Debashis Sahu

Regioselectivity of Vinyl Sulfone Based 1,3-Dipolar Cycloaddition Reactions with Sugar Azides by Computational and Experimental Studies

DFT (M06-L) calculations on the transition state for the 1,3-dipolar cycloadditions between substituted vinyl sulfones with sugar azide have been reported in conjunction with new experimental results, and the origin of reversal of regioselectivity has been revealed using a distortion/interaction model. This study provides the scientific justification for combining organic azides with two different types of vinyl sulfones for the preparation of 1,5-disubstituted 1,2,3-triazoles and 1,4-disubstituted triazolyl esters under metal-free conditions.

Benzimidazolium-based chemosensors: selective recognition of H2PO4−, HP2O73−, F− and ATP through fluorescence and gelation studies

Benzimidazolium-based receptors 1 and 2 have been designed and synthesized. The receptors with identical binding sites exhibit different sensing properties towards different anions under identical conditions. In a lower equivalent amount of guests, receptors 1 and 2 show fluorescence selectivity towards phosphate-based anions. In the presence of higher equivalent amounts of guests, while structure 1 reveals selectivity in sensing of phosphate derivatives such as hydrogen pyrophosphate and dihydrogenphosphate in CH3CN, under identical conditions receptor structure 2 senses F−. Furthermore, compounds 1 and 2 validate the visual sensing of hydrogen pyrophosphate and dihydrogenphosphate, respectively, through the formation of gels. Binding studies have been carried out using fluorescence, UV-vis, 1H NMR and 31P NMR spectroscopic techniques. Experimental results have been correlated with the theoretical findings.

Azaindole-1,2,3-triazole conjugate as selective fluorometric sensor for dihydrogenphosphate

A new receptor 1 has been designed and synthesized. The open cavity of 1 selectively recognizes H2PO4− over a series of other anions in CH3CN containing 0.01% DMSO by exhibiting a ratiometric change in emission. In sensing, the cooperativity of the azaindoles in 1 has been proved using the model compound 2. Also the interaction behavior of the nitrogen in the azaindole has been proved by considering compound 3, which did not show any discrimination towards the anions. Binding studies have been carried out using fluorescence, UV-vis, 1H NMR and 31P NMR spectroscopic techniques.

In silico studies on the origin of selective uptake of carbon dioxide with cucurbit[7]uril amorphous material

The efficient capture and storage of flue gases is of current interest due to environmental problems. We report the adsorption of flue gases (CO2, N2 and CH4) on amorphous solid Cucurbit[7]uril (CB[7]) computationally. The DFT calculations revealed that CO2 can be adsorbed more strongly inside the cavity of CB[7] compared to N2 and CH4 molecules. The glycoluril units of CB[7] are the preferential sites for the adsorption of CO2 gas molecules. The cooperative binding of CO2 molecules inside the cavity of CB[7] has been observed. The geometrical analysis reveals that the carbon atom of CO2 is in close proximity to the nitrogen atom of the glycoluril of CB[7] and the CO2 oxygen atom is in close contact to the carbonyl carbon of the glycoluril unit. The calculated results show that four CO2 and four CH4 molecules can reside inside the CB[7] cavity. However, five N2 gas molecules can be accommodated inside the CB[7] cavity. The energy decomposition analysis (EDA) performed with the adsorbed CO2 on the wall of CB[7] shows that the dispersive force is playing an important role for the uptake of CO2 inside the cavity. The process of desorption was also examined with the desorption enthalpies (ΔHDE) calculated per gas molecule, which suggests that both adsorption and desorption processes are kinetically feasible. The origin of the interactions between the amorphous solid CB[7] and the flue gases can help to design materials to maximize the capture and separation of such gases.

In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines.

Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.

The role of non-covalent interaction for the adsorption of CO2 and hydrocarbons with per-hydroxylated pillar[6]arene: a computational study

A systematic study has been performed with DFT calculations for the physisorption of CO2, CH4, and n-butane gases by pillar[6]arene (PA[6]) in gas phase. The DFT(B3LYP)-D3 calculations showed that CO2 and n-butane could be adsorbed more efficiently inside the cavity of PA[6] compared to the CH4 molecule. The order of the binding energies of the adsorbed gases by PA[6] is n-butane > CO2 > CH4 at 1 atm and 298 K. The hydroquinone units of PA[6] play an important role in the adsorption of the gas molecules. The strong cooperative binding of n-butane compared to CO2 and CH4 inside the cavity of PA[6] facilitates adsorption of n-butane inside the PA[6] cavity. The structural analysis of the gas-adsorbed PA[6] shows that the carbon atom of CO2 is in close proximity to the aromatic hydroquinone ring of PA[6], and the oxygen atom of CO2 is in close contact to the hydrogen atom of the hydroxyl group of the hydroquinone unit of PA[6]. Similarly, the hydrogen atoms of the hydrocarbon (methane and n-butane) closely interact with the aromatic Pi-electron walls of the hydroquinone ring of PA[6], and the electronegative oxygen (O) atoms of the hydroxyl group (–OH) belong to the hydroquinone unit of PA[6]. The calculated results show that four CO2, four CH4, and two n-butane molecules can reside inside the cavity of PA[6]. The atoms in a molecule (AIM) analyses performed with adsorbed CO2, CH4 and n-butane inside the cavity of PA[6] reveal the strong ‘closed shell’ type interactions for n-butane to be held inside the PA[6] cavity. In addition to adsorption, the desorption of CO2, CH4, and n-butane from PA[6] was accounted with the desorption enthalpies (ΔHDE) calculated per gas molecule, indicating that both adsorption and desorption are feasible in nature. The DFT studies of PA[6] with CO2, CH4, and n-butane gases may help to understand the development of new design materials that can efficiently capture and separate such gases. The (B3LYP-D3) computed results corroborate the experimental observations that n-butane can adsorb better with PA[6] compared to CH4 gas molecules. The associative butane–butane interactions seem to be superior over the CO2–CO2 interactions inside the PA[6] cavity that promotes the adsorption of hydrocarbons.