Aysen E. Ozel

Calculation and analysis of IR spectrum of 2-aminopyridine

Abstract Normal coordinate analysis of 2-aminopyridine (2AP) and ND 2 -pyridine have been performed in valance force field approximation. 2AP was taken as planar because of the low barrier to amino group inversion. The IR absorption intensities have been calculated and the electro–optical parameters (EOP) were fitted to experimental data in order to produce the experimental relative intensities. The created force field and EOP reproduce the IR spectrum of the molecule studied well.

Infrared-spectra and normal-coordinate analysis of quinoline and quinoline complexes

Abstract Normal coordinate analysis was performed on the vibrational spectra data of quinoline and the force field parameters of the free molecule were determined by the refinement of the corresponding parameters of benzene and pyridine molecules. The results of semiempirical (AM1) and ab initio (4-31G∗) calculations were taken into account during the refinement procedure. A partially common and well-transferable force field has been obtained for free quinoline. In order to investigate the coupling peculiarities of the vibrational modes of quinoline by metal–ligand vibrations, the calculated force field parameters of the free ligand were used in calculating the IR spectra of the transition metal (II) quinoline complexes, without any alterations and only force field parameters related to the M–N(Q) bond were introduced. The calculated spectra have been compared with the experimental spectra of the quinoline metal (II) complexes.

FT-IR AND LASER RAMAN SPECTROSCOPIC INVESTIGATION OF TRANSITION METAL HALIDE COMPLEXES OF BENZIDINE

Abstract FT-IR and Raman spectra of MX 2 Bzn {where M=Mn or Co, X=Cl; M=Cd, X=Cl or I; and Bzn=benzidine; C 12 H 8 (NH 2 ) 2 } complexes have been investigated in the region between 200–4000 cm −1 and all the bands observed are assigned. Spectroscopic investigation indicates that benzidine molecules are bound to metal through both nitrogen lone pairs and bidentate ligands. It is found that benzidine molecules are centrosymmetric in the complexes. Coordination effects on internal modes of benzidine, particularly on the NH 2 group vibrations are discussed. The general influence of the metal on the state of the coordinated amino-group is found to be similar to the characteristics of the aniline complexes.

Raman micro-spectroscopic analysis of cultured HCT116 colon cancer cells in the presence of roscovitine

Raman micro-spectroscopic analysis of cultured HCT116 colon cancer cells in the presence of roscovitine, [seliciclib, 2-(1-ethyl-2-hydroxy-ethylamino)-6-benzylamino-9-isopropylpurine], a promising drug candidate in cancer therapy, has been performed for the first time. The aim of this study was to investigate modulations in colon cancer cells induced by roscovitine. Raman spectra of the cultured HCT116 colon cancer cells treated with roscovitine at different concentrations (0, 5, 10, 25 and 50 μM) were recorded in the range 400-1850 cm(-1). It was shown that the second derivative profile of the experimental spectrum gives valuable information about the wavenumbers and band widths of the vibrational modes of cell components, and it eliminates the appearance of false peaks arising from incorrect baseline corrections. In samples containing roscovitine, significant spectral changes were observed in the intensities of characteristic protein and DNA bands, which indicate roscovitine-induced apoptosis. Roscovitine-induced apoptosis was also assessed by flow cytometry analysis, and analysis of propidium iodide staining. We observed some modifications in amide I and III bands, which arise from alterations in the secondary structure of cell proteins caused by the presence of roscovitine.

Conformational analysis and vibrational spectroscopic investigation of L-alanyl-L-glutamine dipeptide

In this study conformational behavior of anticancer chemotherapy dipeptide Ala-Gln and its dimers have been investigated by molecular mechanic and ab-initio calculations. The calculations on Ala-Gln dipeptide as a function of side chain torsion angles, enable us to determine their energetically preferred conformations. The relative positions of the side chain residues of the stable conformations of dipeptide were obtained, depending on the obtained conformational analysis results. The lowest energy conformation of the dipeptide has been determined by using the Ramachandran maps (Biopolymers 6 (1963), 1494; J. Mol. Biol.7 (1963), 95) and compared with the quantum chemical ab-initio results. The geometry optimization, vibrational wavenumbers and intensity calculations of Ala-Gln dipeptide were carried out with the Gaussian03 program by using DFT with B3LYP functional and 6-31

Structural and vibrational study of primidone based on monomer and dimer calculations

Primidone (Mysoline), with the chemical formula 5-ethyl-5-phenyl-hexahydropyrimidine- 4,6-dione (C12H14N2O2), has been a valuable drug in the treatment of epilepsy. In the present work, the experimental IR and Raman spectra of solid phase primidone were recorded, and the results were compared with theoretical wavenumber values of monomer and dimer forms of the title molecule. Vibrational spectral simulations in the dimer form were carried out to improve the assignment of the bands in the solid phase experimental spectra. The possible stable conformers of free molecule were searched by means of torsion potential energy surfaces scan studies through two dihedral angles. The molecular geometries of the monomer and dimer forms of title molecule were optimized using DFT method at B3LYP/6-31++G(d,p) level of theory. Using PEDs determined the contributions of internal (stretching, bending, etc.) coordinates to each normal mode of vibration. Further, HOMO–LUMO energy gap and NBO properties of the investigated molecule in monomer and dimer forms were also calculated.

Structural and vibrational spectroscopic elucidation of sulpiride in solid state

The study on the conformational and vibrational behaviors of sulpiride molecule which is known as a neuroleptic or antipsychotic drug that is widely used clinically in the treatment of schizophrenic or depressive disorders is an important scientific and practical task. In here, a careful enough study of monomer and dimeric forms of sulpiridine {5-(aminosulfonyl)-N-[(1-ethyl-2-pyrrolidinyl) ethyl]-2-methoxy-benzamide (C15H23N3O4S)} is undertaken by density functional theory (DFTB3LYP) method with the B3LYP/6-31G(d,p) basis set. The conformations of free molecule were searched by means of torsion potential energy surfaces scan studies through dihedral angles D1 (8 N, 18C, 20C, 23 N), D2 (18C, 20C, 23 N, 25C) and D3 (28C, 30C, 41S, 44 N) in electronically ground state, employing 6-31G basic set. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G(d,p) theory level. Afterwards, the possible dimer forms of the molecule were formed and their energetically preferred conformations were investigated. Moreover, the effect of basis set superposition error on the structure and energy of the three energetically favourable sulpiride dimers has been determined. The optimized structural parameters of the most stable monomer and three low energy dimer forms were used in the vibrational wavenumber calculations. Raman and IR (4000–400 cm−1) spectra of sulpiride have been recorded in the solid state. The assignment of the bands was performed based on the potential energy distribution data. The natural bond orbital analysis has been performed on both monomer and dimer geometries in order to elucidate delocalization of electron density within the molecule. The predicted frontier molecular orbital energies at DFT/B3LYP/6-31G(d,p) theory level show that charge transfer occurs within the molecule. The first-order hyperpolarizability (β0) and related properties (μ and α) of the title molecule were also calculated.

Structural and Vibrational Study on Monomer and Dimer Forms and Water Clusters of Acetazolamide

Experimental IR and Raman spectra of solid acetazolamide have been analysed by computing the molecular structures and vibrational spectra of monomer and dimer forms and water clusters of acetazolamide. The possible stable conformers of free acetazolamide molecule in the ground state were obtained by scanning the potential energy surface through the dihedral angles, D1 (1S-2C-6S-9N), D2 (4N-5C-12N-14C), and D3 (5C-12N-14C-16C). The final geometry parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with −.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.

Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies

Background N-acetylcarnosine (NAC), a dipeptide with powerful antioxidant properties that is extensively used as a pharmaceutical prodrug for the treatment of cataract and acute gastric disease, was investigated by molecular dynamics with the GROMACS program in order to understand the solvent effect on peptide conformation of the peptide molecule used as a component of a drug and which presents substantial information on where drug molecules bind and how they exert their effects. Besides, molecular docking simulation was performed by using the AutoDock Vina program which identify the kind of interaction between the drug and proteins. A delivery system based on poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with NAC (NAC-PLGA-NPs) for the treatment of cataract was prepared for the first time in this study in order to enhance drug bioavailability and biocompatibility. The objective of this work was to prepare and evaluate the structural formulation, characterization, and cytotoxicity studies of NAC-loaded NPs based on PLGA for cataract treatment. Methods PLGA and NAC-loaded PLGA NPs were prepared using the double emulsion (w/o/w) method, and characterizations of the NPs were carried out with UV–Vis spectrometer to determine drug concentration, the Zeta-sizer system to analyze size and zeta potential, FTIR spectrometer to determine the incorporation of drug and PLGA, and TEM analysis for morphological evaluation. Results NAC-loaded PLGA NPs were successfully obtained according to UV–Vis and FTIR spectroscopy, Zeta-sizer system. And it was clearly observed from the TEM analysis that the peptide-loaded NPs had spherical and non-aggregated morphology. Also, the NPs had low toxicity at lower concentrations, and toxicity was augmented by increasing the concentration of the drug. Discussion The NAC molecule, which has been investigated as a drug molecule due to its antioxidant and oxidative stress-reducing properties, especially in cataract treatment, was encapsulated with a PLGA polymer in order to increase drug bioavailability. This study may contribute to the design of drugs for cataract treatment with better reactivity and stability.