Research

Research

Welcome to Aloke Das group

Our Research

The n→π* interaction, a recently discovered weak non-covalent interaction, is extensively present in biomolecules and materials. This interaction is very much analogous to the hydrogen bond, the most popular non-covalent interaction, in terms of the orbitals involved in the delocalization of the electrons between the donor and acceptor groups. The primary aim of this project is to study the modulation of the strength of the weak intramolecular and intermolecular n→π* interaction by substitution of electron-donating and withdrawing groups at the n→π* donor and acceptor sites using mass-selected Resonant 2-Photon Ionization (R2PI) and IR-UV double resonance spectroscopy. The knowledge acquired from this research will be immensely valuable to tune the strength of the n→π* interaction in synthesizing drugs, supramolecular assemblies etc. As an example, one of our recent studies on the n→π* interaction in phenyl formate is depicted here.

 1. Modulating the strength of intra- and inter-molecular weak n→π* non-covalent interactions

 2. Study of the n→π* non-covalent interactions in the secondary structures of small peptides

We are interested here to understand the C=Oi…C=Oi+1 n→π* interaction present in the backbone of peptides and proteins. We study the peptides containing proline residue as this is the most important building block in collagen, PPII helices etc. Our goal is to understand the structures of the conformations of the peptides with trans-amide orientation of the neighboring C=O groups which favors the n→π* interaction. We are also exploring the possibility of the contribution of the n→π* interaction involving the nitrogen atom in the proline ring and the neighboring C=O group present there. We use combination of laser desorption, jet-cooling, Resonantly Enhanced Multiphoton Ionization (REMPI) and IR-UV double resonance techniques to perform this research. Recently, we have studied C=O…C=O n→π* interactions in a capped Hyp residue, a monomeric building block of collagen.

 3. Physical nature and strength of Unconventional Hydrogen-Bonding (UHB) interactions involving Sulfur (S) and Selenium (Se)

The nature and strength of unconventional hydrogen bonding interactions are poorly understood in the literature. In the case of an unconventional hydrogen-bond, either the hydrogen-bond donor or acceptor or even both the acceptor and donor atoms are weakly electronegative. We are interested to study unconventional hydrogen bonds where S and Se are either hydrogen bond donor or acceptor or both donor and acceptors. We try to understand this interaction by studying model complexes as well Protein Data Bank (PDB) analysis. As for example, study of water-mediated Se hydrogen bonding interaction through IR spectroscopy study of a model complex and PDB analysis is highlighted here.

 4. Study of secondary structures of peptides and various unusual non-covalent interactions present there

Specific folded structures of peptides and proteins depend on the sequence of various amino acid residues as well as different types of non-covalent interactions induced by the backbone as well as side-chains of those residues. We are interested to study secondary structures of small peptides containing different amino acid residues. We would like to study folding motifs of those peptides as a function of the sequence of the residues and compare the results with the propensity of the local secondary structures of the corresponding peptide units in proteins. Our aim is also to scrutinize various unusual non-covalent interactions found from the analysis of the PDB. A representative example of our recent spectroscopic study on a dipeptide Z-Gly-Pro-OH showing the most stable conformer with an extended b-strand type structure stabilized by C5 hydrogen-bonding interaction is portrayed here.

 5. Conformation-specific Electronic Circular Dichroism (CD) spectroscopy in gas phase

Circular dichroism (CD) spectroscopy is a very sensitive tool to probe the conformations of any chiral molecule as well as biomolecules (proteins, peptides, nucleic acids). This technique is also very useful to determine the conformational changes in proteins due to external factors (temperature, PH) as well as protein-protein interaction, protein-DNA interaction, protein-ligand interaction etc. Although CD spectroscopy performed in the solution phase is quite important to probe the conformations of molecules, the information we obtain is very qualitative. In the case of solution phase CD spectroscopy, we generally get an average CD value derived from multiple conformations of a flexible molecule. We have built a jet-cooled R2PI-CD spectrometer to measure conformation-specific high resolution electronic CD spectra of molecules in isolated gas phase by measuring resonant two photon ionization (R2PI) spectra using left and right circularly polarized laser light. We use a photoelastic modulator to generate alternative left and right circularly polarized light pulses from plane polarized laser light (10 Hz). We would like to study R2PI-CD spectra of amino acids, peptides, and other chiral molecules.