TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

March 26, 2018 at 4.00 pm in AG-69

Title :

Seminal Electrode Materials for Battery and Supercapacitor Applications

March 21, 2018 at 2.30 pm in AG-80

Title :

Variational Random Phase Approximation Method for Accurate Ionization Potentials and Interaction Energies

Abstract :

A critical and outstanding challenge of electronic structure method development is to deliver both accurate total energy differences and quasiparticle spectra. I will address this challenge using a generalized Kohn-Sham (GKS) approach that variationally minimizes the random phase approximation (RPA) ground-state energy as a functional of the one-particle density matrix. The GKS-RPA approach enables highly accurate predictions of all observables from derivatives of a single variationally stable energy functional, and leads to remarkable advancements. Intermolecular binding-energies and quasiparticle spectra from GKS-RPA improve significantly upon those from state-of-the-art post-Kohn-Sham RPA or G0W0 theory. Anions, which are often unstable and poorly described by semi-local density functional approximations, are well described within GKS-RPA. Core ionization energies, which are traditionally hard to compute, can be accurately estimated using GKS-RPA; pilot applications for modeling solvation effects in conjunction with X-ray photoelectron spectroscopy will be discussed. Overall, the GKS scheme alleviates some of the most serious problems with semi-local density functional approximations, and paves the way for a new generation of electronic structure methods.

References:

  1. G. Chen, V. K. Voora, M. Agee, S. Balasubramani, and F. Furche. “Random phase approximation methods”, Annu. Rev. Phys. Chem., 2017, 68, 421. 
  2. V. K. Voora, S. G. Balasubramani, and F. Furche. “Variational Generalized Kohn-Sham Approach Combining Random Phase Approximation and Green’s Function Methods”, https://escholarship.org/uc/item/7gf3h1h9. 

 

March 20, 2018 at 2.30 pm in AG-80

Title :

Nonvalence Correlation-Bound Anionic States: A New Doorway to Electron Transfer 

Abstract :

The mechanistic details and the dynamics of electron transfer to molecules continue to be poorly understood. The key to unraveling this fundamentally important chemical process hinges upon a sound understanding of electron binding states. Here I will discuss the discovery, theoretical characterization and role of nonvalence correlation-bound (NVCB) states as a new low-energy doorway for electron capture and transfer. In the NVCB states of anions, the excess electron occupies a very diffuse orbital while its binding to the molecule or cluster is dominated by long-range dispersion-type correlation forces. Ab initio methods and one-electron model Hamiltonians will be used to characterize the NVCB anionic states. The existence of NVCB states and its implications for gas-  and condensed-phase electron transfer will be illustrated using examples ranging from small molecules to large fullerene systems. 

 

References:

  1. V. K. Voora, A. Kairalapova, T. Sommerfeld, and K. D. Jordan. “Theoretical approaches for treating non-valence correlation-bound anions”, J. Chem. Phys., 2017, 147, 214114.
  2. V. K. Voora, and K. D. Jordan. “Nonvalence correlation-bound anion states of spherical fullerenes”, Nano Lett., 2014, 14, 4602. 
  3. V. K. Voora, L. S. Cederbaum, and K. D. Jordan. “Existence of a correlation bound s-type anion state of C60”, J. Phys. Chem. Lett., 2013, 4, 849. 
  4. J. P. Rogers, C. S. Anstöter, and J. R. R. Verlet. “Ultrafast dynamics of low-energy electron attachment via a non-valence correlation-bound state”, Nat. Chem., 2018, http://dx.doi.org/10.1038/nchem.2912.  

 

March 14, 2018 at 2.30 pm in AG-80

Title :

Proton Coupled Electron Transfer and Charge Transfer Reactions at Solid-Liquid Interfaces and Homogeneous Environment

Abstract :

Proton coupled electron transfer (PCET) reactions are integral part of several catalytic processes that are crucial for energy storage, fuel cell research and several biological processes. On the other hand, excited state charge transfer reactions are at the heart of many photoinduced processes. In this presentation, I will discuss (i) computational study of PCET reaction between ZnO nanocrystal and an organic radical (ii) new theoretical methods to calculate solvent reorganization energies for electron transfer and PCET reactions in electrochemical systems, and (iii) implementation of a novel method to incorporate nuclear quantum effects in charge transfer dynamics. In the first part of the presentation I will show how to estimate rate constant for PCET between photoreduced ZnO nanocrystal and TEMPO. For reactions that involve a substantial redistribution of charge density in a polar environment, it is important to estimate the energy penalty involved in rearranging the solvent dipoles in order to estimate rate constant for the charge transfer process. In the second part of this talk I will describe a new method for calculating this important parameter, solvent reorganization energy, in the context of electrochemical electron transfer and PCET reactions. In the final part of this talk I will introduce my ongoing research on incorporating nuclear quantum effects in charge transfer dynamics within the framework of ring polymer surface hopping algorithm.

March 13, 2018 at 2.30 pm in AG-80

Title :

Homogeneous and Interfacial Proton Coupled Electron Transfer Reactions

Abstract :

Proton coupled electron transfer (PCET) reactions are integral part of several catalytic processes, e.g. reduction of dioxygen to water, oxidation of water to dioxygen, carbon dioxide reduction, reduction of dinitrogen to ammonia, that are crucial for energy storage, fuel cell research and several biological processes. In this presentation, I will discuss (i) computational investigations of role of PCET reaction in the mechanism of oxygen reduction reaction by a Co-salophen complex in the presence of p-hydroquinone as a co-catalyst, (ii) computational study of PCET reaction between ZnO nanocrystal and an organic radical. In the first part of the talk we will see that my calculations along with substantial experimental studies provide ample evidence for reduction of dioxygen to a coordinated hydrogen peroxide intermediate, which is subsequently reduced to water. The role of p-hydroquinone as electron proton transfer mediator is explored in details. In the second part of the presentation I will show how to estimate rate constant for PCET between photoreduced ZnO nanocrystal and TEMPO. We will further explore the role of proton diffusion inside the ZnO nanocrystal coupled to PCET reaction at the surface to explain the experimental studies of reaction dynamics of the PCET reaction mentioned above at longer timescales.

March 12, 2018 at 4.00 pm in AG-69

Title :

High Surface Area Aluminosilicates : Novel synthesis and unraveling the active sites by catalysis and Solid State NMR

March 5, 2018 at 4.00 pm in AG-69

Title :

Xeno-nuclei enable protein-specific modulation of order-disorder transition

Abstract :

The ability to modulate the order to disorder or vice versa transition of a specific protein in a milieu of many proteins can be an important tool for chemical biology and pharmacology. Kinetics and thermodynamics of protein folding are routinely modulated by changing solvent conditions, but such changes are not very protein specific. Specific ligands with the ability to alter the stability of a 

protein are rarely available. Here, we propose a general approach for designing such ligands by mimicking the folding nucleus of a protein. The key idea is to choose a part of the protein itself, which is suspected/known to be the nucleation site for the folding pathway, and then to put it in a pre-formed shape to modulate the folding/unfolding. This xeno-nucleus can in principle, be used to selectively modulate the folding of a particular protein from a mixture of different proteins. 

We show that the ⓵ - ⓶ part (residues 1 to 17) of ubiquitin [1], which is known to fold into a β-hairpin shape and to nucleate the folding of the rest of the protein, can make folding faster when it is introduced as a separate peptide at excess concentrations. No such acceleration is observed when the xeno-nucleus is unfolded to start with. Interestingly, the protein also becomes less stable, as the unfolding rate becomes even faster. We show that this effect is protein-specific, as another protein with no such β-hairpin (e.g. bovine serum albumin) remains unaffected by the peptide. Our results suggest that the folding of almost any protein that possesses a well-defined folding nucleus can be modulated, if a nucleus-mimicking molecule with a stabilized structure can be constructed. 

References: 

1. Atomic-level description of ubiquitin folding. PNAS, 2013, 110 (15), 5915–5920.

 

February 28, 2018 at 2.30 pm in AG-66

Title :

Science Stories: Communicating Science as Career, Hobby, or Habit

Abstract :

Whether it’s a new, better battery material, a company with controversial new drug, or tracking the impacts of climate change, science is an important part of the news. Science journalists translate research from the lab for public audiences—and they rely on working scientists to be a part of that process. Jessica Marshall will speak about the ins and outs of producing chemistry news for C&EN readers, and she’ll discuss her prior work as a freelance science writer. She’ll also talk about ways that working scientists can improve their communication—whether in speaking with other scientists or as sources for the news media. Science communication can be a rewarding career for science graduates—and those who remain at the bench can increase their work’s impact by clear communication. This session will discuss both roles: science communicator and communicating scientist. Come join the conversation.

About the Speaker:

Jessica Marshall is an associate editor at Chemical & Engineering News. Prior to joining C&EN, she spent a decade as a freelance science and environment writer. Her work appeared in Nature, TheAtlantic.com, Discover, Proceedings of the National Academy of Sciences, New Scientist, and other outlets. She contributed to The Science Writers’ Handbook: Everything You Need to Know to Pitch, Publish and Prosper in the Digital Age. She attended the University of California, Santa Cruz Science Communication Program. Prior to that, she earned a Ph.D. in chemical engineering at the University of California, Berkeley, and a B.S.E. in chemical engineering at Princeton University.  She lives in Seattle with her husband and three children.

 

February 27, 2018 at 2.30 pm in AG-80

Title :

Discovery and Characterization of Microproteins

Abstract :

The human genome project was supposed to have identified all protein-coding genes in the human genome, but recent work has revealed that gene finding algorithms had a blind spot; they failed to recognize protein-coding small open reading frames (smORFs). By definition, smORFs contain less than 150 codons and encode peptides or small proteins, collectively referred to as microproteins. Recent advances in the Mass Spectrometry and the Ribosome Profiling technology has led to the discovery of hundreds to thousands of these microproteins. The functional characterization of the microproteins is essential to understand their biological and cellular importance. The biological functions of a few microproteins have been elucidated, and these microproteins have fundamental roles in biology ranging from limb development to muscle function, highlighting the value of characterizing these molecules. Bioactive microproteins operate through microprotein-protein interactions (MPIs) and I’ll talk about the application of an in situ proximity tagging method that relies on an engineered ascorbate peroxidase (APEX) to elucidate MPIs. The APEX tagging method has been shown to be superior to traditional immunoprecipitation methods for microproteins. Furthermore, the application of APEX-tagging to uncharacterized microproteins called C11orf98 and MIEF revealed their interaction with protein complexes in nucleus and mitochondria respectively, thus, demonstrating the ability of this approach to identify novel hypothesis-generating MPIs.

February 26, 2018 at 4.00 pm in AG-69

Title :

Extracting the features of complex multidimensional energy landscape of proteins : a reaction coordinate free approach

February 23, 2018 at 2.30 pm in AG-66

Title :

Complete Enumeration of BN-doped Polycyclic Aromatic Hydrocarbon Libraries in the MolDis repository

Abstract :

The MolDis repository under development at TIFR Centre for Interdisciplinary Sciences aims to provide an analytics platform for Big Data of computed molecular properties. Presently massively large datasets are being generated for a multitude of domains of application.  The level-1 phase of data generation involves combinatorial enumeration of all possible molecules satisfying a few design rules. Starting with all possible plane-filling polycyclic aromatic hydrocarbons (PAHs), we have enumerated all possible doped analogues by substituting pairs of C atoms with B and N atom pairs. I will discuss the mathematics of this approach based on Polya enumeration theorem and show how a single PAH with six benzene rings can be doped into 241,813,226,150 different molecules providing a continuous spectrum of band-gap and other properties. 

Febrauary 22, 2018 at 2.30 pm in AG-80

Title :

Development of mixed N, O donor ligands for in vivo metal ion chelation and sensing

February 19, 2018 at 4.00 pm in AG-69

Title :

Breaking the RET barrier using metamaterials

Abstract :

Resonance Energy Transfer (RET) is a form of direct energy transfer between two dipoles. It has a very precise distance dependence that has allowed the technique to be widely used in particular for determining complex molecular structures. However, it is only effective over ˜ 15 nm separations. I will discuss our proof-of-principle experiments which extend the RET range of effectiveness by an order-of-magnitude and show RET between a donor-acceptor pair separated by 160 nm. This increase is facilitated by using metamaterials a class of custom-made nanophotonic structures that are designed to have unique optical properties, specifically, a topological transition from a closed to an open form which can be tuned for individual RET pairs. We will go over the design of the metamaterial for our experiment and also discuss the experimental demonstration of long distance RET using time resolved and steady state spectroscopy.

February 13, 2018 at 2.30 pm in AG-66

Title :

Nonadiabatic Reaction Dynamics at Conical Intersection

Abstract :

Excited-state reactions take place via couplings among near-lying electronic states. These electronic state couplings are mediated by nuclear momenta associated with vibrational motions and become most efficient at conical intersections where two or more electronic states are degenerate at the same nuclear configuration. Thereafter, nonadiabatic reaction pathways are open so that chemical reactions are driven into particular reaction outcomes. Even though conceptual description for nonadiabatic reactions as above is nicely conceived, actual experimental evidences are quite rare. Here, we present experimental cases where conical intersections are spectroscopically characterized and associated nonadiabatic dynamic pathways are identified in energy and time domains. Specifically, predissociation dynamics of thioanisoles in the supersonic jet are thoroughly investigated to unravel detailed mechanism involved in nonadiabatic transitions taking place in the vicinity of the conical intersection encountered along the reaction coordinate.

References :

K.C. Woo, D. H. Kang, and S. K. Kim, J. Am. Chem. Soc. 139, 17152 (2017).

H. S. You et. al., Int. Rev. Phys. Chem. 34, 429 (2015).

H. S. You, S. Han, J. S. Lim, S. K. Kim, J. Phys. Chem. Lett. 6, 3202 (2015).

J. S. Lim, S. K. Kim, Nat. Chem. 2, 627 (2010).

 

February 12, 2018 at 4.00 pm in AG-69

Title :

Tracking Phospholipid Induced Coil-Helix Transitions in Phosphoinositide-binding Motifs of Actin Binding Proteins