Ömer Tamer

Theoretical investigation of 5-(2-acetoxyethyl)-6-methylpyrimidin-2,4-dione: conformational study, NBO and NLO analysis, molecular structure and NMR spectra.

Structural and conformational, natural bond orbital (NBO) and nonlinear optical (NLO) analysis was performed, and (1)H and (13)C NMR chemical shifts values of 5-(2-Acetoxyethyl)-6-methylpyrimidin-2,4-dione [C9H12N2O4] in the ground state were calculated by using Density Functional Theory (DFT-B3LYP/6-311++G(d,p)) and Hartree-Fock (HF/6-311++G(d,p)) methods. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. In addition, the molecular frontier orbital energies, thermodynamic parameters (in the range of 200-700 K), molecular surfaces, Mulliken charges and atomic polar tensor-based charges were investigated. Besides, the analysis of all possible conformational of the title compound, a detailed potential energy curve for τ1(C8O3C10O4), τ2 (C8O3C10C11) and τ3 (C5C7C8O3) dihedral angles were performed in steps of 10° from 0° to 360°, and depicted to find the most stable form. Finally, the calculated HOMO and LUMO energies show that charge transfer occurs within the title compound.

Quantum chemical characterization of N-(2-hydroxybenzylidene)acetohydrazide (HBAH): a detailed vibrational and NLO analysis.

The molecular modeling of N-(2-hydroxybenzylidene)acetohydrazide (HBAH) was carried out using B3LYP, CAMB3LYP and PBE1PBE levels of density functional theory (DFT). The molecular structure of HBAH was solved by means of IR, NMR and UV-vis spectroscopies. In order to find the stable conformers, conformational analysis was performed based on B3LYP level. A detailed vibrational analysis was made on the basis of potential energy distribution (PED). HOMO and LUMO energies were calculated, and the obtained energies displayed that charge transfer occurs in HBAH. NLO analysis indicated that HBAH can be used as an effective NLO material. NBO analysis also proved that charge transfer, conjugative interactions and intramolecular hydrogen bonding interactions occur through HBAH. Additionally, major contributions from molecular orbitals to the electronic transitions were investigated theoretically.

Spectroscopic characterization, X-ray structure, antimicrobial activity and DFT calculations of novel dipicolinate copper(II) complex with 2,6-pyridinedimethanol

Novel dipicolinate complex of copper(II) ion, [Cu(dmp)(dpc)]·0.8H(2)O [dmp: 2,6-pyridinedimethanol; dpc: dipicolinate or pyridine-2,6-dicarboxylate], has been prepared and fully characterized by single crystal X-ray structure determination. The central copper(II) ion is bonded to dpc and dmp ligands through pyridine nitrogen atom together with two oxygen atom, forming the distorted octahedral geometry. The complex molecules, connected via O-H···O hydrogen bonds, form a supramolecular structure. H(2)dpc, [Cu(dpc)(H(2)O)(3)] and [Cu(dmp)(dpc)]·0.8H(2)O were screened for antimicrobial activity against Gram-positive, Gram-negative bacteria and yeast. H(2)dpc and [Cu(dpc)(H(2)O)(3)] exhibited antibacterial and antifungal activity, while [Cu(dmp)(dpc)]·0.8H(2)O exhibited activity only for Gram-positive bacteria. The geometry optimization and EPR parameters were carried out using the following unrestricted hybrid density functionals: LSDA, BPV86, B3LYP, B3PW91, MPW1PW91, PBEPBE and HCTH. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, calculated data show that the predicted geometries can reproduce the structural parameters. The electronic station in the frontier orbitals of the copper complex calculated from the experimental data is compared to the results of time-depended DFT calculations with the polarizable continuum model. Calculated vibrational frequencies are consistent with the experimental IR data.

An experimental and theoretical study on the novel (Z)-1-((naphthalen-2-ylamino)methylene)naphthalen-2(1H)-one crystal

A novel compound has been synthesized, and its structure has been characterized by IR, UV-vis, NMR and X-ray single-crystal determination techniques. The title compound crystallizes in the orthorhombic space group P212121 with a=6.2120(4)Å, b=10.8242(7)Å, c=22.3857(15)Å and Z=4. The crystal structure has intramolecular N-H···O hydrogen bond and C-H···Cg interaction. These hydrogen bonds and interactions are effective in crystal packing. The optimum molecular geometry, conformational analysis, normal mode wavenumbers, infrared and Raman intensities, corresponding vibrational assignments, chemical shift assignments, and thermo-dynamical parameters have been investigated with the help of Density Functional Theory (DFT). Detailed vibrational assignments have been made on the basis of potential energy distribution (PED). In order to understand the electronic transitions of the compound, time dependent DFT (TD-DFT) calculations were performed in gas phase. Also, the dipole moment, linear polarizabilities, anisotropy and first hyperpolarizabilities values have been computed.

The synthesis, characterization and theoretical study on nicotinic acid [1-(2,3-dihydroxyphenyl)methylidene]hydrazide.

In this study, we reported a combined experimental and theoretical study on nicotinic acid [1-(2,3-dihydroxyphenyl)methylidene]hydrazide (C13H11N3O3) molecule. The title compound was prepared and characterized by 1H and 13C FT-NMR, FT-IR and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a=6.2681(3) Å, b=16.5309(7) Å, c=12.4197(6) Å, α=90°, β=111.603(4)°, γ=90° and Z=4. In addition, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO), continuous set of gauge transformations (CSGT), individual gauges for atoms in molecules (IGAIM) 1H and 13C NMR chemical shift values, natural bond orbital (NBO), nonlinear optical (NLO) and HOMO-LUMO analyses, molecular electrostatic potentials (MEPs) and thermodynamic properties of the title compound in the ground state were investigated by using Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p). Besides, the hardness and electronegativity parameters were obtained from HOMO and LUMO energies. Obtained results indicate that there is a good agreement between the experimental and theoretical data.

1-Pentamethylbenzyl-3-(n)buthylbenzimidazolesilver(I)bromide complex: synthesis, characterization and DFT calculations.

A novel NHC complex of silver(I) ion, 1-pentamethylbenzyl-3-(n)buthylbenzimidazolesilver(I)bromide, was prepared and fully characterized by single crystal X-ray structure determination. FT-IR, NMR and UV-vis spectroscopies were employed to investigate the electronic transition behaviors of the complex. Additionally, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) (1)H and (13)C chemical shift and electronic transition values of silver(I) complex were calculated by using density functional theory levels (B3LYP and PBE1PBE) with LANL2DZ basis set. Also, the vibrational frequencies were supported on the basis of the potential energy distribution (PED) analysis calculated for PBE1PBE level. We were also investigated total static dipole moment (μ), the mean polarizability (〈α〉), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (〈β〉) of the title complex. Natural bond orbital (NBO) analysis was performed to determine the presence of hyperconjugative interactions, and charge distributions.

Effects of donor-acceptor groups on the structural and electronic properties of 4-(methoxymethyl)-6-methyl-5-nitro-2-oxo-1,2-dihydropyridine-3-carbonitrile.

Quantum chemical calculations on the geometric parameters, harmonic vibrational wavenumbers and 1H and 13C nuclear magnetic resonance (NMR) chemical shifts values of 4-(methoxymethyl)-6-methyl-5-nitro-2-oxo-1,2-dihydropyridine-3-carbonitrile [C9H9N3O4] molecule in ground state were performed using the ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The results of optimized molecular structure were presented and compared with X-ray diffraction results. The theoretical vibrational frequencies and 1H and 13C NMR chemical shifts values were compared with experimental values of the investigated molecule. The observed and calculated values were found to be in good agreement. Since the title compound contains different electron-donor and -acceptor groups as well as lone pair electrons, and multiple bonds, the effects of these groups on the structural and electronic properties are found out. In addition, conformational, natural bond orbital (NBO), nonlinear optical (NLO) analysis, frontier molecular orbital energies, molecular surfaces, Mulliken charges and atomic polar tensor based charges were investigated using HF and DFT methods.

Quantum chemical calculations on the geometrical, conformational, spectroscopic and nonlinear optical parameters of 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine.

The optimized geometry, (1)H and (13)C NMR chemical shifts, conformational and natural bond orbital (NBO) analyses, thermodynamic parameters, molecular surfaces, Mulliken, NBO and APT charges for 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine [C7H7Cl3N2] were investigated by the ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The calculated structural parameters (bond lengths, bond angles and dihedral angles) and (1)H and (13)C NMR chemical shifts values are compared with experimental values of the investigated compound. The observed and the calculated values are found to be in good agreement. The energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were calculated, and the obtained energies displayed that charge transfer occurs in 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine compound. In addition, the linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated compound have been computed by using HF and DFT methods.

Conformational, spectroscopic and nonlinear optical properties of biologically active N,N-dimethyltryptamine molecule: A theoretical study

The effective psychoactive properties of N,N-dimethyltryptamine (DMT) known as the near-death molecule have encouraged the imagination of many research disciplines for several decades. Although there is no theoretical study, a number of paper composed by experimental techniques have been reported for DMT molecule. In this study, the molecular modeling of DMT was carried out using B3LYP and HSEh1PBE levels of density functional theory (DFT). Our calculations showed that the energy gap between HOMO and LUMO is low, demonstrating that DMT is a biologically active molecule. Large hyperconjugation interaction energies imply that molecular charge transfer occurs in DMT. Moreover, NLO analysis indicates that DMT can be used an effective NLO material.

Quantum chemical computational studies on bis-thiourea zinc acetate

In this study, quantum chemical calculations of vibrational spectra, Raman spectra, electronic properties (total energy, dipole moment, electronegativity, chemical hardness and softness), Mulliken atomic charges and thermodynamic parameters of bis-thiourea zinc acetate (BTZA) have been performed using Gaussian 09 program. Additionally, nonlinear optical (NLO), conformational, natural bond orbital (NBO) analyses of BTZA have been carried out using the same program. The structural and spectroscopic data of the molecule in the ground state have been calculated using Hartree-Fock (HF) and density functional method (DFT/B3LYP) with the 6-311++G(d,p) basis set. In addition, the molecular frontier orbital energies (HOMO, HOMO-1, LUMO and LUMO+1) of the title compound have been calculated at the HF and B3LYP levels. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Finally, the calculated results were applied to simulate infrared and Raman spectra of the title compound which showed good agreement with the experimental ones.