natural bond orbital (NBO)

In an effort to identify the factors that affect the reactivity of nitrogen mustards, we prepared two phosphoramide mustard derivatives in interaction with DNA. The activity of these drugs was compared to that of cyclophosphamide and phosphoramide mustard. The effect of drug interaction on DNA aggregation and condensation was investigated in aqueous solution under physiological conditions, using a constant DNA concentration (6.25 mM) and various ligand/polynucleotide (phosphate) ratios of 1/160, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2, and 1/1. Fourier transform infrared, two-dimensional infrared (2D IR), and ultraviolet (UV)-visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of the drug–DNA complexes in aqueous solution. Density functional theory (DFT) calculations followed by a natural bond orbital (NBO) analysis, Fukui functions, electron localization functions (ELF), generalized valence bond (GVB) calculations, and quantum theory of atoms in molecules (QTAIM) were used to find the relationship between the structure and reactivity of phosphoramide mustard derivatives. Together with these methods, docking studies were applied to understand the features that dominate the molecular orbitals, charges, and other binding parameters. Theoretical results that coincided with the experimental values were obtained under similar conditions of pH and temperature. The results showed that the reactivity of these compounds is controlled by the frontier molecular orbitals, as well as the factors affecting them, such as negative hyperconjugation.

1,3,3-Trinitroazetidine (TNAZ) and its derivatives are highly desirable energetic compounds, which can be used in explosive and/or propellant formulations. In this paper, the quantities of activation barriers, enthalpies, entropies and free energies of a few initial steps in the decomposition pathways of TNAZ and some of its derivatives with –F, –CN and –OCH3 groups have been computed by means of

... Interestingly, the change in the conformation is accompanied by a significant change in the S–S bond length: for the 384 skewed fragments and for the eight fragments in the trans conformation calculated mean values of the S–S bond lengths are 2.04(2) Å and 2.12(3) Å ...

Free radical oxygen species act on biological constituents like lipid, cell membrane and deoxyribonucleic acids by changing their biological functions. These effects are associated with the appearance of anomalies like allergies, cancer, viral infections, inflammations, etc. Antioxidants like flavonoids are abundant in plants and are good scavengers of reactive oxygen species (ROS). Their antioxidant activities are measured through hydrogen atom transfer or charge transfer. These mechanisms depend on the structure of the flavonoid or the nature of the free radical. In this paper, we study the interaction of one of the most reactive flavonoid quercetin with two ROS: hydroxyl radical (·OH) and superoxide radical (·O2-) using B3LYP/6-31++G*level of theory. Correlations between structural changes and antioxidant activity are shown. The potential energy surfaces (PES) are calculated in both cases and indicate a transition state (TS) only for the reaction of quercetin with the hydroxyl radical. This transition state is only localized at the B3LYP/3-21G level of theory. This comparison between the reactants, the TS and the products of the reaction with the ·OH radical indicate the nature of the transfer. As far as the reaction of quercetin with the superoxide anion radical is concerned, the PES shows the inexistence of one transition state. The nature of the charge transfer is thus determined using the natural bond orbital (NBO) and the singlet occupied molecular orbital (SOMO) analysis.

Density functional theory (DFT), Hartree–Fock (HF) and Möller–Plesset second order perturbation (MP2) calculations were applied to study the mechanism of the two-step substitution reaction of cis-[Pt (en)(H2O) 2] 2+(en= ethylenediamine) and thiourea. ...

The present work demonstrates a computational exploration of the intramolecular H-bond (IMHB) interaction in two model heterocyclic compounds - 2-thiazol-2-yl-phenol (2T2YP) and 2-benzothiazol-2-yl-phenol (2B2YP) by meticulous application of various quantum chemical tools. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇(2)ρ(r) at the bond critical point using the Atoms-In-Molecule methodology. Topological features based on ρ(r) suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of a covalent interaction. The interplay between aromaticity and Resonance-Assisted H-Bond (RAHB) has also been discussed using both geometrical and magnetic criteria. The occurrence of IMHB interaction in 2T2YP and 2B2YP has also been criticized under the provision of the Natural Bond Orbital (NBO) analysis. The ESIPT phenomenon in the molecular systems is also critically addressed on the le...