MCBÜ Açıkerişim Sistemi :: Browsing by Author "Bardak, F"

Browsing by Author "Bardak, F"

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Intermolecular interactions and molecular docking investigations on 4-methoxybenzaldehyde
Ghalla, H; Issaoui, N; Bardak, F; Atac, A
In this work, a structural and electronic properties of 4-methoxybenzaldehyde (4MBA) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The 4MBA crystal is stabilized by C-H center dot center dot center dot O intermolecular interactions along with pi center dot center dot center dot pi interactions. Various intermolecular interactions involved in 4MBA crystal have been analyzed deeply through topological atom-in-molecules (AIM) analysis and noncovalent interactions (NCI) method. Besides, Hirshfeld surface (HS) analysis and fingerprint plots are performed to determine the contribution of intermolecular contacts in 4MBA crystal packing. The electronic properties of the title compound have been investigated. Nonlinear optic (NLO) properties of 4MBA have been interpreted through the calculated first hyperpolarizability value. 4-substituted benzaldehydes, including 4MBA, are known with their competitive inhibitory activity on Tyrosinase, which also known as polyphenol oxidase (PPO). This enzyme is a rate limiting enzyme that controls the production of melamine and brown coloring of foods. Thus, molecular docking behaviors of 4MBA are presented in comparison with that of benzaldehyde (BA), 4-ethylBA, 4-tertbutylBA, 4-isoprophylBA, 4-propoxyBA, 4-butoxyBA, and Hexylresorcinol on four selected PPOs from sweet potato, grape, and mushroom.
Single and binary nickel, copper, and zinc-based nanosized oxides as anode materials in lithium-ion batteries
Egesoy, E; Kap, O; Bardak, F; Horzum, N; Ataç, A
The demand for portable power sources with higher energy density and longer lifespan has prompted researchers to focus on developing better electrode materials for lithium-ion batteries (LIBs). Metal oxide nanoparticles have potential due to their low cost, high surface-area-to-volume ratio, strong reactivity, excellent size distribution, high theoretical capacities, and eco-friendly synthesis methods. However, there is still room for improvement in capacity retention and rate performance. To cope with this entail, the cycle performance of LIBs has been initially investigated utilizing single metal oxide anode materials including NiO, CuO, and ZnO nanostructures. Subsequently, binary oxides of Ni-Cu, Ni-Zn, and Cu-Zn have been synthesized to examine whether the binary structures boost the battery performance. NiCuO is the optimum anode material combining the benefits of NiO with the highest initial discharge capacity of 691 mAh g(-1) and the highest retention rate of CuO (49% after 30 cycles).
Determination of structural and vibrational spectroscopic features of neutral and anion forms of dinicotinic acid by using NMR, infrared and Raman experimental methods combined with DFT and HF
Kose, E; Bardak, F; Atac, A; Karabacak, M; Cipiloglu, MA
In this study; the experimental (NMR, infrared and Raman) and theoretical (HF and DFT) analysis of dinicotinic acid were presented. H-1 and C-13 NMR spectra were recorded in DMSO solution and chemical shifts were calculated by using the gauge-invariant atomic orbital (MO) method. The vibrational spectra of dinicotinic acid were recorded by FT-Raman and FT-IR spectra in the range of 4000-10 cm(-1) and 4000-400 cm(-1), respectively. To determine the most stable neutral conformer of molecule, the selected torsion angle was changed every 10 degrees and molecular energy profile was calculated from 0 degrees to 360 degrees. The geometrical parameters and energies were obtained for all conformers form from density functional theory (DFT/B3LYP) and HF with 6-311++G(d,p) basis set calculations. However, the results of the most stable neutral and two anion forms (anion(-1) and anion(-2) forms) of dinicotinic acid are reported here. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational wavenumbers, calculated with scaled quantum mechanics (SQM) method and PQS program. (C) 2013 Elsevier B.V. All rights reserved.
Heterogeneous dynamics in ionic liquids at the glass transition: Fluorescence recovery after photobleaching measurements of probe rotational motion from Tg-6 K to Tg+4 K
Bardak, F; Rajian, JR; Son, P; Quitevis, EL
The rotational dynamics of tetracene and rubrene in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)C(1)im][PF6]) at the glass transition (T-g = 196 K), from T-g - 6 K to T-g + 4K, were measured using the technique of fluorescence recovery after photobleaching. The rotational anisotropy decays of these probes in [C(4)C(1)im][PF6] were found to be non-exponential and well fit by the Kohlrausch-Williams-Watts (KWW) function with the stretching parameter beta(KWW) equal to 0.70 +/- 0.03 for tetracene and 0.88 +/- 0.04 for rubrene in the temperature range of the measurements. The rotational correlation time tau(c) at T-g is equal to 19 +/- 1 s for the smaller probe tetracene and 180 +/- 40 s for the larger probe rubrene. Below T-g, tau(c) shows a slight decoupling from the extrapolation of fits of the Vogel-Fulcher-Tammann equation to the viscosity eta. This decoupling is characterized by a fractional Debye-Stokes-Einstein relation, tau(c) proportional to eta(xi)/T, with xi equal to 0.78 +/- 0.02 for rubrene and 0.85 +/- 0.01 for tetracene. The dependence of beta(KWW) on probe size is consistent with the dynamics in [C(4)C(1)im][PF6] being heterogeneous and is rationalized in terms of the time scale of the probe rotational motion compared to the domain exchange time. (c) 2014 Elsevier B.V. All rights reserved.
Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT
Bardak, F; Karaca, C; Bilgili, S; Atac, A; Mavis, T; Asiri, AM; Karabacak, M; Kose, E
Isophthalic acid (C6H4(CO2H)(2)) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, H-1 and C-13 NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts CH and C-13) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm(-1) and 3500-50 cm(-1), respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311 ++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The C-13 and H-1 nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained. (C) 2016 Elsevier B.V. All rights reserved.
The investigation of fluorine substitution in difluoroanilines with focus on 2,6-difluoroaniline by spectroscopic methods, density functional theory approach, and molecular docking
Kose, E; Bardak, F; Atac, A
In this study, the spectroscopic features and reactive nature of difluoroanilines, with special attention on 2,6-difluoroaniline (2,6-DFA), are explored thoroughly to gain insight into the effect of fluorine substitution in aniline derivatives. The quantum chemically obtained spectral properties including Fourier transform infrared, Raman, ultraviolet, and H-1 and C-13 nuclear magnetic resonance spectra were obtained by using Density Functional Theory (DFT) calculations at B3LYP/6-311++G(d,p) level of theory, and given along with the ones measured experimentally. The reactivity characteristics such as Fukui descriptor, electrostatic potential, and electronegativity were defined based on electron density generated theoretically. The position of fluorine substitution does not significantly alter the amide group reactivity making all difluoroanilines compatible to each other in terms of the reactivity. The time-dependent DFT was used to calculate the electronic properties such as excitation energies, maximum wavelengths, oscillator strengths, and molecular orbitals energies, and given along with the density of state diagrams. The intramolecular interactions were mapped by reduced density gradient method to reveal possible fluorine influence on the amide group and its reactivity, and the strongest van der Waals interactions in 2,6-DFA were observed. Besides, the thermodynamic and nonlinear optical properties of the title molecule were also investigated. The 2,6-DFA molecule seems to be appealing for multidisciplinary studies about the relevant nonlinear optical properties. To explore the binding capability of 2,6-DFA and see the influence of fluorine substitution in difluoroanilines, molecular docking was performed on a model enzyme structure of T4 lysozyme. Ligand-enzyme binding energies of 2,6-DFA is nearly the same with that of 2,5 DFA and 3,5 DFA at the same binding site which differs from the remaining derivatives. (C) 2019 Elsevier B.V. All rights reserved.
Theoretical and experimental investigation of the spectroscopic features of and interionic interactions in 1-hexyl-3-methylimidazolium chloride, 1-hexyl-3-methylimidazolium tetrafluoroborate and 1-hexyl-3-methylimidazolium hexafluorophosphate ionic liquids
Bilgili, S; Atac, A; Bardak, F
In this work, the spectroscopic and electronic properties of three imidazolium-based ionic liquids (ILs) with 1-Hexyl-3-methylimidazolium cation and chloride, tetrafluoroborate, and hexafluorophosphate anions have been investigated theoretically and experimentally. The ground state electronic structure features such as molecular electrostatic potential, IR and Raman spectra, have been achieved through density functional theory (OFT) calculations at the B3LYP/6-311++G(d,p) level of theory in Gaussian 16. The resulting electron density has been analyzed to reveal intra- and interionic non-covalent interactions via atoms in molecules (AIM) approach and interpreted in terms of both the anion dependency and interaction type. The electronic transition characteristics have been carried out by time-dependent OFT calculations at the same level. The nuclear magnetic resonance shielding constants and chemical shifts have been computed by applying the DFT/gauge-including atomic orbitals (GIAO) method. The experimental measurements associated with the performed calculations include FT-IR and FT-Raman, UV-Vis, and H-1 and C-13 NMR spectra. The experimental spectroscopic signatures have been interpreted under the light of theoretical calculations. The effect of anion on the electronic structure and spectroscopic features are interpreted in accordance with the that of the density, viscosity, surface tension, refractive index, and the electrical conductivity results from previous works on the physicochemical properties of [Hmim][Cl], [Hmim][BF4] and [Hmim][PF6] ionic liquids. (C) 2020 Elsevier B.V. All rights reserved.
Investigation of the interionic interactions and spectroscopic features of 1-Octyl-3-methylimidazolium chloride, tetrafluoroborate, and hexafluorophosphate ionic liquids: An experimental survey and DFT modeling
Bilgili, S; Bardak, F; Kose, E; Atac, A
This study presents the spectroscopic and electronic properties of some imidazole-based ionic liquids (ILs) consisting of 1-Octyl-3-methylimidazolium cation and chloride, tetrafluoroborate, and hexafluorophosphate anions from experimental and theoretical perspectives. The ground state structural and vibrational characteristics of the ionic liquids have been achieved through Density Functional Theory (DFT) calculations at the Becke's and the Lee-Yang-Parr (B3LYP) and 6-311 ++G(d,p) level of theory in Gaussian 16. The electronic and magnetic features of the ILs have been examined by using electronic absorption spectra and Nuclear Magnetic Resonance spectroscopy (NMR) techniques along with the calculations from Time-Dependent Density Functional Theory (TD-DFT) and using Gauge-Including Atomic Orbital (GIAO) method. The intra-and interionic noncovalent interactions in the ionic liquids have been revealed via the electron density analysis based on the Atoms in Molecules (AIM) approach, and decomposed as hydrogen bonding, van der Waals interactions, and steric effects via Reduced Density Gradient (RDG) analysis. To gain insight into the possible effects of anion-cation interaction on the physicochemical properties of ionic liquids, interionic interactions, reactivity properties, topological critical points, and electrostatic potential surfaces were obtained. These interactional characteristics were interpreted in terms of both the anion dependency and interaction type. Notably, the results of this study were evaluated together with the results obtained from our previous study on ILs consisting of the same anions with the 1-Hexyl-3methylimidazolium cation to achieve the effects of the extension in the chain length of the cation in the presence of the same anion on the spectroscopic and electronic properties of ionic liquids. (c) 2022 Elsevier B.V. All rights reserved.
A comprehensive study on the effect of substitution position and solvent effect on absorption and emission characteristics of n-methylindoles via linear response and State-Specific formalisms
Karaca, C; Bardak, F; Kose, E; Atac, A
The light absorption emission characteristics of n-methylindoles (n = 1-7) have been explored thoroughly by taking solvatochromic, substitution position, and solvation model effects into account. Experimental UV-Vis and Fluorescence spectra were recorded between 200 and 400 nm, and 250-800 nm, respectively, in cyclohexane, dichloromethane, and acetonitrile. Molecular geometry optimizations and excited state calculations were conducted using DFT and TD-DFT methods with a long-range corrected hybrid exchange-correlation functional CAM-B3LYP. Absorption emission characteristics were determined based on the polarizable continuum model accompanied with Linear-Response and State-Specific formalisms. Absorption spectra were resolved using Franck-Condon analysis for a more accurate representation of experimental data and underlying vibronic transitions were determined. Overall, although the Linear-Response and State-Specific approaches provide a quantitative explanation of experimental spectra, the approach used for the calculations can affect the solvent polarity-dependent shifts by nearly an order of magnitude. Besides, the State-Specific model provides slightly better results in the determination of Stokes shifts. The shouldered fluorescence peak observed in weakly polar solvents diminishes at higher polarities indicating the elimination of solute-solute interactions and domination of solute-solvent interactions with increasing solvent polarity.
Spectroscopic and luminescence properties of an isonicotinic acid
Can, N; Ataç, A; Bardak, F; Can, SES
An isonicotinic acid N-oxide Zn(II) compound was characterized on the basis of elemental analysis. FTIR spectra of the compound and free isonicotinic acid N-oxide (INO) were recorded in the range 4000-400 cm(-1). Cathodoluminescence (CL) spectra from the Zn(INO)(2) complex were recorded. The luminescence data were interpreted in terms of the emission band at 470 inn. The green luminescence (similar to 470 nm) arises from Zn2+ transition T-4(1) ((4)G) --> (6)A(1) (S-6). It shows a weak vibronic structure. and short lifetimes less than 150 mu s. The lifetime and intensity of the signal are temperature dependent, and the parameters are reported for the 470 nm emission line.
Structural characterization and luminescence properties of an isonicotinic acid N-oxide Mn(II) complex
Can, N; Can, SES; Ataç, A; Bardak, F
An isonicotinic acid N-oxide Mn(II) compound was synthesized and characterized on the basis of elemental analysis and X-ray crystallography. In the complex, Mn(II) ions are coordinated by six water molecules, and the coordination number of the Mn(II) ion is six. FTIR spectra of the compound free isonicotinic acid N-oxide (INO) have been recorded in the range 4000-400 cm(-1) Cathodoluminescence (CL) spectra from the Mn(II) complex have been recorded. The luminescence data were interpreted in terms of the emission band at 480 nm. The green luminescence (similar to480 nm) arises from the Mn2+ transition T-4(1) ((4)G)-->(6)A(1) (S-6). It shows weak vibronic structure. short lifetimes less than 250 mus, and indicates that Mn2+ is octahedrally coordinated, occupying sites with similar distortions. The lifetime and intensity of the signal is temperature dependent, and the parameters are reported for the 480 nm emission line. (C) 2004 Elsevier Ltd. All rights reserved.
Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra
Kose, E; Karabacak, M; Bardak, F; Atac, A
One of the most significant aromatic amines is aniline, a primary aromatic amine replacing one hydrogen atom of a benzene molecule with an amino group (NH2). This study reports experimental and theoretical investigation of 2,5-difluoroaniline molecule (2,5-DFA) by using mass, ultraviolet-visible (UV-vis), H-1 and C-13 nuclear magnetic resonance (NMR), Fourier transform infrared and Raman (FT-IR and FT-Raman) spectra, and supported with theoretical calculations. Mass spectrum (MS) of 2,5-DFA is presented with their stabilities. The UV-vis spectra of the molecule are recorded in the range of 190-400 nm in water and ethanol solvents. The H-1 and C-13 NMR chemical shifts are recorded in CDCl3 solution. The vibrational spectra are recorded in the region 4000-400 cm(-1) (FT-IR) and 4000-10 cm(-1) (FT-Raman), respectively. Theoretical studies are underpinned the experimental results as described below; 2,5-DFA molecule is optimized by using B3LYP/6-311++G(d,p) basis set. The mass spectrum is evaluated and possible fragmentations are proposed based on the stable structure. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, frontier molecular orbitals (FMO), HOMO and LUMO energies, are determined by time-dependent density functional theory (TD-DFT). The electrostatic potential surface (ESPs), density of state (DOS) diagrams are also prepared and evaluated. In addition to these, reduced density gradient (RDG) analysis is performed, and thermodynamic features are carried out theoretically. The NMR spectra (H-1 and C-13) are calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of 2,5-DFA molecule are obtained by using DFT/B3LYP method with 6-311++G(d,p) basis set. Fundamental vibrations are assigned based on the potential energy distribution (PED) of the vibrational modes. The nonlinear optical properties (NLO) are also investigated. The theoretical and experimental results give a detailed description of the structural and physicochemical properties of the title molecule and contribute to understanding of the nature of di-substituted aniline derivatives. (C) 2016 Elsevier B.V. All rights reserved.
Effect of anion and methylation on the interionic interactions and reactivity of 1-butyl-2,3-dimethyl imidazolium-based ionic liquids
Bilgili, S; Bardak, F; Atac, A
The study presents the investigation of anion and methylation effects on the interionic interactions, thus explaining the variations in the reactivity, electronic, and spectroscopic features in 1-butyl-2,3-dimethyl imidazolium-based ionic liquids with chloride, tetrafluoroborate, and hexafluorophosphate anions. Ground state electronic structures, IR and Raman spectra, electronic transition characteristics, and chemical shifts of the ionic liquids were obtained using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. The calculated electron densities were analyzed to determine intra- and interionic interactions at critical points using Reduced Density Gradient and topological analysis through the atoms-in-molecules approach. Experimental spectroscopic characterizations were performed using the FT-IR, FT-Raman, NMR, and UV-vis techniques. These techniques and DFT calculations provide essential contributions to interpreting spectral features concerning the structure and dynamics of ionic liquids. Furthermore, molecular docking studies were performed to determine the binding status of studied ionic liquids with human serum albumin to explore their activity, thus reporting their potential due to their demand in pharmacology.
Anionic dependency of electronic and nonlinear optical properties of ionic liquids
Bardak, F; Bardak, C; Karaca, C; Kose, E; Bilgili, S; Atac, A
Nonlinear optical phenomena play significant roles in the bulk properties and responsive characteristics of ionic liquids, especially when used under strong electric fields. The variability of the anion-cation pair in ionic liquids makes them designer solvents; thus, the anion or cation dependency of the physicochemical properties should be understood in depth. Accordingly, the electric field-induced characteristics of eight ionic liquids with [Br] , [BE4] , [PF6] , [Ac] , [TFAc] , [MS] , [NTf2] , and [Tos] anions paired with the 1-butyl-3-methyl imidazolium cation were investigated using density functional theory modeling at four theoretical levels: B3LYP-6-31G(d), M06-2X 6-31G(d), M06-2X 6-311++G(d,p), and M06-2X aug-ccPVTZ. The frontier molecular orbitals, electrostatic potential surface, and electron density difference maps were obtained to visualize the electrostatic characteristics. The permanent electric dipole moment, linear electric polarizability, and first-order and second-order hyperpolarizabilities were also determined. While the static dipole moment and dipole polarizabilities could be obtained using low-level quantum chemistry at a satisfactory level, the functionalization of more intensive methods was required to accurately obtain the nonlinear optical properties. (C) 2021 Elsevier B.V. All rights reserved.
Electric field modulation of electronic structure, charge transfer, and nonlinear optical properties of crocetin for dye-sensitized solar cells
Bardak, F; Bardak, C
Natural sensitizing dyes in solar energy applications have gained attention due to their sustainability, costeffectiveness, and environmental friendliness. However, enhancing their performance, light-harvesting efficiency, and durability requires a deeper understanding of their structural and electronic properties under solar irradiance. Accordingly, this study explores the electronic structure and nonlinear optical properties of crocetin dye (cis and trans conformers) under varying external electric fields using M06-2X/6-311+G(d,p) model chemistry. The absorption characteristics strongly depend on field intensity, with electron injection efficiency expected to decrease as the field increases. Key nonlinear optical (NLO) parameters, such as dipole moment, polarizability, and hyperpolarizabilities, were calculated at solar irradiance peak frequencies. The NLO properties are wavelength-independent in the infrared region but show significant wavelength dependency in the visible region, increasing substantially near the absorption energy.
External field intensity and wavelength dependency from IR to deep UV of linear and nonlinear optical properties of 1-butyl-3-methylimidazolium dicyanamide ionic liquid
Bardak, F; Bardak, C
The electronic structure, inter-ionic interactions and charge transfer, polarizability, and first-order and secondorder hyperpolarizabilities of 1-butyl-3-methylimidazolium dicyanamide ionic liquid have been explored via modeling at M06-2X/6-311++G(d,p) level of theory. External field intensity dependence of electronic properties was investigated by utilization of field intensity from 0.0001 to 0.002 au applied in the direction of anion-cation. Interionic interactions have been characterized through the reduced density gradient method to reveal and distinguish hydrogen bonding and other non-covalent interactions. Extraordinary bonding interactions were observed between the anion and ring system of the cation. Electronic excitation characteristics were analyzed based on the inter-fragment charge transfer method to distinguish charge transfer contributions from local excitations. Static and dynamic nonlinear optical parameters namely the total dipole moment mu, the mean polarizability a(0,0) and a(-co; co), the anisotropy of polarizability Aa(0,0) and Aa(-co; co) the first hyperpolarizability in the direction of dipole moment 13(0,0,0), 13(- co; co,0), and 13 (-2co; co,co), the average second hyperpolarizability y(0;0,0,0), y(- co; co,0,0) and y(-2co; co,co,0) have been calculated for specific laser wavelengths corresponding to the UV, visible, and infrared region. Thus, a novel way of mapping the field intensity and wavelength dependence of NLO properties was achieved. The hyperpolarizability calculations indicate that 1-butyl-3-methylimidazolium dicyanamide has a significant potential to be used in electro-optics Pockels effect, second-harmonic generation, and electro-optical Kerr effect applications. NLO property maps indicate that the wavelength dependence in the IR and visible region is almost ignorable when compared with that of the UV region where the first hyperpolarizabilities can increase by ten thousand and the second hyperpolarizabilities can reach up to ten billion times.
Experimental and DFT analysis of structural and spectroscopic features of nitroterephthalic acid, and computational insights into its molecular interactions with hER-α via molecular docking
Bardak, F
It has become clear that the exposure to the ubiquitous xenoestrogens are the first line causatives for human breast cancer. Besides, terephthalic acid (TPA), the major chemical constituent in the synthesis of polyethylene terephthalate (PET), also shown to have carcinogenic effects. Nitroterephthalic acid (NTPA) modified PET or polyethylene glycol (PEG) polymers are suggested to have lower risk, however little known about the reactive nature of NTPA especially in terms of its interactions with estrogen receptors. Therefore, this study focuses on the investigation of structural and spectroscopic features of NTPA through experimental and theoretical methods, and the exploration of interactions with human estrogen receptor alpha (hER-alpha) in comparison with that of benzoic acid (BA), phthalic acid (PA), and terephthalic acid (TPA) by using molecular docking methodology. Essential quantum descriptors obtained for NTPA include electrostatic potential surface, electrophilicity and nucleophilicity from Fukui analysis, aromaticity indexes from nuclear independent chemical shift (NICS) analysis, and electronic properties like band gap and ionization potentials from population analysis. Infrared, Raman, and UV spectra are presented both experimentally and via ab initio density functional theory calculations obtained at the B3LYP 6-311++G(d,p) level of theory. Ligand-enzyme interactions were discussed within a dependency on the structural variations in four ligands in docking analysis. NTPA was found to behave like phthalic acid and highly rich in terms of conformations in monomeric and dimeric forms. (C) 2018 Elsevier B.V. All rights reserved.
Computational Insight into Warfarin Blockage by Silymarin Components via DFT and Molecular Docking
Bardak, F
Silymarin has been utilized as a traditional, complementary, and integrative medicine for centuries, despite a poor molecular-level understanding of its interactions with other medicinal compounds and enzyme structures. However, recent studies indicate that this supplement, as with many others, should be considered with caution because it has the potential to interact with many drugs, medical plants, and foods. Silymarin is composed of several compounds that are either enantiomeric or have similar structures. Thus, this study presents the electronic structure properties and reactivity characteristics of silymarin components and warfarin through density functional theory modeling at the M06-2X/6-311 + G(d,p) level of theory. The ligand-protein interactions of the compounds with human serum albumin, cytochrome P450 (CYP2C9, CYP2C19, CYP2D6, and CYP3A4) enzymes, and alanine transaminase were presented using molecular docking. The critical residue-based interactions of silymarin components and warfarin were fingerprinted. Furthermore, their drug-likeness and toxicity characteristics were compared to those of warfarin and the well-known flavonoids, taxifolin, and quercetin. The possibility of inhibiting the target enzymes to reduce the effectiveness of warfarin has been highlighted.
Experimental and computational insights into the electronic structures and absorption-emission characteristics of coumarin, C-6H, C-153, and C-343 dyes
Karaca, C; Bardak, F; Köse, E; Ataç, A
This paper explores the electronic structure and spectral characteristics of coumarin (C), C-6H, C-153, and C-343 in the protic polar solvent acetonitrile, combining computational methods via Density Functional Theory (DFT) and time-dependent Density Functional Theory (TD-DFT) with experimental analysis of UV-Vis and fluorescence spectra. The optoelectronic features of C, C-6H, C-153, and C-343 are primarily utilized in the solution phase for various applications, such as lasers and dye-sensitized solar cells. Computational studies were conducted using four different Modal Chemistry methods [MC1: CAM-B3LYP/6-311++G(d.p), MC2: CAM-B3LYP/6-31 + G(d.p), MC3: B3LYP/6-311++G(d.p), and MC4: B3LYP/6-31 + G(d.p)]. The excited state features were investigated based on TD-DFT/Polarizable Continuum Model-Linear Response and TD-DFT/Polarizable Continuum ModelState Specific formalisms. Molecular orbital configurations, molecular electrostatic potentials, and electron density difference isosurface of the dyes were analyzed to uncover the factors influencing the absorption and emission properties. The decomposed UV-Vis and fluorescence spectra of compounds indicate that emission characteristics are complex and contribute to low-lying energy transitions. The state-specific solutions provide more reliable estimates for smaller molecular structures with less intramolecular charge transfer, whereas the linear response approach excels when more electron-donating functional groups are present. The effect of the basis set in determining both absorption and emission features is almost negligible compared to Hartree-Fock exchange contributions in DFT functionals. B3LYP appears to provide satisfactory results for systems where long-range HF exchange is not as crucial.
Effect of the external electric field on the electronic structure, spectroscopic features, NLO properties, and interionic interactions in ionic liquids: A DFT approach
Bardak, C; Atac, A; Bardak, F
Ionic liquid (IL)s are a unique group of chemicals with extraordinary physical and chemical properties. Due to the advantage of the tunability of their features by varying the ion compositions and either IL/IL or IL/conventional solvent mixing ratios, uncountable functions of them have been discovered. In the field of electrochemistry and energy applications, the function of ILs under external field should also be understood well. The most fundamental way of gaining insight into the function of a substance is to study the structure. Therefore, this work focuses on the investigation of structural variations of an exemplary IL, 1-hexyl 3-methylimidazolium chloride (HmimCl), under external electric field (EEF) via ab initio quantum chemistry calculations. Field dependent geometry analysis show that the interionic bond and the molecular conformation can be modulated by the strength and the direction of the applied field, and the disassociation occurs at similar to 0.7 V/angstrom level. Mulliken, atomic polar tensor, and natural bond orbital charges were obtained within field dependency and their correlation was examined. Charge displacement curves were constructed to visualize the field inducement on the charge transfer. Interionic interactions were profiled as hydrogen, van der Walls, and steric effect by using reduced density gradient analysis and the breaking of the single hydrogen bond was determined to occur at similar to 0.6 V/angstrom level. The vibrational spectra (IR and Raman) were simulated and the critical peaks that are affected by the field inducement were interpreted. The analysis of the field dependent Nonlinear Optical (NLO) properties shows that the only important component is in the field direction for the field intensity >0.2 V/angstrom. Electronic transition properties determined via TD-DFT calculations with B3LYP/6-311G** level of theory indicate that the UV-Vis spectrum and underlying transitions are depended on the direction of the field, and experience a bathochromic shift with increasing inducement showing that the IL becomes more susceptible to excitation. (C) 2018 Elsevier B.V. All rights reserved.

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