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

Conformational study of octopamine in gas phase and effect of hydrochloride

This work deals with the molecular modeling and vibrational spectra of all the twenty conformers of an important biomolecule octopamine which have been investigated using the DFT/B3LYP level of theory in combination with the 6-31++g(d,p) as a suitable basis set. The experimental FTIR and FTRaman spectra of octopamine neurotransmitter were recorded in the spectral region 400-4000 cm^-1 and 50-4000 cm^-1 respectively and correlated with the calculated spectra of the most stable conformer. The effect of hydrochloride on the important geometrical parameters of most stable conformer of octopamine was also studied. The normal coordinate analysis was performed to scale the theoretical frequencies and to calculate potential energy distributions for precise normal mode assignment. Most of the frequencies were in good agreement with experimental one. However, some have been modified. Natural bond orbital analysis was performed in order to confirm the stability of electronic structure of octopamine molecule. HOMO-LUMO analysis for all the twenty conformers was also performed to give the transition profile and to study the chemical reactivity of octopamine.

Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

The present work deals with the conformational and vibrational spectroscopic study of an important bio-molecule named norepinephrine in gas phase. The FTIR and FTRaman spectrum of norepinephrine in amorphous form were recorded in wavenumber range 4000-400 cm^-1 and 4000-50 cm^-1 respectively. We have investigated twenty-seven stable conformational structures of norepinephrine molecule. All the calculations have been done using Density Functional Theory with exchange functional B3LYP incorporated with the 6-31++G(d, p) basis set. The effect of hydrochloride on different bond lengths, bond angles and dihedral angles in the most stable conformer has also been studied. The total potential energy distribution for both the most stable conformer and the most stable conformer in hydrochloride was performed with the help Normal coordinate analysis method. Most of the calculated vibrational frequencies are in good agreement with the experimental frequencies. The natural bond orbital analysis was also performed to ensure the stability of electronic structures of norepinephrine. To know chemical reactivity of norepinephrine molecule we have calculated the energy gap between HOMO and LUMO orbitals and it has found above 5 eV in all the conformers.

Conformational study of neutral histamine monomer and their vibrational spectra

Molecular modeling and potential energy scanning of histamine molecule, which is an important neurotransmitter, with respect to the dihedral angle of methylamine side chain have done which prefer three different conformers of histamine monomer. We have calculated molecular structures and vibrational spectra with IR and Raman intensities of these conformers using Density Functional Theory (DFT) with the exchange functional B3LYP incorporated with the basis set 6-31++G(d,p) and Hartree-Fock (HF) with the same basis set. We have also employed normal coordinate analysis (NCA) to scale the theoretical frequencies and to calculate potential energy distributions (PEDs) for the conspicuous assignments. Normal modes assignments of some of the vibrational frequencies of all the three conformers are in good agreement with the earlier reported experimental frequencies of histamine whereas others have modified. The standard deviations between the theoretical and experimental frequencies fall in the region 13-20cm(-1) for the three conformers. NBO analyses of histamine conformers were also performed. The net charge transfers from ethylamine side chain to the imidazole ring. The intensive interactions between bonding and anti-bonding orbitals are found in imidazole ring. The HOMO-LUMO energy gap is nearly 5.50eV.

Spectroscopic signatures and structural motifs in isolated and hydrated serotonin: a computational study

The conformational landscapes of neutral serotonin characterized by MP2, CC2 and DFT methods. The Gph-out/anti conformation is found most stable.

FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach

In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

Theoretical vibrational spectra and thermodynamics of organic semiconductive tetrathiafulvalene and its cation radical

Molecular structure in optimum geometry and vibrational frequencies of pentafulvalene [bicyclopentyliden-2,4,2',4'-tetraene], tetrathiafulvalene [2,2'-bis(1,3-dithiolylidene)] and its cation are calculated. All the calculations are carried out by employing density functional theory incorporated with a suitable basis set. Normal coordinate analysis is also employed to scale the DFT calculated frequencies and to calculate potential energy distributions. The molecular structures and vibrational frequencies are compared for both the pentafulvalene and tetrathiafulvalene molecules. The effect upon geometry and vibrational frequencies of TTF due to charge transfer has also been studied. The vibrational partition function and hence, the thermodynamical properties, such as Helmholtz free energy, entropy, specific heat at constant volume and enthalpy are also calculated and compared for the title molecules. The reason of conductivity of tetrathiafulvalene has been tried to explain on the basis of molecular geometry and normal modes. Study of vibrational partition function exhibits that below 109 K, PFV starts to condense.