TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

February 18, 2020 at 2.30 pm in AG-80

Title :

Morphology Optimization and Photophysical Studies of Perovskite Solar Cell

Abstract :

There is an urgent need to shift all existing power systems such as household electricty, transportation, etc. on renewable and clean sources of  energy such as solar and wind energy etc. To harness solar energy lot of new materials have been discovered that caused the generational evolution of solar cells. Recently, organic-inorganic hybrid perovskite solar cells (PSCs), a third generation solar cell, have received significant research interest due to its high efficiency and low cost fabrication. The major research focus of PSCs is on interface modification, compositional engineering and morphology tailoring since these factors plays crucial role in efficiency modulation. We found that perovskite film morphology and photophysics are the crucial factors in fabricating highly efficient and stable solar cells. We optimized the morphology ofCH3NH3PbI3  perovskites film at room temperature using dual solvent elimination method, antisolvent treatment and solvent annealing and found that these methods are very important to grain size engineering.

February 13, 2020 at 2.30 pm in AG-80

Title :

Allele-Specific Engineering of Methyllysine Writers and Readers for Controlling Chromatin-Dependent Processes

Abstract :

One of the key players in regulating the gene pattern is the post-translational modifications (PTMs) of histone proteins. Histone modifications regulate the transcriptional potential of genes by interacting with reader/effector protein domains. Post-translational modifications on methyllysine are ubiquitous in biological systems and critical for mammalian development. Specific perturbation of such interactions has remained a challenging endeavor. We hypothesized that incorporation of an unnatural modification with the aid of an engineered writer domain and its recognition by reader domain would regulate the downstream genes (epigenetic editing) leading to modification of the epigenetic landscape. The engineered orthogonal pairs together with catalytically inactive Cas9 would specifically modulate the expression of a gene of interest, thereby providing control on transcription machinery. We employed the allele-specific strategy towards engineering the epigenetic landscape at protein-protein interface orthogonal to the human proteome. We generated a hole-modified methyltransferase (writer) that would install an aryllysine moiety on histones in-cellulo. We established the orthogonality of the engineered system, overcame the permeability issue of SAM analogues, developed an antibody and established the applicability of the system in cells. Our data confirms successful benzylation of histone proteins in mammalian cells at sites known to be regulated by SUV39h2 (writer protein) in cellulo. Further we engineered a chromodomain (reader) with a pocket to accommodate the bulky modifications. We established the biochemical integrity of the engineered interface, provided structural evidence for domain integrity, demonstrated the generality of the approach, and validated its applicability to identify transcriptional regulators. We have shown that the orthogonal reader domain on binding to the unnatural modification remains functionally intact and to regulate the epigenetic landscape similar engineering can be translated to other reader-histone proteins as well. 

February 11, 2020 at 2.30 pm in AG-80

Title :

Designing nano-biocatalyst with improved enzymatic activity and stability

Abstract :

In the current scenario, there is a need to develop clean, reliable, biocompatible and benign processes for the industrial manufacturing of chemicals. Notwithstanding all these advantages of enzymes, industrial application of enzymes is often hampered by a lack of long-term operational stability and difficult recovery and re-use of the enzyme. Hence, re-engineering of enzymes with high activities in the given environments is required for enzymatic catalysis in industrial biocatalytic processes. The redesign of enzyme can be achieved by chemical approaches including immobilization and chemical modification which represents a simple but effective route. In most of the conventional immobilization methods, the activity of enzymes is usually lower than its native counterpart which is mainly due to the hindered substrate accessing and/or unfavourable conformational transition of enzyme within the matrix. Hence, it is necessary to develop new method which can amplify catalytic activity along with the improvement in the enzyme properties. Recently, the construction of organic–inorganic hybrid material is a rapidly expanding field of material chemistry for its advanced designs with a specific structure and functionality. Organic–inorganic hybrid platform can be prepared simply by using metal ions as the inorganic component and the organic component at room temperature under aqueous conditions. The main advantages of using hybrid organic-inorganic matrix for enzyme immobilization are: (i). Organic-inorganic platform can help to form strong bonding with enzyme which can prevent the leaching of enzyme in reaction mixture. (ii) The presence of metallic counterpart in hybrid material can exhibit the allosteric effect on enzyme which can ultimately enhance the enzyme activity. (iii) Hybrid material can stabilize the conformational structure in various in-hospitalized conditions and chemical environment.

To enhance robustness, thermal stability, and extended the shelf-life time for industrial applications, in this research work, an organic-inorganic hybrid platform for enzyme immobilization has been developed via rapid single pot technique using biomineralization methodology. The allosteric effect (due to metal ion) and structural configuration of enzyme not only helped to enhance the enzyme activity but also improved the stability (mechanically robustness and thermally stable) due to protective shield. Further, the immobilized enzyme was characterized by powdered X-ray diffraction (XRD), Fourier transform infrared (FT-IR) and confocal scanning laser microscopy. The size and morphology were analysed by scanning electron microscopy (SEM). Also, the kinetic parameters (Vmax and KM) and thermal stability of free and immobilized enzyme were determined in terms of thermal deactivation constant (kd), half-life(t1/2) and deactivation energy (Ed). In addition, conformational changes occurring after immobilization were estimated by FT-IR data analysis tools. Lastly, reusability and storage stability of enzymes were studied to check its durability and industrial feasibility. This exploration of immobilization technology is anticipated to inspire further advancement in the novel design and functionality of the support matrix for a wide range of applications.

February 10, 2020 at 4.00 pm in AG-69

Title :

Double Similarity Transformed Coupled Cluster Theory: Non-Covalent Interactions and Excited State Energetics

Abstract :

The existing ab-initio theories often require high computational scaling to account for the ground and excited state energetics in a quantitatively correct manner. In this talk, I shall propose an inexpensive dual exponential Ansatz based recursive similarity transformed Coupled Cluster methodology, which accurately captures dynamical correlation of weakly correlated molecular systems in an affordable manner. The superior accuracy of the proposed method in describing non-covalent interactions is ensured by the inclusion of high rank correlation effects and a balanced treatment of screened Coulomb interactions. Further, starting with a correlated description of the ground state, I shall propose a Linear Response formulation to describe electronically excited states of isolated gas phase molecules. I will demonstrate how our method strikes the right balance between computational cost and accuracy. The efficacy of the formulation will be demonstrated with a number of numerical examples.

February 7, 2020 at 11.30 am in AG-80

Title :

Molecular Structure and Weak Interactions Explored by Broadband Microwave Spectroscopy

Abstract :

Microwave spectroscopy allows details of structure to be measured for molecules and complexes which are isolated in the gas phase. One aim is to quantify weak interactions with high selectivity such that intrinsic character can be separated from effects of a solvent or matrix. This theme will be illustrated through recent studies of molecules containing imidazole. It will be shown that two isomers of a complex formed between this molecule and water can be isolated and spectroscopically-characterised in the gas phase. A second aim is to explore the gas phase chemistry prompted by laser vaporisation of solids in the presence of a mixture of chemical precursors, a process known to allow the generation of small molecules that can be found in interstellar and circumstellar environments. Laser vaporisation of platinum in the presence of gaseous hydrocarbons allows very efficient generation of PtC3, an atypical and exotic platinum carbene which has structural similarities with the oxycarbon species, OC3. Experiments are performed using a unique broadband rotational spectrometer that allows the simultaneous observation of many rotational transitions across a broad bandwidth.  

February 6, 2020 at 2.30 pm in AG-80

Title :

Design and characterization of Ferritin based bio-catalyst

February 3, 2020 at 4.00 pm in AG-69

Title :

From atoms and molecules to solids… A glimpse into my research journey so far…

Abstract :

It is a well-known fact that every material in the universe is composed of atoms, which in turn comprise nuclei and electrons. A comprehensive understanding of the interactions among such sub-atomic particles have enabled us to tailor materials for a plethora of applications that heavily govern our day-to-day living. Thanks to advances in computation and theory development, investigating these interactions systematically has been possible. Based on the type of system, different computational methods are used to achieve this. For example, at the atomic scale, quantum chemistry simulations implemented within a localized orbital (or atomic orbital) basis set are performed routinely. On the other hand, for periodic solids, density functional theory (DFT) generally implemented within a plane-wave basis set, is used. Obviously, the list of methods is not restricted to those mentioned above. My talk will attempt to cover my journey so far, where I have been exposed to both perspectives of thinking. I will be providing a glimpse of my current work on time-dependent thermally-assisted-occupation DFT (TDTAO-DFT) which is a low-cost method to study excited states. This method is based on a modified DFT scheme known as TAO-DFT, which explicitly incorporates the non-dynamical correlation effect in ground-state simulations, but retains the low computational complexity of conventional DFT. In line with the title of my presentation, which coincides with the reverse chronology of my research journey, I will present my earlier works on solid state simulations using phosphorene (a quasi–two-dimensional sheet of phosphorus atoms) as an example. Here, I will be demonstrating how the electronic properties are tuned without affecting its excellent transport properties as well mechanical and structural stability.

January 30, 2020 at 2.30 pm in AG-80

Title :

Distribution of Isomerized and Racemized Amyloid b Isoforms in the Sporadic Alzheimer’s Disease using Ion-Mobility Mass Spectrometry

Abstract :

Extracellular amyloid plaques and intracellular neurofibrillary tangles are the pathological hallmarks of Alzheimer’s Disease (AD). It takes on average 19 years for amyloid b (Ab) peptides to deposit as insoluble plaques from onset to clinical dementia symptoms in AD. Such long-lived proteins and peptides without degradation and clearance can undergo further post-translational modifications (PTM). Several biochemical and analytical approaches have estimated very high degree of isomerization and racemization of Asp and Ser residues in Ab purified from the insoluble plaques, along with sequential loss of the N-terminal amino acids. In this study we have characterized the most common isomerization and racemization of the Asp-1 and Asp-7 residues of the Ab peptides present in AD brain based on both their chromatographic resolution as well as their collisional cross section (CCS) using high resolution ion mobility (IM) Q-TOF mass spectrometer (Agilent 6560). Using stable isotope labeled peptides we have also quantified the amount of these isomers/racemers in the different fractionated biochemical pools of the temporal cortex grey matter of human AD and control brains. Distribution of these isomerized and racemized peptides change from lower levels in the soluble/peripheral memebraneous to higher levels in the insoluble/aggregated debris in AD brain, also indicating loss in the biochemical exchange of the pool of Ab with the progression of the disease. These findings have implications in Ab neurotoxicity, oligomerization, structures of amyloid fibrils present in the AD brain as well establishing CSF/blood-based biomarkers.

January 28, 2020 at 2.30 pm in D-406

Title :

Vibrational spectroscopy of biological systems at the micro and nano level - RERS, SERS, TERS & AFM-IR

Abstract :

Raman spectroscopy is an excellent tool for interrogating biomolecules or biological systems in natural environments because water is such a weak Raman scatterer. This is particularly the case when there are chromophoric materials such as hemes, chlorophyll, carotenes that are strong scatterers or give rise to resonance Raman. Over a number of years we have applied Raman, Resonance Raman, Surface Enhanced Raman and Tip enhanced Raman spectroscopies to live cells such as erythrocytes in order to understand and develop probes for disease states. A number of these studies will be used to highlight instrumental and sampling techniques and data analysis in Raman spectroscopy of biosystems. Infrared spectroscopy also has a role, especially nano-IR and a study of DNA methylation will be used to show the power of nano-IR

January 27, 2020 at 4.00 pm in AG-69

Title :

Role of Acetylation at Active Site Lysine in Maintaining the Functional State of CDK1-Cyclin B Complex

January 20, 2020 at 2.30 pm in AG-80

Title :

Planarization of Anthracene fused Cyclooctatetraene

January 13, 2020 at 4.00 pm in AG-69

Title :

Maneuvering the stability and reactivity of ‘[3]Dendralenes”, an exciting class of oligo-enes for diversity oriented organic synthesis

Abstract :

Organic synthesis is mainly concerned with C-C and C-X (X = heteroatom) bond forming reactions. The biggest challenge is to perform them under strict control of regio-, stereo- and enantio-selectivity, and also to achieve diverse structural complexity in fewer steps. Carbon-carbon double bond (olefin) is an important synthon in organic chemistry for further C–C bond formation, diverse functional group generation and for construction of complex organic structures. Olefins also exhibit great structural diversity when several such bonds are put together in a molecule. Depending upon the type of connectivity of the ethylene units, conjugated polyenes can be classified into various classes. A geminal linkage results in a class of cross conjugated polyenes called as "Dendralenes". Despite being in existence in Nature and having been synthesized as early as in 1955, they remained "unmanageable" until the turn of this century mainly owing to their unpredictable stability and reactivity.

Due to the abundance of fused hetero- and carbocyclic ring systems in numerous bio-active compounds, such motifs have intrigued synthetic organic chemists. Besides, an efficient synthesis of such architecturally complex scaffolds is an uphill task and hence poses a formidable challenge. In this regard, [3]dendralenes are fascinating molecules because they possess huge potential for the quick generation of diverse and complex multicyclic scaffolds when subjected to tandem Diels–Alder (DA) reactions, also known as diene transmissive Diels–Alder (DTDA) sequences. But their synthesis is a tall order.

The chronicles of our roller-coaster journey and systematic approach beginning from the development of new olefination protocols, synthesis of extremely unstable, non-isolable [3]dendralenes through moderately stable examples and finally, highly functionalized stable [3]dendralenes will be presented. The attributes affecting their stability and reactivity have been recognized. Also, how these dendralenes, upon judicious maneuvering, can be engaged in a DTDA sequence, thus harnessing their full potential by construction of a small but diverse library of complex frameworks in a quick and efficient manner, with step and atom economy will be discussed.

 

Selected References

1. S. K. Ghosh, R. Singh and S. M. Date, Chem. Commun., 2003, 636.

2. S. M. Date and S. K. Ghosh, Angew. Chem. Int. Ed., 2007, 46, 386.

3. R. Singh and S. K. Ghosh, Org. Lett., 2007, 9, 5071.

4. R. Singh and S. K. Ghosh, Chem. Commun., 2011, 47, 10809.

5. G. S. Naidu, R. Singh and S. K. Ghosh, RSC Adv., 2016, 6, 37136.

6. R. Singh, G. S. Naidu and S. K. Ghosh, Proc. Natl. Acad. Sci., India, Sect. A Phys. Sci., 2016, 86, 619.

7. G. S. Naidu, R. Singh, M. Kumar and S. K. Ghosh, J. Org. Chem., 2017, 82, 3648.

 

8. G. S. Naidu, R. Singh and S. K. Ghosh, Synlett, 2018, 29, 282.

 

January 13, 2020 at 11.30 am in AG-80

Title :

Multiphoton femtosecond laser spectroscopy of anisotropic molecular probes

Abstract :

The talk presents a review of theoretical and experimental investigations of polarized fluorescence in anisotropic molecular probes excited via two-color two-photon transitions by femtosecond laser pulses.  

The molecular probes under study were small biomolecules which are of importance for bio-medical applications: indole, tryptophan, and NADH (nicotinamide adenine dinucleotide). The polarized fluorescence was excited in molecular solutions by simultaneous absorption of two laser photons with different and variable wavelengths thus allowing for tuning of the total excitation energy in the range 4,04-7,09 eV. By alternating the polarization of each of the three photons involved in the photoprocess a set of molecular parameters describing the photoprocess dynamics were determined. Analysis of the results obtained was performed on the basis of ab initio computations of excited state molecular structure and transition dipole moments.  

As pointed out in the talk, the molecular parameter values are very sensitive to the molecular microenvironment thus allowing for investigation of thin details of enegry transfer processes in excited molecules characterized by: anisotropic distribution of molecular axes, lifetimes, rotation correlation times, and the dynamics of nonadiabatic transitions between different potential energy surfaces. As shown, investigation of polarized fluorescence from molecular probes imbedded into biological structures opens a new information channel on protein structure, folding, hydration, and on the mechanizms of redox reactions in living organisms. 

1. P. S. Shternin, K.-H. Gericke, O. S. Vasyutinskii, Molecular Physics, 2010, 108(7), 813.

2. S. Denicke, K.-H. Gericke, A. G. Smolin, P. S. Shternin, O. S. Vasyutinskii, J. Phys. Chem. A  2010, 114, 9681.

3. S. Herbrich, K.-H. Gericke, A. G. Smolin, O. S. Vasyutinskii, J. Phys. Chem. A. 2014, 118, 5248.

4. S. Herbrich, T. Al-Hadhuri, K.-H. Gericke, P. S. Shternin, A. G. Smolin, O. S. Vasyutinskii, J. Chem. Phys. 2015, 142, 024310.

5. M. E. Sasin, A. G. Smolin, K.-H. Gericke, E. Tokunaga, O. S. Vasyutinskii, PCCP, 2018, V.20, pp. 19922.

 

January 10, 2019 at 11.30 am in AG-80

Title :

Medium Matters: Dynamics of Molecules in a Confined Space

Abstract :

From time immemorial it is well known that curtailment of freedom often leads to changes in the behaviour of living beings. Similar restriction of freedom leads to selectivity in the chemical behaviour of molecules embedded in biological systems. Extending these well-known behaviours, supramolecular chemists have established that even small molecules upon confinement in synthetic hosts exhibit behaviour distinctly different from the ones in a bulk isotropic solution.

In this lecture the role a “Medium” in bringing about changes in the well-established behaviour of excited molecules would be illustrated with select examples. Results of steady state and ultrafast experiments will be presented that highlight how the confinement alters the excited state dynamics of molecules such as stilbenes, azobenzenes, anthracene, dibenzyl ketones etc. Another reaction to be discussed concerns with electron transfer and spin transfer that play a fundamental role in a number of biological events including photosynthesis. Examples and ultrafast dynamics of electron and spin transfer between a confined and a free molecule would be presented.

The main message of the talk is that molecules like humans behave differently when confined within synthetic cages.

Selected references

[1] V. Ramamurthy, S. Jockusch and M. Porel, Langmuir, 2015, 31, 5554-5570

[2] V. Ramamurthy, Acc. Chem. Res. 2015, 48, 2904-2917.

[3] A. Mohan Raj, M. Porel, P. Mukherjee, X. Ma, R. Choudhury, E. Galoppini, P. Sen and V. Ramamurthy, J. Phys. Chem. C, 2017, 121, 20205−20216.

[4] C-H. Chuang, M. Porel, R. Choudhury, C. Burda and V. Ramamurthy, J. Phys. Chem. B, 2018, 122, 328−337.

[5] C. J. Otolski, A. Mohan Raj, V. Ramamurthy and C.G. Elles, J. Phys. Chem. Lett. 2019, 10, 121−127

January 2, 2019 at 11.30 am in AG-80

Title :

L-Amino acid Based Polyester Nanocarriers for Drug Delivery and Bio-imaging

Abstract :

The past generation therapeutic agents are increasingly failing in combating new-age threats. Therapeutics based on polymers are advantageous as they possess advanced targeting, can target hard to reach agents, and carry multiple cargos of conflicting nature. These can be extremely selective, owing to several phenomena such as Enhanced Permeation (EPR) effect and carrying multiple cargoes in a single particle, which can have synergistic effects, leaving them more potent than any of the medicine alone. 

L-Amino acid-based synthetic polypeptides non-peptides are extensively explored for biomedical applications owing to their structural diversity and biocompatibility. My talk is aimed to explore new classes of amphiphilic and biodegradable polyester and their fluorescent nano-assemblies based on natural L-aspartic acid resources for accomplishing anticancer drug delivery and intracellular bioimaging in cancer cells. These polymers were designed with the dual response to acidic conditions and enzyme-rich environment stimuli. Different therapeutically active drugs were loaded into the polymer scaffolds, and their cytotoxicity was studied in the cancer cell lines. 

The uptakes of these drugs were monitored using confocal microscopy. L-amino acid-based amphiphilic luminescent polyester was developed using π- conjugated oligo-phenylenevinylene (OPV) custom made diols, while Aggregation induced emission (AIE) capable hydroxyl functionalized tetraphenylethyelene (TPE) diol was tailor-made through multi-step reaction and was subjected to melt transesterification with L-aspartic acid monomer to yield new blue-luminescent amphiphilic polyesters. 

Hydroxyl and carboxylic functionalized polyesters were also synthesized. The hydrophilic hydroxyl and carboxylic groups along with the hydrophobic aliphatic backbone made these polymer amphiphilic in nature and enabled these to self-assemble into spherical nanoparticles in water, which exhibited superior encapsulation capabilities to load wide ranges of both water-soluble and water-insoluble anticancer drugs and fluorophores. The amphiphilic polyesters designed and developed based on L-aspartic acid residues presented in the talk are new entries as enzymatic-biodegradable polymers in the literature, and the custom-designed OPV-tagged and TPE-tagged fluorescent polymers are excellent nano-scaffolds for constructing a wide range of FRET probes with drugs and fluorophores which could be employed for early diagnostics of cancer and other bio-imaging applications. Thus, the work opens up a new platform of opportunities in the biomaterials arena based on L-Amino acid polymers.