TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

August 10, 2015 at 4.00 pm in AG-69

Title :

Domino Strategies for Syntheses of Natural Products and New Molecular Scaffolds

Abstract :

Domino and multicomponent reactions are always attractive and they are expected to provide the target molecules efficiently in a shortest possible route. Our group has been engaged in designing simple and efficient domino strategies for the syntheses of biologically active natural products and natural product like molecules. In this lecture, our efforts leading to syntheses of vinigrol, cyclic guanidines and N-heterocyclic amides will be discussed in details.

Vinigrol,1 a unique diterpene containing the decahydro-1,5-butanonaphthalene carbon skeleton was shown to exhibit a broad spectrum of biological activity. Besides the multiple sites of oxygenation, vinigrol contains a tricyclic core having a cis-fused [4.4.0] system bridged by an eight-membered ring and eight contiguous stereocenters. We recently reported2 an enantioselective formal synthesis of vinigrol involving a1-2-3 strategy: one pot and 2-reactions with the formation of3-rings leading to the core structure of vinigrol from its stereochemically well-defined acyclic precursor.

The cyclic guanidines3 and N-heterocyclic amides4 are important structural units present in biologically active drug molecules. However, the existing methods suffer from harsh conditions, narrow functional group tolerance, poor atom economy, low yielding and so; it warrants an efficient protocol for their syntheses. We have developed a one-pot Cu-catalyzed cascade routes to these unique cyclic guanidines and N-heterocyclic amides5 from readily available starting materials.

References:

1. Uchida, I.; Ando, T.; Fukami, N.; Yoshida, K.; Hashimoto, M.; Tada, T.; Koda, S.; Morimoto, Y.J. Org. Chem. 1987, 52, 5292–5293.

2. Betkekar, V. V.; Sayyad, A. A.; Kaliappan, K. P.Org. Lett.2014,16, 5540-5543.

3. Subramanian, P.; Kaliappan, K. P. Eur. J. Org. Chem. 2014, 5986–5997.

4. Hou, H.; Wei, Y.; Song, Y.; Mi, L.; Tang, M.; Li, L.; Fan, Y. Angew. Chem. Int. Ed. 2005, 44, 6067-6074.

5. Subramanian, P.; Indu, S.; Kaliappan, K. P. Org. Lett.2014,16, 6212-6215.

August 3, 2015 at 4.00 pm in AG-69

Title :

Musings with Intermolecular Interactions

Abstract :

In general intermolecular interactions between pair of closed shell molecules can be represented by [-1, -6, +12] potential. Various intermolecular interaction varies significantly due to the differences in the weightage for each of the three terms. Spectroscopy and computational chemistry provide the reasonable understanding of many intermolecular interactions. However, each method has specific shortfalls. Physically meaningful models can only be constructed by adequately addressing these shortfalls while interpreting the data. The importance of each of the components of [-1, -6, +12] potential in understating hydrogen bonding, π-π stacking and in foldamers will be highlighted

 

July 31, 2015 at 11.30 am in AG-80

Title :

Accelerating virtual discoveries by augmenting quantum mechanics with
machine learning

Abstract :

Acceleration of socio-economically important researches such as the design of catalysts, drugs, or conducting materials, lies in reliable virtual screening to identify candidate molecules or materials with desired properties. Any attempt to address this problem exclusively via brute force high-throughput computation is doomed to fail due to the combinatorial hardness of the problem, and the limitations of the compute power that is available on the planet. In my talk, I will highlight some out-of-the-box approaches to navigate chemical space with a focus on the application of supervised machine-learning combined with legacy quantum chemistry methods such as even semi-empirical models. This strategy has very recently been shown to reach desirable quantum chemical accuracy, for forecasting a multitude of properties, ranging from thermochemistry to NMR chemical shifts, even for new molecules which had no part in
training. I will present an overview of this emerging sub-discipline of theoretical chemistry, and discuss some of the prominent contributions in this venue.


References
[1] Snyder, et al., Finding density functionals with machine learning, Physical Review Letters, 108 (2012) 253002.
[2] Ramakrishnan, et al., Big data meets quantum chemistry approximations: The ∆-
machine learning approach, Journal of Chemical Theory and Computation, 11 (2015)
2087.
[3] Ghiringhelli, et al., Big data of materials science: Critical role of the descriptor, Physical Review Letters, 114 (2015) 105503.
[4] Special Issue: Machine learning and quantum mechanics, International Journal of Quantum Chemistry, 115 (August 2015).

July 30, 2015 at 2.30 pm in D-406

Title :

Rapid and accurate simulation of electron dynamics across nanostructures

Abstract :

Accurate first-principles modeling of electron dynamics is a challenging area of research. To follow the dynamics of molecular electron density one has to solve the time-dependent electronic Schrödinger equation (TDSE). Straight-forward extensions of common quantum chemistry methods to the time-dependent domain reveal density functional theory (DFT), or even the coupled cluster theories to be extremely unsuited for this purpose. In a series of studies, we have demonstrated linear equations of motions to be one of the fundamental requirements to reliably model electonic wavepacket dynamics, or coherent controlled state-to-state excitation. To this end, we have developed one of the most effcient implementations of the time-dependent configuration-interaction (TDCI) methodology to solve the TDSE. Our
implementation has been successfully applied to follow the electron transport across molecular wires and nanostructures terminating in a small metal cluster or a model gold surface. When combined with imaginary time propagation, or other variational schemes TDCI can be utilized also to perform time-independent task of computing the bound states. The present talk will provide an overview of the TDCI methodology and summarize the results of some recent applications.


References
[1] Raghunathan, et al., Critical examination of explicitly time-dependent density functional theory for coherent control of dipole switching Journal of Chemical Theory and Computation, 7 (2011) 2492.
[2] Ulusoy, et al., The multi-configuration electron-nuclear dynamics method applied to LiH, The Journal of chemical physics, 136 (2012) 054112.
[3] Ramakrishnan, et al., Control and analysis of single-determinant electron dynamics,
Physics Review A, 85 (2012) 054501.
[4] Ramakrishnan, et al., Electron dynamics across molecular wires: A time-dependent configuration interaction study, Chemical Physics, 420 (2013) 44.
[5] Ramakrishnan, et al., Charge transfer dynamics from adsorbates to surfaces with single active electron and configuration interaction based approaches, Chemical Physics, 446 (2015) 24.

July 28, 2015 at 2.30 pm in AG-69

Title :

Towards Understanding Natural and Artificial Light Harvesting – New Theoretical Insights and Optical Techniques

Abstract :


With substantial budget hikes towards renewable energy technologies, all the leading and developing world economies are recognizing the need to reduce their dependence on fossil fuels. Understanding the fundamental physics of light-harvesting in both natural and artificial systems is the key to development of efficient light-harvesting technologies. I will be presenting my thesis work on the following topics: i) The non-adiabatic energy funnel (Tiwari et al. PNAS 2013) underlying the remarkably efficient electronic energy transfer in natural light harvesting antennas. Future experiments to further investigate this new mechanism will also be discussed. ii) A novel femtosecond time-resolved photonumeric technique to quantitatively characterize transient chemical species. Preliminary measurements on PbSe quantum dots relevant for third generation photovoltaic technologies will also be presented.This talk will mainly focus on the first topicwhile briefly touching the key ideas of the second topic.

 

July 27, 2015 at 11.30 am in AG-66

Title :

Probing Plant Metabolism and Bio-molecular Interaction: Studies by NMR

July 20, 2015 at 4.00 pm in AG-69

Title :

New strategies for the stereoselective synthesis of oxa and aza-cycles

Abstract :

Synthesis of oxa- and aza-cycles is a topic of contemporary interest owing to the presence of these moieties in structurally challenging and biologically important natural products. Our group is involved in developing strategies for their synthesis using vinylogous carbonates and carbamates under radical as well as non-radical conditions. In this regard, we have developed a highly stereoselective synthesis of new oxa-cages and angular oxa-triquinanesvia alkyl radical cyclisation to vinylogous carbonates. To expand the scope of vinylogous carbonates and carbamates in non-radical pathways, a highly diastereoselective method for the synthesis of cyclopropafuranones and cyclopropapyrrolidinones from vinylogous carbonates and carbamates, respectively, has been established. These donor-acceptor substituted cyclopropanes (DACs) have been converted into diversely functionalized THFs, THPs, lactones, pyrrolidine, piperidine and lactam derivatives by regioselective ring opening of the cyclopropane ring. An efficient strategy for the synthesis of THF, THP and oxepane derivatives has been developed employing a tandem SN2-Michael addition to vinylogous carbonates. Further, we have shown that the intramolecular Pictet-Spengler type cyclization of the indole moiety to the vinylogous carbonates under Lewis acidic conditions can be effected leading to N-fused oxazino indoles. We have demonstrated that Lewis acid mediated reductive etherification can be used for gaining stereoselective access to diverse array of 1,4-heterocycles like morpholines, which are important pharmacophores. Very recently, we have developed divergent synthesis of N-fused indolylidine, indole, and indoline derivatives using alkyne iminium ion cyclization. The talk will highlight some of thesestudies for the stereoselective construction of bioactive oxa- and aza-cycles.

 

References:(a) Gharpure, S. J.; Shukla, M. K.; Vijayasree, U. Org. Lett.2009, 10, 5466. (b) Gharpure, S. J.; Sathiyanarayanan, A. M. Chem. Commun.2011, 47, 3625. (c) Gharpure, S. J.; Prasad, J. V. K.J. Org. Chem.2011, 76, 10325.(d) Gharpure, S. J.; Vijayasree, U.; Reddy, S. R. B.Org. Biomol. Chem., 2012, 10, 1735. (e) Gharpure, S. J.; Prasad, J. V. K. Eur. J. Org. Chem. 2013, 2076. (f) Gharpure, S. J.; Prasath, V. Org. Biomol. Chem., 2014, 12, 7397. (g) Gharpure, S. J.; Nanda, L. N.; Shukla, M. K. Org. Lett.2014, 16, 6424. (h)Gharpure, S. J.; Anuradha, D.; Prasad, J. V. K.; Rao, P. S.Eur. J. Org. Chem. 2015, 86. (i) Gharpure, S. J.; Shelke, Y. G.; Kumar, D. P. Org. Lett.2015, 17, 1926.

 

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).