Department of Chemical Sciences
School of Natural Sciences


October 26, 2015 at 4.00 pm in AG-69

Title :

Molecular Probes and Templates for DNA Structures

Abstract :

DNA exists in variety of structural forms supported by canonical (A, B and Z-DNA) and non-canonical [H-DNA, G-quadruplex, i-motif, A-motif etc] hydrogen bonding interactions. Small molecules play key role in the study of DNA structures, biological significance, and to treat diseases related to their structure and function. On the other hand, the unique molecular recognition, persistence length and size of DNA inspire researchers to create novel molecular architectures for numerous applications. In this context, we have been developing mutually templated novel small molecule-ss DNA architectures using canonical and non-canonical hydrogen bonding interactions of nucleobases. In this talk, I shall present our recent results on fluorescence probes and nucleobase conjugates to study canonical and non-canonical hydrogen bonded DNA structures as well as to create hybrid DNA ensembles for applications ranging from biology to materials science.




1.    J. Choi and T. Majima, Chem. Soc. Rev. 2011, 40, 5893; A. Rich, D. R. Davies, F. H. C. Crick and J. D. Watson, J. Mol. Biol., 1961, 3, 71.

2.    N. Narayanaswamy, M. Kumar, R. Sharma, P. K. Samanta, S. K. Pati, S. K. Dhar, T. K. Kundu and T. Govindaraju, Sci. Rep. 2014, 4, 6476.

3.    N. Narayanaswamy, S. Das, P. K. Samanta, K. Banu, S. K. Dhar, S. K. Pati and T. Govindaraju, Nucleic Acids Res. (2015)DOI: 10.1093/nar/gkv875.

4.    N. Narayanaswamy, M. Unnikrishnan, M. Gupta and T. Govinadaraju. Bioorg. Med. Chem. Lett. 2015, 25, 2395.

5.    M. B. Avinash and T. Govindaraju, Nanoscale2014,6, 13348.

6.    N. Narayanaswamy, G. Suresh, U. D. Priyakumar, and T. Govindaraju, Chem. Comm. 2015, 51, 5493-5496.


October 12, 2015 at 4.00 pm in AG-69

Title :

Molecular Tools for the Manipulation of Size, Surface Chemistry and Assemblies of Metal Nanoparticles

Abstract :

Nanoscale particles have been envisioned to be the building blocks of a wide variety of future technologies including catalysis, electronic, optical and information technologies.As the nanoparticles have enhanced surface activity a layer of organic molecules are often used as passivating or capping agents. The surface functioanlization assumes significance not just for their stability in diverse solvent media but defines the way nanoparticles interact either with themselves or with the environment/biological systems. For example, water dispersibility is an essential criterion to realize bio-applications of nanoparticles.On the other hand, dispersions in organic media can be utilized to obtain interesting assemblies. In this connection, we have been working on a procedure called “digestive ripening” process in which a colloidal metal suspension in a solvent is refluxed at or above the solvent boiling temperature in the presence of the surface active agent like thiols resulting in the conversion of a highly polydisperse colloid into a monodispersed one (s< 5%). It is hypothesized that the thiols bind and remove reactive surface atoms/clusters from big nanoparticles and redeposit them on smaller nanoparticles.  In this way, large particles become smaller, while small particles become larger and eventually, an equilibrium size is obtained that is specific to each of the digestive ripening agent used. While the original work on digestive ripening has been largely carried out with gold nanocrystals, it has recently been extended to several other nanoparticle systems. Once again, the mechanism of this process is not understood, which is extremely important to generate nanocrystals with controlled and desired size distributions. In this presentation we will review the state of the art in digestive ripening and some of our recent experimental results that we hope will help in developing a mechanistic model for digestive ripening.



J. Seth, C. N. Kona, S. S. Das and B. L. V. Prasad, Nanoscale, 2015, 7, 872–876.

P. Sahu and B. L. V. Prasad, Langmuir, Langmuir, 2014, 30, 10143−10150.

P. Sahu and B. L. V. Prasad, Col. Surf A., 2014, 447, 142-147

P. Sahu and B. L. V. Prasad, Nanoscale, 2013, 5, 1768 – 1771

P. Sahu and B. L. V. Prasad, Chem. Phys. Lett. 2012 525–526, 101–104.

D. S. Sidhaye and B. L. V. Prasad, New J. Chem. 2011, 35, 755–763


October 5, 2015 at 4.00 pm in AG-69

Title :

Nano-bioconjugation of Mutant Cytochrome P450cam (CYP101) for Biocatalysis

September 10, 2015 at 2.30 pm in AG-66

Title :

Design and Construction of Protein Molecules with Novel Properties

Abstract :

One of the most important challenges in chemical biology is to understand the molecular basis of protein function. Developing new methodologies using chemistry and the ability to apply those methodologies to proteins plays a crucial role in addressing this challenge. I propose to direct my future research program towards applying chemistry to design and engineer novel protein molecules, and to systematically develop a new class of therapeutics with controlled biochemical properties. Part of my research will be focused on the design and total chemical synthesis of medicinally relevant protein molecules with complex polypeptide backbone topologies that are rare or do not occur in natural proteins. I will develop a novel technology, using virtual structure-based screening of peptide fragment libraries from protein data bank, to identify small protein molecules of opposite handedness that will be used as candidate therapeutics. A significant portion of my research will be dedicated to develop and apply chemistry tools to enhance the conformational rigidity, introduced by the incorporation of fixed elements of secondary structures that will improve the stability and receptorbinding affinity of the small protein drug candidates. I will also explore and extend racemic and quasi-racemic crystallography to unravel complex biological questions. All these research projects will be pursued with the goal of addressing a wide range of questions having implications in fundamental as well as in
applied research.

September 9, 2015 at 2.30 pm in AG-66

Title :

A Mirror Image Protein Antagonist of VEGF-A: Total Chemical Synthesis and Racemic Crystallography of A Heterochiral Protein Complex

Abstract :

Using a unique combination of total chemical protein synthesis and mirror image phage display, we have systematically developed a D-protein antagonist of VEGF-A function. The bottleneck in mirror-image phage display is the preparation of the D-protein form of the target molecule, which can only be achieved by chemical synthesis. We prepared the mirror-image form of VEGF-A, i.e. D-VEGF-A, from three unprotected synthetic peptide segments stitched together by one-pot native chemical ligations. Phage displayed libraries of a novel L-protein scaffold were then screened against the D-VEGF-A to identify high affinity binders. The mirror-image form of the selected L-protein binder, i.e. the corresponding D-protein binder, was then chemically synthesized and was shown to specifically bind to native VEGF165 and to inhibit receptor binding. As expected, the D-protein antagonist was found to be non-immunogenic and had a longer half-life in vivo in mice. The binding mode of the D-protein antagonist was determined by high-resolution racemic X-ray crystallography of the {VEGF–A plus D-protein antagonist} heterochiral protein complex. The detailed structural information obtained from this crystal structure will enable the development of improved D-protein antagonists of VEGF-A.

September 7, 2015 at 4.00 pm in AG-69

Title :

Ultrafast 2D and 3D electronic spectroscopy and its applications to the study of Photosynthetic Light Harvesting Complexes

Abstract :

Recently, there has been much interest in the application of ultrafast multi-dimensional electronic spectroscopy in studying various chemical, physical and biological systems. We will review the basic principles of multi-dimensional electronic spectroscopy.  We report on our development and applications of ultrafast coherent 3rd order two-dimensional (2D) and 5ththree-dimensional (3D) spectroscopiesbased on a pulse shaper assisted pump-probe setup [1,2].In 5th order 3D optical spectroscopy, we obtain purely absorptive 3D spectra using five ultrashort optical pulses. For the first time, we also directly observe multistep excitation energy transfer (EET) processes in LHCII using the newly developed ultrafast fifth-order three-dimensional electronic spectroscopy (3DES) [3]. Ultrafast 3rd order two-dimensional electronic spectroscopy (2DES) is an important tool to study EET processes in photosynthetic complexes. However, the multistep EET processes can only be indirectly inferred by correlating different cross peaks from a series of 2DES spectra. Here we observe cross peaks in room temperature 3DES spectra of LHCII that directly indicate energy transfer from excitons in the chlorophyll b (Chl b) manifold to the low-energy level chlorophyll a (Chl a) via mid-level Chla energy states. This new spectroscopic technique will allow scientists to move a step towards mapping the complete complex EET processes in photosynthetic systems.


References :

1.    1.  Z. Zhang, K.L. Wells, and H.-S. Tan. "Purely absorptive fifth-order three-dimensional electronic spectroscopy" Opt. Lett. 37, 5058-5060 (2012).

2.      2.  K.L. Wells, P.H. Lambrev, Z. Zhang, G. Garab and H.-S. Tan. "Pathways of energy transfer in LHCII revealed by room-temperature 2D electronic spectroscopy" Phys. Chem. Chem. Phys. 16, 11640-11646 (2014).

3.    3.   Z. Zhang, P.H. Lambrev, K.L. Wells, G. Garab, H.-S. Tan. "Direct observation of multistep energy transfer in LHCII with fifth-order 3D electronic spectroscopy" Nat. Comm. 6, 7194 (2015).


August 31, 2015 at 4.00 pm in AG-69

Title :

Rational Design of Functional Materials: A Chemist's Approach

Abstract :


Functional materials have assumed prominent position in several high tech areas. Such materials are not classified on the basis of their origin, nature of bonding or processing techniques but are classified on the basis of functions which they can perform.  The synthesis of such materials has been a challenge and also opportunity to chemists. New functional materials can be designed by interplay of synthesis and crystallographic structure. Other approaches for design of these materials are defects engineering and concepts of hybrids. Unconventional synthetic routes play an important role in this direction as many of these new materials are metastable and hence it is not possible to prepare them by conventional solid state synthesis.  We have prepared [1-18] a number of new functional materials guided by crystallographic approach coupled with novel synthesis protocols. Some typical materials which will be discussed in this talk are La1-xCexCrO3 (materials with tunable band gap and magnetic properties), CeScO3 (with unusual reversible conversion to fluorite lattice), Gd1-xYxInO3, GdSc1-xInxO3, YIn1-xFexO3 (tunable dielectrics) and several lead free relaxor materials. Perovskite and fluorite-type materials with trivalent Ce3+ were successfully prepared from suitable precursor powders by a controlled heating under low pO2. Several interesting pyrochlore based oxygen storage materials, viz. Ce2Zr2O7+x (x = 0.0 to 1.0), Gd2-xCexZr2O7 andGd2-xCexZr2-xAlxO7 (x = 0.0 to 2.0) have been prepared, which have shown interesting redox catalysis. The simple concepts like rA/rB ratio of A2B2O7 pyrochlores could be used to tailor the functional properties. The major focus of this talk will be on the role of synthesis, novel properties exhibited by these functional materials, and their crystallographic correlation.




Our recent publications in the field functional materials


[1]  Chem. Mater. 21 (2009) 125

[2]  J. Phys. Chem. C 113 (2009) 12663

[3]  Inorg. Chem. 48 (2009) 11691


[4]  Inorg. Chem. 49 (2010) 10415


[5]  Inorg. Chem 49 (2010) 1152


[6]  Chem.- A Eur. J.17 (2011) 12310


[7]  Chem. Mater. 24 (2012) 2186


[8]  Analysts 137 (2012) 760


 [9]   Nano Letters 12 (2012) 3025


 [10]      J. Phys. Chem C 117 (2013) 10929


[11]  J. Phys. Chem. C  117 (2013) 2382


[12]  Inorg. Chem. 52 (2013) 7873


[13]  Inorg. Chem. 52  (2013) 13179


[14]  J. Mater. Chem. C, 1 (2013) 3710


[15]  J. Phys. Chem. C 118 (2014) 20819


[16]  Inorg. Chem. 53 (2014) 10101


[17]  Dalton Transaction 44 (2015) 10628


August 25. 2015 at 2.30 pm in AG-69

Title :

Teaching Sponges New Tricks: Redox Reactivity and Charge Transport in Microporous Metal-Organic Frameworks

Abstract :

Traditional applications of metal-organic frameworks (MOFs) are focused on gas storage and separation, which take advantage of the inherent porosity and high surface area of these materials. The MOFs’ use in technologies that require charge transport have lagged behind, however, because MOFs are poor conductors of electricity. We show that design principles honed from decades of previous research in molecular conductors can be employed to produce MOFs with remarkable charge mobility and conductivity values that rival or surpass those of common organic semiconductors and even graphite. We expect that such high surface area, ordered, and crystalline conductors will be used for a variety of applications in thermoelectrics, energy storage, electrocatalysis, electrochromics, or new types of photovoltaics. Another virtually untapped area of MOF chemistry is related to their potential to mediate redox reactivity through their metal nodes. We show that MOFs can be thought of as unique macromolecular ligands that give rise to unusual molecular clusters where small molecules can react in a matrix-like environment, akin to the metal binding pockets of metalloproteins. By employing a mild, highly modular synthetic method and a suite of spectroscopic techniques, we show that redox reactivity at MOF nodes can lead to the isolation and characterization of highly unstable intermediates relevant to biological and industrial catalysis, and to unusual reactivity patterns for small molecules.


August 17, 2015 at 4.00 pm in AG-69

Title :

The W(Hole) Story of β-barrel Pore-forming Toxin Vibrio cholerae Cytolysin

Abstract :

Bacterial β-barrel pore-forming toxins (β-PFTs) constitute a unique class of membrane-damaging cytolytic proteins.β-PFTs are, in general, produced by the pathogenic bacteria as water-soluble monomeric molecules. In contact with their target eukaryotic cells, they assemble into transmembrane oligomeric β-barrel pores, thus destroying the natural permeability barrier function of the target cell membranes. Vibrio cholerae cytolysin (VCC) is a prominent member in the β-PFT family. It is produced by most of the pathogenic strains of V. cholerae, the causal organism of the severe diarrheal disease cholera.VCC is shown to evoke critical cytotoxic effects in wide array of host eukaryotic cells, and therefore, it is considered as a potent virulence factor of V. cholerae. High-resolution three-dimensional structures are known for both the water-soluble monomeric form as well as the oligomeric pore state of VCC. However, mechanistic details of the membrane pore formation process employed by the toxin remain only partly described.One of our major research interests is focused toward elucidating the detail structure-function mechanisms associated with the b-barrel membrane pore formation process of VCC. In my talk, I will present some of our recent studies that have provided new insights regarding the mechanism of action of VCC, in the context of the generalized β-PFT mode of actions.

August 12, 2015 at 11.00 am in AG-80

Title :

Structures and Dynamics using two-dimensional infrared and sum frequency generation spectroscopies

Abstract :

Two dimensional infrared (2D IR) spectroscopy, which is the infrared analog of 2D NMR, has the ability to resolve congested spectra better than linear infrared spectroscopy by adding an extra dimension. When multiple vibrational modes are present in the system of interest, the 2D IR spectrum depends critically on whether these modes are coupled to one another. One of the major strengths of 2D IR over conventional linear IR is that coupling between different modes is probed directly, and existence of cross-peaks in a 2D IR spectrum is evidence for coupling between different vibrations. In the event that there are chemically distinct species present in equilibrium, wherein fast chemical processes like hydrogen bond making and breaking interchange populations between the species, cross peaks appear on the time scales of the equilibrium kinetics of this chemical exchange. Examples of such exchange dynamics, observed for aromatic nitriles in methanol will be presented. Similar interpretations can be applied to the ultrafast dynamics of liquids, which can be thought of as a distribution of well-defined structures characterized by different solvation environments evolving spectrally on a range of time scales. Hence, the spectral diffusion seen in 2D IR experiments that derives from decay of the vibrational frequency correlations might be thought of as exchange among multiple solvent−solute configurations, and these underlying configurations are resolvable when the solvent dynamics are significantly slower than bulk. 2D IR spectra of amide vibrations in proteins and peptides exhibit solvent exchange under certain conditions, thus verifying the above hypothesis, and examples of the same will be discussed. The capabilities of 2D spectroscopy can be extended to surfaces through two-dimensional sum frequency generation (2D SFG) spectroscopy, which is a novel technique capable of measuring spectra analogous to 2D IR but with monolayer sensitivity and SFG selection rules. Applications of 2D SFG to exploring structures of a peptide segment FGAIL, a conserved sequence found in the islet amyloid polypeptide, will be presented. The 2D SFG spectra of FGAIL on model membranes reveal how hydrogen bonding interactions can play a vital role in the formation of aggregates on membranes, which is at the heart of understanding amyloid diseases such as type II diabetes. New technological advances that implement multi beam detection schemes in 2D IR experiments using mid-IR focal plane arrays will be shown. Details of future research plans will also be presented.

August 11, 2015 at 2.30 pm in AG-80

Title :

Vibrational dynamics in proteins using two-dimensional infrared spectroscopy

Abstract :

The time course of a vibrational probe is ultra-sensitive to the motions of nearby atoms, particularly those with net charges like water, which cause instantaneous fluctuations of the vibrational frequency. Two dimensional infrared spectroscopy (2D IR) leads to direct quantitative inferences on these motions. Over the past decade, 2D IR spectroscopy has developed into a promising method for probing site-specific structure and dynamics of peptides, proteins and other biological assemblies. The principles of 2D IR spectroscopy and approaches for extracting the vibrational frequency correlation function from 2D spectra will be discussed. The application of 2D IR methodologies, employed to investigate the pH induced ebb and flow of water in the M2 proton channel in influenza viruses through the spectral dynamics of the backbone amide modes, will be presented. The 2D IR spectroscopy of pore lining amides in the M2 channel reveal that the conformational equilibrium in M2 entails a change in the mobility of the channel water similar to what might be expected for phase transition from frozen to liquid water. This approach was extended to address drug binding modes in the channel. 2D IR experiments with drug-free and drug-bound channels expose water mobility in the channel under different drug binding conditions, which is reflected in the spectral dynamics of the Ala30 and Gly34 amides. The results suggest a favorable entropic factor for drug binding owing to disruption of water structures, thus revealing a functional model of drug binding in the channel that is in qualitative consistency with the model proposed from MD simulations. The unique capabilities of Fourier transform infrared spectroscopy can be utilized for imaging applications, and a new table-top technique for collecting wide-field Fourier transform infrared (FTIR) microscopic images by combining a femtosecond pulse shaper with a mid-IR focal plane array will be presented. Infrared absorption images were collected for a mixture of W(CO)6 or Mn2(CO)10 absorbed polystyrene beads, demonstrating that this technique can spatially resolve chemically distinct species. Extension of this method to hyperspectral 2D IR microscopy will also be discussed.