Non-Linear Optical Organic Micro-Resonators
Bottom-up molecular self-assembly technique has emerged as one of the powerful methods to produce miniaturized organic photonic structures, such as optical waveguides, lasers, resonators, filters, circuits and modulators. Optical waveguides and modulators are used to control the light propagation down to microscale and modulate the light propagation speed, respectively. In optical resonators their mirror-like geometry allows them to tightly trap the photons by repeated total internal reflection at the air-matter interface and act as optical gain media exhibiting high-quality factor (Q) with the low optical loss. We have been performing single-particle micro-PL spectroscopy studies to exploit the geometrical features of diverse self-assembled organic structures for photonic applications. In my talk, I will discuss some original results achieved in our group in linear and non-linear optical organic optical waveguide and microresonators useful for signal enhancement, sensing and lasing applications. I will also discuss our attempts towards creation and study of photonic molecules.
Adv. Mater. 2017, 29, 1605260.
Adv. Mater. 2013, 25, 2963.
 Angew. Chem. Int. Ed. 2012, 51, 3556.
Adv. Funct. Mater. 2013, 23, 5875.
Adv. Funct. Mater. 2011, 21, 667.
Adv. Opt. Mater. 2018, in the press [progress Report].
Adv. Opt. Mater. 2017, 5, 1600613.
Adv. Opt. Mater. 2016, 4, 112-119.
Adv. Opt. Mater. 2015, 3, 1035.
Adv. Opt. Mater. 2013, 1, 305.
 ACS Appl. Mater. Interfaces, 2018, 10, 16723.
 J. Mater. Chem. C 2018, DOI: 10.1039/C8TC02638F.
 J. Mater. Chem. C 2017, 5, 7262.
 J. Mater. Chem. C 2017, 2, 1404.
 Chem.Nano.Mat. 2018, 4, 764.
Exploring the Challenges in Computational Enzyme Design
Enzymes are nature’s most efficient catalysts and are also harnessed in synthetic chemistry for the sustainable production of several non-natural products. However, the design of new enzymes presents a major practical and fundamental challenge. Despite an interesting progress, the main advances are achieved through directed evolution and not by computational design.1 Moreover, several designed systems adopt the less efficient route of ground state destabilization instead of transition state stabilization. In the talk, I will discuss the design of two enzymes; Kemp eliminases and haloalkane dehalogenase. Kemp eliminases are computationally designed enzymes that catalyze the conversion of 5-nitrobenzisoxazole to cyanophenol product. Haloalkane dehalogenase; DhlA is an important enzyme that helps in breaking down the toxic haloalkanes (1,2-dichloroethane) to alcohol via a series of steps. EVB (Empirical valence bond) approach is used to calculate the activation energies for the wild type and mutants. For Kemp eliminases, the origin of catalysis in different systems is rationalized on the basis of solvation free energies.2 The different trends observed in the directed evolution of different systems is investigated to understand the effect of multiple mutations. For halolalkane dehalogenase, after successfully reproducing the activation barriers of known mutants, new mutations are proposed on the basis of structural data.3 We mutated residues that are known to contribute to catalysis and then attempted to restore the activity by mutating residues in the first and second solvation shells. Various factors responsible for certain anomalies and the challenges encountered during computational enzyme design will be discussed.
 Frushicheva, M. P.; Cao, J.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16869.
 (a) Jindal, G.; Ramachandran, B.; Bora, R. B.; Warshel, A. ACS Catal. 2017, 7, 3301. (b) Jindal, G.; Mondal, D.; Warshel, A. J. Phys. Chem. B 2017, 121, 6831.
 Jindal, G.; Slánská, K.; Kolev, V.; Damborsky, J.; Prokop, Z.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2018 (Under Revision).
Computational Studies on Mechanism and Stereoinduction in Asymmetric Catalysis
One of the leading goals in contemporary catalysis is to render improved efficiency to existing catalytic protocols.1 While different forms of catalysis have witnessed tremendous success in the synthesis of complex molecules, there is minimal clarity at the mechanistic front. Further developments in the new form of catalysis/catalysts require a thorough knowledge of the reaction pathways. In asymmetric catalysis, the rationalization of selectivity is of prime importance as it paves the way for rational catalyst design. In the current talk, I will discuss the use of use of computational tools in providing a mechanistic understanding and insights into the factors controlling the stereoselectivity in a few landmark asymmetric reactions catalyzed by axially chiral catalysts/ligands. In particular, all calculations have been carried out with hybrid density functional theory (DFT) methods (B3LYP, M06, M06-2X and B3LYP-D3). The talk will focus on three forms of catalysis; 1) organocatalysis, 2) metal catalysis and, 3) cooperative catalysis. The first part encompasses the role of a newly developed class of chiral imidodiphosphoric acids in inducing selectivity in an asymmetric sulfoxidation reaction.2 The second part will focus on the fine tuning of noncovalent interactions to design new phosphoramidite ligands for an asymmetric diamination reaction.3 In the last part, the role of chiral Brønsted acids when used in conjunction with Pd metal and the importance of ligand exchange in the formation of spirocyclic ring formation will be elucidated.4
 Houk, K. N.; Cheong, P. H.-Y. Nature 2008, 455, 309.
 Jindal, G.; Sunoj, R. B. Angew. Chem. Int. Ed. 2014, 53, 4432.
 (a) Jindal, G.; Sunoj, R. B. Chem. Eur. J. 2012, 18, 7045. (b) Jindal, G.; Sunoj, R. B. Org. Biomol. Chem. 2014, 12, 2745.
 (a) Jindal, G.; Sunoj, R. B. J. Am. Chem. Soc. 2014, 136, 15998. (b) Jindal, G.; Sunoj, R. B. Org. Lett. 2015, 17, 2874.
Carbonyl-carbonyl interactions in small molecules and proteins
The carbonyl group is ubiquitous in both chemistry and biology. Apart from being involved in numerous chemical transformations, it can also participate in various distinct weak noncovalent interactions including hydrogen bonding (C=O•••H), carbonyl-chalcogen interactions (C=O•••X; X = S, Se, Te) and nucleophile-carbonyl interactions. In recent years, carbonyl-carbonyl (CO•••CO) interaction has emerged as an important noncovalent interaction that was observed in various small molecules, polyesters, peptoids, protein secondary structures and collagen-like peptides. It is believed that this interaction is n→π* in nature where the lone pair of oxygen of the donor carbonyl group is delocalized over the antibonding π orbital of C=O bond of another nearby acceptor carbonyl group. In this talk, I will discuss our current understanding of CO•••CO interactions with a focus on the “reciprocal” variant of n→π* interaction that we recently discovered. I will also discuss about the various structural motifs of CO•••CO interactions and put forward a hypothesis based on CO•••CO interactions that could explain the stabilization of polyproline II and collagen triple helices.
GroEL Chaperonin Assisted Protein Folding: studied by PETFCS and SmFRET
Many newly synthesized unfolded polypeptides require assistance by molecular chaperones in order to reach their active folded states. The GroEL/GroES chaperonin system is one of the most important bacterial chaperonin systems, which fulfills an essential function in assisting the folding of cytosolic proteins. GroEL is a homo-tetradecameric double-ring assembly of 60 kDa subunits with two opposing central cavities stacked back to back. Upon binding of ATP and the co chaperone GroES, GroEL transiently encapsulates newly synthesized or misfolded substrate proteins, which then can fold to the native state while being shielded from the crowded cytosolic environment. The mechanism of GroEL remains controversial whether GroEL acts as a passive cage, merely providing an aggregation preventing micro compartment, or whether GroEL actively accelerates the refolding of a subset of substrate proteins by modulation of the folding energy landscape.
We resorted to a variety of single molecule fluorescence techniques to address this controversy. A novel and sensitive dual color fluorescence cross-correlation spectroscopy assay shows the absence of transient aggregates at single molecular concentration. Using a single molecule FRET (SmFRET) based assay, we show that the acceleration of substrate protein folding by GroEL is preserved under single molecule conditions, where aggregation is excluded. We apply photoinduced electron transfer fluorescence quenching correlation spectroscopy (PETFCS) to demonstrate that the acceleration of substrate protein folding is achieved by encapsulation of a dynamic folding intermediate inside the GroEL cavity. Furthermore, we provide evidence that modulation of the folding energy landscape is a result not only of steric confinement during encapsulation, but also of the net negative charge of the GroEL cage wall. Taken together, these results represent a substantial advance in our understanding of the mechanism of the prokaryotic chaperonin system and our findings suggest that GroEL, by an active chaperonin mechanism, promotes substrate protein folding by entropic destabilization of folding intermediates.
Direct observation of the Mechanical Foldase Activity of Trigger Factor Chaperone by Magnetic tweezers
Proteins fold under mechanical forces in a number of biological processes, ranging from muscle contraction to co-translational folding at the mouth of the ribosome. As force hinders the folding reaction, chaperones must play a crucial role in this scenario. Nevertheless, to date, it has not been possible to monitor the direct influence of a chaperone on a protein folding under force. Here, we introduce single molecule magnetic tweezers to study the folding dynamics of protein L in presence of the prototypical molecular chaperone Trigger Factor (TF) over the range of physiological forces (4 to 10 pN). Our results show that TF modulates the folding of protein L by prominently increasing the probability of folding against the force and accelerating the refolding kinetics. Moreover, we find that the ability of TF to catalyze the folding reaction depends on the pulling force; as the force increases, higher concentrations of TF are needed for rescue folding, although no effect is observed above 12 pN even with saturating amounts of TF. Here, we propose for the first time that chaperones such as TF can work as foldases under force, playing a relevant role in many biological processes such as protein translation.
Design of Catalysts and Nano-Heaters by Decorating Ultrasmall Nanoparticles and Pseudo-Single Atoms of Metal on DFNS: Tuning their Plasmonic Response by Hot Spot Engineering
Charge Transport and Catalysis Reactions at the Electrified Interfaces
Possibility of studying the properties of molecules or nanostructures at single enity level offers huge opportunities to tune structure property relationships at nanoscale. The problem with current state-of-the-art nanomaterials and energy research involving charge or electron transport at electrode|molecule interface as a key process is centered in the fact that no single experimental technique can independently provide complete information on nanoscale structure-property relationships. The development of fast, cost effective and structure sensitive characterization methods at single entity level is the target of much current nanotechnology research.
During this presentation, I will try to show the experimental framework (experimental technique and methodologies development) that I am planning to implement/develop in my future laboratory to address the key issue of nanoscale structure-property relationships under in-operando conditions.1-4
1. Kaliginedi et al., Nanoscale. 2015, 7 (42), 17685-17692.
2. Rudnev, A., Kaliginedi et al., Science Advances. 2017, 3, e1602297.
3. Seth, C., Kaliginedi et al., Chemical Science. 2017, 8, 1576-1591.
4. Atesci, H., Kaliginedi et al., Nature Nanotechnology. 2018, 13, 117.
Charge transport at Electrode|Molecule interface: From Molecular Electronics to Energy Research Applications
The idea of building electronic devices using single molecule as an active component was first proposed by Aviram and Ratner in the early seventies.1 Indeed, molecules are of great interest for application in electronic devices because of their small size, recognition properties, ability of self-organization, possibility of chemical modification and customisation. Thus, the ability to measure and control charge transport across metal|molecule|metal junction is of considerable fundamental interest and represents a key step towards the development of molecular electronic and spintronics devices.2-6
In addition to the applications in molecular electronics and spintronics research, studying charge or electron transport properties at metal|molecule interfaces under the influence of external stimuli like light, temperature, electrochemical potential or magnetic field will have a variety of applications in other research fields like (i) energy research (for example, solar cells, where the charge or electron transfer at metal|molecule interfaces plays a crucial role in determining the efficiency of the solar cell); (ii) photocatalysis and electrocatalysis (activity of a catalyst depends on the effective charge transport at electrode|catalyst interface); (iii) Sensors (sensitivity and selectivity of a sensor may depend on the effective charge transport at electrode|sensor moiety interface) and etc.5,7
In the first part of my presentation, I will introduce working principle of measurement techniques (i.e STM break junctions (STM-BJ), mechanically controllable break junction (MCBJ) and conducting probe AFM (CP-AFM) techniques) and data analysis procedures used to extract conductance properties of molecular junctions.2 Using the results from several case studies, I will try to demonstrate a frame work for building structure-property correlations of metal|molecule|metal junctions at single and multi-molecular level.2-6 In the later part of my presentation, I will discuss the molecular conductance measurement results which will have direct consequences in electrocatalysis and energy researh.3,5,7
1. Aviram, A.,Ratner, M., Chem. Phys. Lett. 1974, 29, 277.
2. Kaliginedi et al., Journal of American chemical society. 2012, 134, 5262–5275.
3. Rudnev, A., Kaliginedi et al., Science Advances. 2017, 3, e1602297.
4. Seth, C., Kaliginedi et al., Chemical Science. 2017, 8, 1576-1591.
5. Atesci, H., Kaliginedi et al., Nature Nanotechnology. 2018, 13, 117.
6. Kaliginedi et al., PCCP. 2015, 16, 23529.
7. Kaliginedi et al., Nanoscale. 2015, 7, 17685.
Circular permutations in azurin: Creating new termini for pulling along different directions
Plant Viruses for the Delivery of Platinum Anticancer Therapeutics
Platinum-based anticancer drugs such as cisplatin, carboplatin, and oxaliplatin are used in the treatment of nearly half of the population of the cancer patients undergoing chemotherapy. These drugs, however, lack selectivity and have dose-limiting toxicities, low bio-availability, rapid clearance from the body, and may encounter drug resistance mechanisms, leading to the recurrence of the cancer. Therefore, efficient loading of drugs in novel delivery agents has the potential to substantially improve therapy by directly targeting the diseased tissue and avoiding unwanted side effects. Given that the development of new drugs is expensive, reducing toxicity caused by existing drugs by packaging them into delivery vehicles is attractive and can be achieved by controlled and targeted methodologies. Although presently available nano-sized delivery agents impart safety, their limited efficacy and inability to penetrate tissue adequately are some of the limitations. Consequently, development of new drug delivery methods has been a subject of recent burgeoning interest.
Viruses are very simple in structure and composition, and they can be considered as biology-derived nanocarriers, naturally evolved to carry and delivery cargos to target cells. Moreover, they can transfect host cells with a very high efficiency. However, their immunogenic nature hinders their development as drug carriers. In this regard, plant viruses form an emerging platform technology as they offer several advantages over mammalian vectors.
In this talk, I will highlight the use of tobacco mosaic virus (TMV) for the delivery of platinum anticancer therapeutics. It has been shown previously by our research group that the highly potent analogues of cisplatin, phenanthriplatin (1) and its aqua-form (2), are differentially taken up in the TMV channel. Whereas ~1000 molecules of 1 are loaded in TMV, 2 is taken up in higher quantities (~2000 molecules per TMV particle). Studies on delineating the mechanism of their differential uptake and their stabilization in the TMV channel will be discussed in detail. Furthermore, I will also discuss on the heat-transition of TMV nanorods to nanospheres (SNPs) in the presence of 1, which leads to significant uptake of 1 in the bulk of SNPs, and their mechanism of formation. These SNPs are stable in the fetal bovine serum (FBS) medium and they do not release 1 at pH 7.4 and pH 5, which may further prevent the toxicity arising due to off-target release of drugs. To an added advantage, the release of 1 is only triggered by proteolytic enzyme like trypsin which is a constituent of endosome. SNP delivery system presents a comparable to better anticancer efficacy in the panel of cancer cell lines. These investigations inform the design of future drug analogues that can be efficiently encapsulated, stabilized in different morphologies of TMV, and delivered to the tumor site.
1.A. E. Czapar, Y. Zheng, I. A. Riddel, S. Shukla, S. G. Awuah, S. J. Lippard, N. F. Steinmetz, ACS Nano, 2016, 10, 4119-4126.
2.A. A. Vernekar, G. Berger, A. E. Czapar, F. A. Veliz, D. Wang, N. F. Steinmetz, S. J. Lippard, J. Am. Chem. Soc., 2018, 140, 4279-4287.
3.A. A. Vernekar, F. A. Veliz, N. F. Steinmetz, S. J. Lippard, (SNP work will be submitted soon).
Bioinorganic Chemistry Approach to Nanozymes for Cellular Redox Regulation
Organic/metal organic compounds that mimic the functional role of enzymes have been extensively investigated. Recently, few nanomaterials such as gold nanoparticles, ferromagnetic nanoparticles and graphene-based materials have been innovatively shown to exhibit unprecedented biochemical catalysis by mimicking certain enzymes (nanozymes). Owing to their simplicity of preparation and storage and stability, nanozymes have been investigated for their application in many fields such as biosensing, immunoassays, cancer diagnostic, therapeutic and pollutant removal, etc. Despite current interest on nanozymes, tackling with some of the difficulties associated with them such as selectivity, cooperativity with other enzymes, limited surface area due to functionalization, biocompatibility and activity in cells, etc. is a challenging task.
In this seminar, I will discuss about the novel antioxidant and phosophotriesterase nanozymes. We have recently reported the graphene-hemin hybrid material for its remarkable peroxynitrite reductase and isomerase antioxidant activities. Noncovalent interactions of hemin and reduced graphene oxide (RGO) resulted in synergistic activity to effectively scavenge peroxynitrite, which is a potent reactive nitrogen species (RNS) found in vivo.
In another related study, we found that vanadium pentoxide (V2O5), an oxidant, reveals an unexpected antioxidant role in its nano-form and exerts tremendous cytoprotective effects. The vanadia nanozyme exhibit excellent glutathione peroxidase (GPx)-like catalytic antioxidant activity and prevents oxidative damage to cells from reactive oxygen species (ROS) without affecting the expression level of other antioxidant enzymes. This work demonstrates the first experimental evidence that the biological property of a metal ion in its nano-form can be completely different from that of a bulk material. In a similar line, I will also briefly highlight about MnFe2O4 nanooctahedrons as oxidase and vacancy-engineered nanoceria as phosphotriesterase nanozymes for antibody-free detection of major biomarkers of oxidative stress and detoxification of sarin gas-related nerve agents, respectively.
1. A. A. Vernekar, G. Mugesh, Chem. Eur. J. 2012, 18, 15122-15132.
2. A. A. Vernekar, G. Mugesh, Chem. Eur. J. 2013, 19, 16699-16706.
3. A. A. Vernekar, D. Sinha, S. Srivastava, U. P. Prasath, P. D’Silva, G. Mugesh, Nature Commun. 2014, 5, 5301.
4. A. A. Vernekar, T. Das, S. Ghosh, G. Mugesh, Chem. Asian J. 2016, 11, 72-76.
5. A. A. Vernekar, T. Das, G. Mugesh, Angew. Chem. Int. Ed.2016, 55, 1412-1416.
When Nano Break H2O
While H2O (water) is life to all living organisms on earth, it is also one of the key technological components of hydrogen economy. In an electrolysis cell, water can be decomposed into hydrogen and oxygen due to an electric current passing through it. Although hydrogen evolution reaction (HER) is the major reaction of interest, oxygen evolution reaction (OER) is the most energy intensive step. To overcome the activation barrier of splitting water, a catalyst is needed. The more active and stable the catalyst, more effective is the splitting. One of our major research interests is to develop nanoheterostructured electrocatalysts for OER and HER,1,2 thereby leading to overall water splitting.3 The best performances are obtained not only by designing a suitable catalyst but also by optimizing the substrate on which the catalyst nanoparticles are supported, among which flexible substrates are fascinating.4 When the electrolyzer is integrated to solar cells, water photolysis with high solar-to-hydrogen efficiency also becomes possible.
1.Datta, A.; Kapri, S.; Bhattacharyya, S. J. Mater. Chem. A 2016, 4, 14614-14624.
2.Debnath, B.; Kumar, A.; Salunke, H. G.; Bhattacharyya, S. J. Phys. Chem. C 2017, 121, 25594-25602.
3.Kumar, A.; Bhattacharyya, S. ACS Appl. Mater. Interfaces 2017, 9, 41906-41915.
4.Sahasrabudhe, A.; Dixit, H.; Majee, R.; Bhattacharyya, S. Nat. Commun. 2018, 9, 2014.
Investigations on photocatalytic H2 generation using modified TiO2 and g-C3N4 semiconductors
Generation of hydrogen from renewable sources like water and solar energy is considered to be an attractive and viable solution for replacing fossil fuels. Photocatalytic water splitting has attracted much attention as it involves conversion of solar energy into useful chemical energy. The major challenge involved in the process is the development of stable and visible light active photocatalyst with required solar to fuel energy conversion efficiency (SFE). In the present work, studies were undertaken to improvise the optical and photocatalytic properties of several photocatalysts; conventionally known UV active TiO2 and novel organic semiconductor, graphitic carbon nitride (g-C3N4). Various strategies such as cationic doping by Cu in TiO2, composite formation with NiO and CuO inducing pn heterojunctions, carbon and TiO2 heterojunction to improve electronic conductivity, surface modification of g-C3N4 by dispersing carbon nanodots (CND) and noble metal (Pt, Pd, Cu, Ag and Au) were adopted to limit the e-/h+ recombination reaction and to enhance the photoresponse under visible light illumination. All samples were thoroughly characterized by relevant techniques and their potential for H2 generation was evaluated under sunlight and UV-visible light in presence of sacrificial reagent. Density functional theory calculations were performed and life time of e-/h+ from PL decay curves was measured to support the activity trend. Parameters such as illumination area, catalyst concentration, form of catalyst (powder/films) and different sacrificial reagents were optimized for maximum H2 yield. Performance of the screened photocatalysts was also tested in up-scaled photoreactors (volume = 0.5, 1 and 2 L). H2 yield @ 16 ml/h/g with apparent quantum efficiency (AQE) of 7.5 % and SFE of 3.9 % over Cu0.02Ti0.98O2-δ (without cocatalyst) was observed under sunlight suggesting that 0.96 m2 illumination area will yield H2 @ 1 L/h photocatalytically. Among modified g-C3N4 photocatalysts, maximum H2 yield of 398 μmol/h over 80 mg of Pt/CND/ g-C3N4 (0.48 wt %) under sunlight with AQE of 4.0 % and SFE of 2.0 % was achieved as compared to almost negligible yield over pristine carbon nitride. The present study is targeted to provide valuable inputs for actual large scale solar photocatalytic H2 production.
Development of metal oxide based photocatalysts for the CO2 reduction to fuel
Continuous depletion of fossil fuel resources and growing environmental concerns due to the huge CO2 emissions, have focused the need to develop renewable and clean energy resources. CO2 is a major greenhouse gas and cause of global warming. CO2 capture, storage and utilization particularly, catalytic conversions of CO2 to fuels and chemicals have attracted much attention in recent years. Activation of CO2 requires high amount of energy due to its stability. Harvesting the photon energy and its storage in the form of fuels hold promise to address the current and future demand of energy supply. The photocatalytic conversion of CO2 over heterogeneous photocatalysts is a potential approach to mitigate CO2.
Designing of material with suitable band gap and product selectivity remained key challenges. Problems associated are: (i) massive recombination of generated charge carriers and (ii) low yield and less selectivity for product formation and (iii) development of stable visible light active catalyst. Metal oxides with suitable properties can convert solar energy to chemical energy using artificial photosynthesis and it will be a good technique to develop sustainable environment.
The talk will cover my work on designing and synthesis of metal oxide catalysts for the photocatalytic reduction of CO2 to fuel.