Lydia Rhyman

Nickel(II) and copper(II) complexes of allyl 2-(thiophen-2-ylmethylene)hydrazinecarbodithioate: synthesis, X-ray crystal structures, and theoretical study

We report allyl 2-(thiophen-2-ylmethylene)hydrazine-carbodithioate (HL) and its Ni(II) and Cu(II) complexes, [ML2]. The compounds were fully characterized by elemental analysis, IR, 1H-NMR, UV-Vis, and molar conductivity. The crystal structure analysis indicates that the metal is four-coordinate square planar and that a parallel stacking of the molecular planes is present in the crystals, with stacking distances of 3.642 and 3.676 Å for the Ni(II) and Cu(II) complexes, respectively. Gas phase DFT computations indicate that the thione tautomeric form of the free ligand is more stable than the thiol form by 14.52 kJ mol–1. For HL and ML2, comparison between the computed and experimental data shows good agreement.

A DFT study of the [3 + 2] versus [4 + 2] cycloaddition reactions of 1,5,6-trimethylpyrazinium-3-olate with methyl methacrylate.

The reaction between 1,5,6-trimethylpyrazinium-3-olate and methyl methacrylate (MMA) yielding a lactone-lactam has been studied using the DFT method at the B3LYP/6-31G(d) level. It is concluded that formation of the lactone-lactam is a domino process involving three consecutive reactions: (i) a 1,3-dipolar cycloaddition (13DC) reaction between the pyrazinium-3-olate and MMA yielding a [3 + 2] cycloadduct (CA); (ii) a skeletal rearrangement, which converts the [3 + 2] CA into a formal [4 + 2] CA, possessing a diazabicyclo[2.2.2]octane structure; and finally, (iii) an S(N)2 reaction, promoted by halide anion, with concomitant nucleophilic attack of the created carboxylate anion on an iminium carbon with formation of the lactone ring present in the lactone-lactam. Analysis of the four competitive channels associated with the 13DC reaction indicates that this cycloaddition takes place with complete endo stereoselectivity and 6 regioselectivity, yielding [3 + 2] CA. The subsequent skeletal rearrangement also takes place in an elementary step via a non-concerted mechanism. Electron localization function bonding analysis makes it possible to establish that the bicyclo[2.2.2]octane skeleton present in the lactone-lactam complex structure is not attained via a Diels-Alder reaction between pyrazinium-3-olate and MMA.

Understanding the formation of [3+2] and [2+4] cycloadducts in the Lewis acid catalysed reaction between methyl glyoxylate oxime and cyclopentadiene: a theoretical study

The formation of the formal [3+2] and [2+4] cycloadducts in the Lewis acid (LA) catalysed reaction of cyclopentadiene (Cp, 1) with methyl glyoxylate oxime (MGO, 2a) has been theoretically studied using DFT methods. Coordination of BF3 LA to the oxygen atom of MGO 2a not only increases the electrophilicity of the oxime, but also makes the corresponding tautomeric BF3:nitrone complex 8b the reactive species. The reaction is characterised by the nucleophilic attack of Cp 1 on the carbon atom of the corresponding BF3:nitrone complex 8b. The subsequent ring closure at the end of the reaction allows the formation of the [3+2] or [2+4] cycloadducts. ELF bonding analysis of selected points on the intrinsic reaction coordinate of the two competitive endo paths enables us to establish that the formation of the formal [3+2] or [2+4] cycloadducts takes place through stereoisomeric transition state structures with a similar electronic structure.

Synthesis, molecular structure, FT-IR, Raman, XRD and theoretical investigations of (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one

A novel (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one [C17H11ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The isomers, optimized geometrical parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of the density functional theory method, employing, the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the monoclinic space group P2₁/c with the unit cell parameters a=5.7827(8)Å, b=14.590(2)Å, c=16.138(2)Å and β=89.987 (°). The CC bond of the central enone group adopts an E configuration. There is a good agreement between the theoretically predicted structural parameters and vibrational frequencies and those obtained experimentally.

Ion‐Pair SN2 Substitution: Activation Strain Analyses of Counter‐Ion and Solvent Effects

The ion-pair SN 2 reactions of model systems MnF(n-1) +CH3Cl(M(+) =Li(+), Na(+), K(+), and MgCl(+); n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6-31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M(+) modifies ion-pair SN 2 reactivity relative to the parent reaction F(-) +CH3Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion-pair SN2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor-made substitution reactions.

DFT Studies of the Photophysical Properties of Fluorescent and Semiconductor Polycyclic Benzimidazole Derivatives

The photophysical and electrochemical properties of eleven polycyclic benzimidazole fused organic pigments (four based on phthalic anhydride, four based on naphthalic anhydride and three based naphthalene tetra carboxylic acid dianhydride) were investigated using density functional theory and time dependent density functional theory methods (B3LYP/6-31G(d) and M06/6-31G(d)). The predicted geometries are comparable using both functionals. The electrochemical properties are in good agreement with the experimental results. However, the experimental absorption-emission properties are closer to the values computed using the M06/6-31G(d) method. Both the methods perform equally well in explaining the intramolecular charge transfer characteristics. This work can help to understand the modern age functional materials at molecular level and to design new molecules.

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations

The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.Graphical abstract

Discovery of anti-Ebola drugs: a computational drug repositioning case study

Computational drug repositioning has complemented and guided the experimental drug repositioning assignments in the recent past. Structure- and ligand-based strategies have been tried for the generation of novel repositioning ideas. In the present computational work, an attempt has been made to reposition a set of approved/existing drugs as novel anti-Ebola agents, targeting VP35 viral protein. One of the crystal structure ligands bound to VP35 protein was used as a query for the initial shape- and electrostatics-based virtual screening using OpenEye Scientific Software suite. The top-ranking hits from the ligand-based virtual screening were further docked in the ligand-binding pocket of the VP35 protein. The virtual hits from both the ligand- and structure-based screening were examined carefully in terms of tightness of their binding interactions with the macromolecular target. Several top hits belonged to therapeutic categories like antidiabetics (e.g., nateglinide), antihypertensives (e.g., telmisartan) and antibiotics (e.g., ticarcillin), etc., totally unrelated to the proposed antiviral indication. The computational repositioning hypotheses generated at the end of this study are likely to interest several researchers around the globe that are desperately looking for a breakthrough treatment to curb the recent menace created by a relatively older virus. The proposed hits that are approved/existing drugs may serve as starting points for the clinical repositioning for anti-Ebola indication or as lead structures in fast-track anti-Ebola drug discovery campaigns.

4-Mercaptophenylboronic acid: Conformation, FT-IR, Raman, OH stretching and theoretical studies

4-Mercaptophenylboronic acid (4-mpba, C6H7BO2S) was investigated experimentally by vibrational spectroscopy. The molecular structure and spectroscopic parameters were studied by computational methods. The molecular dimer was investigated for intermolecular hydrogen bonding. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. The present work provides a simple physical picture of the OH stretch vibrational spectra of 4-mpba and analogues of the compound studied. When the different computational methods are compared, there is a strong evidence of the better performance of the BLYP functional than the popular B3LYP functional to describe hydrogen bonding in the dimer. The findings of this research work should be useful to experimentalists in their quests for functionalised 4-mpba derivatives.

Synthesis and Photophysical Properties of Polycarbo-Substituted Quinazolines Derived from the 2-Aryl-4-chloro-6-iodoquinazolines

The reactivity of the 2-aryl-4-chloro-6-iodoquinazolines towards palladium catalyzed sequential (Sonogashira/Suzuki-Miyaura) and one-pot two-step cross-coupling (bis-Sonogashira, and successive Sonogashira/Stille) reactions to afford novel unsymmetrical polycarbo-substituted quinazolines has been evaluated. In contrast to the chloro-bromo substituted quinazolines in which selectivity has been previously found to generally favor substitution at the more activated C(4)-Cl bond over the weaker Csp2-Br bond, substitution in the case of the chloro-iodo derivatives favors cross-coupling through the intrinsically more reactive Csp2-I bond. The electronic absorption and emission properties of the prepared 2,3-diaryl-6-(phenylethynyl)quinazolines were studied in solvents of different polarity (dichloromethane, toluene, DMF, methanol) and CH2Cl2-TFA mixture using UV-Vis and emission spectroscopic techniques complemented with density functional theory method to establish the effect of substituents on intramolecular charge transfer properties.