Sevim Akyüz - Academia.edu (original) (raw)

Papers by Sevim Akyüz

All possible conformations of Cyclo (Arg-Gly-Asp-D-Phe-Val) (C26H38N8O7) with antitumor activity ... more All possible conformations of Cyclo (Arg-Gly-Asp-D-Phe-Val) (C26H38N8O7) with antitumor activity were determined and the most stable conformer elucidated by MMFF method using the Spartan06 program. The differences in energy between the conformers were determined, and the low energy conformers, which are required for determination of the biological activity, were characterized. Since as an anticancer candidate, the investigated molecule is expected to be an integrin inhibitor, a molecular docking study was conducted with αvβ3 integrin to determine the mechanism of interaction. As a result of docking simulations, the binding affinity (G =-10.5 kcal/mol) and the interactions between the investigated peptide and target integrin were determined.

Open Journal of Nano

Acalabrutinib is an inhibitor of Bruton's tyrosine kinase (BTK) activity and prevents the activat... more Acalabrutinib is an inhibitor of Bruton's tyrosine kinase (BTK) activity and prevents the activation of the B-cell antigen receptor (BCR) signaling pathway. For having these properties acalabrutinib recently was approved for medical use as an anticancer drug. Determining the conformational properties of a bioactive molecule is necessary to reveal its bioactivity. For this reason, the conformational states of the acalabrutinib were examined first. The AM1, a semiexperimental method, was used to examine the stable conformations of the acalabrutinib molecule. Nine lowest energy conformers of the acalabrutinib molecule were determined and their relative energies were calculated. Afterwards, the interactions of the most stable conformer of acalabrutinib with DNA and integrin were examined by docking simulations, and the most active interaction sites and binding affinities were determined.

Current Computer - Aided Drug Design, Mar 31, 2020

Background: Sulpiride, which has selective dopaminergic blocking activity, is a substituted benza... more Background: Sulpiride, which has selective dopaminergic blocking activity, is a substituted benzamide antipsychotic drug playing a prominent role in the treatment of schizophrenia, which more selective and primarily blocks dopamine D2 and D3 receptor. Objective: This study has two main objectives, firstly; the molecular modeling studies (MD and Docking, ADME) were conducted to define the molecular profile of sulpiride and sulpiridereceptor interactions, another to synthesize polymeric nanoparticles with chitosan, having the advantage of slow/controlled drug release, to improve drug solubility and stability, to enhance utility and reduce toxicity. Method: Molecular dynamic simulation was carried out to determine the conformational change and stability (in water) of the drug and the binding profile of D3 dopamine receptor was determined by molecular docking calculations. The pharmacological properties of the drug were revealed by ADME analysis. The ionic gelation method was used to prepare sulpiride loaded chitosan nanoparticles (CS NPs). The Dynamic Light Scattering (DLS), UV-vis absorption (UV), Scanning Electron Microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy techniques were carried out to characterize the nanoparticles. In vitro cell cytotoxicity experiments examined with MTT assay on mouse fibroblast (L929), human neuroblastoma (SH-SY5Y) and glioblastoma cells (U-87). The statistical evaluations were produced by ANOVA. Results: The residues (ASP-119, PHE-417) of D3 receptor provided a stable docking with the drug, and the important pharmacological values (blood brain barrier, Caco-2 permeability and human oral absorption) were also determined. The average particle size, PdI and zeta potential value of sulpiride- loaded chitosan NPs having a spherical morphology were calculated as 96.93 nm, 0.202 and +7.91 mV. The NPs with 92.8% encapsulation and 28% loading efficiency were found as a slow release profile with 38.49% at the end of the 10th day. Due to the formation of encapsulation, the prominent shifted wave numbers for C-O, S-O, S-N stretching, S-N-H bending of Sulpiride were also identified. Mitochondrial activity of U87, SHSY-5Y and L929 cell line were assayed and evaluated using the SPSS program. Conclusion: To provide more efficient use of Sulpiride having a low bioavailability of the gastrointestinal tract, the nanoparticle formulation with high solubility and bioavailability was designed and synthesized for the first time in this study for the treatment of schizophrenia. In addition to all pharmacological properties of drug, the dopamine blocking activity was also revealed. The toxic effect on different cell lines have also been interpreted.

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2021

In this study, the lowest energy molecular structures were determined by conformational analysis ... more In this study, the lowest energy molecular structures were determined by conformational analysis of six drugs commonly used in cancer treatment, in order to use as initial data for docking simulations. Using the AutoDock Vina software, the interaction mechanisms of the 6 FDA approved drugs (Pemetrexed, Irinotecan, Tamoxifen, Gemcitabine, Topotecan and Temozolomide) with DNA were investigated. In addition, MM/PB(GB)SA calculations for the drug-DNA structures under investigation have been performed. The calculated binding affinities and binding free energies of interactions were showed the stability of the structures. It has been found that the active site where these molecules interact with DNA is the same and that their various interactions, primarily hydrogen bond, play an important role in this stability of the structures. Furthermore, the pharmacophoric features of the investigated molecules were determined.The aim of the work is to deeply investigate the binding properties of the title drugs with DNA.

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2021

Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etki gösteren Cyclo(Tyr-Tyr) d... more Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etki gösteren Cyclo(Tyr-Tyr) dipeptidinin olası en kararlı yedi konformasyonu tirozin aminoasitlerinin χ yan zincir dihedral açılarına bağlı olarak konformasyon analizi yapılarak belirlenmiştir. Konformasyon analizi sonrasında belirlenen konformasyonlara ait geometrik yapılar, yan zincire ait dihedral açıdaki değişimler ve konformerlerin toplam ve bağıl enerjileri ile bu konformasyonların toplam enerjilerine katkı sağlayan van der Waals, elektrostatik, torsiyon enerji katkıları ayrı ayrı hesaplanmıştır. Konformasyon analizi ile belirlenen en kararlı konformer, Gaussian03 programı kullanılarak, DFT (Density Functional Teory), B3LYP fonksiyoneli ve 6-31++G(d,p) baz seti ile optimize edilmiş ve optimize yapının temel titreşim dalga sayıları aynı teori düzeyinde hesaplanmıştır. Ayrıca, IR şiddetleri, Raman aktiviteleri, potansiyel enerji dağılımları MOLVIB programı kullanılarak saptanmış, Simirra programı ile ölçeklendirilmiş Raman aktiviteleri, Raman şiddetlerine dönüştürülmüştür. Ek olarak bu dipeptidin dimerik formu oluşturulmuş ve DFT/B3LYP/6-31G(d,p) teori düzeyinde optimize edilerek halka yapıya ait w, φ, Ψ dihedral açıları monomer form ile karşılaştırmalı olarak verilmiştir. Dimerik yapının oluşumunda rol oynayan moleküller arası hidrojen bağları belirlenmiştir.

Журнал технической физики, 2020

People have started to look for alternative sources because of the health problems created by pet... more People have started to look for alternative sources because of the health problems created by petrochemical products used in all areas of human life and environmental problems that remain intact in nature for years. In this study, molecular structure analysis of cellulose triacetate II (CTA II) molecule, obtained from cellulose II and acetate, was carried out. There is an important relationship between the structure and activity of molecules, so it is very important to determine the geometric structure of a molecule. Therefore, using density functional theory (DFT) the most stable molecular geometries of the cellulose triacetate II monomer (C12H18O9) as well as dimer (C24H36O18), which included intermolecular H-bonding, were calculated. The analogous calculations were carried out for the (CTA-II)2 nano-cluster (C24H34O17), which represents the local structure of CTA-II crystal, and created by binding the two most stable CTA II molecules by covalent bond. Scaled wavenumbers and poten...

Journal of Biomolecular Structure and Dynamics, 2019

A new anthraquinone [1-(2-Aminoethyl)piperazinyl-9,10-dioxo-anthraquinone], derivative was synthe... more A new anthraquinone [1-(2-Aminoethyl)piperazinyl-9,10-dioxo-anthraquinone], derivative was synthesized and characterized by DFT calculations, experimental and theoretical vibrational spectroscopy and NMR techniques. The most stable molecular structure of the title molecule was determined by Density Functional Theory (DFT) B3LYP method with 6-31++G(d,p) and 6-311++G(d,p) basis sets. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of the investigated molecule were calculated and compared with the experimental vibrational spectra. The vibrational assignment of the molecule was done using the potential energy distribution analysis. The molecular electrostatic potential (MEP), HOMO and LUMO orbitals were also calculated. The antibacterial activities of the new antraquinone derivative against gram positive and gram-negative bacteria was determined and it was shown that the highest effectiveness was against S. aureus and S. epidermidis while no activity against gram-negative bacteria. Moreover the antimycotic activity of the title compound was examined and the cytotoxicity of anthraquinone derivate was determined. In order to find the possible inhibitory activity of the title compound, molecular docking of the molecule was carried out against DNA. The results A c c e p t e d M a n u s c r i p t indicated that the mentioned compound has a good binding affinity to interact with the DC3, DG4, DA5, DC21 and DC23 residues of DNA via the intermolecular hydrogen bonds.

Journal of biomolecular structure & dynamics, Jan 26, 2016

In this study conformational behavior, structural and vibrational characterisation of the carboxy... more In this study conformational behavior, structural and vibrational characterisation 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 by 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 -0.78 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 dens...

Asian Journal of Chemistry, 2015

Primidone is a white crystalline substance with a molecular weight 218.28. It is an anticonvulsan... more Primidone is a white crystalline substance with a molecular weight 218.28. It is an anticonvulsant, used mainly to treat generalized tonic-clonic seizures. It is also occasionally used in treatment of neuropathic pain, trigeminal neuralgia and migraine. Bogue and Carrington synthesized primidone in 1949 and Handley and Stewart reported the first trial at David Lewis Epileptic Colony 1-4. Primidone is a proper substance in monotherapy or adjunctive therapy for the management of generalized tonic-clonic, psychomotor epilepsy and focal seizures in both adults and children. In addition to these, primidone is used for the control of Jacksonian seizures, mycoclonic jerks and akinetic attacks 5. In this study we report results of DFT/B3LYP/6-31++G(d,p) level of theory calculations on primidone molecule. The aim of this study is to show nonlinear optical activity, the dipole moment, linear polarizability and first-order hyperpolarizability of the monomeric and dimeric structures of primidone. COMPUTATIONAL METHODS The non-linear optical activity of pyrimidone the dipole moment (µ), linear polarizability (α) and first-order hyperpolarizability (β0) of the monomer and dimers of primidone

Vibrational Spectroscopy, 2008

The molecular structure, vibrational frequencies and the corresponding vibrational assignment of ... more The molecular structure, vibrational frequencies and the corresponding vibrational assignment of Zn(biq)X 2 (X = Cl and Br; biq = 2,2 0biquinoline) have been studied by employing the hybrid density functional theory (B3LYP) method and the complete basis set (DFT) method together with the 6-31G(d,p) basis set for X = Cl and Br. The FT-IR (400-4000 cm À1) and Raman (100-3200 cm À1) spectra of compounds were recorded and compared with that of the calculated spectra, which allowed authors to assign most of the observed bands. It was demonstrated that cis conformer is suitable for the Zn(biq)X 2 compounds. The fundamental vibrational modes were characterized by their total energy distribution. The coordination effects on vibrational wavenumbers of biq were discussed in detail.

Journal of Structural Chemistry, 2005

The vibrational wavenumbers and the fundamental modes of 2,2′-biquinoline were obtained by densit... more The vibrational wavenumbers and the fundamental modes of 2,2′-biquinoline were obtained by density functional theory (DFT) with the B3LYP functional using the 6-31G(d,p) basis set. The calculated wavenumbers were scaled by a single factor of 0.965 to correct them for vibrational anharmonicity, but the force constants were overestimated. Normal coordinate analysis of the molecule was also carried out by using the force field of the quinoline molecule and the force field parameters of quinoline are shown to be transferable to 2,2′-biquinoline. The potential energy distribution associated with the normal modes is also given. The theoretical wavenumbers are found to be in good agreement with the experimental data.

Journal of Molecular Structure, 1997

FTIR spectroscopy has been employed in order to investigate α-tocopherol (α-T) and α-tocopheryl a... more FTIR spectroscopy has been employed in order to investigate α-tocopherol (α-T) and α-tocopheryl acetate (α-TA) induced effects on the molecular organization of dimyristoyl-l-α-phosphatidylcholine (DMPC) bilayers, at various temperatures and concentrations. It was concluded that α-T interacts much more strongly than α-TA, indicating that α-T has a more polar location in the membrane than α-TA. The observed changes in the carbonyl and phosphate group vibrational modes of DMPC on addition of α-T or α-TA are discussed

Journal of Molecular Structure, 2007

ABSTRACT In this study the molecular structure and vibrational spectra of Zn(2,2′-bipyridine)X2 (... more ABSTRACT In this study the molecular structure and vibrational spectra of Zn(2,2′-bipyridine)X2 (X=Cl and Br) complexes were studied in their ground states by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimization, vibrational wavenumber and intensity calculations of free and coordinated 2,2′-bipyridine were carried out with the Gaussian03 program package by using Hartree–Fock (HF) and Density Functional Theory (DFT) with B3LYP functional and 6-31G (d,p) basis set. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Fundamentals were characterised by their total energy distributions. Coordination sensitive modes of 2,2′-bipyridine were determined.

Journal of Molecular Structure, 2009

Combined experimental and computational vibrational spectra of 5-aminoquinoline (5-AQ) and its zi... more Combined experimental and computational vibrational spectra of 5-aminoquinoline (5-AQ) and its zinc chloride complex {Zn(5-AQ) 2 Cl 2 }, together with the computational results of 5-AQ interacting with H 2 O through the ring nitrogen {5-AQÁH 2 O} have been reported. The geometry of the free 5-AQ were optimized using DFT method at B3LYP/6-31G(d,p) and 6-31++G(d,p) levels of theory. Coordinated 5-AQ molecules; {5-AQÁH 2 O} and {Zn(5-AQ) 2 Cl 2 } were optimized using DFT/B3LYP/6-31G(d,p) level of theory. Harmonic and anharmonic vibrational frequencies and infrared intensities were calculated at the same level of theory. The fundamental vibrational modes were characterised depending on their total energy distribution (TED%). Coordination effects on 5-AQ vibrational frequencies were investigated.

Journal of Biomolecular Structure and Dynamics, 2014

Primidone (Mysoline), with the chemical formula 5-ethyl-5-phenyl-hexahydropyrimidine- 4,6-dione (... more 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.

Applied Clay Science, 2017

In this study, the adsorption of 5-Chlorouracil (5-ClU) on natural montmorillonite from Anatolia ... more In this study, the adsorption of 5-Chlorouracil (5-ClU) on natural montmorillonite from Anatolia was investigated using FT-IR and Raman spectroscopy. The 5-ClU is a thymine antagonist and has some antitumor properties. The comparison of the vibrational spectra of the adsorbed 5-ClU with those of the free molecule provided data on the nature and characteristics of the clay organic complexes. The intercalation of 5-ClU within montmorillonite has been shown by X-ray diffraction to increase the interlayer spacing. Vibrational spectroscopy indicates that adsorbed 5-ClU molecules on montmorillonite are coordinated to exchangeable cations, directly or indirectly through water bridges.

High resolution Raman spectra of GeSe 2 glass were measured and fitted using individual component... more High resolution Raman spectra of GeSe 2 glass were measured and fitted using individual components. The structural origin of the components were interpreted using the results of ab initio DFT calculations which were performed on Ge n Se m nanoclusters (n=2-6,12; m=6-9,12,14-16,30) that represent the local structure of GeSe 2 glass and on some "defect" Ge n Se m clusters that are thought to be related to the inhomogeneity of the structure at the nanoscale. The calculated vibrational properties of Ge n Se m nanoclusters and their couplings with the local and medium range order structure formations in GeSe 2 glass are analysed and discussed.

All possible conformations of Cyclo (Arg-Gly-Asp-D-Phe-Val) (C26H38N8O7) with antitumor activity ... more All possible conformations of Cyclo (Arg-Gly-Asp-D-Phe-Val) (C26H38N8O7) with antitumor activity were determined and the most stable conformer elucidated by MMFF method using the Spartan06 program. The differences in energy between the conformers were determined, and the low energy conformers, which are required for determination of the biological activity, were characterized. Since as an anticancer candidate, the investigated molecule is expected to be an integrin inhibitor, a molecular docking study was conducted with αvβ3 integrin to determine the mechanism of interaction. As a result of docking simulations, the binding affinity (G =-10.5 kcal/mol) and the interactions between the investigated peptide and target integrin were determined.

Open Journal of Nano

Acalabrutinib is an inhibitor of Bruton's tyrosine kinase (BTK) activity and prevents the activat... more Acalabrutinib is an inhibitor of Bruton's tyrosine kinase (BTK) activity and prevents the activation of the B-cell antigen receptor (BCR) signaling pathway. For having these properties acalabrutinib recently was approved for medical use as an anticancer drug. Determining the conformational properties of a bioactive molecule is necessary to reveal its bioactivity. For this reason, the conformational states of the acalabrutinib were examined first. The AM1, a semiexperimental method, was used to examine the stable conformations of the acalabrutinib molecule. Nine lowest energy conformers of the acalabrutinib molecule were determined and their relative energies were calculated. Afterwards, the interactions of the most stable conformer of acalabrutinib with DNA and integrin were examined by docking simulations, and the most active interaction sites and binding affinities were determined.

Current Computer - Aided Drug Design, Mar 31, 2020

Background: Sulpiride, which has selective dopaminergic blocking activity, is a substituted benza... more Background: Sulpiride, which has selective dopaminergic blocking activity, is a substituted benzamide antipsychotic drug playing a prominent role in the treatment of schizophrenia, which more selective and primarily blocks dopamine D2 and D3 receptor. Objective: This study has two main objectives, firstly; the molecular modeling studies (MD and Docking, ADME) were conducted to define the molecular profile of sulpiride and sulpiridereceptor interactions, another to synthesize polymeric nanoparticles with chitosan, having the advantage of slow/controlled drug release, to improve drug solubility and stability, to enhance utility and reduce toxicity. Method: Molecular dynamic simulation was carried out to determine the conformational change and stability (in water) of the drug and the binding profile of D3 dopamine receptor was determined by molecular docking calculations. The pharmacological properties of the drug were revealed by ADME analysis. The ionic gelation method was used to prepare sulpiride loaded chitosan nanoparticles (CS NPs). The Dynamic Light Scattering (DLS), UV-vis absorption (UV), Scanning Electron Microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy techniques were carried out to characterize the nanoparticles. In vitro cell cytotoxicity experiments examined with MTT assay on mouse fibroblast (L929), human neuroblastoma (SH-SY5Y) and glioblastoma cells (U-87). The statistical evaluations were produced by ANOVA. Results: The residues (ASP-119, PHE-417) of D3 receptor provided a stable docking with the drug, and the important pharmacological values (blood brain barrier, Caco-2 permeability and human oral absorption) were also determined. The average particle size, PdI and zeta potential value of sulpiride- loaded chitosan NPs having a spherical morphology were calculated as 96.93 nm, 0.202 and +7.91 mV. The NPs with 92.8% encapsulation and 28% loading efficiency were found as a slow release profile with 38.49% at the end of the 10th day. Due to the formation of encapsulation, the prominent shifted wave numbers for C-O, S-O, S-N stretching, S-N-H bending of Sulpiride were also identified. Mitochondrial activity of U87, SHSY-5Y and L929 cell line were assayed and evaluated using the SPSS program. Conclusion: To provide more efficient use of Sulpiride having a low bioavailability of the gastrointestinal tract, the nanoparticle formulation with high solubility and bioavailability was designed and synthesized for the first time in this study for the treatment of schizophrenia. In addition to all pharmacological properties of drug, the dopamine blocking activity was also revealed. The toxic effect on different cell lines have also been interpreted.

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2021

In this study, the lowest energy molecular structures were determined by conformational analysis ... more In this study, the lowest energy molecular structures were determined by conformational analysis of six drugs commonly used in cancer treatment, in order to use as initial data for docking simulations. Using the AutoDock Vina software, the interaction mechanisms of the 6 FDA approved drugs (Pemetrexed, Irinotecan, Tamoxifen, Gemcitabine, Topotecan and Temozolomide) with DNA were investigated. In addition, MM/PB(GB)SA calculations for the drug-DNA structures under investigation have been performed. The calculated binding affinities and binding free energies of interactions were showed the stability of the structures. It has been found that the active site where these molecules interact with DNA is the same and that their various interactions, primarily hydrogen bond, play an important role in this stability of the structures. Furthermore, the pharmacophoric features of the investigated molecules were determined.The aim of the work is to deeply investigate the binding properties of the title drugs with DNA.

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2021

Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etki gösteren Cyclo(Tyr-Tyr) d... more Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etki gösteren Cyclo(Tyr-Tyr) dipeptidinin olası en kararlı yedi konformasyonu tirozin aminoasitlerinin χ yan zincir dihedral açılarına bağlı olarak konformasyon analizi yapılarak belirlenmiştir. Konformasyon analizi sonrasında belirlenen konformasyonlara ait geometrik yapılar, yan zincire ait dihedral açıdaki değişimler ve konformerlerin toplam ve bağıl enerjileri ile bu konformasyonların toplam enerjilerine katkı sağlayan van der Waals, elektrostatik, torsiyon enerji katkıları ayrı ayrı hesaplanmıştır. Konformasyon analizi ile belirlenen en kararlı konformer, Gaussian03 programı kullanılarak, DFT (Density Functional Teory), B3LYP fonksiyoneli ve 6-31++G(d,p) baz seti ile optimize edilmiş ve optimize yapının temel titreşim dalga sayıları aynı teori düzeyinde hesaplanmıştır. Ayrıca, IR şiddetleri, Raman aktiviteleri, potansiyel enerji dağılımları MOLVIB programı kullanılarak saptanmış, Simirra programı ile ölçeklendirilmiş Raman aktiviteleri, Raman şiddetlerine dönüştürülmüştür. Ek olarak bu dipeptidin dimerik formu oluşturulmuş ve DFT/B3LYP/6-31G(d,p) teori düzeyinde optimize edilerek halka yapıya ait w, φ, Ψ dihedral açıları monomer form ile karşılaştırmalı olarak verilmiştir. Dimerik yapının oluşumunda rol oynayan moleküller arası hidrojen bağları belirlenmiştir.

Журнал технической физики, 2020

People have started to look for alternative sources because of the health problems created by pet... more People have started to look for alternative sources because of the health problems created by petrochemical products used in all areas of human life and environmental problems that remain intact in nature for years. In this study, molecular structure analysis of cellulose triacetate II (CTA II) molecule, obtained from cellulose II and acetate, was carried out. There is an important relationship between the structure and activity of molecules, so it is very important to determine the geometric structure of a molecule. Therefore, using density functional theory (DFT) the most stable molecular geometries of the cellulose triacetate II monomer (C12H18O9) as well as dimer (C24H36O18), which included intermolecular H-bonding, were calculated. The analogous calculations were carried out for the (CTA-II)2 nano-cluster (C24H34O17), which represents the local structure of CTA-II crystal, and created by binding the two most stable CTA II molecules by covalent bond. Scaled wavenumbers and poten...

Journal of Biomolecular Structure and Dynamics, 2019

A new anthraquinone [1-(2-Aminoethyl)piperazinyl-9,10-dioxo-anthraquinone], derivative was synthe... more A new anthraquinone [1-(2-Aminoethyl)piperazinyl-9,10-dioxo-anthraquinone], derivative was synthesized and characterized by DFT calculations, experimental and theoretical vibrational spectroscopy and NMR techniques. The most stable molecular structure of the title molecule was determined by Density Functional Theory (DFT) B3LYP method with 6-31++G(d,p) and 6-311++G(d,p) basis sets. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of the investigated molecule were calculated and compared with the experimental vibrational spectra. The vibrational assignment of the molecule was done using the potential energy distribution analysis. The molecular electrostatic potential (MEP), HOMO and LUMO orbitals were also calculated. The antibacterial activities of the new antraquinone derivative against gram positive and gram-negative bacteria was determined and it was shown that the highest effectiveness was against S. aureus and S. epidermidis while no activity against gram-negative bacteria. Moreover the antimycotic activity of the title compound was examined and the cytotoxicity of anthraquinone derivate was determined. In order to find the possible inhibitory activity of the title compound, molecular docking of the molecule was carried out against DNA. The results A c c e p t e d M a n u s c r i p t indicated that the mentioned compound has a good binding affinity to interact with the DC3, DG4, DA5, DC21 and DC23 residues of DNA via the intermolecular hydrogen bonds.

Journal of biomolecular structure & dynamics, Jan 26, 2016

In this study conformational behavior, structural and vibrational characterisation of the carboxy... more In this study conformational behavior, structural and vibrational characterisation 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 by 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 -0.78 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 dens...

Asian Journal of Chemistry, 2015

Primidone is a white crystalline substance with a molecular weight 218.28. It is an anticonvulsan... more Primidone is a white crystalline substance with a molecular weight 218.28. It is an anticonvulsant, used mainly to treat generalized tonic-clonic seizures. It is also occasionally used in treatment of neuropathic pain, trigeminal neuralgia and migraine. Bogue and Carrington synthesized primidone in 1949 and Handley and Stewart reported the first trial at David Lewis Epileptic Colony 1-4. Primidone is a proper substance in monotherapy or adjunctive therapy for the management of generalized tonic-clonic, psychomotor epilepsy and focal seizures in both adults and children. In addition to these, primidone is used for the control of Jacksonian seizures, mycoclonic jerks and akinetic attacks 5. In this study we report results of DFT/B3LYP/6-31++G(d,p) level of theory calculations on primidone molecule. The aim of this study is to show nonlinear optical activity, the dipole moment, linear polarizability and first-order hyperpolarizability of the monomeric and dimeric structures of primidone. COMPUTATIONAL METHODS The non-linear optical activity of pyrimidone the dipole moment (µ), linear polarizability (α) and first-order hyperpolarizability (β0) of the monomer and dimers of primidone

Vibrational Spectroscopy, 2008

The molecular structure, vibrational frequencies and the corresponding vibrational assignment of ... more The molecular structure, vibrational frequencies and the corresponding vibrational assignment of Zn(biq)X 2 (X = Cl and Br; biq = 2,2 0biquinoline) have been studied by employing the hybrid density functional theory (B3LYP) method and the complete basis set (DFT) method together with the 6-31G(d,p) basis set for X = Cl and Br. The FT-IR (400-4000 cm À1) and Raman (100-3200 cm À1) spectra of compounds were recorded and compared with that of the calculated spectra, which allowed authors to assign most of the observed bands. It was demonstrated that cis conformer is suitable for the Zn(biq)X 2 compounds. The fundamental vibrational modes were characterized by their total energy distribution. The coordination effects on vibrational wavenumbers of biq were discussed in detail.

Journal of Structural Chemistry, 2005

The vibrational wavenumbers and the fundamental modes of 2,2′-biquinoline were obtained by densit... more The vibrational wavenumbers and the fundamental modes of 2,2′-biquinoline were obtained by density functional theory (DFT) with the B3LYP functional using the 6-31G(d,p) basis set. The calculated wavenumbers were scaled by a single factor of 0.965 to correct them for vibrational anharmonicity, but the force constants were overestimated. Normal coordinate analysis of the molecule was also carried out by using the force field of the quinoline molecule and the force field parameters of quinoline are shown to be transferable to 2,2′-biquinoline. The potential energy distribution associated with the normal modes is also given. The theoretical wavenumbers are found to be in good agreement with the experimental data.

Journal of Molecular Structure, 1997

FTIR spectroscopy has been employed in order to investigate α-tocopherol (α-T) and α-tocopheryl a... more FTIR spectroscopy has been employed in order to investigate α-tocopherol (α-T) and α-tocopheryl acetate (α-TA) induced effects on the molecular organization of dimyristoyl-l-α-phosphatidylcholine (DMPC) bilayers, at various temperatures and concentrations. It was concluded that α-T interacts much more strongly than α-TA, indicating that α-T has a more polar location in the membrane than α-TA. The observed changes in the carbonyl and phosphate group vibrational modes of DMPC on addition of α-T or α-TA are discussed

Journal of Molecular Structure, 2007

ABSTRACT In this study the molecular structure and vibrational spectra of Zn(2,2′-bipyridine)X2 (... more ABSTRACT In this study the molecular structure and vibrational spectra of Zn(2,2′-bipyridine)X2 (X=Cl and Br) complexes were studied in their ground states by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimization, vibrational wavenumber and intensity calculations of free and coordinated 2,2′-bipyridine were carried out with the Gaussian03 program package by using Hartree–Fock (HF) and Density Functional Theory (DFT) with B3LYP functional and 6-31G (d,p) basis set. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Fundamentals were characterised by their total energy distributions. Coordination sensitive modes of 2,2′-bipyridine were determined.

Journal of Molecular Structure, 2009

Combined experimental and computational vibrational spectra of 5-aminoquinoline (5-AQ) and its zi... more Combined experimental and computational vibrational spectra of 5-aminoquinoline (5-AQ) and its zinc chloride complex {Zn(5-AQ) 2 Cl 2 }, together with the computational results of 5-AQ interacting with H 2 O through the ring nitrogen {5-AQÁH 2 O} have been reported. The geometry of the free 5-AQ were optimized using DFT method at B3LYP/6-31G(d,p) and 6-31++G(d,p) levels of theory. Coordinated 5-AQ molecules; {5-AQÁH 2 O} and {Zn(5-AQ) 2 Cl 2 } were optimized using DFT/B3LYP/6-31G(d,p) level of theory. Harmonic and anharmonic vibrational frequencies and infrared intensities were calculated at the same level of theory. The fundamental vibrational modes were characterised depending on their total energy distribution (TED%). Coordination effects on 5-AQ vibrational frequencies were investigated.

Journal of Biomolecular Structure and Dynamics, 2014

Primidone (Mysoline), with the chemical formula 5-ethyl-5-phenyl-hexahydropyrimidine- 4,6-dione (... more 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.

Applied Clay Science, 2017

In this study, the adsorption of 5-Chlorouracil (5-ClU) on natural montmorillonite from Anatolia ... more In this study, the adsorption of 5-Chlorouracil (5-ClU) on natural montmorillonite from Anatolia was investigated using FT-IR and Raman spectroscopy. The 5-ClU is a thymine antagonist and has some antitumor properties. The comparison of the vibrational spectra of the adsorbed 5-ClU with those of the free molecule provided data on the nature and characteristics of the clay organic complexes. The intercalation of 5-ClU within montmorillonite has been shown by X-ray diffraction to increase the interlayer spacing. Vibrational spectroscopy indicates that adsorbed 5-ClU molecules on montmorillonite are coordinated to exchangeable cations, directly or indirectly through water bridges.

High resolution Raman spectra of GeSe 2 glass were measured and fitted using individual component... more High resolution Raman spectra of GeSe 2 glass were measured and fitted using individual components. The structural origin of the components were interpreted using the results of ab initio DFT calculations which were performed on Ge n Se m nanoclusters (n=2-6,12; m=6-9,12,14-16,30) that represent the local structure of GeSe 2 glass and on some "defect" Ge n Se m clusters that are thought to be related to the inhomogeneity of the structure at the nanoscale. The calculated vibrational properties of Ge n Se m nanoclusters and their couplings with the local and medium range order structure formations in GeSe 2 glass are analysed and discussed.