) reaction is one of the most common types of cycloaddition reaction which leads to the formation of six-membered ring. The DA reaction plays a pivotal role in the synthesis of diverse polymer and natural products. However, the mechanism through which the DA reaction occurs makes it difficult to elucidate experimentally but can be fully addressed in silico. The DA reaction has found its applications in several aspects of chemistry and it has also been proposed as a key transformation in the biosynthesis of many cyclohexene-containing secondary metabolites. For instance, the key step in the biosynthesis of spinosyn A is a DA reaction which converts the putative macrocyclic lactone into the tricyclic compound (Figure 1) which may be catalyzed by an enzyme. In order to confirm this hypothesis, it is mandatory to demonstrate the concertedness of the transition state and thus, the enzyme would be known as Diels-Alderase. We have used computational methods to locate and characterize the transition state by making use of a theozyme, also known as theoretical enzyme.

 

 

 

Figure 1: Cyclisationreaction.

 

This presentation describes the fundamentals of cycloaddition and DA reactions. This is followed by our sustained efforts to understand these reactions using model systems and then culminating to an enzyme-catalysed reaction.

 

 

 

January 5, 2015 at 4.00 pm in AG-69

Title :

Finding homes to orphan enzymes

Abstract :

My graduate research in the Raushel lab at TAMU focused on the functional annotation of orphan bacterial enzymes and biological pathways. During my graduate studies, I realized the gigantic problem of misannotation of enzymes or lack of thereof in the post-genomic era. Following completion of my graduate studies, I decided to apply my background in biochemistry and mechanistic enzymology, to functionally annotate orphan enzymes in mammalian diseases, and pathophysiology in the Cravatt Lab at TSRI. Here, using a combination of activity based protein profiling, chemoproteomics, and lipidomics, I have identified and functionally characterized an as of yet uncharacterized serine hydrolase enzyme ABHD16A (also BAT5) as the major phosphatidylserine (PS) lipase in mammalian cells and tissues and as the enzyme responsible for biosynthesizing immunomodulatorylyso-PSs in vivo. I validated this annotation of ABHD16A using pharmacological studies performed with first generation small molecule inhibitors of ABHD16A, and from genetic data obtained from ABHD16A-directed shRNA probes, and ABHD16A–/– mice. This functional validation of ABHD16A has potential therapeutic implications in the neurological disorder PHARC (polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, cataract) and other immunological disorders involving deregulated lyso-PS signaling.

December 22, 2014 at 4.00 pm in AG-69

Title :

In support of Nitric Oxide Dioxygenase function: Algal Hemoglobins and their Reduction partners

Abstract :

The ubiquity of hemoglobins as a superfamily to life has enthused the field with renewed vigor. Reactions like oxygen binding and nitric oxide (NO) dioxygenation appear to be characteristic to the hemoglobin superfamily, as revealed from investigation of recombinant globins, irrespective of whether they are associated to any particular function like oxygen transport/storage, sensing, electron transport, protection against hypoxia and other possibilities. NO dioxygenase reaction, common in vitro, however, was limited by lack of report of specific enzymes that can convert ferric hemoglobin, formed during reaction of oxy hemoglobin with NO, into ferrous hemoglobin – the species that reacts with NO. Absence of a known cognate reductase would prevent reduction of ferric species of hemoglobin to ferrous form and the oxidation-reduction cycle would be incomplete for NO related function to be fruitful. Assignment of NO dioxygenase activity as a physiological function requires the design of experiments that address reduction mechanisms. We used Chlamydomonas reinhardtii as model system since we have identified 12 globins and 3 putative genes that can potentially function as reductase of ferric hemoglobin. Organism database annotated these reductases as dihydrolipoamide dehydrogenase, cytochrome b5 reductase and monodehydroascorbate reductase. So far, we have characterized 3 hemoglobins and 3 putative cognate reductases using biochemical and biophysical methods. Spectroscopic studies reveal that Chlamydomonas contains both pentacoordinate and hexacoordinate hemoglobins. The enzymes were found to contain flavin domain and could reduce ferric Chlamydomonas hemoglobins in vitro to their functional ferrous state. The interactions between hemoglobins and these reductases might support NO scavenging/detoxification function of globins with potential implications in biotechnology.

December 8, 2014 at 4.00 pm in AG-66

Title : Exploring Energy Landscapes : From Molecules to Nanodevices

Abstract :

The potential energy landscape provides a conceptual and computational framework forinvestigating structure, dynamics and thermodynamics in atomic and molecular science. This talk will summarise new approaches for global optimisation, quantum dynamics, the thermodynamic properties of systems exhibiting broken ergodicity, and rare event dynamics. Applications will be presented that range from prediction and analysis of high-resolution spectra, to conformational changes of biomolecules and coarse-grained models of mesoscopic structures.


Selected Publications:
D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010)
D.J. Wales, J. Chem. Phys., 130, 204111 (2009)
B. Strodel and D.J. Wales, Chem. Phys. Lett., 466, 105-115 (2008)
D.J. Wales and T.V. Bogdan, J. Phys. Chem. B, 110, 20765-20776 (2006)
D.J. Wales, Int. Rev. Phys. Chem., 25, 237-282 (2006)
D.J. Wales, "Energy Landscapes", Cambridge University Press, Cambridge, 2003

December 2, 2014 at 2.30 pm in AG-69

Title :

Mechanistic Investigation of Membrane Fusion through a Model Caged SNARE Protein

Abstract :

Intracellular membrane fusion is directed by the formation of a specific complex of proteins such as SNARE [Soluble NSF (N-ethylmaleimide-sensitive factor) Attachment Protein Receptor]. There are several mechanisms of SNARE mediated membrane fusion, but the exact nature of these processes remains debated. In particular, little is understood about the molecular mechanisms governing trans-SNARE complex nucleation and zippering in driving fusion. Assembly strength and fusion kinetics in these systems are highly complex, and the downstream events of membrane contact (docking), stalk formation, hemifusion, and fusion pore opening along the fusion pathway is still unclear. Moreover, the exact role of the transmembrane domain (TMD) of synaptobrevin and syntaxin-1A is unknown. In this presentation, I will demonstrate light triggered mechanistic investigation of membrane fusion using artificial caged SNAREs. Caging of a biologically active molecule with a photolabile protecting group at a key functional position can temporarily mask the functionality and inactivate the biomolecule. The activity of the molecule can be restored by uncaging, externally triggered by light of appropriate wavelength. However, caging group strategy has not been applied yet to temporarily block the membrane fusion activity of SNARE protein to get deeper structural insights into the SNARE zippering and assembly pathway. I will illustrate the design of artificial caged SNAREs with photolabile protecting groups to dissect the mechanism of SNAREs in membrane docking, hemifusion, and fusion. I will also provide a method to arrest and study the intermediates such as partially zipped trans-SNARE complexes which is used for light triggered stepwise recognition/two-stage zippering of membrane fusion. Our recent findings of light triggered membrane fusion using artificial caged SNAREs can be a significant starting point to address many compelling questions surrounding the topic of SNARE-induced membrane fusion.

At the end, I will present my future research proposal: 1) Synthetic Transmembrane Peptide-Based Ion Channel and 2) Synthetic Molecular/Supramolecular Machines.

December 1, 2014 at 4.00 pm in AG-69

Title :

Manipulation of Membrane Structure and Function Using Light

Abstract :

The 1st part of my presentation will focus on light triggered mechanistic investigation of membrane fusion using artificial caged SNAREs [Soluble NSF (N-ethylmaleimide-sensitive factor) Attachment Protein Receptor]. Membrane fusion is a fundamental process in life and plays a key role in exo- and endocytosis, fertilization, intracellular trafficking, enveloped virus infection, etc. All intracellular membrane fusion is directed by the formation of a specific complex of proteins, such as SNARE. Two SNARE proteins residing in the plasma membrane are syntaxin-1A (Sx) and SNAP-25. A SNARE protein residing in the membrane of synaptic vesicle is synaptobrevin (Syb). The SNAREs assemble into four-α-helix bundles. There are several mechanisms of SNARE mediated membrane fusion, but the exact nature of these processes is still unknown. I will demonstrate the design of artificial caged SNAREs using photolabile protecting groups to temporarily mask the functionality of the recognition site with the goal of obtaining deeper structural insights into the SNARE-mediated membrane fusion mechanism.

In the 2nd part of my presentation, I will illustrate how an understanding of membrane events can be used to promote drug molecules at tumor sites by passive and active targeting to tumor. Another goal is to target local pH of tumor site. A tumor microenvironment (cytosol) usually has a pH of 6.5-7.2, an endosomal pH of 5.0–6.0 and a lysosomal pH of 4.0−5.0, which is different from the normal tissues pH of 7.4. This pH gradient is of particular importance, since several drugs and carriers for cancer therapy are internalized through endocytosis and trapped within endosomal and lysosomal compartments. I will explain NIR pH switchable liposomal formulation where laser-induced photothermal heating is turned on at acidic pH (> 6.5) and turned off at physiological pH 7.4 which could show major toxic effects against tumors, without causing damage to normal cells. Drug release from thermosensitive liposome will be demonstrated using logical application of pH and photothermal heating. This liposomal formulation with laser could be a promising strategy for ‘Photothermal Cancer Theranostics’.

November 24, 2014 at 4.00 pm in AG-69

Title

Development of spectral simplification methods in NMR spectroscopy

Abstract :

Importance of NMR spectral simplification methods for unambiguous structural determinations of small organic molecules in solid and solution-state will be discussed. The development of solid-state NMR experimental techniques are aimed for obtaining desired spectral information, both scalar and dipolar couplings (inter nuclear distances), by simplifying complex NMR spectra.  Whereas, in solution-state all the anisotropic interactions average to zero, thereby yield NMR spectra representing only the features of chemical-shift and scalar (J) couplings.  However, often the solution-state 1H NMR spectra suffer from intense overlaps due to spread of J-multiplets. In solution-state, the enhanced spectral resolution has been accomplished by employing new real-time pure-shift pulse schemes that involve broadband and band-selective homodecoupling. 

 

November 21, 2014 at 2.30 pm in AG-69

Title :

 Change of Protein Conformation and Function Associated with Amyloid Aggregation

November 17, 2014 at 4.00 pm in AG-69

Title :

Probing Energetic and Spatiotemporal Heterogeneity using Single-Emitter Spectroscopy

Abstract :

While ensemble measurements have been extremely successful in understanding the structure and dynamics in the condensed phase, they have often failed to capture the underlying details of the physical processes which give rise to the observed “bulk” behaviors. In this context, single-molecule fluorescence microscopy has emerged as a valuable technique to extract information regarding local (nanoscale) properties in complex (disordered) systems and understand the extent of spatiotemporal as well as energetic heterogeneities therein. This presentation will exemplify the efficacy of single-emitter spectroscopy to elucidate energetic inhomogeneity in two categories of luminescent semiconductor nanocrystals (undoped and dopedquantum-dots). Further, I will discuss the utility of single-molecule translational and rotational mobility measurements to provide insights on the extent of spatial and dynamic heterogeneity in polymer thin-films during plasticization, a process which involves solvent induced lowering of the glass transition temperature.

 

November 13, 2014 at 11.30 am in AG-66

Title :

Synthesis, Characterization and Applications of Mixed Metal Oxide Nanoparticles

Abstract :

Metal oxide nanoparticles play a very important role in various fields as they exhibit interesting optical, electronic and magnetic properties. Moreover the combination of two or more metal oxides can lead to materials with multi-functional properties. Aim of my research work was to control of size, shape and homogeneity for mixed metal oxide nanoparticles, studies on their optical and magnetic properties and explore some possible applications. During my doctorate research, I have synthesized core-shell nanoparticles CuO@NiO and SiO2@NiO core-shell nanoparticles by homogeneous precipitation method, binary mixed metal oxide nanoparticles SnO2-MgO, TiO2-MgO, NiO-ZnO, NiO-CuO and NiO-MgO and aluminate nanoparticles (CoAl2O4, NiAl2O4 and CuAl2O4) by sol-gel method. The synthesized nanoparticles have been characterized using different analytical techniques as XRD, TGA, CHN analysis, FT-IR, FE-SEM, EDXA, TEM, SAED, surface area analyser, UV-Vis DRS and SQUID. Some possible applications have also been explored such as catalytic reduction of 4-nitrophenol (4-NP), photocatalytic degradation of methylene blue (MB), adsorption of MB, and destructive adsorption of paraoxon. The CuO@NiO core-shell nanoparticles show better efficiency in the reduction of 4-NP compared to that of pure NiO and CuO nanoparticles. The NiO@SiO2 core-shell nanoparticles act as better adsorbent for MB compared to pure NiO nanoparticles and silica spheres. The SnO2-MgO nanoparticles act as an efficient photocatalyst towards the photodegradation of MB. The reactivity of the metal aluminate nanoparticles was investigated using the destructive adsorption of paraoxon and catalytic reduction of p-nitrophenol.