Sedat Karabulut

Supramolecular lead(II) azide complex of 2,6-diacetylpyridine dihydrazone: synthesis, molecular structure, and biological activity

The complex of 2,6-diacetylpyridinedihydrazone (L) with lead(II) and azide has been characterized by elemental analyses, FTIR, and single-crystal X-ray analysis. The Pb(C9H13N11) (1) crystallized in the monoclinic space group C2/c. The coordination of 1 exhibits a gap around the lead(II), possibly occupied by a stereochemically active electron lone pair on lead(II) resulting in a hemidirected complex. Antimicrobial activity of the complex is higher than the free ligand.

A DFT-based QSAR study on inhibition of human dihydrofolate reductase

Diaminopyrimidine derivatives are frequently used as inhibitors of human dihydrofolate reductase, for example in treatment of patients whose immune system are affected by human immunodeficiency virus. Forty-seven dicyclic and tricyclic potential inhibitors of human dihydrofolate reductase were analyzed using the quantitative structure-activity analysis supported by DFT-based and DRAGON-based descriptors. The developed model yielded an RMSE deviation of 1.1 a correlation coefficient of 0.81. The prediction set was characterized by R2=0.60 and RMSE=3.59. Factors responsible for inhibition process were identified and discussed. The resulting model was validated via cross validation and Y-scrambling procedure. From the best model, we found several mass-related descriptors and Sanderson electronegativity-related descriptors that have the best correlations with the investigated inhibitory concentration. These descriptors reflect results from QSAR studies based on characteristics of human dihydrofolate reductase inhibitors.

Anomeric and rotameric preferences of glucopyranose in vacuo, water and organic solvents

Glucopyranose is the most stable form of glucose in solution. Identification of molecular structure of glucopyranose is very important because of its biological and synthetic significance; it is not an easy task because of the large number of possible configurations. Relative energies of exocyclic hydroxymethyl rotamers and α-β anomers of D-glucopyranose have been determined at the reference MP2/6-31G(d,p) level geometry by ab initio calculations at the infinite basis set limit of MP2 approach and with inclusion of CCSD(T) correction term evaluated with the aug-cc-pVDZ basis set in vacuum, water, dimethylsulfoxide, tetrahydrofurane and ethanol. The infinite basis set limit of MP2 level was determined by two point extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Solvent effects, relative energies and binding energies have been considered applying explicit calculations and implicit solvent models.

Reduction of aflatoxin B1 to aflatoxicol: a comprehensive DFT study provides clues to its toxicity.

BACKGROUND Aflatoxicol (AFL) is one of most the important metabolites of aflatoxin B1 (AFB1). AFL can be formed through enzymatic or synthetic reduction of AFB1. Various experimental and theoretical studies have been focused on the AFB1 due to its high toxicity and carcinogenicity. RESULTS The selective reduction of AFB1 carbonyls, molecular structure of AFL and its effect on toxicity has been studied here by the density functional theory (DFT) method. Although the toxicity of AFL is 18 times lower than that of AFB1, it has been concluded that both molecular structures have similar potency to form an exo-epoxide (AFEP) analogue which can bind to DNA. CONCLUSION Calculations revealed that only one of the three possible tautomers of AFL is stable, both in the gas phase and water. The electronic properties of aflatoxicol are calculated as similar to aflatoxin B1 and this may be an explanation of similar carcinogenicity and toxicity of these compounds, which has been proved by experimental results.

Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint

Molecular structures of stable tautomers of dimedone [5,5-dimethyl-cyclohexane-1,3-dione (1) and 3-hydroxy-5,5-dimethylcyclohex-2-enone (2)] were optimized and vibrational frequencies were calculated in five different organic solvents (dimethylsulfoxide, methanol, acetonitrile, dichloromethane and chloroform). Geometry optimizations and harmonic vibrational frequency calculations were performed at DFT 6-31+G(d,p), DFT 6-311++G(2d,2p), MP2 6-311++G (2d,2p) and MP2 aug-cc-pVDZ levels for both stable forms of dimedone. Experimental FT-IR spectra of dimedone have also been recorded in the same solvents. A new approach was developed in order to determine tautomers’ ratio using both experimental and theoretical data in Lambert–Beer equation. Obtained results were compared with experimental results published in literature. It has been concluded that while DFT 6-31+G(d,p) method provides accurate enol ratio in DMSO, MeOH, and DCM, in order to obtain accurate results for the other solvents the MP2 aug-cc-pVDZ level calculations should be used for CH3CN and CHCl3 solutions.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings.

A new hybrid (experimental–theoretical) quantitative method for detection of relative anomer concentrations in water

A novel and inexpensive hybrid (combined experimental and theoretical) approach was used to quantitatively identify anomer proportions of d-glucose, d-galactose and d-mannose in water. The study involves three parts: recording of experimental FT-IR spectra of monosaccharides in water, calculation of vibrational frequencies of all stable anomers of monosaccharides and regression analysis of theoretical and experimental intensities. No expensive experimental processes and high-level calculations were needed during the study. The results were compared with the data from pure experimental and molecular dynamic studies. It has been concluded that in water while d-glucose and d-mannose have two stable anomers, α-pyranose and β-pyranose, d-galactose has four stable anomers, α-pyranose, β-pyranose, α-furanose and β-furanose. Comparison of detected results with the literature data showed that the developed method is working for the quantitative detection of anomer proportions of monosaccharides in water.