Department of Chemical Sciences
School of Natural Sciences


April 6, 2015 at 4.00 pm in AG-69

Title :

Molecular Basis for Optimizing Organic Photovoltaics

March 30, 2015 at 4.00 pm in AG-69

Title :

Selective C-H Functionalization Reaction

Abstract :

Palladium catalyzed coupling between aryl halides and alkenes (Mizoroki-Heck reaction) is one of the most popular reactions for synthesizing complex organic molecules. The limited availability, problematic synthesis, and higher cost of aryl halide precursors (or their equivalents) have encouraged exploration of direct olefination of aryl carbon-hydrogen (C–H) bonds (Fujiwara-Moritani reaction). Despite significant progress, the restricted substrate scope, in particular noncompliance of unactivated aliphatic olefins, has discouraged the use of this greener alternative. Overcoming this serious limitation, a palladium-catalyzed chelation-assisted ortho-C–H bond olefination of phenyl acetic acid derivatives with unactivated, aliphatic alkenes in good to excellent yields with high regio- and stereoselectivities has been reported. The versatility of this operationally simple method has been demonstrated through drug diversification and for synthesizing divinyl benzene derivatives.

March 23, 2015 at 4.00 pm in AG-69

Title :

Spectroscopic and Ab-initio Studies of OH---S and CH---Y(Y=O,S) H-bonded Systems

March 18, 2015 at 2.30 pm in AG-69

Title :

Modeling the Metabolic Pathways

March 11, 2015 at 2.30 pm in AG-69

Title :

Stability, metastability and aggregation in Prion proteins: Importance of capturing the rare events

Abstract :

In contrast to the molecular machinery where nature performs fascinatingly well, there are many examples where things may go terribly wrong leading to life-threatening diseases! In this talk we shall try to understand the elusive problem of “prion propagation” and their aggregation into insoluble fibrils that cause a multitude of neurodegenerative disorders. I shall talk about our recent efforts in identifying the mysterious misfolded scrapie (PrPSc) form of a prion protein that is considered to infect the healthy cellular prions (PrPC) by inducing misfolding in them. Using extensive Replica Exchange Molecular Dynamics (REMD) simulations we have been able to identify many low-lying transient misfolded states that might catalyze the aggregation pathway through hydrophobic interactions. We also speculate that the secondary structural elements in a cellular Prion are in fact stabilized by weak tertiary contacts leading to very low barrier towards misfolding.

We shall also discuss our futuristic ideas about understanding the hydrophobic effects around a complex molecular surface (e.g. proteins), which seem to play a very important role in various self-assembly, aggregation and binding processes. Our long term goal would be to build a computationally efficient, yet quantitative implicit solvation model that would give us solvation thermodynamics of any arbitrary molecular surface.


March 10, 2015 at 2.30 pm in AG-69

Title :

The curious case of Cytochrome c Oxidase: Role of protein electrostatics in biomolecular structure-function correlation

Abstract :

Nature has created a wide array of fascinating molecular machinery, and their efficiency is unparalleled when compared to their man-made counterparts. Be it photosynthesis (conversion of light into chemical energy), or enzyme catalysis (speeding up difficult chemical reactions), or ion channels (filtration device with high degree of specificity), or self-assembly of small molecules into organized structures, we have a lot to learn from biology! The need for a molecular level understanding of nature has been dramatically asserted by Richard Feynman: Everything that living things do can be understood in terms of the jiggling and wiggling of atoms. Following this ambitious approach, my goal is to understand the complex biomolecular functions and properties from a molecular point of view. Using statistical mechanics based computational techniques, we are able to connect the molecular interactions (energetics) to their structural, thermodynamic and kinetic properties. The ultimate challenge is to obtain the underlying free energy surfaces for any (bio)chemical processes with quantitative accuracy and computational efficiency.

In this talk, I shall take up the example of the fascinating molecular machinery involved in the proton transport processes in a trans-membrane enzyme Cytochrome c Oxidase (CcO), which reduces oxygen (O2) to water in our respiratory cycle and uses the released energy to pump protons across the membrane. I shall discuss the importance of electrostatic interactions, the role of dielectric heterogeneity of the protein interior in affecting the pKa and protonation state of the key ionizable residues, and the role of internal water molecules therein. We shall demonstrate how molecular thermodynamics can provide physical insights into the function of complex biomolecules.


March 9, 2015 at 4.00 pm in AG-69

Title :

Fluorescent Sensors for Signaling Phospholipids

March 5, 2015 at 4.00 pm in AG-80

Title :

Elucidating the Structural Basis of Substrate Recognition by the Proteasomes: A Global Approach

Abstract :

PSMD9, a non-ATPase subunit of the 19S regulatory complex of the 26S proteasome harbours an uncharacterized PDZ-like domain which is well known for protein-protein interaction. PDZ domains interact with C-terminal residues of the interacting partner. In quest for partners of PSMD9, we performed C-terminal tetrapeptide screen representing the C-termini of proteins of human proteome to test the ability of these peptides to bind to PSMD9 and consequently demonstrate that proteins harbouring those C-terminal residues interact with PSMD9. Here, we report that PSMD9 interacts with the C-terminal residues of hnRNPA1, S14, a ligand growth hormone and IL6 receptor via its PDZ-like domain. Studies in our lab have also shown that PSMD9-hnRNPA1 interaction is important for NF-κB signaling. Through homology modeling, docking studies, site directed mutagenesis and simulation, we provide an insight into the probable structure of PDZ domain of PSMD9 and the residues important for the interaction and functions of PSMD9.

March 2, 2015 at 4.00 pm in AG-69

Title :

New Solids having Novel Interfaces with Tunable Properties

Abstract :


Ultra-thin atomic layers open a possibility for interacting with individual atoms in a material. At the same time, control over their synthesis, bulk production, large area single crystal synthesis, amenabilities in transfer processesetc. open avenues for engineering them for suitable applications. Recently, development of new solids from interfacing distinct atomic layers received tremendous scientific attention. A new solid from in-plane bond saturated and electronically dissimilaratomic sheets, such as graphene and hexagonal boron nitride (hBN), called van der Waals solids is one such solid where new and unprecedented phenomena are found to be emanating from the interface. This is a paradigm shift in the materials science since these interface induced phenomena are found to be tunable to large extends. Moreover, some of these tunable phenomena at the interfaces are useful in energy harvesting and storage applications. The solids generated by other means of interfacing atomic layers are also found to be excelling in various fields. My talk will be focusing on some of the engineering aspects of 2D materials for various fields.




 1.  Artificially stacked atomic layers: towards new van der Waals solids, Gao et al. Nano Letters, 12, 3518-3525 (2012).Two dimensional materials: Mix and Match”Nature Nanotechnology, doi:10.1038/nnano.2012.139.


2.      Engineering photophenomena in large three-dimensional van der Waals heterostructures, Krishna et al. NaturePhysics(Under Review).


3.    Cross-linked 3D Graphene Nanoribbon Monolith Electrodes, Vineesh et al. Nanoscale (Under Review).


4.   Low Density Three-Dimensional Foam Using Self-reinforced Hybrid Two-Dimensional Atomic Layers, S. Vinod et al. Nature Communications,5, 4541, doi:10.1038/ncomms5541 (2014).


5.     Wu et al. A three-dimensionally bonded spongy graphene material with both super compressive elasticity and near-zero Poisson's ratio,Nature Communications (Accepted).




March 2, 2015 at 11.00 a.m. in AG-80

Title :

Metabolic Paradigm of Sleep

Abstract :

Reduced sleep duration is a hallmark of modern-day society and is increasingly associated with medical conditions, such as diabetes, obesity, metabolic syndrome, and cardiovascular disease. Therefore, altered metabolism is a key to understand the processes related to sleep debt and clinical conditions associated to sleep. A metabolomic investigation by our lab has shown significant metabolic alteration in sleep deprived mice compared to baseline metabolic status. Major circulatory lipid component was found to be altered. In addition, we also showed presence of cross-species metabolic markers of sleep debt across rodents and humans. In addition, we also made progress investigating metabolic correlates of brain function during sleep. These results will be discussed in light of the clinical phenotypes of reduced sleep and sleep disorders. 

February 23, 2015 at 4.00 pm in AG-69

Title :

Understanding Amyloid Beta Aggregation in terms of its Distal Folding Contacts

February 16, 2015 at 4.00 pm in AG-69

Title :

Photocatalytic Application of Atomic Layer Deposited (ALD) TiO2 on Fibrous Nano-Silica (KCC-1)

February 12, 2015 at 4.00 pm in AG-80

Title :

Single Molecular Spectroscopy of Single Live Cell

Abstract :

The 2014 Nobel Prize in Chemistry has been awarded for the development of Single Molecule Spectroscopy. We will discuss some recent application of this technique to the study of a single live cell. In a confocal microscope, the size of the focused spot (~200 nm = 0.2 m) is one-hundredth of the dimension of a cell. Thus one can probe different regions/organelles in a cell. Utilizing this, we will describe several new phenomena inside a live cell [1-5]. Specifically, we have discovered found substantial differences between a cancer cell and a normal cell [1-4]. The gold nano-clusters preferentially enter or stain a cancer cell compared to a non-malignant cell [1]. The red-ox processes (thiol-disulfide interconversion) lead to intermittent structural oscillations leading to fluctuations in fluorescence intensity in a single live cell [2-3]. Such oscillations are absent for a cancer cell [2]. The number of lipid droplets are much higher in a cancer cell. We detected stochastic resonance during gene silencing in a cancer cell [5].

1.  S. Chattoraj, et al.  "Fluorescent Gold Nano-Cluster inside a Live [UTF-8?]Cell,” J. Phys. Chem. C 118

     (2014, in press).
2.  S. Chattoraj, et al.  "Role of Red-Ox Cycle in Structural Oscillations and Solvation Dynamics in Mitochondria,"

     J. Phys. Chem. B 118 (2014, in press).
3.  S. Ghosh, et al. "Solvation Dynamics and Intermittent Oscillation of a Cell Membrane: " J. Phys. Chem. B 118

     (2014) 2949-2956.  
4.  R. Chowdhury, et al. "Confocal Microscopy of Cytoplasmic Lipid Droplets in a Live Cancer  Cell”

     Med. Chem. Comm. 5 (2014) 536-539.
5.  S. Chattoraj, et al. "Dynamics of Gene Silencing in a Live Cell," J. Phys. Chem. Lett. 5 (2014) 1012-16.

February 9, 2015 at 4.00 pm in AG-69

Title :

Examining Protein Ligand Interactions Using Single Molecule Force Spectroscopy