Mechanistic investigation in the [1,4] and [1,2] Wittig rearrangement reactions: a DFT study.

The mechanistic pathways for the [1,4] and [1,2] Wittig rearrangements of 2-silyl-6-aryl-5,6-dihydro-(2H)-pyrans have been studied at the M06-2X/6-31+G(d,p), 6-311++G(d,p) and cc-pVTZ level of theory. The crucial C-O bond cleavage step in the mechanism has been analysed initially, using two model reactions covering aliphatic as well as cyclic allylic ethers. The barriers for the one-step as well as two-step pathways have been calculated and the mechanisms for both the [1,4] and [1,2] Wittig rearrangement reactions are predicted to occur through a two-step mode. An energetic analysis of the reaction pathways reveals that the [1,4]-rearrangement has a lower barrier than the [1,2]-Wittig rearrangement. The C-O cleavage transition state was found to have the highest barrier and is thus the rate determining transition state for all of the studied molecules. This is in agreement with the previously published experimental studies. The role of the allylic trimethylsilane group in the stabilization of the intermediate anions of the Wittig reactants has also been investigated while comparing it with the phenyl and allylic t-butyl groups through Natural Bond Orbital (NBO) calculations.

iEDDA Reaction of the Molecular Iodine-Catalyzed Synthesis of 1,3,5-Triazines via Functionalization of the sp3 C-H Bond of Acetophenones with Amidines: An Experimental Investigation and DFT Study.

The present work reports an inverse electron demand Diels-Alder (iEDDA)-type reaction to synthesize 1,3,5-trizines from acetophenones and amidines. The use of molecular iodine in a catalytic amount facilitates the functionalization of the sp3 C-H bond of acetophenones. This is a simple and efficient methodology for the synthesis of 1,3,5-triazines in good to excellent yields under transition-metal-free and peroxide-free conditions. The reaction is believed to take place via an in situ iodination-based oxidative elimination of formaldehyde. DFT calculations at the M062X/6-31+G(d,p) level were employed to investigate the reaction mechanism. Reaction barriers for the cycloaddition as well as a formaldehyde expulsion steps were computed, and a multistep mechanism starting with the nucleophilic attack by benzamidine on an in situ generated imine intermediate has been proposed. Both local and global reactivity descriptors were used to study the regioselectivity of the addition steps.

PyGlobal: A toolkit for automated compilation of DFT-based descriptors.

Density Functional Theory (DFT)-based Global reactivity descriptor calculations have emerged as powerful tools for studying the reactivity, selectivity, and stability of chemical and biological systems. A Python-based module, PyGlobal has been developed for systematically parsing a typical Gaussian outfile and extracting the relevant energies of the HOMO and LUMO. Corresponding global reactivity descriptors are further calculated and the data is saved into a spreadsheet compatible with applications like Microsoft Excel and LibreOffice. The efficiency of the module has been accounted by measuring the time interval for randomly selected Gaussian outfiles for 1000 molecules. © 2016 Wiley Periodicals, Inc.

Theoretical studies on the electronic structure, charge distribution and vibrational spectra of diglyme-M(+)-AsF(6)(-) (M=Li, Na, K).

Electronic structure and the vibrational spectra of CH(3)(OCH(2)CH(2))(2)OCH(3)-M(+)-AsF(6)(-) (M=Li, Na, K) have been obtained using the density functional theory. Lithium ion exhibits a pentavalent coordination via 3 oxygens from diglyme and two fluorines of AsF(6)(-) whereas Na(+) and K(+) exhibit coordinate number 6 with 3 fluorines of the anion binding to alkali metal in these complexes. Analysis of calculated spectra reveal that the CH(2) wag (840-1120 cm(-1)) vibrations in the complex are sensitive to metal ion coordination. A frequency downshift relative to the free anion has been predicted for the vibrations of AsF(6)(-) anion when the fluorines are directly bonded (denoted by F) to metal ion. Consequent reorganization of electron density in the complex engenders a frequency shift in the opposite direction for As-F vibrations wherein the fluorine atoms are not coordinating to the alkali metal ion. An approach based on the molecular electron density topography coupled with the difference electron density map explains the direction of the frequency shifts of C-O-C and the As-F stretchings compared to those of free diglyme or AsF(6) anion. A new method, which includes the color-mapping function for the difference molecular electron density (MED), superimposed on the bond critical points in MED topography has been suggested to explain the direction of the frequency shifts in a single attempt.

Exploring isoxazole and carboxamide derivatives as potential non-nucleoside reverse transcriptase inhibitors.

Nonnucleoside reverse transciptase inhibitors (NNRTI) are a class of drug molecules with a specific target of HIV-1 reverse transcriptase (RT). In the present work, we evaluated a set of selected oxazole and carboxamide derivatives to identify potential pharmacophoric features using molecular docking approach. The docking approach employed has been validated by enrichment factor calculation at top 1% (EF1%). It shows a considerable improvement in EF1%value compared to earlier reported study carried out on specific dataset of ligands and decoys for RT, in the directory of useful decoys (DUD). The carboxamide derivatives show better activity as NNRT inhibitors than oxazole derivatives. From this study, four pharmacophoric groups including a triazine ring, an aniline substituent, a benzyl amide moiety and a trimethylphenoxy substituent have been recognized and used for designing new NNRT inhibitors. Newly designed molecules show significant enhancement in docking scores over the native ligand, parent and other training set molecules. In addition, some functional groups have also been identified to assist in improving the activity of these pharmacophores. Thus a nitrile group, an amide and fluoro substitution turn out to be an important requisite for NNRT potential inhibitors.

Molecular electrostatic potentials in aromatic substituted 4-hydroxyquino-2-lones: glycine/NMDA receptor antagonists.

Hydroxyquinolone derivatives have proven to be useful for inhibition at the glycine binding site of N-methyl-D-aspartate (NMDA) receptor. In this work the electronic structure, molecular electrostatic potential (MESP) and vibrational characteristics of a set of C(3) substituted 4-hydroxyquino-2-lone (HQ) derivatives, which act as Glycine/NMDA receptor antagonists, have been investigated using the density functional calculations. In the optimized structures a substituent at the C(3) site of HQ tends to adopt a helical structure. MESP investigations reveal that the ligands showing better inhibition activity should possess electron-rich regions extending over the substituent and carbonyl group of HQ. A correlation of inhibitory activity to the molecular electrostatic potential topography at the carbonyl oxygen as well as to the molecular electron density topography turns out to be a significant output of the investigation.

Theoretical studies on hydrogen bonding, NMR chemical shifts and electron density topography in alpha, beta and gamma-cyclodextrin conformers.

Hydrogen-bonded interactions in alpha-, beta-, and gamma-CD conformers are investigated from the molecular electron density topography and chemical shift in the nuclear magnetic resonance (NMR) spectra calculated by using the Gauge Invariant Atomic Orbital (GIAO) method within the framework of density functional theory. For the lowest-energy CD conformers in the gas phase, the O3-H...O2' hydrogen-bonding interactions are present. Calculated 1H NMR chemical shifts (delta H) correlate well with the hydrogen-bond distance as well as electron density at the bond critical point in the molecular electron density (MED) topography. The conformers of beta- and gamma-CD comprised of relatively strong secondary hydroxyl interactions are stabilized by solvation from polar solvents.

Molecular electrostatic potentials and hydrogen bonding in alpha-, beta-, and gamma-cyclodextrins.

Cyclodextrins (CDs) are cyclic oligomers of glucose having the toroid of sugars elaborating a central cavity of varying size depending on the number of glucoses. The central hydrophobic cavity of CD shows a binding affinity toward different guest molecules, which include small substituted benzenes to long chain surfactant molecules leading to a variety of inclusion complexes when the size and shape complementarity of host and guest are compatible. Further, interaction of guest molecules with the outer surface of alpha-CD has also been observed. Primarily it is the electrostatic interactions that essentially constitute a driving force for the formation of inclusion complexes. To gain insights for these interactions, the electronic structure and the molecular electrostatic potentials in alpha-, beta-, and gamma-CDs are derived using the hybrid density functional theory employing the three-parameter exchange correlation functional due to Becke, Lee, Yang, and Parr (B3LYP). The present work demonstrates how the topography of the molecular electrostatic potential (MESP) provides a measure of the cavity dimensions and understanding of the hydrogen-bonded interactions involving primary and secondary hydroxyl groups. In alpha-CD, hydrogen-bonded interactions between primary -OH groups engender a "cone-like" structure, while in beta- or gamma-CD the interactions from the primary -OH with ether oxygen in glucose ring facilitates a "barrel-like" structure. Further, the strength of hydrogen-bonded interactions of primary -OH groups follows the rank order alpha-CD > beta-CD > gamma-CD, while the secondary hydrogen-bonded interactions exhibit a reverse trend. Thus weak hydrogen-bonded interactions prevalent in gamma-CD manifest in shallow MESP minima near hydroxyl oxygens compared to those in alpha- or beta-CD. Furthermore, electrostatic potential topography reveals that the guest molecule tends to penetrate inside the cavity forming the inclusion complex in beta- or gamma-CD.