Research

Superoxide & Peroxide species are crucial intermediates in O2 activation process. Chemists have succeeded in elucidating the structures of several dioxygen adducts by mimicking the structure or function of the reactive sites of metalloenzymes associated with the dioxygen activation process. There are many computational and experimental investigations on metal-superoxide and -peroxide intermediates, but there are few strong examples of these two species' natural inter conversion.

Herein, we examine the feasibility of formation and inter conversion of metal oxides and using Quantum Mechanical calculations to decipher the mechanistic pathway of other chemical reaction mechanisms. 

Disulfide bonds are the second most prevalent covalent interactions in proteins. Redox switching reactions involving these bonds are crucial to gram-negative bacterial viability, and they are catalyzed by enzymes of the disulfide bond (DSB) superfamily. The disulfide redox chemistry has been well characterized for oxidating folding (formation of S-S bond). The proton motive force (PMF) is believed to be responsible for this reversible cyclic reaction (also known as the thiol-disulfide exchange). Wide chemical reaction mechanisms are also found to supplement the thiol-disulfide interchange, which includes nucleophilic and elimination reactions. 

Herein, we examine the feasibility of reactions other than the proposed PMF pathway in DSB's using state of the art QM/MM MD Metadynamics simulations to decipher the mechanistic pathway of other chemical reaction mechanisms. 

It is great to see how nature organizes the packaging of its sub units to make meaningful and yet fully functional working units out of them. Proteins, thought to be one of the fundamental building blocks of life is one such example of its kind. One of the interesting aspect of the proteins are the formation of different structural types while packing themselves. 

Herein, we are interested basically in understanding the folding, unfolding mechanisms and kinetics in certain alpha α-helices and β-hairpin loops of proteins, which forms a part of the secondary motifs in proteins.

Disulfide bonds play a crucial role in the smooth functioning of protein machinery. Among the proteins, basically the disulfides are  classified into two distinct sets - "Structural" and "Functional" disulfides. The structural disulfides are believed to be added in different protein systems during the evolution to enhance the stability of proteins owing to its strong covalent nature. On the other hand, the comparatively newly defined class of disulfides known as the functional ones are those which are capable of regulating the chemico-biological activity of the protein by themselves undergoing frequent reduction and oxidation. These disulfide bonds are enriched by the very chemistry of sulfur bonds, which can easily undergo redox reactions at mild, physiological conditions. Thus, studying the cleavage reactions and the reformation of the disulfides in proteins becomes extremely crucial as it could be deterministic in defining distinct biological processes.

We in here mainly focus on the disulfide bond cleavage and its various mechanisms under the influence of a mechanical tension.

Electronic devices that utilize an organic layer as the active material are called organic electronics. An important area of research among these applications is Organic Light Emitting Diodes (OLEDs). An OLED working principle starts with the production of electron-hole pairs (excitons), which occupy excited singlet states (S1) and excited triplet states (T1) in a 1:3 ratio. De-excitation of excitons from the S1 excited state to the singlet ground state (S0) results in fluorescence. A breakthrough in OLEDs occurred in 2011 when Adachi et al. demonstrated a 100% efficient OLED material based on the Thermally Activated Delayed Fluorescence (TADF) phenomenon. The process involves the Reverse Intersystem Crossing (RISC) of excitons from T1 to S1 , followed by further de-excitation to S0. Recent studies have found that polymeric carbazole-benzophenone (CzBP) derivatives are TADF active, while its monomer is non-TADF. We identify here that when the second (lower) benzene group is substituted (mono and di) by deactivating groups such as -NO2, -SO3H, -COOH and -CN, the TADF properties can be tuned accordingly and in particular 2,6-CzBP-COOH could be a potential candidate for TADF, where orbital overlap, and spatial separation dominate the SOC in lowering ∆EST (≈ 0.03 eV) and thereby enhancing the TADF properties.

The role played by long side chains (like polyethylene oligomers) in transducing external tensile forces on to different mechanophores plays a great role in defining the chemistry of these mechanophores.

Herein, we demonstrate that the oligomer chains do indeed exert a notable influence on the force dependence of the activation energies of ring openings in benzocyclobutene moeities, with both conrotatory and disrotatory ring-opening processes being effected considerably. This could be instrumental in tuning the properties of mechanoresponsive materials not only by changing the properties of the mechanophore itself, but also by tailoring the force-transducing chain molecules attached to it. It is found that these chains even have a profound impact on the topology of the force-transformed potential energy surface in the vicinity of conrotatory transition states.

Calculating and simulating the mechanical behavior of single biopolymer (Pectin) chains. DFT calculations on monomers, diamers and trimers of pectin to look at their conformations during force induced stretching and characterization of the biopolymer. Brownian Dynamics Simulations on larger chains to look at stretching and the collapse of the chain in different solvent and chain stiffness. Steered Molecular Dynamics (SMD), looking at the stretching of a ten member polymer chain and its force-extension behavior.