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Öğe 1-Formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline: Synthesis, characterization, antimicrobial activity and DFT studies(Elsevier Science Bv, 2016) Sid, Assia; Messai, Amel; Parlak, Cemal; Kazanci, Nadide; Luneau, Dominique; Kesan, Gurkan; Rhyman, Lydia; Alswaidan, Ibrahim A.; Ramasami, PonnaduraiThe structure of 1-formy1-3-phenyl-5-(4-isopropylpheny1)-2-pyrazoline synthesized as single crystal was investigated by FTIR, NMR, XRD. Experimental data were complemented by quantum mechanical calculations. XRD data show that the compound crystallizes in the triclinic system (P-1) via trans isomer (a = 6.4267(4) angstrom, b = 10.9259(12) angstrom, c = 12.4628(9) angstrom and alpha = 102.894(8)degrees, beta = 102.535(6)degrees, gamma = 101.633(7)degrees). Anti-microbial screening results indicate that the compound shows promising activity. The theoretically predicted and experimentally obtained parameters reveal further insight into pyrazoline systems. (C) 2016 Elsevier B.V. All rights reserved.Öğe 2-halojen-4-klorobenzaldehitlerin yapısal titreşim ve elektronik özellikleri üzerine halojen ve çözücü etkilerinin incelenmesi(Ege Üniversitesi, 2020) Parlak, CemalBiyolojik ve farmasötik bilim alanlarında yaygın kullanıma sahip olan benzaldehit türevlerinden 2-halojen-4-klorobenzaldehit (Halojen = Flor (FCB), Cl (CCB) ve Br (BCB)) moleküllerinin yapısal, titreşim ve elektronik özellikleri araştırılarak, bu özellikler üzerindeki halojen atom ve çözücü etkileri incelenmektedir. Sunulan proje kapsamında moleküllerin gaz fazı konformasyon analizleri için ilgili Schrödinger denklemleri Hartree-Fock (HF), Møller-Plesset 2 (MP2) ve yoğunluk fonksiyonel teorisi (YFT) metotlarından Becke, üç-parameter, Lee-Yang-Parr (B3LYP) yöntemleri ele alınarak ve aug-cc-pVDZ baz seti kullanılarak çözülmektedir. Çözücü ortamındaki hesaplamalar ve zamana bağlı Schrödinger denklemleri için farklı çözücüler, B3LYP fonksiyoneli, 6-31G(d, p) baz seti ve polarize süreklilik modeli kullanılmaktadır. Konformasyonel tercih, geometrik parametreler gibi yapısal özellikler, dipol moment, karbonil gerilme frekansı gibi titreşim özellikleri ve bant aralığı, moleküler sınır orbitalleri, uyarılmış durumlar gibi elektronik özellikler ele alınmaktadır. Ayrıca, Kirkwood-Bauer-Magat, akseptör sayısı, Swain parametreleri ve lineer çözünme enerji ilişkisi gibi bazı çözücü modelleri ile karbonil gerilme frekansları incelenmektedir. Deneysel çalışmalar IR ve UV spektroskopileri ile yürütülmektedir. Proje kapsamında elde edilen tüm deneysel ve teorik bulgular iki halojen atomlu benzaldehitlerin konformasyonları, kullanım alanları ve amaçları ile ilgili yapılacak çalışmalar için yararlı ve yönlendirici olacaktır.;Yoğunluk Fonksiyonel Teorisi, Çözücü Modelleri, Benzaldehit Türevleri, IR, UV, Bant Aralığı.;Density Functional Theory, Solvent Models, Benzaldehyde Derivatives, IR, UV, Band Gap.Öğe Absorption mechanism, structural and electronic properties of MC19 (M = B and Si) fullerenes with 1-acetylpiperazine(Sage Publications Inc, 2018) Alver, Ozgur; Parlak, Cemal; Elzagheid, Mohamed I.; Ramasami, PonnaduraiThe interaction mechanisms of undoped, silicon- and boron-doped C20 fullerenes and 1-acetylpiperazine (1-ap) were investigated. Stability, electronic properties, influence of water on the solubility and stability, molecular parameters, descriptive vibrational bands and nuclear magnetic resonance shielding values are reported. The quantum mechanical calculations were carried out using the M06-2X functional and the 6-31G(d) basis set. It is observed that all the complexes are more stabilized in water compared to the gas phase. The most stable complex was found as silicon-doped fullerene interacting with the carbonyl edge of 1-ap releasing energy of 64.13kcal/mol in water.Öğe Adsorption mechanism, structural and electronic properties: 4-Phenylpyridine & undoped or doped (B or Si) C60(Elsevier Science Bv, 2017) Gokpek, Yenal; Bilge, Metin; Bilge, Duygu; Alver, Ozgur; Parlak, CemalInteraction mechanisms of fullerene derivatives and various types of molecules have been paid increasing attention. In this research, interaction mechanism, structural and electronic properties, natural bond orbital (NBO) analyses of 4-Phenylpyridine (4-phpy) interacted undoped or doped (B or Si) C60 fullerenes were examined based on quantum mechanical calculations. Bond order and binding energy results suggest a possible chemisorption between nitrogen atom of 4-phpy and boron or silicon atoms of doped fullerene cages and the examined B or Si-doped complexes yielded with higher binding energies in water media calculations. Results also show that unlike C60...4-phpy indicating a very weak binding energy, B or Si doped C60 fullerenes can be used to carry 4-phpy molecule for various purposes including drug delivery systems. (C) 2017 Elsevier B.V. All rights reserved.Öğe Adsorption Mechanisms of 6-Chloro-3-Hydroxy-2-Pyrazinecarboxamide on Pristine, Si- and Al-Doped C-60 Fullerenes: A DFT Study(Springer/Plenum Publishers, 2017) Parlak, Cemal; Alver, Ozgur; Ramasami, PonnaduraiFullerenes have been of research interest and they have been particularly studied for their possible applications as drug delivery vehicles. In the present research, the optimized molecular geometries, electronic properties and the possible interaction mechanisms between C-60, Si- or Al-doped C-60 and 6-chloro-3-hydroxy-2-pyrazinecarboxamide were investigated using quantum mechanical calculations. The calculated binding energies to the Si- and Al-doped fullerenes suggest that doping of fullerene nanocage enhances the interaction mechanism and alters the chemical and electronic properties. The results and parameters found in this research reveal further insight into drug delivery systems.Öğe Adsorption of ibuprofen on silicon decorated fullerenes and single walled carbon nanotubes: A comparative DFT study(Elsevier Science Bv, 2019) Parlak, Cemal; Alver, OzgurIbuprofen (IBP) is known as a widely prescribed drug for its non-steroidal, anti-inflammatory, analgesic, and antipyretic effects. Carbon nanotubes and fullerenes are the novel elements of drug delivery and sensor applications. In this work using M062X and B3LYP functionals with 6-31G(d) basis set, adsorption energies, possible sensor applications or sensitivity of single walled carbon nanotube (SWCNT) and fullerene C-60 to IBP along with some electronic properties including conductivity, gap energies of frontier orbitals and natural bond orbital (NBO) analyses were reported in comparison. It was found that SiC59 is more strongly interacts with IBP and electronic sensitivity of it higher than that of Si@SWCNT system. (C) 2019 Elsevier B.V. All rights reserved.Öğe Assessing a double silicon decorated fullerene for the delivery of interacting flurbiprofen and salicylic acid drugs: A DFT approach(Elsevier, 2023) Catal, Esin; Baglayan, Ozge; Koroglu, Ahmet; Parlak, Cemal; Alver, OzgurSince the number of drugs increases constantly, drug interactions appear as a critical issue to handle. The effective use of multiple drugs appears as another important subject to discuss and the use of targeted and se-lective delivery of drugs is becoming more important. Impurity doped C60 fullerenes with various dopant atoms such as silicon or boron appear as promising drug delivery vehicles. Therefore, in the framework of this study, we investigated the interaction between salicylic acid and flurbiprofen and their controlled delivery by using double silicon decorated C60 fullerene using density functional theory. Stability and reactivity considerations were also examined by investigating some important structural parameters, interaction energies and frontier molecular orbitals. The interactions were also monitored by examining important diagnostic vibrational bands. The strength of the interactions between atoms at the interaction sites was also identified by using the quantum theory of atoms in molecules.Öğe Atmospheric reaction of chlorine radical and cyclic amide: A theoretical approach(Elsevier, 2024) Samai, Salima; Ferhati, Azedine; Direm, Amani; Parlak, CemalThe atmosphere is considered a chemical reactor where many chemical reactions occur. Theoretical investigations are useful for understanding the mechanisms involved in the reaction with atmospheric radicals. Density functional theory (DFT) with B3LYP, CBS-QB3 and G3B3 methods were used to investigate the reactivity, mechanism and structure-reactivity relationship as well as the kinetics of N-methyl-2-pyrrolidinone (NMP) reaction with chlorine. Furthermore, the Rice-Ramsperger-Kassel-Marcus (RRKM) theory was employed to compute the rate constants. This study provides rate coefficients and a detailed H -abstraction mechanism for the reaction of chlorine with NMP. Kinetic and mechanistic results showed that the mechanism of this reaction goes with small barriers through H -atom transfer from the -N-CH3 group and -CH2- adjacent to the -N-CH3 site within a branching ratio slightly in favour of the -N-CH3 site.Öğe B, Al and Si doping of fullerene-C60 and the limits of selective drug delivery assessments of ifosfamide: A DFT approach(Elsevier, 2024) Kolsuz, Demet; Baglayan, Ozge; Parlak, Cemal; Alver, OzgurSelective drug delivery studies using fullerene-based systems have become an important research field. In the framework of this study, theoretical calculations based on the density functional theory, and the controlled and selective delivery trials of boron, silicon and aluminium decorated fullerene-C60 were investigated. The structural and reactivity properties along with some important diagnostic vibrational bands of triple doped fullerene-C60 and its interacted form with the ifosfamide drug molecule were examined. It was observed that by decorating the surface of C60 with B, Si and Al dopants, it is possible to produce controlled drug delivery carries with fullereneC60 nano cages.Öğe Bazı fiziksel kavramların ekonomiye uygulanması(Ege Üniversitesi, 2018) Parlak, CemalEkonomide finansal piyasalar ve kurumlar fonları tasarruf sahiplerinden yatırım yapanlara aktarmada çok önemli bir rol oynarlar. Tasarruflarını finansal piyasalarda değerlendirmek isteyen yatırımcılar ise riske maruz kalırlar. Finansal piyasalardaki hareketleri modellemek için birçok teknik geliştirilmiştir. İktisadi sistemler büyük miktarda sayısal verinin olduğu ve birbiriyle etkileşim içindeki kompleks sistemlerdir. Aynı şekilde birbirine bağımlı çok değişken içeren sistemleri ve o sistemin dinamikleri hakkında sonuçlara ulaşma çalışmaları da termodinamik olarak değerlendirilmektedir. Termodinamiğin temel ve direk uygulamaları fabrikalar, nükleer santraller, diğer enerji üretim ve tüketim sistemleri, makro ve mikro ölçekli kimyasal reaksiyonlar olup, daha pek çok gündelik olaylarla hayatımıza girmiştir. Esasen modern termodinamiğin kökeni ise istatistiksel fiziktir. Bu projede ekonomi ve fizik arasındaki ilişkiyi anlamak için öncelikle fizikte kullanılan nicelik ve terimlerin finans piyasasındaki karşılıkları incelenmekte ve yenileri türetilmektedir. Daha sonra, ilk kez Maxwell – Boltzmann dağılımı ile tiftik, yumurta ve bal için uygulamalar yapılmaktadır.Öğe Bazı fiziksel kavramların ekonomiye uygulanması(Ege Üniversitesi, 2018) Parlak, CemalEkonomide finansal piyasalar ve kurumlar fonları tasarruf sahiplerinden yatırım yapanlara aktarmada çok önemli bir rol oynarlar. Tasarruflarını finansal piyasalarda değerlendirmek isteyen yatırımcılar ise riske maruz kalırlar. Finansal piyasalardaki hareketleri modellemek için birçok teknik geliştirilmiştir. İktisadi sistemler büyük miktarda sayısal verinin olduğu ve birbiriyle etkileşim içindeki kompleks sistemlerdir. Aynı şekilde birbirine bağımlı çok değişken içeren sistemleri ve o sistemin dinamikleri hakkında sonuçlara ulaşma çalışmaları da termodinamik olarak değerlendirilmektedir. Termodinamiğin temel ve direk uygulamaları fabrikalar, nükleer santraller, diğer enerji üretim ve tüketim sistemleri, makro ve mikro ölçekli kimyasal reaksiyonlar olup, daha pek çok gündelik olaylarla hayatımıza girmiştir. Esasen modern termodinamiğin kökeni ise istatistiksel fiziktir. Bu projede ekonomi ve fizik arasındaki ilişkiyi anlamak için öncelikle fizikte kullanılan nicelik ve terimlerin finans piyasasındaki karşılıkları incelenmekte ve yenileri türetilmektedir. Daha sonra, ilk kez Maxwell - Boltzmann dağılımı ile tiftik, yumurta ve bal için uygulamalar yapılmaktadır.;Fiziksel Kavramlar, İstatistiksel Fizik, Ekonofizik, Termodinamik, Maxwell - Boltzmann dağılımı.;Physical Concepts, Statistical Physics, Econophysics, Thermodynamics, Maxwell - Boltzmann distribution.Öğe Cadmium oxide nanoparticles from new organometallic Cd(II)-Schiff base complex and in vitro biological potentials: dual S. aureus and E. coli DNA gyrase inhibition by the precursors via in silico binding modes' study(Springer, 2024) Ejidike, Ikechukwu P.; Direm, Amani; Parlak, Cemal; Bamigboye, Mercy O.; Oluade, Olajumoke; Adetunji, Juliana B.; Ata, AtharAt the nanoscale level, several biological processes take place, owing to the potential that engineered nanomaterials might interrelate with bio-molecules and cellular procedures. This study aimed to synthesize cadmium oxide nanoparticles via a one-step calcination process of tetradentate Schiff base-Cd(II) complex at different temperature ranges. The as-synthesized compounds were carried out via a viz UV-visible, elemental analysis, H-1 NMR, molar conductivity, transmission electron microscopy (TEM), FT-IR spectroscopy, and X-ray diffraction (PXRD). The band gap energy and average particle sizes of the CdO particles are respectively (2.69 eV, 3.54 eV), 26.88 nm for CdO@250, and (3.20 eV, 3.57 eV), 25.67 nm for CdO@300, while CdO@350 exhibited the 3.78 eV and 28.42 nm values. The antioxidant accomplishments of the test samples through the scavenging activity of DPPH radicals showed CdO@300 to possess (IC50 = 5.18 +/- 0.56 mu g/mL). Similarly, the as-synthesized CdO nanoparticles exhibited higher antibacterial activities against S. aureus and E. coli as compared to the corresponding Cd-HMB and ligand (HMB), while ciprofloxacin acted as a standard antibiotic. Furthermore, HMB and its complex Cd-HMB were docked against the DNA gyrase enzymes of S. aureus (PDB IDs: 5CDQ) and E. coli (PDB IDs: 6F86) as receptors. The binding sites docking results showed that the binding energies of HMB and Cd-HMB to 5CDQ ranged from - 3.44 to - 4.99 kcal/mol and from - 6.45 to - 6.64 kcal/mol, while the binding energies related to the target 6F86 are in the ranges of (- 3.64, - 4.76) kcal/mol and (- 6.08, - 6.09) kcal/mol respectively. Therefore, the significant antioxidant and antibacterial activities of the ligand (HMB), Cd-HMB, and CdO NPs review the broad application prospects of these compounds as therapeutic agents for wide-ranging biomedical applications.Öğe Can the Antivirals Remdesivir and Favipiravir Work Better Jointly? In Silico Insights(Georg Thieme Verlag Kg, 2022) Parlak, Cemal; Alver, Ozgur; Ouma, Cecil N. M.; Rhyman, Lydia; Ramasami, PonnaduraiThe proverb Old is gold is applicable in drug discovery and the proverb All that Glitters is not Gold is also appropriate. In the COVID-19 era, there has been a race for drugs to be effective against SARS-CoV-2. There are reports about the uses of Remdesivir and Favipiravir as existing antivirals against virus but none have been conclusive so far. In the attempts for innovations, the combination of drugs is also undertrials. Therefore, we used the densityfunctional theory method and quantum theory of atoms in moleculesto investigate drug-drug interactions involving Remdesivir and Favipiravir. The computed parameters were related to the antiviral actions of both drugs together. The results indicate enhanced antiviral activity and it will be worthy to consider additional investigations with the combination of these two drugs.Öğe Carbonyl stretching vibrations of 5-halogen-2-thiophenecarboxaldehydes: KBM, AN, SWAIN and LSER parameters(2016) Parlak, Cemal; Alver, Özgür5-halojen-2-tiyofenkarboksaldehitlerin (C5H3XOS; X=F, Cl veya Br) yapısal denge ve karbonil gerilme titreşimleri üzerindeki çözücü ve halojen etkileri yoğunluk fonksiyoneli teorisi ile B3LYP fonksiyoneli, 6-311+G(3df,p) baz seti ve kutuplanabilir süreklilik modeli kullanılarak incelendi. Hesaplamalar on sekiz farklı çözücü içinde moleküllerin cis ve trans konformasyonları ele alınarak yürütüldü. Çözücü içindeki karbonil gerilme titreşim frekansları Kirkwood-Bauer-Magat denklemi, çözücü akseptör sayısı, Swain parametreleri ve lineer çözünme enerji ilişkisi gibi çözücü skalaları ile incelendi. Bu çalışmanın sonuçları tiyofen-karboksaldehit türevleri için faydalı olacaktır.Öğe Carbonyl stretching vibrations of 5-halogen-2-thiophenecarboxaldehydes: KBM, AN, SWAIN and LSER parameters(Pamukkale Univ, 2016) Parlak, Cemal; Alver, OzgurHalogen and solvent influence on the conformational stability and carbonyl stretching vibration of 5-Halogeno-2-thiophene-carboxaldehydes (C5H3XOS; X=F, Cl or Br) were investigated by the density functional theory using the B3LYP functional, 6-311+G(3df,p) basis set and polarizable continuum model. Calculations were performed by the cis and trans forms of the compounds in eighteen different solvents. The carbonyl stretching frequencies were correlated with some solvent parameters such as the Kirkwood-Bauer-Magat equation, the solvent acceptor number, Swain parameters and the linear solvation energy relationships. The findings of this research will be useful for thiophenecarboxaldehydes.Öğe A comparative DFT study of tetracyanoquinodimethane and its difluoro and tetrafluoro analogs(Elsevier, 2021) Umar, Yunusa; Parlak, Cemal; Haque, S. K. Manirul; Appu, Sreekumar P.; Ashwaq, Omar; Ramasami, PonnaduraiThe optimized molecular structures, harmonic vibrational wavenumbers and corresponding vibrational assignments, frontier molecular orbitals and UV data of 7,7,8,8-tetracyanoquinodimethane, 2,5-difluoro-7,7,8,8-tetracyanoquinodimethane and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane were computed using quantum mechanical code. Calculations were carried out at Becke-3-Lee-Yang-Parr (B3LYP) functional with density functional theory (DFT) and time-dependent density functional theory (TD-DFT) using the 6-311++G (d,p) basis set. The theoretical results were successfully compared with some of the available experimental data. The influence of fluorine on the structural, vibrational and electronic properties were investigated. The addition of fluorine reduces both the electrical and optical band gaps. The findings of this research can be useful for analogs of the molecules studied which have potential applications in the design of organic semiconductors for electronic devise applications.Öğe A comparative study of two novel unsymmetrically substituted triazacyclohexanes(Elsevier Science Bv, 2017) Lamraoui, Hanane; Messai, Amel; Bilge, Duygu; Bilge, Metin; Bouchemma, Ahcen; Parlak, CemalNovel unsymmetrically N-substituted N,N'-R1N"-R-2-1,3,5-triazacyclohexanes (1b and 2b; R-1 = p-chlorophenyl or p-methoxyphenyl and R-2 = butyl or cyclohexyl) have been synthesized in a good yield from condensation reaction by excess amine. Both triazacyclohexane rings have chair conformation. However, 1b adopts diaxial orientation of aryl groups and an equatorial form of alkyl group whereas 2b prefers an axial orientation of the alkyl group and diequatorial forms of aryl groups. 1b is consolidated by weak C-H center dot center dot center dot pi interactions. Intra-molecular C-H center dot center dot center dot O or C-H center dot center dot center dot N hydrogen bonds and C-H center dot center dot center dot pi may be effective in the stabilization of 2b. Both compounds have showed moderate antimicrobial activity, but 1b exhibits higher activity than 2b. All experimental results are found in good support to theoretical data. Findings of research may be helpful guide for the medicinal chemists and the field is further open for pharmacokinetics studies. (C) 2017 Elsevier B.V. All rights reserved.Öğe Computational study on favipiravir adsorption onto undoped-and silicon-decorated C60 fullerenes(World Scientific Publ Co Pte Ltd, 2017) Parlak, Cemal; Alver, Ozgur; Senyel, MustafaAdsorption and interaction mechanisms of fullerene-based complex systems for possible drug delivery vehicles have been at the center of increasing attention. In the scope of this work, the interaction mechanism between an important antiviral drug favipiravir and silicon-doped/undoped C60 fullerenes have been investigated using density functional theory (DFT). Calculations were carried out in both gas phase and water media to see the possible solvent effects. The effect of adsorption of the favipiravir on the SiC59 fullerene system and the nature of interaction were examined by analyzing the band shifts in the carbonyl stretching vibrations and natural bond orbital (NBO) properties of the examined complexes. Some important structural and electronic properties were reported and discussed as well. It was observed that doping the C60 fullerene nanocages with silicon atom enhanced the adsorption mechanism and calculations performed in water media gave rise to more stable complexes for silicon-doped systems compared to the results obtained for the gas phase. Results and parameters found in the present search reveal further insights into the drug delivery systems.Öğe Conformational and electronic properties of hydroquinone adsorption on C60 fullerenes: Doping atom, solvent and basis set effects(Elsevier Science Bv, 2018) Ergurhan, Orkun; Parlak, Cemal; Alver, Ozgur; Senyel, MustafaHydroquinone (HQ) is widely used as a reducing agent with well-known antioxidant properties. The interaction with pristine and doped fullerenes seems to have a promising research field particularly for the drug delivery and sensor applications. In this research, sensitivity of silicon or boron doped and undoped fullerenes to the HQ molecule and adsorption energies of HQ interacted fullerene cages and dopant effect on the electronic properties were mainly examined with density functional theory (DFT).M06-2X and B3LYP functionals were used for the gas phase and water media. The effect on the basis sets for the investigated systems was also searched by using 6-31G(d) and ccpvdz basis sets. (C) 2018 Elsevier B.V. All rights reserved.Öğe Conformational and electronic properties of N-methacryloyl-(L)-glutamic acid(Taylor & Francis Ltd, 2017) Parlak, Cemal; Kesan, Gurkan; Kazanci, Nadide; Rhyman, Lydia; Ramasami, Ponnadurai; Alver, Ozgur; Akgol, SinanConformers of N-methacryloyl-(L)-glutamic acid (MAGA, C9H13NO5) in the gas phase, benzene or methanol environment were searched by the density functional theory (DFT) and time-dependent DFT. Selected conformational isomers based on potential energy surface analysis were studied by considering the structural and electronic properties. B3LYP functional, and HF and MP2 levels were used with the 6-31+G(d,p), 6-311+G(3df,p) and aug-cc-pVDZ basis sets. We explored the effect of medium on the conformational preferences, UV spectra and frontier molecular orbitals of the conformers. The outcomes of this research will be useful for future studies including moieties analogous to MAGA.
