Experimental IR, Raman, and UV-Vis Spectra DFT Structural and Conformational Studies: Bioactivity and Solvent Effect on Molecular Properties of Methyl-Eugenol.

Structural, conformational, and spectroscopic investigations of methyl-eugenol were made theoretically at the B3LYP-6-311++G**level. Experimental IR, Raman, and UV-vis spectra were investigated and analyzed in light of the computed quantities. Conformational analysis was carried out with the help of total energy vs. dihedral angle curves for different tops, yielding 21 stable conformers, out of which only two have energies below the room temperature relative to the lowest energy conformer. The effect of the solvent on different molecular characteristics was investigated theoretically. MEP and HOMO-LUMO analysis were carried out and barrier heights and bioactivity scores were determined. The present investigation suggests that the molecule has three active sites with moderate bioactivity. The solvent-solute interaction is found to be dominant in the vicinity of the methoxy moieties.

Structural and vibrational study of a neurotransmitter molecule: Dopamine [4-(2-aminoethyl) benzene-1,2-diol].

Structural and vibrational studies for the most stable conformer of dopamine {4-(2-Aminoethyl) benzene-1, 2-diol} have been carried out at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. The IR and Raman spectra have been recorded and analyzed in light of the computed vibrational parameters using the DFT and the PEDs computed with the help of the GAR2PED software. Some of the fundamentals have considerably changed frequencies in going from benzene to dopamine. Except the rocking and wagging modes of the NH2 group the other four modes are pure group modes. The rocking and wagging modes of the NH2 group show mixing with the other modes. The two OH stretching vibrations are highly localized modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO study suggests the existence of charge transfer within the molecule and the energy gap supports the pharmacological active property of the dopamine molecule. The NBO analysis has been carried out to understand the proper and improper hydrogen bonding.

Comparative structural and vibrational study of the four lowest energy conformers of serotonin.

A computational investigation of all possible lowest energy conformers of serotonin was carried out at the B3LYP/6-311++G** level. Out of the 14 possible lowest energy conformers, the first 4 conformers were investigated thoroughly for the optimized geometries, fundamental frequencies, the potential energy distributions, APT and natural charges, natural bond orbital (NBO) analysis, MEP, Contour map, total density array, HOMO, LUMO energies. The second third and fourth conformers are energetically at higher temperatures of 78, 94 and 312K respectively with respect to the first one. Bond angles and bond lengths do not show significant variations while the dihedral angles vary significantly in going from one conformer to the other. Some of the vibrational modes of the indole moiety are conformation dependent to some extent whereas most of the normal modes of vibration of amino-ethyl side chain vary significantly in going from one conformer to conformer. The MEP for the four conformers suggested that the sites of the maximum positive and negative ESP change on changing the conformation. The charges at some atomic sites also change significantly from conformer to conformer.

DFT-B3LYP computations of electro and thermo molecular characteristics and mode of action of fungicides (chlorophenols).

Density functional theoretical (DFT) calculations of the pesticides; 2-chlorophenol (2-CP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP) have been carried out using 6-311++G** basis set available on Gaussian-09 software in order to optimize the molecular structures. The optimized geometry of the molecules has been found to possess Cs symmetry. The charge transfer phenomena occurring in the molecules have been exhibited by (HOMO-LUMO) analysis. The molecular ESP values and mappings of electron density iso-surface with the molecular electrostatic potential (MEP), have been carried out to achieve the information of the size, shape, charge density distribution and site of chemical reactivity of the molecules. Thermo molecular characteristics have been computed to achieve essential environmental influence on the activities of fungicides.

Investigation of crystal structure, vibrational characteristics and molecular conductivity of 2,3-dichloro-5,6-dicyno-p-benzoquinone.

Molecular geometries and vibrational spectra for the ground state of 2,3-dichloro-5,6-dicyno-p-benzoquinone (DDQ) and its anion (DDQ(-)) were computed using DFT method at the B3LYP level employing 6-311++G(d,p) basis set whereas for the first excited state (DDQ(∗)), these were calculated using TD-DFT at the B3LYP level employing the 6-311++G(d,p) basis set available with the Gaussian 09 package. The spectra have been experimentally investigated and the observed IR and Raman bands have been assigned to different normal modes on the basis of the calculated potential energy distributions (PEDs). XRD of single crystal has been investigated to determine molecular and crystal structures of DDQ. In order to elucidate the transfer of electrons, electronic structure and electronic absorption have been calculated with the TD-DFT method. Vibronic interaction and its role in the appearance of superconductivity in the DDQ, DDQ(-) and DDQ(∗) molecules have been investigated. The present XRD, molecular, electronic and vibronic studies indicate that mainly the ag C=O stretching and ring stretching modes participate in the charge transfer process.

Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion.

Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5C6 bond length increases and loses its double bond character while the C4C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled NH stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule.

The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G(**) level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G(**) method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed.

Experimental Raman and IR spectral and theoretical studies of vibrational spectrum and molecular structure of Pantothenic acid (vitamin B5).

Vibrational spectrum of Pantothenic acid has been investigated using experimental IR and Raman spectroscopies and density functional theory methods available with the Gaussian 09 software. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed using GAR2PED software. Optimized geometrical parameters suggest that the overall symmetry of the molecule is C1. The molecule is found to possess eight conformations. Conformational analysis was carried out to obtain the most stable configuration of the molecule. In the present paper the vibrational features of the lowest energy conformer C-I have been studied. The two methyl groups have slightly distorted symmetries from C3V. The acidic OH bond is found to be the smallest one. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.

Synthesis, characterization and quantum chemical investigation of molecular structure and vibrational spectra of 2,5-dichloro-3,6-bis-(methylamino)1,4-benzoquinone.

2,5-Dichloro-3,6-bis-methylamino-[1,4]benzoquinone has been synthesized by condensing methyl amine hydrochloride with chloranil in presence of condensing agent sodium acetate. FT-IR (4000-400 cm(-1)) and FT-Raman (4000-400 cm(-1)) spectral measurements of dmdb have been done. Ab initio and DFT (B3LYP/6-311+G(**)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, infrared intensities and Raman activities. The optimized molecular structure of the compound is found to possess C2h point group symmetry. A detailed interpretation of the observed IR and Raman spectra of dmdb is reported on the basis of the calculated potential energy distribution. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The thermodynamic functions of the title compound have also been computed.

Experimental and theoretical studies of vibrational spectrum and molecular structure and related properties of pyridoxine (vitamin B6).

Vibrational spectrum of pyridoxine has been investigated using experimental IR and Raman spectroscopic and density functional theory (DFT) methods. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed. Optimized geometrical parameters suggest that if the OH groups of the two methyl groups are replaced by H atoms the resulting molecule has Cs point group symmetry. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.

Vibrational studies of benzene, pyridine, pyridine-N-oxide and their cations.

IR and Raman spectra of pyridine and pyridine-N-oxide have been recorded and analyzed. The optimized molecular geometries, APT charges and vibrational characteristics for benzene, pyridine, pyridine-N-oxide and their cations have been computed using DFT method. Due to attachment of O atom at N site or removal of electron all the modes are affected in magnitudes. However, significant changes are noticed in their IR intensities, Raman activities and depolarization ratios of the Raman bands in going from pyridine to its N-oxide or in going from neutrals to their cations. It is interesting to note that in going from benzene to benzene cation charge redistribution takes place to reduce the symmetry from D6h to D2h. The calculated frequencies have been correlated with the experimental frequencies for the pyridine and pyridine-N-oxide molecules.

Theoretical DFT study on spectroscopic signature and molecular dynamics of neurotransmitter and effect of hydrogen removal.

Vibrational spectroscopic study has been made for the serotonin molecule and its deprotonated form. The Infrared and Raman spectra in optimum geometry of these two molecules are calculated using density functional theorem and the normal modes are assigned using potential energy distributions (PEDs) which are calculated using normal coordinate analysis method. The vibrational frequencies of these two molecules are reported and a comparison has been made. The effect of removal of the hydrogen atom from the serotonin molecule upon its geometry and vibrational frequencies are studied. Electronic structures of these two molecules are also studied using natural bond orbital (NBO) analysis. Theoretical Raman spectrum of serotonin at different exciting laser frequencies and at different temperatures are obtained and the results are discussed. Present study reveals that some wrong assignments had been made for serotonin molecule in earlier study.

Ab initio determination of geometries and vibrational characteristics of building blocks of organic super-conductors: TTF and its derivatives.

Molecular behavior of the building block {[2-(1,3-dithiole-2-ylidene)-1,3-dithiole] ≡ tetrathiafulvalene (TTF)} of organic superconductors have been investigated along with its three derivatives, namely, {[2-(1,3-dioxole-2-ylidene)-1,3-dioxole] ≡ tetraoxafulvalene (TOF)}; [2,2]-bi -[[1,3] oxathiolylidene] ≡ Der I and 2-(3H-Furan-2-ylidene)-[1,3] oxathiole ≡ Der II. The properties of the molecules such as molecular geometries, frontier MOs and vibrational spectra have been investigated by using DFT method at the B3LYP level employing 6-311++G(d,p) basis set. The geometrical parameters and atomic charges on various atomic sites of the TTF, TOF, Ders I and II suggest extended conjugation in these systems. The present calculations lead to the reassignments for of some of the fundamentals and new interpretations for some of the observed IR and Raman frequencies. One of the two modes involved in the Fermi resonance giving rise to the doublet 1555 and 1564 cm(-1) needed to be revised and another doublet 3083 and 3108 cm(-1) could be interpreted as a Fermi resonance doublet. Out of the two ν(C = C) modes under the a(1) species, the lower frequency mode is assigned to the ν(C = C) of the ring and the higher one to the ν(C = C) of the central C = C bond contrary to the assignment reported in literature. The conducting properties of these molecules depend mainly on this mode.

Experimental IR and Raman spectra and quantum chemical studies of molecular structures, conformers and vibrational characteristics of L-ascorbic acid and its anion and cation.

IR and spectra of the L-ascorbic acid (L-AA) also known as vitamin C have been recorded in the region 4000-50 cm(-1). In order to make vibrational assignments of the observed IR and Raman bands computations were carried out by employing the RHF and DFT methods to calculate the molecular geometries and harmonic vibrational frequencies along with other related parameters for the neutral L-AA and its singly charged anionic (L-AA(-)) and cationic (L-AA(+)) species. Significant changes have been found for different characteristics of a number of vibrational modes. The four ν(O-H) modes of the L-AA molecule are found in the order ν(O(9)-H(10))>ν(O(19)-H(20))>ν(O(7)-H(8))>ν(O(14)-H(15)) which could be due to complexity of hydrogen bonding in the lactone ring and the side chain. The CO stretching wavenumber (ν(46)) decreases by 151 cm(-1) in going from the neutral to the anionic species whereas it increases by 151 cm(-1) in going from the anionic to the cationic species. The anionic radicals have less kinetic stabilities and high chemical reactivity as compared to the neutral molecule. It is found that the cationic radical of L-AA is kinetically least stable and chemically most reactive as compared to its neutral and anionic species.

Vibrational fundamentals and natural bond orbitals analysis of some tri-fluorinated benzonitriles in ground state.

The theoretical IR and Raman spectra of the 2,3,4-, 2,3,6-, 2,4,5- and 3,4,5-tri-fluorobenzonitrile molecules have been calculated by using the density functional method in the ground state. The rigorous normal coordinate analyses based upon both an empirical force field and quantum chemical calculations have been performed and the detailed vibrational assignment has been made on the basis of the calculated potential energy distributions (PEDs). A comparison of molecular geometries, atomic charges and vibrational fundamentals of these molecules has been reported. The effects of fluorination upon the geometries, atomic charges and vibrational frequencies of benzonitrile have been discussed. Several ambiguities and contradictions in the previously reported vibrational assignments have been clarified. In addition, the variation of Raman intensity with excitation frequency and with temperature has also been studied.

Experimental IR and Raman spectra and quantum chemical studies of molecular structures, conformers and vibrational characteristics of nicotinic acid and its N-oxide.

FTIR and Raman spectra of nicotinic acid and its N-oxide have been recorded and analyzed. The stabilities, optimized molecular geometries, APT charges and vibrational characteristics for the two possible conformers of nicotinic acid and its N-oxide have been computed using DFT method. The E (trans) conformers of both the molecules are found to be more stable and less polar than their respective Z (cis) conformers. Due to addition of an O atom at the N1 site in nicotinic acid the magnitudes of atomic charges on all the H atomic sites of the nicotinic acid N-oxide molecule are found to increase. Most of the vibrational frequencies have nearly the same magnitude for the two conformers of both the molecules. However, significant changes are noticed in their IR intensities, Raman activities and depolarization ratios of the Raman bands. The calculated frequencies have been correlated with the experimental frequencies.

FTIR and Raman spectra and optimized geometry of 2,3,6-tri-fluorobenzoic acid dimer: a DFT and SQMFF study.

Raman and FTIR spectra of the 2,3,6-tri-fluorobenzoic acid molecule have been recorded in the regions 50-4000cm⁻¹ and 400-4000cm⁻¹, respectively. Vibrational frequencies have been calculated by employing DFT method in dimeric form in optimum state. SQM force field has also been used to calculate potential energy distributions in order to make conspicuous vibrational assignments. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. Optimized bond lengths and angles of the title molecule have been interpreted and compared with the earlier reported experimental values for benzoic acid and some mono and di-fluorinated benzoic acids. Some of the vibrational frequencies of the title molecule are effected upon profusely with the fluorine substitutions in comparison to benzoic acid and these differences have been interpreted. The strong doubly hydrogen-bonded interface of the dimerized system is well demonstrated by the red shift in OH stretching frequency concomitant with the elongation of bond length.

Ab initio determination of geometries and vibrational characteristics of building blocks of organic superconductors: 4,5-Ethylenedithio-1,3-dithiole-2-thione, and 4,5-ethylenedithio-1,3-dithiole-2-one.

RHF and DFT calculations were carried out to study the optimized molecular geometries and vibrational characteristics of the 4,5-ethylenedithio-1,3-dithiole-2-thione (EDT-DTT) and 4,5-ethylenedithio-1,3-dithiole-2-one (EDT-DTO) molecules and their radical cations and anions. It is found that the anionic radical of the EDT-DTO molecule is unstable. Both the neutral molecules and their radical cations have non-planar structures with C(2) symmetry while the radical anion of the EDT-DTT molecule has non-planar structure with C(1) symmetry. It is found that the most of the vibrational characteristics of the radicals are similar to their corresponding neutral molecules, however, for some of the modes significant changes are noticed. As a result of anionic radicalization of EDT-DTT, the IR intensity and Raman activity increase and Raman band becomes polarized for both the CH(2) twisting modes. Drastic enhancements in the Raman activity and reduced IR intensity are noticed for the C=S/O stretching mode in going from neutral molecules to their radical ions consistent with charge separation along this bond. The C=S and C=C stretching wavenumber changes are consistent with corresponding bond length changes in going from neutral to their radical ions.

Ab initio studies of molecular structures, conformers and vibrational spectra of heterocyclic organics: I. Nicotinamide and its N-oxide.

FTIR spectra of nicotinamide and its N-oxide have been recorded and analyzed in the range 400-4000 cm(-1). The stabilities, optimized molecular geometries, APT charges and vibrational characteristics for the two possible conformers of nicotinamide and its N-oxide have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. The E (trans) conformers of nicotinamide and its N-oxide are found to be more stable and less polar than their respective Z (cis) conformers. Due to addition of an O atom at the N(1) site in the NA molecule the magnitudes of atomic charges on all the H atomic sites are found to increase. For all the studied molecules, magnitude of the wagging mode of the NH(2) group is found to be higher than its torsion mode, which is in the reverse order as compared to that for the aniline molecule. Most of the vibrational frequencies have nearly the same magnitude for the two conformers of nicotinamide and its N-oxide, however, significant changes are noticed in their IR intensities, Raman activities and depolarization ratios of the Raman bands. The frequency of the ring breathing mode for the NA molecule is found to decrease by 100 cm(-1) in going to the NANO molecule for both the conformers. The IR intensity for the scissoring mode of the CON(H(2)) group is found to decrease significantly for the NA-II conformer as compared to that for the NA-I conformer.

DFT study of molecular geometries and vibrational characteristics of uracil and its thio-derivatives and their radical cations.

DFT calculations at the B3LYP/6-311++G** level have been carried out to study the vibrational characteristics of the neutral molecules, anionic and cationic radicals of uracil, 2-thiouracil and 4-thiouracil. In the U molecule, C=C bond loses its double bond character and magnitude of the C=C stretching frequency decreases significantly as a result of radicalization. Frequency for the in-plane deformation mode of C=O increases when a sulfur atom is substituted for the oxygen atom at the site C(2) in the uracil molecule but decreases when a sulfur atom is substituted for the oxygen atom at the site C(4). The magnitude of both the N-H stretching frequencies decreases in all the radical cations as compared to their neutral molecules. Radicalization leads to significant changes in the magnitudes and intensities corresponding to some of the normal modes for all the three cases. Removal of an electron leads to decrease in the electronic charge mainly from the sulfur atom in the case of 2-TU and 4-TU, whereas it is distributed over the sites N(1), C(5), O(8) and O(10) in case of the U molecule.