Kalyanashis Jana

Hydrogen bonding interaction between active methylene hydrogen atoms and an anion as a binding motif for anion recognition: experimental studies and theoretical rationalization.

Two new reagents, having similar spatial arrangements for hydrogen atoms of the active methylene functionalities, were synthesized and interactions of such reagents with different anionic analytes were studied using electronic spectroscopy as well as by using (1)H and (31)P NMR spectroscopic methods. Experimental studies revealed that these two reagents showed preference for binding to F(-) and OAc(-). Detailed theoretical studies along with the above-mentioned spectroscopic studies were carried out to understand the contribution of the positively charged phosphonium ion, along with methylene functionality, in achieving the observed preference of these two receptors for binding to F(-) and OAc(-). Observed differences in the binding affinities of these two reagents toward fluoride and acetate ions also reflected the role of acidity of such methylene hydrogen atoms in controlling the efficiencies of the hydrogen bonding in anion-Hmethylene interactions. Hydrogen bonding interactions at lower concentrations of these two anionic analytes and deprotonation equilibrium at higher concentration were observed with associated electronic spectral changes as well as visually detectable change in solution color, an observation that is generally common for other strong hydrogen bond donor functionalities like urea and thiourea. DFT calculations performed with the M06/6-31+G**//M05-2X/6-31G* level of theory showed that F(-) binds more strongly than OAc(-) with the reagent molecules. The deprotonation of methylene hydrogen atom of receptors with F(-) ion was observed computationally. The metal complex as reagent showed even stronger binding energies with these analytes, which corroborated the experimental results.

In silico studies with substituted adenines to achieve a remarkable stability of mispairs with thymine nucleobase

DNA nucleobases are prone to undergo modification by deamination, oxidation, alkylation or hydrolysis processes because of their reactive nature. Many of these damaged DNA nucleobases are highly susceptible to mutagenesis when formed in cellular DNA, and such modified nucleobases can be mispaired by a DNA polymerase during replication. Mispair formation has largely been carried out with modified uracil and guanine nucleobases, while the reports on mispair formation with modified adenines are scarce in the literature. Research into adenine mispairs is limited due to the lower number of hydrogen bonding sites and orientations of hydrogen bonding donor and acceptor in such mispairs. We have explored mispair formation between modified adenine and thymine nucleobases and found that substitutions at the 2-position of adenine with –NH2/–OH groups augmented the stability compared to the typical A–T base pair. Furthermore, substituents at the remote position of adenine nucleobase also enhanced the interaction energies of the mispairs. The nitrogen/oxygen-lithiated adenines showed remarkable stability for mispairs with a thymine base. The di-coordinated N/O-lithiated adenine and thymine mispairs were found to be stable at ∼12.0 kcal mol−1 compared to the A–T base pair. We also studied the mispairing interaction with a tetra-coordinated lithiated adenine and thymine mispair, where lithium was coordinated with two water molecules. The interaction free energy calculated with a M06-2X/6-31+G(d,p) level of theory for such tetra-coordinated lithiated adenine thymine mispairs is ∼−30.0 kcal mol−1. The EDA analysis suggested that the electrostatic interaction energy contributes more to the total interaction energy calculated for such mispairs. The ab initio molecular dynamics (ADMP) simulations showed that the formation of mispairs with modified adenine is stable and the deviations in their geometries are minimal with time. This study reveals that suitable modifications in adenine nucleobase can lead to very stable mispairs with the thymine nucleobase, which are in some cases comparable to G–U mispairs.

Improved Shoot Regeneration, Salinity Tolerance and Reduced Fungal Susceptibility in Transgenic Tobacco Constitutively Expressing PR-10a Gene.

Plants in ecosystems are simultaneously exposed to abiotic and biotic stresses, which restrict plant growth and development. The complex responses to these stresses are largely regulated by plant hormones, which in turn, orchestrate the different biochemical and molecular pathways to maneuver stress tolerance. The PR-10 protein family is reported to be involved in defense regulation, stress response and plant growth and development. The JcPR-10a overexpression resulted in increased number of shoot buds in tobacco (Nicotiana tabacum), which could be due to high cytokinin to auxin ratio in the transgenics. The docking analysis shows the binding of three BAP molecules at the active sites of JcPR-10a protein. JcPR-10a transgenics showed enhanced salt tolerance, as was evident by increased germination rate, shoot and root length, relative water content, proline, soluble sugar and amino acid content under salinity. Interestingly, the transgenics also showed enhanced endogenous cytokinin level as compared to WT, which, further increased with salinity. Exposure of gradual salinity resulted in increased stomatal conductance, water use efficiency, photosynthesis rate and reduced transpiration rate. Furthermore, the transgenics also showed enhanced resistance against Macrophomina fungus. Thus, JcPR-10a might be working in co-ordination with cytokinin signaling in mitigating the stress induced damage by regulating different stress signaling pathways, leading to enhanced stress tolerance.

In silico studies to explore the mutagenic ability of 5-halo/oxy/li-oxy-uracil bases with guanine of DNA base pairs.

DNA nucleobases are reactive in nature and undergo modifications by deamination, oxidation, alkylation, or hydrolysis processes. Many such modified bases are susceptible to mutagenesis when formed in cellular DNA. The mutagenesis can occur by mispairing with DNA nucleobases by a DNA polymerase during replication. We have performed a study of mispairing of DNA bases with unnatural bases computationally. 5-Halo uracils have been studied as mispairs in mutagenesis; however, the reports on their different forms are scarce in the literature. The stability of mispairs with keto form, enol form, and ionized form of 5-halo-uracil has been computed with the M06-2X/6-31+G** level of theory. The enol form of 5-halo-uracil showed remarkable stability toward DNA mispair compared to the corresponding keto and ionized forms. (F)U-G mispair showed the highest stability in the series and (Halo)(U(enol/ionized)-G mispair interactions energies are more stable than the natural G-C basepair of DNA. To enhance the stability of DNA mispairs, we have introduced the hydroxyl group in the place of halogen atoms, which provides additional hydrogen-bonding interactions in the system while forming the 5-membered ring. The study has been further extended with lithiated 5-hydroxymethyl-uracil to stabilize the DNA mispair. (CH2OLi)U(ionized)-G mispair has shown the highest stability (ΔG = -32.4 kcal/mol) with multi O-Li interactions. AIM (atoms in molecules) and EDA (energy decomposition analysis) analysis has been performed to examine the nature of noncovalent interactions in such mispairs. EDA analysis has shown that electrostatic energy mainly contributes toward the interaction energy of mispairs. The higher stability achieved in these studied mispairs can play a pivotal role in the mutagenesis and can help to attain the mutation for many desired biological processes.

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.

Transformation of Substituted Glycals to Chiral Fused Aromatic Cores via Annulative π-Extension Reactions with Arynes

The Diels-Alder addition of arynes to appropriately substituted vinyl/aryl glycals followed by π-extension via pyran ring opening smoothly furnished meta-disubstituted fused aromatic cores containing a stereodefined orthogonally protected chiral side chain. The method is broad in terms of aryl homologation, affording benzene, naphthalene, and phenanthrene derivatives. Base-induced deprotonation followed by cleavage of the allylic C-O bond appear to be the crucial steps leading to the development of aromaticity, which is the driving force behind the annulative π-extension process. The present protocol can be used for the synthesis of meta-disubstituted naphthalene aldehydes and substrates for aldolases.

Stereoselective Metabolism of Omeprazole by Cytochrome P450 2C19 and 3A4: Mechanistic Insights from DFT Study

The efficacy of S-omeprazole as a proton pump inhibitor compared with that of its enantiomer R-omeprazole is studied using density functional theoretical calculations. The pharmacokinetic studies suggest that the efficacy of S-omeprazole presumably depends on metabolic pathway and excretion from the human body. The density functional theory calculations at SMDwater-B3LYP-D3/6-311+G(d,p)/LANL2DZ//B3LYP/6-31G(d)/LANL2DZ with triradicaloid model active species, [Por•+FeIV(SH)O], of CYP2C19 enzyme with high-spin quartet and low-spin doublet states demonstrate C-H bond activation mechanism through a two-state rebound process for the hydroxylation of R-omeprazole and S-omeprazole. The calculated activation free energy barriers for the hydrogen abstraction are 15.7 and 17.5 kcal/mol for R-omeprazole and S-omeprazole, respectively. The hydroxylation of R-omeprazole and S-omeprazole is thermodynamically favored; however, the hydroxylated intermediate of S-omeprazole further disintegrates to metabolite 5- O-desmethylomeprazole with a higher kinetic barrier. We have examined the sulfoxidation of S-omeprazole to omeprazole sulfone metabolite by CYP3A4, and the observed activation free energy barrier is 9.9 kcal/mol. The computational results reveal that CYP2C19 exclusively metabolizes R-omeprazole to hydroxyomeprazole, which is hydrophilic and can easily excrete, whereas CYP3A4 metabolizes S-omeprazole to lipophilic sulfone; hence, the excretion of this metabolite would be relatively slower from the body. The spin density analysis and molecular orbital analysis performed using biorthogonalization calculations indicate that R-omeprazole favors high-spin pathway for metabolism process whereas S-omeprazole prefers the low-spin pathway.

Revealing the Mechanistic Pathway of Acid Activation of Proton Pump Inhibitors To Inhibit the Gastric Proton Pump: A DFT Study

Acid-related gastric diseases are associated with disorder of digestive tract acidification due to the acid secretion by gastric proton pump, H+,K+-ATPase. Omeprazole is one of the persuasive irreversible inhibitor of the proton pump H+,K+-ATPase. However, the reports on the mechanistic pathway of irreversible proton pump inhibitors (PPIs) on the acid activation and formation of disulfide complex are scarce in the literature. We have examined the acid activation PPIs, i.e., timoprazole, S-omeprazole and R-omeprazole using M062X/6-31++G(d,p) in aqueous phase with SMD solvation model. The proton pump inhibitor is a prodrug and activated in the acidic canaliculi of the gastric pump H+,K+-ATPase to sulfenic acid which can either form another acid activate intermediate sulfenamide or a disulfide complex with cysteine amino acid of H+,K+-ATPase. The quantum chemical calculations suggest that the transition state (TS5) for the disulfide complex formation is the rate-determining step of the multistep acid inhibition process by PPIs. The free energy barrier of TS5 is 5.5 kcal/mol higher for timoprazole compared to the S-omeprazole. The stability of the transition state for the formation of disulfide bond between S-omeprazole and cysteine amino acid of H+,K+-ATPase is governed by inter- and intramolecular hydrogen bonding. The disulfide complex for S-omeprazole is thermodynamically more stable by 4.5 kcal/mol in aqueous phase compared to disulfide complex of timoprazole, which corroborates the less efficacy of timoprazole as irreversible PPI for acid inhibition process. It has been speculated that sulfenic acid can either form sulfenamide or a stable disulfide complex with cysteine amino acid residue of H+,K+-ATPase. The M062X/6-31++G(d,p) level of theory calculated results reveal that the formation of tetra cyclic sulfenamide is unfavored by ∼17 kcal/mol for S-omeprazole and 11.5 kcal/mol for timoprazole compared to the disulfide complex formation in each case. The DFT calculations have further shed light on the acid activation process of R- and S-isomers of omeprazole. The calculated results suggest that the efficacy of these isomers lie on their metabolic pathway and excretion from human body.

Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies

The neutral oxime reactivator RS194B with a seven-membered ring has shown better efficacy towards the tabun-inhibited AChE than that of RS69N with a six-membered ring and RS41A with a five-membered ring. The difference in the efficacy of these reactivators has remained unexplored. We report here the origin of the difference of efficacy of these reactivators based on the conformational analysis, quantum chemical calculations and steered molecular dynamics (SMD) simulations. The conformational analysis using B3LYP/6-31G(d) level of theory revealed that RS41A and RS194B are more stable in gauche conformation due to the gauche effect (–N–C–C–N– bonds) whereas RS69N prefers anti-conformation. The SMD simulations show that RS194B retains in more stable gauche conformation inside the active gorge of AChE during different time intervals that experiences more hydrogen bonding, hydrophobic interactions with the catalytic anionic site (CAS) residues and weaker interactions with the peripheral anionic site (PAS) residues compared to RS41A and RS69N. In an effort to design an even superior reactivator, RS194B-S has been chosen with a subtle change in the geometry of RS194B by replacing the carbonyl oxygen with the sulfur atom. The newly designed reactivator RS194B-S can also be a promising candidate to reactivate tabun-inhibited AChE.

DFT Study To Explore the Importance of Ring Size and Effect of Solvents on the Keto–Enol Tautomerization Process of α- and β-Cyclodiones

We have explored the effect of ring size on keto–enol tautomerization of α- and β-cyclodiones using the M062X-SMDaq/6-31+G(d,p)//M062X/6-31+G(d,p) level of theory. The calculated results show that the activation free energy barrier for the keto–enol tautomerization process of α-cyclopropanedione (1) is 54.9 kcal/mol, which is lower compared to that of the other cyclic diketo systems studied here. The four-membered α- and β-cyclobutanedione (2 and 6) do not favor keto–enol tautomerization unlike other studied cyclic systems because of the ring strain developed in the transition-state geometries and their corresponding products. Water-assisted keto–enol tautomerization with one molecule reveals that the free energy activation barriers reduce almost half compared to those for the uncatalyzed systems. The two-water-assisted process is favorable as the activation free energy barriers lowered by ∼10 kcal/mol compared to those of the one-water-assisted process. The ion-pair formation seems to govern the lowering of activation barriers of α- and β-cyclodiones with two water molecules during the keto–enol tautomerization process, which however also overcomes the favorable aromatization in the three-membered ring system. The free energy activation barriers calculated with the M062X-SMDaq/6-31+G(d,p) level predicted that the keto–enol tautomerization process for the α-cyclodiones follows the following trend: 2 > 3 > 4 > 5 > 1. Water-assisted tautomerization of α-cyclodiones also predicted 1-W and 1-2W as the most favored processes; however, 5-W and 5-2W were found to be disfavored in this case. The β-cyclodione systems also showed similar trends as obtained with α-diketone systems. The influence of bulk solvent on the keto–enol tautomerization process favors the formation of the enol form in a more polar solvent medium even under mixed solvent conditions in acetonitrile and hexane at M062X-SMDacetonitrile/6-31+G(d,p) and M062X-SMDhexane/6-31+G(d,p) levels of theory.