FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2-amino-5-chloropyridine

Spectroscopic characterization, DFT, antimicrobial activity and molecular docking studies on 4,5-bis[(E)-2-phenylethenyl]-1H,1'H-2,2'-biimidazole

The newly synthesized imidazole derivative namely, 4,5-bis[(E)-2-phenylethenyl]-1H,1'H-2,2'-biimidazole (KA1), was studied for its molecular geometry, docking studies, spectral analysis and density functional theory (DFT) studies. Experimental vibrational frequencies were compared with scaled ones. The reactivity sites were determined using average localized ionization analysis (ALIE), electron localized function (ELF), localized orbital locator (LOL), reduced density gradient (RDG), Fukui functions and frontier molecular orbital (FMO). Due to the solvent effect, a lower gas phase energy gap was observed. Through utilization of the noncovalent interaction (NCI) method, the hydrogen bond interaction, steric effect and Vander Walls interaction were investigated. Molecular docking simulations were employed to determine the specific atom inside the molecules that exhibits a preference for binding with protein. The parameters for the molecular electrostatic potential (MESP) and global reactivity descriptors were also determined. The thermodynamic characteristics were determined through calculations employing the B3LYP/cc-pVDZ basis set. Antimicrobial activity was carried out using the five different microorganisms like Escherichia coli, Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae and Candida albicans.

Novel benzoylthiourea derivatives had differential anti-inflammatory photodynamic therapy potentials on in vitro stimulated mammalian macrophages

Novel benzoylthioureas, N-((5-chloropyridin-2yl)carbamothioyl)benzamide, (HL¹), N-((2-chloropyridin-3yl)carbamothioyl)benzamide, (HL²), N-((5-bromopyridin-2yl)carbamothioyl)benzamide, (HL³) and N-(Naphthalene-1-yl(phenyl)carbamothioyl)benzamide, (HL⁴), were synthesized. Their characterizations were made by FT-IR,¹H NMR and ¹³C NMR spectrophotometric analysis. Single crystal X-ray diffraction measurements were conducted to determine the crystal structure of HL¹ and HL⁴.  The HL¹ crystallization conditions are: in the monoclinic crystal system with P2₁/c space group, Z = 2, a = 8.118(2) Å, b = 12.056(3) Å, c = 13.753(4) Å. HL⁴crystallization conditions are: in the orthorhombic crystal system with Pbca space group, Z = 8, a = 19.597(9) Å, b = 8.270(4) Å, c = 24.299(11) Å. Investigation of photodynamic and antiinflamatory effects of these compounds revealed that they are potent adducts. Using these derivatives, mammalian macrophages were stimulated with LPS to test their anti-inflammatory activity. Based on pro-inflammatory cytokine production levels, the photodynamic anti-inflammatory activity of these adducts were found to differ. Our results showedthat benzoylthioureas can be used as potential photodynamic therapy agents to suppress the excessive inflammatory reactions encountered in autoimmune and inflammatory disorders.

Vibrational spectra, normal coordinate analysis, and hydrogen bond investigation of pyridinium perchlorate

The IR and Raman spectra of pyridine perchlorate salt (PyHClO₄) have been recorded in the 4000-300 and 3200-200cm^-1 regions, respectively. The structure and vibrational spectra of pyridine salt have been investigated by means of ab initio and density functional theory (DFT) calculations. To examine the efficiency of basis sets in predicting the vibrational spectra of ClO₄^-1 ion, several basis sets were used with the B3LYP and B2PLYP levels of theory. It was shown that the 6-311(3df) basis set gives reasonably vibrational wavenumbers for simulation of perchlorate ion experimental vibrational wavenumbers. Therefore, the B3LYP/6-311G(3df) level was used to calculate the vibrational spectra of pyridine perchlorate salt in CH₃CN solution. For comparison, the vibrational wavenumbers were also calculated at the B3LYP/aug-cc-pVTZ level. The geometry of PyHClO₄ was calculated in the gas phase as well as in solutions, using SCRF-PCM method. According to these calculations, the structure and hydrogen bonding in PyHClO₄ is highly affected by media. Two hydrogen bonding systems between ClO₄^-1 and pyridinium ions were recognized. The nature of these hydrogen bonds is theoretically investigated by using atoms in molecule (AIM) method and natural bond orbital (NBO) analysis. A normal coordinate analysis was performed by using the internal coordinates calculated at the B3LYP/6-311G(3df,p) level for the vibrational normal modes of the titled compound.

Investigation of structure, vibrational, electronic, NBO and NMR analyses of 2-chloro-4-nitropyridine (CNP), 2-chloro-4-methyl-5-nitropyridine (CMNP) and 3-amino-2-chloro-4-methylpyridine (ACMP) by experimental and theoretical approach

This study reports about the optimized molecular structures, vibrational wavenumbers, atomic charges, molecular electrostatic potentials, NBO, electronic properties, (1)H NMR and (13)C NMR chemical shifts for the molecules 2-chloro-4-nitropyridine (CNP), 2-chloro-4-methyl-5-nitropyridine (CMNP) and 3-amino-2-chloro-4-methylpyridine (ACMP). Theoretical calculations were performed by density functional theory (DFT)/B3LYP method using 6-311++G (d,p) basis set. The stability and charge delocalization of the title molecules were studied by natural bond orbital (NBO) analysis. Molecular electrostatic potential maps (MEP) were calculated to predict the reactive sites. The reactivity of the title compounds were investigated by HOMO-LUMO energies and global descriptors. The electronic properties of the compounds were also discussed and the transitions were found to be π→π(∗). In addition, the thermodynamic properties were studied for the title compounds and corresponding relations between the properties and temperature were also discussed. The hyperpolarizability values (βtot) were calculated for the title compounds. Hyperpolarizability value (βtot) of CMNP was found to be high and nineteen times greater than that of urea.

DFT simulations and vibrational spectra of 2-amino-2-methyl-1,3-propanediol

The FTIR and FT-Raman spectra of 2-amino-2-methyl-1,3-propanediol were recorded in the regions 4000-400cm(-1) and 4000-50cm(-1) respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and density functional method (B3LYP) with the augmented-correlation consistent-polarized valence double zeta (aug-cc-pVDZ) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed on the basis of the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Mulliken charges were calculated using both Hartee-Fock and density functional method using the aug-cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. (1)H and (13)C NMR chemical shifts of the molecule were calculated using Gauge-Independent Atomic Orbital (GIAO) method and were compared with experimental results.

Spectroscopic analysis of 3-Bromodiphenylamine with experimental techniques and quantum chemical calculations

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 3500-100cm(-1) and 4000-400cm(-1), respectively, for 3-Bromodiphenylamine (3BDPA). Theoretical calculations were performed by using Density Functional Theory (DFT) method with 6-31G(d,p) and 6-311++G(d,p) basis sets. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The calculated wavenumbers were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. The frontier orbital energy gap and dipole moment illustrates the high reactivity of the title molecule. The first order hyperpolarizability (β0) and related properties (μ, α and Δα) of the molecule were also calculated. Stability of the molecule arising from hyperconjugative interactions and charge delocalization were analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) anti-bonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. Molecular electrostatic potential (MEP) and HOMO-LUMO energy levels are also constructed. The thermodynamic properties of the title compound were calculated at different temperatures and the results reveals the heat capacity (C), and entropy (S) increases with rise in temperature.

Ab initio/DFT calculations of butyl ammonium salt of O,O'-dibornyl dithiophosphate

O,O'-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other.

Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole

The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set.

Synthesis, spectroscopic characterization, X-ray structure and DFT studies on 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine

The title molecule, 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine (C(33)H(25)N(5)), was synthesized and characterized by elemental analysis, FT-IR spectroscopy, one- and two-dimensional NMR spectroscopies, and single-crystal X-ray diffraction. In addition, the molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) (1)H and (13)C NMR chemical shift values of the title compound in the ground state have been calculated using the density functional theory at the B3LYP/6-311G(d,p) level, and compared with the experimental data. The complete assignments of all vibrational modes were performed by potential energy distributions using VEDA 4 program. The geometrical parameters of the optimized structure are in good agreement with the X-ray crystallographic data, and the theoretical vibrational frequencies and GIAO (1)H and (13)C NMR chemical shifts show good agreement with experimental values. Besides, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMO) and non-linear optical properties of the title compound were investigated by theoretical calculations at the B3LYP/6-311G(d,p) level. The linear polarizabilities and first hyper polarizabilities of the molecule indicate that the compound is a good candidate of nonlinear optical materials. The thermodynamic properties of the compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures.

Molecular structure and vibrational spectra of 3-and 4-amino-2-bromopyridine by density functional methods

In this work, experimental and theoretical study on the molecular structure and the vibrational spectra of 3-amino-2-bromopyridine (Compound I) and 4-amino-2-bromopyridine (Compound II) are presented. The vibrational frequencies of these compounds were obtained theoretically by DFT/B3LYP employing the 6-311G(2df,2p) basis set for optimized geometries and were compared with Fourier Transform Infrared solid phase spectra (FTIR) in the region of 400-4000 cm(-1), FT-Raman spectra in the region of 100-4000 cm(-1) and with solution phase spectra in the region of 400-4000 cm(-1). Complete vibrational assignment, analysis and correlation of the fundamental modes for these compounds have been carried based on the potential energy distribution (PED). The vibrational harmonic frequencies were scaled using scale factors, yielding a good agreement between the experimentally recorded and the theoretically calculated values. Finally the calculated HOMO and LUMO energies are localized on the entire ring and substituents.

Spectroscopic (NMR, UV, FT-IR and FT-Raman) analysis and theoretical investigation of nicotinamide N-oxide with density functional theory

The spectroscopic properties of the nicotinamide N-oxide (abbreviated as NANO, C(6)H(6)N(2)O(2)) were examined by FT-IR, FT-Raman, NMR and UV techniques. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The (1)H and (13)C NMR spectra were recorded in DMSO. The UV absorption spectrum of the compound that dissolved in water was recorded in the range of 200-800 nm. The structural and spectroscopic data of the molecule in the ground state were calculated by using Density Functional Theory (DFT) employing B3LYP methods with the 6-311++G(d,p) basis set. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The optimized structure of compound was interpreted and compared with the reported experimental values. The observed vibrational wavenumbers, absorption wavelengths and chemical shifts were compared with calculated values. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.

Vibrational spectra and first order hyperpolarizability studies of dimethyl amino pyridinium 4-nitrophenolate 4-nitrophenol

Vibrational spectra of the organic nonlinear optical crystallized dimethyl amino pyridinium 4-nitrophenolate 4-nitrophenol have been recorded and analyzed. The spectral interpretation has been done based on the density functional theory using the standard B3LYP/LANL2DZ basis set. Total energy distribution is calculated using the scaled quantum mechanic program. Natural bond orbital analysis is also used to explain the inter and intra molecular hydrogen bonding. The relative second harmonic efficiency of the compound is found to be 15 times greater than that of KDP. The effect of intermolecular hydrogen bonding between the phenolate ion of 4-nitrophenol with N-atom of pyridine ring is sufficiently more, enhancing the β value which is the required property of a system to be NLO active.

Intramolecular charge delocalization and nonlinear optical properties of push-pull chromophore 1-(4-N,N-dimethylaminopyridinium) acetic acid bromide monohydrate from vibrational spectra

FT-Raman and FT-IR spectra of the nonlinear optical crystal 1-(4-N,N-dimethylaminopyridinium) acetic acid bromide monohydrate have been recorded and analyzed. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal have been calculated with the help of density functional theory computations. The assignments of the vibrational spectra have been carried out with the help of Scaled Quantum Mechanic force field theory. Optimized geometry gives the charge transfer interaction of the pyridine ring and the amino group in the electron-donor side of the nonlinear optic chromophore. Electron-phonon coupling and O-H⋯O interactions in making the molecule nonlinear optical active have been analyzed based on the vibrational spectral features. The Natural Bond Orbital analysis confirms the occurrence of strong intermolecular O-H⋯O hydrogen bonding.

Vibrational spectra and assignments of 2-amino-5-iodopyridine by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-5-iodopyridine were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set for C, N, H and LANL2DZ pseudopotential for I. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of 2-amino-5-iodopyridine is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.