Spectroscopic investigation on glutamic acid by Coulomb-attenuating and double hybrid density functional theory methods

This study deals with the identification of glutamic acid by means of quantum chemical approach. FT-IR, FT-Raman and UV–vis spectra were recorded in the region 4000–400, 4000–50 cm^? 1 and 200–600 nm, respectively. CAM-B3LYP/6-31G(d,p) and B2PLYP/6-31G(d,p) calculations were performed to obtain the optimised molecular structures, vibrational frequencies and corresponding vibrational assignment, thermodynamic properties and natural bonding orbital (NBO) analysis. The results show that the obtained optimised geometric parameters (bond lengths, bond angles and bond dihedrals) and vibrational frequencies were found to be in good agreement with the experimental results. The calculations of the electronic spectra were compared with the experimental ones. Furthermore, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses and UV–vis spectral analysis were also performed to determine the energy band gaps and transition states. NBO analysis, calculated using density functional theory methods (CAM-B3LYP/6-31G(d,p) and B2PLYP/6-31G(d,p)), was induced to find inter-molecular atoms. ¹³C and ¹H NMR isotropic chemical shifts were calculated and the assignments made were compared with the ChemDraw Ultra values.     

Experimental and DFT computational studies on 5-benzyl-4-(3,4-dimethoxyphenethyl)-2H-1,2,4-triazol-3(4H)-one

The triazole compound, 5-benzyl-4-(3,4-dimethoxyphenethyl)-2H-1,2,4-triazol-3(4H)-one, has been synthesized and characterized by ¹H-NMR, ¹³C-NMR, IR, and X-ray single-crystal determination. The compound crystallizes in the monoclinic space group P2₁ with a?=?11.8844(3) Å, b?=?17.5087(4) Å, c?=?17.3648(6) Å, β?=?99.990(2)? and Z?=?8. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) ¹H- and ¹³C-NMR chemical shift values of the title compound in the ground state have been calculated using the density functional method (B3LYP) with 6-31G(d,p) basis set. The calculated results show that the optimized geometries can well reproduce the crystal structure and the theoretical vibrational frequencies and chemical shift values show good agreement with experimental ones. Besides, molecular electrostatic potential (MEP), natural bond orbital (NBO), and frontier molecular orbitals (FMO) analysis of the title compound were performed by the B3LYP/6-31G(d,p) method.     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Molecular structure and vibrational and chemical shift assignments of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione by DFT and <Emphasis Type="Italic">ab initio</Emphasis> HF calculations

The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values and several thermodynamic parameters of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Also, calculated ¹H chemical shift values compared with the experimental ones. The data of the title compound display significant molecular structure and IR, NMR analysis provide the basis for future design of efficient materials having the of 1,2,4-triazole core.     

An experimental and theoretical approach to the molecular structure of 2-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]thiazol-2-yl}isoindoline-1,3-dione

The title compound, 2-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]thiazol-2-yl}isoindoline-1,3-dione (C₂₄H₂₂N₂O₂S), was synthesized and characterized by IR-NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a?=?19.7799(13) Å, b?=?6.7473(4) Å, c?=?15.7259(9) Å and β?=?103.416(5)°. In addition, the molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values of the title compound in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets, and compared with the experimental data. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 5°. Besides, molecular electrostatic potential, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were investigated by theoretical calculations.     

Raman,FT-IR spectroscopic analysis and first-order hyperpolarisability of 3-benzoyl-5-chlorouracil by first principles

3-Benzoyl-5-chlorouracil (3B5CU), a biologically active synthetic molecule, has been analysed at DFT/6-311+ + G(d,p) level and reported for the first time as a potential candidate for nonlinear optical (NLO) applications. The optimised skeleton of 3B5CU molecule is non-planar. The frontier orbital energy gap, dipole moment, polarisability and first static hyperpolarisability have been calculated. The first static hyperpolarisability is found to be almost 15 times higher than that of urea. The high value of first static hyperpolarisability (2.930 × 10^? 30 e.s.u.) due to the intra-molecular charge transfer in 3B5CU has been discussed using first principles. A complete vibrational analysis of the molecule has been performed by combining the experimental Raman, FT-IR spectral data and the quantum chemical calculations. In general, a good agreement of calculated modes with the experimental ones has been obtained. The strong vibrational modes contributing towards NLO activity, involving the whole charge transfer path, have been identified and analysed.     

Quantum chemical study of the structure and properties of citrinin

Detailed structures and electronic properties of three tautomeric forms of the toxin citrinin were investigated using several quantum calculation methods. Energetic preference of the predominant p- and o-quinone methide tautomeric forms is dependent on the method of calculation. A previously unstudied carboxylic acid enol tautomer was calculated to be surprisingly stable in vacuo, being within 2.5 kcal mol^? 1 at the B3LYP/6-311++G(2d,2p) level of theory. Despite differences in bond nature and connectivity of tautomers, the natural bond orbital analysis revealed that tautomeric forms share similar natural charges and natural electron configurations. Calculated bond lengths corresponded with experimentally observed values and assignments for the calculated infrared vibrational frequencies are reported.     

Zwitterionic conformers of pyrrolysine and their interactions with metal ions—a theoretical study

A total of 16 pyrrolysine conformers in their zwitterionic forms are studied in gas and simulated aqueous phase using a polarizable continuum model (PCM). These conformers are selected on the basis of our study on the intrinsic conformational properties of non-ionic pyrrolysine molecule in gas phase [Das and Mandal (2013) J Mol Model 19:1695?1704]. In aqueous phase, the stable zwitterionic pyrrolysine conformers are characterized by full geometry optimization and vibrational frequency calculations using B3LYP/6-311++G(d,p) level of theory. Single point calculations are also carried out at MP2/6-311++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. The calculated relative energy range of the conformers at B3LYP/6-311++G(d,p) level is 5.19 kcal mol^?1 whereas the same obtained by single point calculations at MP2/6-311++G(d,p) level is 4.58 kcal mol^?1. A thorough analysis reveals that four types of intramolecular H-bonds are present in the conformers; all of which play key roles in determining the energetics and in imparting the observed conformations to the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of the H-bonds. This study also points out that conformers with diverse structural motifs may differ in their thermodynamical stability by a narrow range of relative energy. The effects of metal coordination on the relative stability order and structural features of the conformers are examined by complexing five zwitterionic conformers of pyrrolysine with Cu⁺² through their carboxylate groups. The interaction enthalpies and Gibbs energies, rotational constants, vibrational frequencies and dipole moments of the metal complexes calculated at B3LYP level are also reported. The zwitterionic conformers of pyrrolysine are not stable in gas phase; after geometry optimization they are converted to the non-ionic forms.     

Molecular structure and effects of intermolecular hydrogen bonding on the vibrational spectrum of trifluorothymine, an antitumor and antiviral agent

In the present work, the experimental and the theoretical vibrational spectra of trifluorothymine were investigated. The FT-IR (400-4000?cm(-1)) and μ-Raman spectra (100-4000?cm(-1)) of trifluorothymine in the solid phase were recorded. The geometric parameters (bond lengths and bond angles) and vibrational frequencies of the title molecule in the ground state were calculated using ab initio Hartree-Fock (HF) method and density functional theory (B3LYP) method with the 6-31++G(d,p) and 6-311++G(d,p) basis sets for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with results found in the literature. Vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of trifluorothymine was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H?O hydrogen bonds.     

Experimental and theoretical investigation of the molecular and electronic structure of 5-(4-aminophenyl)-4-(3-methyl-3-phenylcyclobutyl)thiazol-2-amine

The title molecule, 5-(4-aminophenyl)-4-(3-methyl-3-phenylcyclobutyl)thiazol-2-amine (C₂₀H₂₁N₃S), was prepared and characterized by ¹H-NMR, ¹³C-NMR, IR and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a?=?9.4350(5) Å, b?=?11.2796(6) Å, c?=?18.4170(8) Å and β?=?113.378(3)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H- and ¹³C-NMR chemical shift values and atomic charges distribution of the title compound in the ground state have been calculated using the Hartree–Fock (HF) and density functional method (DFT) (B3LYP) with 6-31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis was performed by the B3LYP/6-31G(d) method.     

Density functional and Møller–Plesset studies of cyclobutanone⋯HF and ⋯HCl complexes

The molecular structure (hydrogen bonding, bond distances and angles), dipole moment and vibrational spectroscopic data [vibrational frequencies, IR and vibrational circular dichroism (VCD)] of cyclobutanone?HX (X?=?F, Cl) complexes were calculated using density functional theory (DFT) and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6–311G, 6–311G^**, 6–311 + + G^**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2 and B3LYP levels with basis sets including diffuse functions. Surface potential energy calculations were carried out with scanning HCl and HF near the oxygen atom. The nonlinear hydrogen bonds of 1.81 Å and 175° for HCl and 1.71 Å and 161° for HF were calculated. In these complexes the C=O and H–X bonds participating in the hydrogen bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and the band assignments reported are in excellent agreement with experimental IR spectra. The C=O stretching vibrational frequencies of the complexes show red shifts with respect to cyclobutanone.     

Electronic structure simulations of 2,6-dimethyl-2,5-heptadien-4-one by FTIR,FT-Raman,NMR, UV–vis,NBO and density functional theory

Density functional theory (DFT) (B3LYP and B3PW91) calculations have been carried out for 2,6-dimethyl-2,5-heptadien-4-one (DMHD4O) using 6–311++ G** basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out from the FTIR and FT-Raman spectral data. The theoretical electronic absorption has been calculated by using time-dependent DFT (TD-DFT) methods and compared with the experimental spectra. The theoretically computed Frontier energy gaps and TD-DFT calculations are in good agreement with the experimental UV–vis spectral absorption. The chemical hardness measured from the Frontier molecular orbital energies of DMHD4O is 0.0693 eV. Electronic stability of the compound arising from hyperconjugative interactions and charge delocalisation were also investigated based on the natural bond orbital (NBO) analysis. Effective stabilisation energy E ⁽²⁾ associated with the interactions of the π and the lone pair of electrons was determined by the NBO analysis. ¹³C and ¹H NMR chemical shifts of the compound have been calculated by means of Gauge-Invariant Atomic Orbital using B3LYP/6–311++ G** method. The partial ionic character of the carbonyl group due to resonance render a partially positive charge to the carbonyl carbon, and thus C4 chemical shift lie in the very downfield 191.6 ppm. Comparison between the experimental and the theoretical results indicates that B3LYP method is able to provide satisfactory results for predicting vibrational, electronic and NMR properties.     

Density functional theory and ab initio studies of vibrational spectra of 2-bis (2-chloroethyl) aminoperhydro-1,3,2-oxazaphosphorinane-2-oxide

The Fourier transform Raman (FTR) and Fourier transform infrared (FTIR) spectra of 2-bis (2-chloroethyl) aminoperhydro-1,3,2-oxazaphosphorinane-2-oxide were recorded in the regions 4000–100 cm^? 1 and 4000–400 cm¹, respectively, in the solid phase. Molecular electronic energy, geometrical structure, harmonic vibrational spectra, infrared intensities and Raman scattering activities, highest occupied molecular orbital, lowest unoccupied molecular orbital energy, energy gaps and thermodynamical properties such as zero-point vibrational energies, rotational constants, entropies and dipole moment were computed at the Hartree–Fock/6-31G(d,p) and three parameter hybrid functional Lee–Yang–Parr/6-31G(d,p) levels of theory. The vibrational studies were interpreted in terms of potential energy distribution. The results were compared with experimental values with the help of scaling procedures. The observed wave number in FTIR and FTR spectra was analysed and assigned to different normal modes of the molecule. Most of the modes have wave numbers in the expected range and are in good agreement with computed values.     

A theoretical study of cooperative and anticooperative effects on hydrogen-bonded clusters of water and the cyanuric acid

Ab initio and density functional calculations are used to analyse the interaction between a molecule of the cyanuric acid and one, two and three molecules of water at B3LYP/6-311++ G(d,p) and MP2/6-311++ G(d,p) computational levels. Also, the cooperative effect (CE) in terms of the stabilisation energy of clusters is calculated and discussed. Depending on the geometry of clusters under study, the cooperative, non- or anti-CE was found with an increasing cluster size. Red shifts of N–H and C = O stretching frequencies illustrate a good dependence on the CE. The atoms in molecules theory is used to analyse the CE on topological parameters.     

Density functional theory,restricted Hartree–Fock simulations and vibrational spectroscopic studies of nicorandil

Fourier transform infrared and Raman spectra of nicorandil have been recorded. The structure, conformational stability, geometry optimisation and vibrational frequencies have been investigated. Complete vibrational assignments were made for the stable conformer of the molecule using restricted Hartree–Fock (RHF) and density functional theory (DFT) calculations (B3LYP) with the 6-31G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of the molecule and calculated results by RHF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. Natural bond order analysis of the title molecule was also carried out. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibration modes.     

Spectroscopic (FTIR,FT-Raman,NMR and UV) and molecular structure investigations of 1,5-diphenylpenta-2,4-dien-1-one: a combined experimental and theoretical approach

The title molecule 1,5-diphenylpenta-2,4-dien-1-one (cinnamylideneacetophenone, CA) has been synthesised and characterised by FTIR, FT-Raman, NMR and UV–vis spectral analyses. The possible stable conformers of the CA molecule were searched by potential energy surface scan at B3LYP level of theory. The molecular geometry from X-ray determination of the CA molecule in the ground state has been compared using the density functional theory (DFT) with 6-31G(d,p) basis set. The harmonic vibrational modes, the corresponding wavenumbers and IR and Raman intensities of most stable conformer were calculated by the DFT method. The assignments of the fundamentals were proposed on the basis of total energy distribution calculations. The calculated ¹³C and ¹H NMR chemical shifts using gauge including atomic orbitals approach are in good agreement with the observed chemical shifts. The molecular stability and bond strength have been investigated by applying natural bond orbital analysis. Using the time-dependent DFT method, the electronic absorption spectrum of the title compound has been predicted and the electronic transitions within the molecule have been interpreted. The molecular electrostatic potential map was used for predicting possible hydrogen and oxygen bonding sites in the CA molecule.     

Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations

This study examined absorption properties of 2-styrylpyridine, trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)]pyridine, and trans-4-(m-cyanostyryl)pyridine compounds based on theoretical UV/Vis spectra, with comparisons between time-dependent density functional theory (TD-DFT) using B3LYP, PBE0, and LC-ωPBE functionals. Basis sets 6–31G(d), 6–31G(d,p), 6–31+G(d,p), and 6–311+G(d,p) were tested to compare molecular orbital energy values, gap energies, and maxima absorption wavelengths. UV/Vis spectra were calculated from fully optimized geometry in B3LYP/6–311+G(d,p) in gas phase and using the IEFPCM model. B3LYP/6–311+G(d,p) provided the most stable form, a planar structure with parameters close to 2-styrylpyridine X-ray data. Isomeric structures were evaluated by full geometry optimization using the same theory level. Similar energetic values were found: ～4.5 kJ?mol^?1 for 2-styrylpyridine and ～1 kJ?mol^?1 for derivative compound isomers. The 2-styrylpyridine isomeric structure differed at the pyridine group N-atom position; structures considered for the other compounds had the cyano group attached to the phenyl ring m-position equivalent. The energy difference was almost negligible between m-cyano-substituted molecules, but high energy barriers existed for cyano-substituted phenyl ring torsion. TD-DFT appeared to be robust and accurate approach. The B3LYP functional with the 6–31G(d) basis set produced the most reliable λ_max values, with mean errors of 0.5 and 12 nm respect to experimental values, in gas and solution, respectively. The present data describes effects on the λ_max changes in the UV/Vis absorption spectra of the electron acceptor cyano substituent on the phenyl ring, the electron donor methyl substituent, and the N-atom position on the electron acceptor pyridine ring, causing slight changes respect to the 2-styrylpyridine title compound.     

Molecular structure,vibrational spectra and first-order hyperpolarisability analysis of 2-amino-6-nitrobenzothiazole by DFT method

Vibrational analysis of 2-amino-6-nitrobenzothiazole (2A6NBT) molecule has been carried out at room temperature using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of the density functional theory DFT method. The non-linear optical (NLO) behaviour of the examined molecule has been studied followed by the determination of the electric dipole moment μ, the polarisability α and hyperpolarisability β using HF/6-31G(d,p) method. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation have been analysed using the natural bond orbital analysis. The results show that charge in electron density in the σ^* and π^* antibonding orbitals and second-order delocalisation energies (E²) confirms the occurrence of intramolecular charge transfer within the molecule. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis following the scaled quantum mechanical force field methodology. The energy and oscillator strength calculated by time-dependent density functional theory complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental spectra.     

Methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate:A combined experimental and theoretical investigation

The title compound, methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate (C₂₅H₂₀O₇), was prepared and characterized by IR and single-crystal X-ray diffraction (XRD). The compound crystallizes in the triclinic space group P ?1 with a?=?8.9554(9) Å, b?=?10.0018(10) Å, c?=?12.7454(13) Å, α?=?67.678(7)°, β?=?89.359(8)° and γ?=?88.961(8)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry and vibrational frequencies of the title compound in the ground state have been calculated using semiempirical AM1 and PM3 methods, as well as Hartree-Fock (HF) and density functional (B3LYP) levels of theory with 6–31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were performed by the B3LYP/6–31G(d) method.     

Molecular geometry,vibrations and electrode potentials of 2-(4,5-dihydroxy-2-methylphenyl)-2-phenyl-2H-indene-1,3-dione; experimental and theoretical attempts

The electrode potential of 2-(4,5-dihydroxy-2-methylphenyl)-2-phenyl-2H-indene-1,3-dione (DMPID) in acetonitrile has been calculated. The calculations were performed using ab initio molecular orbital calculations (HF), and density functional theory (DFT) with the inclusion of entropic and thermochemical corrections to yield free energies of redox reactions. The electrode potential of DMPID was also obtained experimentally with the aid of an electrochemical technique (cyclic voltammetry). The values for geometric parameters and the vibrational frequencies of DMPID and 2-(6-methyl-3,4-dioxocyclohexa-1,5-dienyl)-2-phenyl-2H-indene-1,3-dione (MDPID) were also computed using the same levels with the basis set of 6-31G(d). The calculated IR spectrum of DMPID used for the assignment of IR frequencies was observed in the experimental FT-IR spectrum and the calculated IR and FT-IR observed spectra of DMPID were compared with correlation factor of 0.996. It should be mentioned that the present work is the first research on coagulant derivative molecules in which the electrode potential of a molecule is calculated. Optimized structures of 2-(6-methyl-3,4-dioxocyclohexa-1,5-dienyl)-2-phenyl-2H-indene-1,3-dione (MDPID)