Journal of Theoretical and Computational Chemistry

The theoretical investigation of the physico-chemical properties of pyrazolooxazine derivatives, which could exhibit anti-inflammatory activity, has been carried out using DFT computations at the B3LYP/6-311$++$G (d, p) level. It appears that both pyrazolooxazin-2-one (1) and pyrazolooxazin-2-thione (2) exhibit thermal stability whereas the electron donating character of the latter is higher than that of the former species. Molecular electrostatic potential surfaces (MESP) have been used in order to determine the activity sites of these species. The HSAB (Hard and Soft Acids and Bases) principle helped to determine the reactivity as well as the effect of substituting groups on the molecules. The stability of these compounds has been analyzed using natural bond orbital analyses NBO. Then, the structure-activity properties of a large series of derivatives were investigated using the HyperChem 8.0.6 software considering the Lipinski’s “rule of five”. The results of QSAR analyses showed that the most promising compound among others, named f₁ (a thiophen ring being attached to the nitrogen atom 3 of 1) should be a good candidate for experimental testing.

Pharmacophore modeling and 3D-Quantitative Structure Activity Relationship (3D-QSAR) studies have been performed on a dataset of thirty-two quinazoline and aminopyridine derivatives to get an insight into the important structural features required for binding to inducible nitric oxide synthase (iNOS). A four-point CPH (Common Pharmacophore Hypothesis), AHPR.29, with a hydrogen bond acceptor, hydrophobic group, positively charged ionizable group and an aromatic ring, has been obtained as the best pharmacophore model. Satisfactory statistical parameters of correlation ($R^2$) and cross-validated ($Q^2$) correlation coefficients, 0.9288 and 0.6353, respectively, show high robustness and good predictive ability of our selected model. The contour maps have been developed from this model and the analysis has provided an interpretable explanation of the effect that various features and substituents have on the potency and selectivity of inhibitors towards iNOS. Docking studies have also been performed in order to analyze the interactions between the enzyme and the inhibitors. Our proposed model can thus be further used for screening a large database of compounds and design new iNOS inhibitors.

The structural, electronic and magnetic properties of the neutral and cationic cobalt oxide clusters (CoO)${}_n^q$ ($n=3-10$, $q=0,+1$) have been studied using a modified basin-hopping Monte Carlo (BHMC) algorithm refined by spin-polarized DFT. A systematic search of global minimum structures predicts new global minima of (CoO)${}_9^{0∕+}$ and reproduced other minima that are in excellent agreement with previous works. For most low-spin and high-spin states, the structural transition from planar-like to compact structure occurs at (CoO)${}_5^{0∕+}$, which is in contrast with the general notion that the structural changes at (CoO)${}_6^{0∕+}$. Supported by the results of the binding energy, second-order total energy difference, chemical hardness, chemical potential and HOMO-LUMO gap confirms the stability of (CoO)₄. Results of the spin magnetic moments for the global minima show that (CoO)₄ and (CoO)₈ spin configurations exhibit a fully antiferromagnetic (AFM) ordering, while (CoO)₉ spin displays the highest ferromagnetic (FM) ordering. Interestingly, elongation of Co–Co bond in (CoO)₄ causes O being polarized by the neighboring Co atoms that accordingly follows the Goodenough-Kanamori-Anderson rule of FM super-exchange coupling for the Co-O-Co structural rearrangement to 90^∘ ($D_{4h}$ structure) in order to accommodate the spin magnetic ordering changes. This rearrangement is a result of the valence band being shifted away from the Fermi level to lower energy causing high population of the spin-up density of state and leading to the asymmetrical polarization of the whole (CoO)₄ structure. As far as the dissociation energy surfaces are concerned, the first ever such surfaces are constructed corresponding to ${(\mathrm{\text{CoO}})}_n^q\to {(\mathrm{\text{CoO}})}_m^q+{(\mathrm{\text{CoO}})}_{(n-m)}$, which identify a complete dissociation pathway linking the cationic and neutral clusters and finally confirm (CoO)${}_4^{0∕+}$ as the most stable cluster compared to the rest.

Binding energies ($E_b)$, geometric and electronic structures for [$2+1$](O/[$2+1$]) additions of O atom on ($n,0$)($n=6$ − 10) single-walled carbon nanotubes with di-vacancies are studied using a GGA-PBE method, and defect curvature ($K_{\mathrm{\text{D-def}}}$) is used to predict reactivities of different C—C bonds at defect area. Calculated results show that the C—C bonds can be divided into two types: broken C—C bonds corresponding to adducts with a C—O—C configuration structure and unbroken C—C bonds corresponding to adducts with a closed-3MR structure. $E_b$ of O/[$2+1$] additions for the adduct with the C—O—C configuration structure monotonously increases with the increase of $K_{\mathrm{\text{D-def}}}$ in any ($n$,0)($n=6-10$) tube and decreases with the increase of $n$ in ($n$,0)($n=6$, 7, 10) tubes. Besides the fact that $E_b$ value is mainly determined by the defect curvature, it is also affected by band gaps, bonding characteristic of C—C bonds in the highest occupied molecular orbital (HOMO) and geometric structures. The study would provide a theoretical basis for surface modifications of carbon nanotubes with atomic vacancy defects.

Modified Si(111) surface with designed nanostructural modifications including grown pits, nanobars and nanoislands as well as deposited hill-, diamond- and cage-like nanoclusters were studied using density-functional theory (DFT) calculations. The thermal stabilities, electronic structures and optical properties of these various nanostructural modifications of the Si(111) surface were calculated and discussed. The results indicate that the optical absorption of the modified Si(111) surface can be enhanced by these surface modifications especially when depositing diamond-like nanoclusters on the surface.

Copper(II) benzoates ($n$OBA-Cu) with various terminal alkoxy carbon numbers, $n=7$–12, were prepared from $p$-$n$-alkoxy benzoic acids (nOBAs). Fourier transform infrared (IR) experiments suggested that dimerization through copper(II) chelating bidentate coordination created $n$OBA-Cu with a linear rod-like structure, similar to the hydrogen-bonded structure of its parent $n$OBA. However, the coordination structure of $n$OBA-Cu changed during heating. Periodic density functional theory calculations provided valuable insight into the possible arrangement of the parent and copper(II)-coordinated $n$OBAs. The formation of binuclear complexes between two adjacent $n$OBA-Cu dimers forced $n$OBA-Cu to arrange itself in a layer and exhibit smectic A mesophase. Accordingly, four types of IR stretching absorption of benzoyl carbonyl were observed in binuclear $n$OBA-Cu complexes, replacing the original symmetric and asymmetric vibrations of benzoyl carboxylate in chelating bidentate coordination. The lateral association by $\pi$–$\pi$ interactions between adjacent parent $n$OBA dimers preferred a progressive smectic C arrangement. The origin of the odd–even effect was understood from the consideration of the molecular structure.

In the present work, the activation of methyl halides bonds under experience of an external electric field (EEF) is explained from the Valence Bond theory perspective. The dissociation mechanism of C–X bonds (X $=$ Cl, Br, I) influenced by a homogeneous and a heterogeneous field placed parallel to the bond axis is presented. For all examples, an increase in the electric field strength have similar consequences: (i) the decrease of the energy depth along the dissociation path, (ii) an increase of the equilibrium interatomic distance (at high EEFs), and (iii) the transition from a homolytic to a heterolytic dissociation after some field magnitude. These general behaviors are explained through the curve crossing between the ionic and the covalent structure at some field strength.