Prasad V. Bharatam

Chiral Solvating Agents for Cyanohydrins and Carboxylic Acids

We have shown that a structure as simple as an ion pair of (R)- or (S)-mandelate and dimethylamminopyridinium ions possesses structural features that are sufficient for NMR enantiodiscrimination of cyanohydrins. Moreover, (1)H NMR data of cyanohydrins of known configuration obtained in the presence of the mandelate-dimethylaminopyridinium ion pair point to the existence of a correlation between chemical shifts and absolute configuration of cyanohydrins. Mandelate-DMAPH(+) ion pair and mandelonitrile form a 1:1 complex with an association constant of 338 M(-1) (DeltaG(0), -3.4 kcal/mol) for the (R)-mandelonitrile/(R)-mandelate-DMAPH(+) and 139 M(-1) (DeltaG(0), -2.9 kcal/mol) for the (R)-mandelonitrile/(S)-mandelate-DMAPH(+) complex. To understand the origin of enantiodiscrimination, the geometry optimization and energy minimization of the models of ternary complexes of (S)-mandelonitrile/(R)-mandelate/DMAPH(+) and (S)-mandelonitrile/(S)-mandelate/DMAPH(+) complexes was performed using DFT methodology (B3LYP) with the 6-31+G(d) basis set in Gaussian 3.0. Further, analysis of optimized molecular model obtained from theoretical studies suggested that (i) DMAP may be replaced with other amines, (ii) the hydroxyl group of mandelic acid is not necessary for stabilization of ternary complex and may be replaced with other groups such as methyl, (iii) the ion pair should form a stable ternary complex with any hydrogen-bond donor, provided its OH bond is sufficiently polarized, and (iv) alpha-H of racemic mandelic acid should also get resolved with optically pure mandelonitrile. These inferences were experimentally verified, which not only validated the proposed model but also led to development of a new chiral solvating agent for determination of ee of carboxylic acids and absolute configuration of aryl but not alkyl carboxylic acids.

Site-selective electrophilic cyclization and subsequent ring-opening: a synthetic route to pyrrolo[1,2-a]quinolines and indolizines.

An efficient strategy for the synthesis of pyrrolo[1,2-a]quinolines and indolizines from pyranoquinolines via site-selective electrophilic cyclization and subsequent opening of pyran ring using silver/iodine under mild reaction conditions is described. This approach involves the preferential attack of the pyridyl nitrogen over aryl ring and leads to the formation of 5-endo-dig cyclized products. Quantum chemical calculations between C-N (ΔE(a) = 9.01 kcal/mol) and C-C (ΔE(a) = 31.31 kcal/mol) bond formation were performed in order to rationalize the observed site selectivity. Structure of the products were confirmed by the X-ray crystallographic studies. Iodo-substituted compounds generated by the electrophilic iodocyclization were further diversified via Pd-catalyzed cross-coupling reactions.

Divalent N(I) Compounds with Two Lone Pairs on Nitrogen

Carbon with the C(0) state has been reported recently, examples of which were known for the past decades. Silicon in the Si(0) state and phosphorus in the P(I) state are also known experimentally. This prompted us to search for divalent N(I) compounds, which resulted in the identification of ::N(←L)(2)(⊕) systems with bicoordinated nitrogen in the N(I) formal oxidation state. It was found that several biguanide derivatives (especially in their protonated state) belong to this class. Quantum chemical analysis provided the structural details, molecular orbitals, charge localization (vs delocalization) trends, etc. This class of compounds has been found to be characterized by two lone pairs on the central nitrogen, very similar to the central carbon in divalent C(0) compounds (::C(←L)(2)). The new bonding environment for nitrogen reported in this article, divalent nitrogen N(I), is clearly different from the nitrenium ions NR(2)(⊕). The electronic structure and reactivity of representative examples of this novel class of divalent nitrogen N(I) systems (::N(←L)(2)(⊕)) have been analyzed in detail, in terms of molecular orbitals, atomic charges, protonation energies, complexation energies with Lewis acids like BH(3), AlCl(3), and AuCl and compared with those of divalent C(0) systems.

To Bend or Not to Bend! The Dilemma of Allenes

Allenes, though expected to be linear, are found to be bent in many examples, especially in the case of cyclic allenes. The bending of allene is attributed to the weakening of π-bond strength across the allene. However, tetrakis(dimethylamino)allene {((CH(3))N)(2)C═C═C(N(CH(3))(2))}, which is characterized by push-push interactions, has been shown to be linear, thus leading to doubts of the current understanding of the bent allenes. In this article, we report the ab initio MO/DFT, NBO based electronic structure analysis of R(2)C═C═CR(2) (R = H, NH(2)) with a gradual increase in the number of amino substituents. The results indicate that the allenic π-bond strength and bending potential decrease, with an increase in the amino substitution. Molecular orbital analysis provides necessary clues regarding the delicate balance between orthogonality of the π orbitals and the p orbitals on the central carbon, which dictates the bending potential of the allenes. The dilemma of to bend or not to bend is a unique feature of tetraaminoallenes (NH(2))(2)C═C═C(NH(2))(2) in comparison to isoelectronic heteroallenes (NH(2))(2)C═N═C(NH(2))(2)(+) and (NH(2))(2)C═B═C(NH(2))(2)(-).

Regioselective [4+2] cycloaddition versus nucleophilic reactions of N-arylamino substituted 1,3-diaza-1,3-butadienes with ketenes: Synthesis of pyrimidinone and fused pyrimidinone derivatives. Part II

Abstract A novel synthetic method for 3-aryl-6-phenyl-2-methylthio/secondaryamino substituted-4(3 H )-pyrimidinones 5 and 9 by the reactions of N -arylamino substituted 1,3-diaza-1,3-butadienes 1 and 6 with phenyl-, vinyl- and isopropenylketenes is explored. Semi emperical AM1 calculations on 1 and 6 are performed to explain the mechanism of their reaction with ketenes. Transformations of 5 and 9 leading to fused pyrimidinones 10 are also reported.

In(III) triflate-mediated solvent-free synthesis and activation of thioglycosides by ball milling and structural analysis of long chain alkyl thioglycosides by TEM and quantum chemical methods.

Conventional solution-phase synthesis of thioglycosides from glycosyl acetates and thiols in the presence of In(III) triflate as reported for benzyl thioglucoside failed when applied to the synthesis of phenolic and alkyl thioglycosides. But, it was achieved in high efficiency and diastereospecificity with ease by solvent-free grinding in a ball mill. The acetates in turn were also obtained by the homogenization of free sugars with stoichiometric amounts of acetic anhydride and catalytic In(OTf)3 in the mill as neat products. Per-O-benzylated thioglycosides on grinding with an acceptor sugar in the presence of In(OTf)3 yield the corresponding O-glycosides efficiently. The latter in the case of a difficult secondary alcohol was nearly exclusive (>98%) in 1,2-cis-selectivity. In contrast, the conventional methods for this purpose require use of a coreagent such as NIS along with the Lewis acid to help generate the electrophilic species that actually is responsible for the activation of the thioglycoside donor in situ. The distinctly different self-assembling features of the peracetylated octadecyl 1-thio-α- and β-D-galactopyranosides observed by TEM could be rationalized by molecular modeling.

A simple, mild, and regioselective method for the benzylation of carbohydrate derivatives promoted by silver carbonate ☆

A simple, mild, and regioselective method has been developed for the selective benzylation and p-methoxybenzylation of carbohydrate derivatives in high yields using Ag(2)CO(3) as the promoter. Benzylation of base-labile substrates, for which other reported methods are of little use, has been performed in high yields.

New PPARγ ligands based on barbituric acid: Virtual screening, synthesis and receptor binding studies

A new series of PPARgamma ligands based on barbituric acid (BA) has been designed employing virtual screening and molecular docking approach. To validate the computational approach, designed molecules were synthesized and evaluated in in vitro radioligand binding studies. Out of the total 14 molecules, 6 were found to bind to the murine PPARgamma with IC(50) ranging from 0.1 to 2.5 microM as compared to reference standard, pioglitazone (IC(50)=0.7 microM).

Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: understanding the factors contributing to selectivity.

Glycogen synthase kinase-3 is a constitutively acting, multifunctional serine threonine kinase, the role of which has been implicated in several physiological pathways and has emerged as a promising target for the treatment of type-II diabetes and Alzheimer’s disease. In order to provide a detailed understanding of the origin of selectivity determinants of ATP competitive inhibitors, molecular dynamics simulations in combination with MM-PBSA binding energy calculations were performed using crystal structures of GSK-3β and CDK-2 in complex with 12 ATP competitive inhibitors. Analysis of energy contributions indicate that electrostatic interaction energy dictates the selectivity of ATP competitive inhibitors against CDK-2. Key interactions as well as residues that potentially make a major contribution to the binding free energy were identified at the ATP binding site. This analysis stresses the need for the inhibitors to interact with Lys85, Thr138, and Arg141 in the binding site of GSK-3β to show selectivity. The residue-wise energy decomposition analysis further suggested the additional role of Gln185 in determining the selectivity of maleimides. The results obtained in this study can be utilized to design new selective GSK-3 ATP competitive inhibitors.

Divalent N(I) Character in 2-(Thiazol-2-yl)guanidine: An Electronic Structure Analysis

Several medicinally important compounds carry a 2-(thiazol-2-yl)guanidine unit. These species are generally (erroneously) represented as 1-(thiazol-2-yl)guanidine species. Quantum chemical studies were performed to identify the appropriate tautomeric state of this class of compounds. B3LYP/6-31+G(d) calculations indicate the preferred tautomeric state of these species is associated with the 2-(thiazol-2-yl)guanidine structure rather than the 1-(thiazol-2-yl)guanidine structure. G2MP2 calculations on the model system were carried out to study the electronic structure, electron delocalization, and protonation energy; MESP, ELF, HOMA, AIM, and NBO analyses were also carried out. The results indicate that this class of compounds may be treated as species with hidden ::N(←L)R character. Upon protonation of the thiazole ring nitrogen, these systems show the electronic structure as in ::N(←L)2(⊕) systems with divalent N(I) oxidation state.