Structural study of 2-(1-oxo-1 H-inden-3-yl)-2H-indene-1,3-dione by DFT calculations, NMR and IR spectroscopy

NMR, FT-IR spectroscopic studies and molecular docking study of 4-acetoxyphenethyl acrylate

Conformational, structural, vibrational spectroscopic properties and nuclear magnetic chemical shift values of 4-acetoxyphenethyl acrylate (4APA) were investigated using spectroscopic and theoretical approaches including FT-IR and NMR spectroscopes and quantum chemical calculations. FT-IR spectroscopic measurement was carried out between 3500[Formula: see text]cm[Formula: see text]–400[Formula: see text]cm[Formula: see text]. Geometric parameters, vibrational wavenumbers and nuclear magnetic chemical shift values were estimated using B3LYP hybrid density functional theory method with 6-311[Formula: see text]G(d, p) basis set. 1H, [Formula: see text]C, APT and HETCOR NMR experiments of 4APA were obtained in DMSO solution. For a quantitative description of vibrational wavenumbers, total energy distribution (TED) values with scaled quantum mechanical (SQM) method were calculated. Moreover, molecular docking study of title molecule was theoretically carried out using Auto Dock Vina Program.

INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY

In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.

Spectral, structural elucidation and coordination abilities of Co(II) and Mn(II) coordination entities of 2,6,11,15-tetraoxa-9,17-diaza-1,7,10,16-(1,2)-tetrabenzenacyclooctadecaphan-8,17-diene

Designing tactics were tailored and followed by synthetic and formulation methodologies to prepare 2,6,11,15-tetraoxa-9,17-diaza-1,7,10,16-(1,2)-tetrabenzenacyclooctadecaphan-8,17-diene. Spectral techniques (MS, infrared, 1H NMR, 13C NMR, electronic and EPR), physiochemical measurements (elemental analysis, molar conductance and magnetic susceptibility), electrochemistry (cyclic voltammetry) and classical mechanics (molecular modeling) were employed for structural elucidation of Co(II) and Mn(II) coordination entities having N2O4 chromophore. Comparative spectral analysis revealed legating nature of N2O4 donor macrocycle and confirmed host/guest connectivity between ligand and metal(s). Mass spectrometry (MS) determined 1:1 stoichiometry in CEs. Further electrochemical study confirmed change in oxidation and reduction patterns of CEs. Inhibiting potential (antifungal screened against Aspergillus flavus) showed enhanced antimicrobial properties of CEs as compared to ligand. Molecular modeling was employed to find out different molecular features along with their stabilization energies.

Quantum chemical calculations to reveal the relationship between the chemical structure and the fluorescence characteristics of phenylquinolinylethynes and phenylisoquinolinylethynes derivatives, and to predict their relative fluorescence intensity

In this paper the relationship between the chemical structure and fluorescence characteristics of 30 phenylquinolinylethyne (PhQE), and phenylisoquinolinylethyne (PhIE) derivatives compounds employing ab initio calculations have been elucidated. Quantum chemical calculations (6-31G) were carried out to obtain: the optimized geometry, energy levels, charges and dipole moments of these compounds, in the singlet (steady and excited states) and triplet states. The relationship between quantum chemical descriptors, and wavelength of maximum excitation and emission indicated that these two parameters have the most correlation with quantum chemical hardness (eta). Also, stokes shift has the most correlation with the square of difference between the maximum of positive charges in the singlet steady and singlet excited states. The quantitative structure-property relationship (QSPR) of PhQE and PhIE was studied for relative fluorescence intensity (RFI). The genetic algorithm (GA) was applied to select the variables that resulted in the best-fit models. After the variable selection, multiple linear regression (MLR) and support vector machine (SVM) were both utilized to construct linear and non-linear QSPR models, respectively. The SVM model demonstrated a better performance than that of the MLR model. The route mean square error (RMSE) in the training and the test sets for the SVM model was 0.195 and 0.324, and the correlation coefficients were 0.965 and 0.960, respectively, thus revealing the reliability of this model. The resulting data indicated that SVM could be used as a powerful modeling tool for QSPR studies. According to the best of our knowledge, this is the first research on QSPR studies to predict RFI for a series of PhQE and PhIE derivative compounds using SVM.

Determination of the formation constant for the inclusion complex between Lanthanide ions and Dansyl chloride derivative by fluorescence spectroscopy: theoretical and experimental investigation

In this paper, a sensitive, easy, efficient, and suitable method for the calculation of K(f) values of complexation between one derivative of Dansyl chloride [5-(dimethylamino) naphthalene-1-sulfonyl 4-phenylsemicarbazide] (DMNP) and Lanthanide(III) (Ln) ions is proposed, using both spectrofluorometric and spectrophotometric methods. Determination of K(f) showed that DMNP was mostly selective towards the erbium (III) ion. The validity of the method was also confirmed calculating the Stern-Volmer fluorescence quenching constants (K(sv)) that resulted in the same consequence, obtained by calculating the K(f) of complexation values. In addition, the UV-vis spectroscopy was applied for the determination of K(f) only for the Ln ions that had interactions with DMNP. Finally, the DFT studies were done on Er(3+) and the DMNP complex for distinguishing the active sites and estimating the pair wise interaction energy. It can be concluded that this derivative of Dansyl chloride with inherent high fluorescence intensity is a suitable reagent for the selective determination of the Er(3+) ion which can be used in constructing selective Er(3+) sensors.

Experimental and quantum chemical study on the IR, UV and electrode potential of 6-(2,3-dihydro-1,3-dioxo-2-phenyl-1H-inden-2-yl)-2,3-dihydroxybenzaldehyde

Electrode potential of 6-(2,3-dihydro-1,3-dioxo-2-phenyl-1H-inden-2-yl)-2,3-dihydroxybenzaldehyde (DPDB) in methanol have been calculated theoretically. For the achievement of this task, the density functional theory (B3LYP/6-31G(d)) was employed with the inclusion of the entropic and thermochemical corrections to yield the free energies of the redox reactions. The electrode potential was also obtained experimentally by means of an electrochemical technique (cyclic voltammetry). The geometric parameters, the vibrational frequency values and the UV spectrum of DPDB and 2-(2,3-dihydro-1,3-dioxo-2-phenyl-1H-inden-2-yl)-5,6-dioxocyclohexa-1,3-dienecarbaldehyde (DPDD is the oxidized form of DPDB), were computed using the same methods. The calculated IR spectrum of DPDB, used for the assignment of the IR frequencies, was observed in the experimental FT-IR spectrum. The correlation between the theoretical and experimental DPDB vibrational frequencies was 0.996. This agreement mutually verified the accuracy of the experimental method and the validity of the applied mathematical model.

Exploring QSARs for antiviral activity of 4-alkylamino-6-(2-hydroxyethyl)-2-methylthiopyrimidines by support vector machine

The support vector machine, which is a novel algorithm from the machine learning community, was used to develop quantitative structure activity relationship models to predict the antiviral activity of 4-alkylamino-6-(2-hydroxyethyl)-2-methylthiopyrimidines. The genetic algorithm was employed to select the variables that resulted in the best-fitted models. A comparison between the obtained results using support vector machine with those of multiple linear regression revealed that support vector machine model was much better than multiple linear regression. The root mean square errors of the training set and the test set for support vector machine model were calculated to be 0.102 and 0.205, and the correlation coefficients (r2) were 0.956 and 0.852, respectively. Furthermore, the obtained statistical parameter of leave-one-out (LOO) and leave-group-out (LGO) cross-validation test on support vector machine model were 0.893 and 0.881, respectively, which prove the reliability of this model. The results suggest that branching, volume and lipophilicity are the main independent factors contributing to the antiviral activities of the studied compounds.

A theoretical study on interactions between mitoxantrone as an anticancer drug and DNA: application in drug design

This research is an effort to further understand the physicochemical interaction between the novel drug, mitoxantrone (MTX) and its biologic receptor, DNA. The ultimate goal is to design drugs that interact more with DNA. Understanding the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA, it should ultimately allow the rational design of novel anti-cancer or anti-viral drugs. Molecular modelling on the complex formed between MTX and DNA presented that this complex was indeed fully capable of participating in the formation of a stable intercalation site. Furthermore, the molecular geometries of MTX and the DNA bases (adenine, guanine, cytosine and thymine) were optimized with the aid of the B3LYP/6-31G* method. The properties of the isolated intercalator and its stacking interactions with the adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were studied with the DFTB method (density functional tight-binding), an approximate version of the DFT method, that was extended to cover the London dispersion energy. The B3LYP/6-31G* stabilization energies of the intercalator...base pair complexes were found 10.06 kcal/mol and 21.64 kcal/mol for AT...MTX and GC...MTX, respectively. It was concluded that the dispersion energy and the electrostatic interaction contributed to the stability of the intercalator.DNA base pair complexes. The results concluded from the comparison of the DFTB method and the Hartree-fock method point out that these methods show close results and support each other.