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- MakaleAçık Erişim2025Scopus SJRQ2Detailed investigation of the spectroscopic features of nicardipine hydrochloride using experimental and quantum chemical methods
Can, Sumeyra; Cinar, Mehmet; Baris, Ozlem
Context: The structural and spectroscopic properties of drug groups can be determined using spectroscopic techniques and quantum chemical calculations. In this study, the structural and spectroscopic properties of nicardipine, a potent calcium channel blocker belonging to the dihydropyridine drug group, were investigated. For this purpose, FT-IR, Raman, NMR, and UV–Vis spectra of nicardipine hydrochloride were recorded. The ground state geometry optimization performed under vacuum conditions showed excellent agreement with X-ray diffraction (XRD) data, with root-mean-square deviations of bond lengths and bond angles calculated as 0.017 Å and 2.2°, respectively. Vibrational spectrum analysis revealed all characteristic modes, and theoretical B3LYP predictions largely agreed with experimental data. NMR spectra recorded in chloroform solvent confirmed the molecular structure of nicardipine. A comparison with previously reported data revealed significant differences in the proton NMR results, while the carbon NMR data showed consistency. The gauge-invariant atomic orbital (GIAO) method, commonly used for NMR spectrum prediction, yielded results within an acceptable error range despite minor inconsistencies arising from differences between experimental and computational conditions. In the UV–Vis spectrum of nicardipine HCl, an absorption peak corresponding to π-π* excitation was observed at 238 nm. Method: The geometric optimizations and vibration spectra of the nicardipine drug molecule were performed using the Gaussian 09 program with the B3LYP functional and the 6–311 + + G(d,p) basis set. Visualizations were performed using the GaussView 5.0 interface program. NMR spectra were recorded in chloroform solvent using the GIAO method. Molecular electrostatic potential (MEP) maps and Mulliken atomic charges were analyzed to gain deeper insight into the electronic properties.
AtıfScopus1WoS1OpenAlex1
İncele - MakaleYalnız künye2025Scopus SJRQ1Tailoring the Electron Density of Functional Groups for Controlled Charge Transfer in SWCNTs
Fiebor, Alphonse; Cinar, Mehmet; Amsalem, Patrick; Achazi, Andreas J.; Gordeev, Georgy; Bartonitz, Florian; Xin, Fan; Koch, Norbert; Adeli, Mohsen; Paulus, Beate
Controlling the position of the Fermi level at the single-particle level in bulk amount of carbon nanotubes is a key technological bottleneck against their use in building nanodevices for electronics, optics, sensing, bioimaging, and beyond. Here are deployed a novel set of molecules built up from the same building blocks (aniline and methoxy groups attached on a triazine anchor) that efficiently p- and n-dope the nanotubes, depending upon the way they are assembled. Independent computational and experimental investigations consistently confirm the tunability-by-assembly concept of the charge transfer agents. The changes of the electronic density localized on the anchor groups and, upon attachment, the consistent variation of the position of the Fermi level in single-walled carbon nanotubes are monitored. The induced shifts reach several hundreds of meV, ranging from p-doping up to n-doping. This is evidenced by changes in the electronic and vibrational behavior of the nanotubes, as observed by Raman, photoelectron, and photoluminescence spectroscopies.
- MakaleYalnız künye2024Scopus SJRQ3Artificial Neural Network and Multiple RegresAnalysis Applied to 2D-QSAR Studies: the Caof Imidazolidine-2,4-dione as PTP1B Inhibito
Aggoun, Siham; Belaidi, Salah; Ghamri, Meriam; Kerassa, Aicha; Cinar, Mehmet; Yamari, Imane; Abchir, Oussama; Chtita, Samir
In this investigation, we undertook a comprehensive quantitative structure-activity relationship (QSAR) analysis using both modern artificial neural network (ANN) methods and classical multiple linear regression methods (MLR). Our primary focus was on revealing the intricate connection between antidiabetic activity and the molecular structure of thirty-nine imidazolidine-2,4-dione derivatives. The B3LYP hybrid functional and 6-31G (d) basis set computed electronic properties at the quantum level. Rigorous benchmarking against experimental data validated the reliability of our quantum theory approach. Our statistical model effectively predicted activities closely aligned with experimental antidiabetic activities, quantified by the IC50 values. They also revealed a significant superiority of the ANN architecture (6-4-1) over the MLR method. This study stands as a meaningful contribution to the field, providing valuable insights for designing new antidiabetic drugs, particularly as potential inhibitors of tyrosine phosphate 1B (PTP1B). The explicit articulation of our primary aim and emphasis on the study’s significance underscore its potential impact on advancing drug development within the realm of antidiabetic therapeutics.
AtıfScopus2İncele - MakaleYalnız künye2024Scopus SJRQ2Diltiazem and Verapamil: Combined experimental and computational approaches to structural and spectroscopic characterization
Cinar, Mehmet; Can, Sümeyra; Baris, Özlem; Demirci, Çiğdem Elif
Diltiazem and Verapamil are two important drug molecules in a separate group of Calcium Channel Blockers. The purpose of this work is to determine and compare the structural and spectroscopic properties of these two molecules using a number of experimental techniques and quantum chemical calculations. Compounds were characterized spectroscopically using FT-IR, Raman, NMR (1H, 13C, and DEPT), and UV–vis methods. Furthermore, the Density Functional Theory (DFT) method, Becke's three-parameter hybrid functional (B3LYP), and the 6–311++G(d,p) basis set were used to determine the ground state geometric structures of molecules, and the spectroscopic properties of the obtained optimum structures were investigated computationally. The optimization studies performed under vacuum circumstances and for the isolated molecules were found to be very close to the experimental results. In fact, r.m.s. values were discovered for Diltiazem and Verapamil with bond lengths of 0.013 and 0.024, and bond angles of 1° and 2°, respectively. The vibration characteristics of the compounds were discovered using the collected FT-IR and Raman spectra, and significant vibrational modes were assigned. After scaling, it was revealed that the quantum chemical data was congruent with the experimental ones, and that the characteristic vibrational modes were appropriately predicted. DFT calculations effectively determine molecules' structures due to internal consistency, despite being slightly distant from experimental data. Theoretical values for carbon and hydrogen atoms are better in agreement with observed values when scaling with 0.92 and 0.90. From the UV–vis spectra, Diltiazem HCl absorbance peaks were found at 207 and 237 nm, whereas Verapamil HCl absorbance peaks were identified at 203, 229, and 278 nm. When the theoretical calculations and experimental findings were compared, the anticipated absorption peaks were found to have shifted nearer the visible area. Furthermore, Hirshfeld surfaces and Molecular Electrostatic Potential surfaces were obtained and analyzed in order to better understand the electronic characteristics. The TDOS and PDOS (total and partial density of state) spectra were also studied. Finally, using the HOMO and LUMO energy values, the critical chemical parameters were evaluated, and it was discovered that both molecules had positive electron affinity and electronegativity values, indicating that they will accept electrons when the electron-nucleus attraction exceeds the electron-electron repulsion.
AtıfScopus9WoS9OpenAlex9İncele - MakaleAçık Erişim2018Scopus SJRQ3Qualitative and quantitative structure-activity relationships studies of quercetin derivatives as chemotherapeutic activity
Rouane, Abderrahmane; Tchouar, Noureddine; Kerassa, Aicha; Cinar, Mehmet; Belaidi, Salah
Qualitative and Quantitative structure activity relationship (SAR/QSAR) analysis was applied to eighteen Quercetin derivatives using a combination of various physicochemical, steric, electronic, and structural molecular descriptors. A multiple linear regression (MLR) procedure was used to model the relationships between molecular descriptors and the chemotherapeutic activity of the Quercetin derivatives. The stepwise regression method was used to derive the most significant models as a calibration model for predicting the inhibitory activity of this class of molecules. The best QSAR models were further validated by a leave one out technique as well as by the calculation of statistical parameters for the established theoretical models. High agreement between experimental and predicted inhibitory values, obtained in the validation procedure, indicated the good quality of the derived QSAR models.
AtıfScopus3OpenAlex3İncele - MakaleYalnız künye2018Scopus SJRQ3Drug likeness scoring and quantitative structure anaplastic lymphoma kinase (ALK) inhibitors activities relationships of pyrazolone derivatives
Ouadah, Karim; Tchouar, Noureddine; Belaidi, Salah; Oukil, Oualid; Cinar, Mehmet
Series of twenty-four compounds was the field for applying multi-parameter optimization (MPO) methods and qualitative approximations of structural activity relationships in order to determine the role of various physico-chemical and quantum descriptors used in QSAR modeling as independent variables. Anaplastic lymphoma kinase (ALK) inhibitory activity was considered as a component in this study. In order to illustrate the quantitative relationships between the molecular descriptors and the activity of pyrazolone derivatives, we have applied a multiple linear regression (MLR) procedure. By adopting cross-validation with the leave-one-out method, we could estimate the predictability of models. Our results suggest a QSAR model based on the following descriptors: S, V, LogP, POL, Ref, HOMO, LUMO, E, , HBA, PSA and NRB, for the inhibitory activities against ALK. Results show high correlation between experimental and predicted activity values, indicating the validation and the good quality of the QSAR model.
AtıfOpenAlex1İncele - MakaleYalnız künye2017Scopus SJRQ4Structural investigation, drug likeness scoring and structure activity/property relationships applied on 1,2,3-thiadiazole derivatives, with kinase inhibitors activity
Oukil, Oualid; Tchouar, Noureddine; Belaidi, Salah; Salah, Toufik; Cinar, Mehmet
All calculations and the equilibrium geometries of 1,2,3-thiadiazole have been performed using ab initio/HF, MP2 and DFT methods with different basis sets. The molecular electrostatic potential surface (MESP) that reveals centers of reactivity of the molecule and substitution effects of the molecular system have been studied using the HSAB principle (Hard Soft Acid and Base). Also, the multi-parameter optimization (MPO) methods and structure activity/property relationship studies were carried out on twenty-one molecules of 1,2,3-thiadiazole derivatives which are potent VEGFR-2/KDR kinase inhibitors. In the present work results such as net charges, bond lengths, dipole moments, QSAR properties, Lipinski’s parameters, Lipophilic Efficiency (LipE), have been calculated and discussed. (Figure Presented).
AtıfScopus7İncele - MakaleYalnız künye2015Scopus SJRQ3Conformational and spectroscopic behaviors of 2,4-xylyl isothiocyanate
Cinar, Mehmet; Karabacak, Mehmet; Chand, Satish; Shukla, Vikas K.; Sinha, Leena; Prasad, Onkar; Singh, Manoj Pratap; Asiri, Abdullah M.
This study aims to identify the conformational and spectroscopic characteristics of 2,4-xylyl isothiocyanate (C9H9NS) compound via experimental and computational methods. To accomplish this, density functional theory (DFT), with the B3LYP functional was used to determine ground state conformation, vibrational wavenumbers and also isotropic chemical shifts of the title molecule. Experimentally, vibrational features of the compound were evaluated by FT-IR and FT-Raman spectroscopic analysis in the solid phase. On the basis of these studies, the conformational and spectroscopic behaviors of 2,4-xylyl isothiocyanate were interpreted. The fundamental vibrational wavenumbers as well as their intensities were computed, and a good correlation between experimental and scaled calculated wavenumbers was observed. The polarizability, first hyperpolarizability and dipole moment values of 2,4-xylyl isothiocyanate were calculated at the same level of theory and basis set. The results show that 2,4-xylyl isothiocyanate molecule possesses nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization was analyzed using natural bond orbital (NBO) analysis.
AtıfScopus7WoS5OpenAlex5İncele - MakaleYalnız künye2015Scopus SJRQ1An experimental and density functional study on conformational and spectroscopic analysis of 5-methoxyindole-2-carboxylic acid
Cinar, Mehmet; Karabacak, Mehmet; Asiri, Abdullah M.
In this article, a brief conformational and spectroscopic characterization of 5-methoxyindole-2-carboxylic acid (5-MeOICA) via experimental techniques and applications of quantum chemical methods is presented. The conformational analysis of the studied molecule was determined theoretically using density functional computations for ground state, and compared with previously reported experimental findings. The vibrational transitions were examined by measured FT-IR and FT-Raman spectroscopic data, and also results obtained from B3LYP and CAM-B3LYP functionals in combination with 6-311++G(d,p) basis set. The recorded proton and carbon NMR spectra in DMSO solution were analyzed to obtain the exact conformation. Due to intermolecular hydrogen bondings, NMR calculations were performed for the dimeric form of 5-MeOICA and so chemical shifts of those protons were predicted more accurately. Finally, electronic properties of steady compound were identified by a comparative study of UV absorption spectra in ethanol and water solution and TD-DFT calculations.
AtıfScopus23WoS22OpenAlex24İncele - MakaleYalnız künye2015Scopus SJRQ2Structure'activity relationships and quantitative structure'activity relationships modeling of some 3-(aryl)-N-(aryl)-1,2,4-Oxadiazol-5-Amine derivatives as anti-proliferative agents
Belaidi, Salah; Kerassa, Aicha; Lanez, Touhami; Cinar, Mehmet
Quantitative structure activity relationship studies were performed on a series of 3-(aryl)-N-(aryl)- 1,2,4-oxadiazol-5-amines as anti-proliferative agents, multiple linear regression analysis was performed to derive quantitative structure activity relationship models which were further evaluated internally for the prediction of activity. The developed models were cross-validated by the 'leave one out' technique as well as by the calculation of statistical parameters. The best QSAR model i.e., model-2 (R2 = 0 906, Fischer's test value F = 12066) has acceptable statistical quality and predictive potential as indicated by the value of cross validated squared correlation coefficient (q2 = 0 907). The present investigation indicates the importance of the quantum chemical descriptors, constitutional descriptors and hydrophobicity to study the anti-proliferative activity.
AtıfScopus7WoS4OpenAlex2İncele - MakaleYalnız künye2014Scopus SJRQ2A comparative study of selected disperse azo dye derivatives based on spectroscopic (FT-IR, NMR and UV-Vis) and nonlinear optical behaviors
Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet
In the present work, a combined experimental and quantum chemical study on ground state equilibrium structure, spectroscopic and nonlinear optical properties of selected disperse azo dye molecules are reported. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state, simulated IR spectra and total energy distribution (TED) of vibrational modes. The chemical shifts were determined from the results of observed 1H and 13C NMR spectra in chloroform and dimethylsulfoxide solution. The DFT/gauge-invariant atomic orbital (GIAO) methodology was applied to predict the magnetic properties. Electronic properties were carried out by UV-Vis spectroscopy and TD-DFT/CIS approach. The nonlinear optical (NLO) features were addressed theoretically. A detailed description of spectroscopic and NLO behaviors of studied disperse azo dyes was reported with the help of comparison of experimental measurements and theoretical calculations.
AtıfScopus30WoS29OpenAlex29İncele - MakaleAçık Erişim2014Scopus SJRQ2FT-IR, FT-Raman, NMR, UV and quantum chemical studies on monomeric and dimeric conformations of 3,5-dimethyl-4-methoxybenzoic acid
Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M.; Cinar, Mehmet; Shukla, Vikas K.
Extensive spectroscopic investigations along with theoretical quantum chemical studies on 3,5-dimethyl-4-methoxybenzoic acid (DMMBA) have been consummated. The fundamental vibrational transitions were addressed by experimental FT-IR (4000-400 cm-1) and FT-Raman (4000-10 cm -1) techniques and density functional calculations at B3LYP/6-311++G(d,p) and B3LYP/6-311++G(df,pd) levels of theory. The 1H, 13C and DEPT 135 NMR spectra of studied compound were recorded in deuterated dimethylsulfoxide (DMSO-d6), and compared with computed data obtained by using gauge including atomic orbital (GIAO) method. The electronic absorption spectra in methanol and ethanol solution were evaluated in the range of 200-400 nm, and TD-DFT method was chosen for computational study. The spectroscopic and theoretical results were compared to the corresponding properties for monomer and dimer structures for the most stable conformer. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Moreover, the thermodynamic and nonlinear optical (NLO) properties were evaluated.
AtıfScopus34WoS34İncele - MakaleYalnız künye2013Scopus SJRQ2Determination of structural, spectrometric and nonlinear optical features of 2-(4-hydroxyphenylazo)benzoic acid by experimental techniques and quantum chemical calculations
Cinar, Mehmet; Yildiz, Nihat; Karabacak, Mehmet; Kurt, Mustafa
The optimized geometrical structure, vibrational and electronic transitions, chemical shifts and nonlinear optical properties of 2-(4-hydroxyphenylazo)benzoic acid (HABA) compound were presented in this study. The ground state geometrical structure and vibrational wavenumbers were carried out by using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman spectrometry in the range of 4000-400 cm-1 and 4000-10 cm-1; respectively. The fundamental assignments were done on the basis of the recorded spectra and total energy distribution (TED) of the vibrational modes. The 1H and 13C NMR spectra were recorded in deuterated DMSO solution, and gauge-invariant atomic orbitals (GIAOs) method was used to predict the isotropic chemical shifts. The UV-Vis absorption spectra of the compound were observed in the range of 200-800 nm in ethanol, methanol and water solvents. To investigate the nonlinear optical properties, the polarizability, anisotropy of polarizability and molecular first hyperpolarizability were computed. A detailed description of spectroscopic behaviors of compound was given based on the comparison of experimental measurements and theoretical computations.
AtıfScopus19WoS19OpenAlex19İncele - MakaleYalnız künye2013Scopus SJRQ2Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations
Sinha, Leena; Karabacak, Mehmet; Narayan, V.; Cinar, Mehmet; Prasad, Onkar
Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated.
AtıfScopus53WoS53OpenAlex58İncele - MakaleYalnız künye2013Scopus SJRQ2Synthesis, conformational and spectroscopic characterization of monomeric styrene derivatives having pendant p-substituted benzylic ether groups
Cinar, Mehmet; Ozcan, Levent; Karabacak, Mehmet; Erol, Ibrahim
Three derivatives of styrene monomer, 4-chlorophenyl-4-vinylbenzyl ether (I), 4-methoxyphenyl-4-vinylbenzyl ether (II) and 4-ethylphenyl-4-vinylbenzyl ether (III) were synthesized. The synthesized two novel compounds (I and III) and one with undefined structural features were identified by experimental spectroscopic techniques and density functional approach. The optimized geometrical structure, vibrational and electronic transitions along with chemical shifts of those compounds were presented in this study. The vibrational spectra of investigated compounds were recorded in solid state with FT-IR spectrometry in the range of 4000-400 cm-1. The computational vibrational wavenumbers and also ground state equilibrium conformations were carried out by using density functional method with 6-311++G(d,p) basis set. Assignments of the fundamental vibrational modes were examined on the basis of the measured data and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. Isotropic chemical shift of hydrogen and carbon nuclei were investigated via observed 1H and 13C NMR spectra in deuterated DMSO solution and predicted data applied with gauge-invariant atomic orbitals (GIAOs) method. The UV absorption spectra of monomers were observed in the range of 200-800 nm in ethanol, and time dependent DFT method was used to obtain the electronic properties. A detailed description of spectroscopic behaviors of compound was given based on the comparison of experimental measurements and theoretical computations.
AtıfScopus1WoS1OpenAlex1İncele - MakaleYalnız künye2013Scopus SJRQ2Determination of conformational and spectroscopic features of ethyl trans-alfa-cyano-3-indole-acrylate compound: An experimental and quantum chemical study
Cinar, Mehmet; Karabacak, Mehmet
The optimized geometrical structure, vibrational and electronic transitions, chemical shifts and non-linear optical properties of ethyl trans-alfa-cyano-3-indole-acrylate (C14H12N 2O2) compound were presented in this study. The ground state geometrical structure and vibrational wavenumbers were carried out by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 cm-1 and 4000-10 cm -1, respectively. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The 1H, 13C and DEPT NMR spectra were recorded in DMSO solution, and gauge-invariant atomic orbitals (GIAO) method was used to predict the isotropic chemical shifts. The UV-Vis absorption spectra of the compound were recorded in the range of 200-800 nm in various solvents of different polarity (acetone, benzene, chlorobenzene, chloroform, DMSO, ethanol, methanol and toluene). Solvent effects were calculated using TD-DFT and CIS method. To investigate the non-linear optical properties, the polarizability, anisotropy of polarizability and molecular first hyperpolarizability were computed. A detailed description of spectroscopic behaviors of compound was given based on the comparison of experimental measurements and theoretical computations.
AtıfScopus12WoS11İncele - MakaleAçık Erişim2013Scopus SJRQ2An experimental and theoretical investigation of Acenaphthene-5-boronic acid: Conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra
Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M.; Cinar, Mehmet
The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400 cm1 and 4000-10 cm 1, respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H·O hydrogen bonding have been discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability (β), its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.
AtıfScopus38WoS36OpenAlex33İncele