M.E. Tuttolomondo

Structural and vibrational analysis of thymoquinone

The molecular structure of 2-isopropyl-5-methyl-1,4-benzoquinone, C(6)O(2)H(2) (CH(3))(3)CH, has been optimized using methods based on density functional theory (DFT) and Moller-Plesset second-order perturbation theory (MP2). As regards C(6)O(2)H(2) (CH(3))(3)CH, two populated conformations with C(1) (trans) and C(s) (cis) symmetries are obtained, the former being more stable than the latter. The theoretical data indicate that although both anti and cis conformers are possible by rotation about the C-C bond, the preferred conformation is trans. The effects governing the torsion barriers and preferred conformations were analyzed at B3LYP/6-311++G** level. The atoms in molecules (AIM) theory and natural bond orbital (NBO) analysis was applied to the cis and trans conformers in order to detect intramolecular contacts. Furthermore, the infrared spectra for the gas and solid phases and the Raman spectrum for the solid one, were recorded and the observed bands assigned to the vibrational modes.

Experimental and theoretical vibrational study of 2,2,2-trifluoroethyl trifluoromethanesulfonate, CF3SO2OCH2CF3

The infrared spectra of 2,2,2-trifluoroethyl trifluoromethanesulfonate (CF3SO2OCH2CF3) were obtained in the gaseous, liquid and solid states as well as the Raman spectrum of the liquid. Quantum chemistry calculations using the density functional theory were used to predict the most stable geometry and conformation of the studied molecule. Subsequently, the harmonic vibrational frequencies and force field were calculated. An assignment of the observed spectral features made after comparison with the related molecules and with the predicted frequencies was used as the basis of a scaling of the original force field in order to reproduce as well as possible the experimental frequencies. With this purpose a set of scale factors was calculated by a least square procedure, leading to a final root mean square deviation (RMSD) of 9.7 cm(-1).

A conformational and vibrational study of CF3COSCH2CH3

The molecular structure and conformational properties of S-ethyl trifluorothioacetate, CF(3)COSCH(2)CH(3), were determined in the gas phase by electron diffraction and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (Moller Plesset of second order) and density functional theory quantum chemical calculations at different levels of theory. Both experimental and theoretical methods reveal two structures with C(s) (anti, anti) and C(1) (anti, gauche) symmetries, although there are disagreements about which is more stable. The electron diffraction intensities are best interpreted with a mixture of 51(3)% anti, anti and 49(3)% anti, gauche conformers. This conformational preference was studied using the total energy scheme and the natural bond orbital scheme. In addition, the infrared spectra of CF(3)COSCH(2)CH(3) are reported for the gas, liquid and solid phases as well as the Raman spectrum of the liquid. Using calculated frequencies as a guide, evidence for both C(s) and C(1) structures is obtained in the IR spectra. Harmonic vibrational frequencies and scaled force fields have been calculated for both conformers.

Layered crystal structure, conformational and vibrational properties of 2,2,2-trichloroethoxysulfonamide: an experimental and theoretical study.

The molecular structure of 2,2,2-trichloroethoxysulfonamide, CCl3CH2OSO2NH2, has been determined in the solid state by X-ray diffraction data and in the gas phase by ab initio (MP2) and DFT calculations. The substance crystallizes in the monoclinic P21/c space group with a = 9.969(3)Å, b = 22.914(6)Å, c = 7.349(2)Å, β = 91.06(3)°, and Z = 8 molecules per unit cell. There are two independent, but closely related molecular conformers in the crystal asymmetric unit. They only differ in the angular orientation of the sulfonamide (SO2NH2) group. The conformers are arranged in the lattice as center-symmetric NH · · · O(sulf)-bonded dimers. Neighboring dimers are linked through further NH · · · O(sulf) bonds giving rise to a crystal layered structure. The solid state infrared and Raman spectra have been recorded and the observed bands assigned to the molecular vibration modes. Also, the thermal behavior of the substance was investigated by TG-DT analysis. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond (NBO) analysis.

DFT calculations of structure and vibrational properties of 2,2,2-trichloroethylacetate, CH3CO2CH2CCl3

The molecular structure and conformational properties of 2,2,2-trichloroethylacetate, CH(3)CO(2)CH(2)CCl(3), were determined by ab initio (MP2) and DFT quantum chemical calculations at different levels of theory. The theoretical study was complemented with experimental measurements such as IR and Raman spectroscopy. The experimental and calculations confirm the presence of two conformers, one with anti, gauche conformation (C1 symmetry) and another with anti, anti form (Cs symmetry). The conformational preference was studied using the total energy scheme, NBO and AIM analysis. The infrared spectra of CH(3)CO(2)CH(2)CCl(3) are reported in the liquid and solid phases and the Raman spectrum in liquid phase. Using calculated frequencies as a guide, evidence for both C1 and Cs conformers is obtained in the IR and Raman spectra.

Interaction of S-methyl methanethiosulfonate with DPPC bilayer

The present study is a first step towards the investigation of S-methyl methanethiosulfonate (MMTS) interaction with membrane model systems like liposomes. In this paper, the interaction of MMTS with dipalmitoylphosphatidylcholine (DPPC) bilayers was studied by FTIR and SERS spectroscopy. Lysolipid effect on vesicle stability was studied. The results show that MMTS interacts to different extents with the phosphate and carbonyl groups of membranes in the gel and the liquid crystalline states. To gain a deeper insight into MMTS properties that may be potentially helpful in the design of new drugs with therapeutic effects, we performed theoretical studies that may be the basis for the design of their mode of action.

Vibrational and structural behavior of (L)-cysteine ethyl ester hydrochloride in the solid state and in aqueous solution.

The aim of this work is to evaluate the vibrational and structural properties of l-cysteine ethyl ester hydrochloride (CE), and its electronic behavior mainly in relation to the action of the thiol and amine groups at different degrees of solvation. The crystal structure of CE was determined at room temperature by X-ray diffraction methods. Infrared and Raman spectra were collected to compare the behavior of different functional groups in the molecule, both in the solid phase and in aqueous solution. Its UV and circular dichroism spectra were also measured in aqueous solution. The influence of an aqueous environment on the CE spectra was simulated by means of implicit (polarizable continuum model) and explicit (molecular dynamics, solute-solvent clusters) methods. Calculations in explicit and continuous solvent are of interest to explain the behavior of bioavailable sites in this medium. The study was completed by natural bond orbital analysis to determine the presence of hyperconjugative interactions.

Bis (trifluoromethyl) sulfone, CF3SO2CF3: Synthesis, vibrational and conformational properties

Bis (trifluoromethyl) sulfone, CF(3)SO(2)CF(3), was obtained as a byproduct in the synthesis of CF(3)SO(2)SCF(3). The compound was characterized by infrared and Raman spectroscopy as well quantum chemical calculations. Quantum mechanical calculations indicate the possible existence of two conformers symmetrically equivalent with C(2) symmetry. The preference for the staggered form was studied using the total energy scheme and the natural bond orbital (NBO) partition scheme. Additionally, the total potential energy was deconvoluted using a sixfold decomposition in terms of a Fourier-type expansion, showing that the hyperconjugative effect was dominant in stabilizing the staggered conformer. Infrared and Raman spectra of CF(3)SO(2)CF(3) were obtained. Harmonic vibrational wavenumbers and a scaled force field were calculated, leading to a final root mean-square deviation of 7.8 cm(-1) when comparing experimental and calculated wavenumbers.

Vibrational spectroscopy and conformation of S-ethyl thioacetate: CH3COSCH2CH3 and comparison with -C(O)S- and -C(O)O- compounds.

The molecular structure and conformational properties of S-ethyl thioacetate, CH3COSCH2CH3, were determined in the gas phase by electron diffraction and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (MP2) and DFT quantum chemical calculations at different levels of theory. Theoretical methods reveal two structures with Cs (anti, anti) and C1 (anti, gauche) symmetries. The infrared and Raman spectra for different phases were also recorded and the bands observed assigned to the vibrational normal modes. Liquid Raman and infrared spectra in liquid and gaseous state measurements revealed the presence of two conformations anti, anti (Cs symmetry) and anti, gauche (C1 symmetry). The study was completed using natural bond orbital (NBO) analysis. We have also analyzed the internal rotation barrier about the C(O)SCC dihedral angle using a variety of computational approaches and natural bond orbital (NBO) analyses to understand the nature of the potential function and to explain the preferred conformation of the molecule.

Weak and strong hydrogen bonds conducting the supramolecular framework of 1-butyl-3-(1-naphthoyl)thiourea: crystal structure, vibrational studies, DFT methods, Pixel energies and Hirshfeld surface analysis

ABSTRACT A detailed structural and spectroscopic study of a new thiourea derivative 1-butyl-3-(1-naphthoyl)thiourea (1) is presented with the assistance of theoretical calculations. The X-ray diffraction structure analysis reveals a planar carbonylthiourea group, favoured by intra-molecular NH···O bond. The compound is arranged in the lattice as NH···O and NH···S bonded polymeric ribbons, that extend along the crystal b-axis. Molecular pairs involving N–H···S hydrogen bonds are a dominant contribution to packing stabilisation coming from coulombic component. Hirshfeld surfaces and two-dimensional-fingerprint plots show different intermolecular contacts and its relative contributions to total surface in each compound. The AIM approach shows the nature and strength of the strong and weak intramolecular interactions and the solvent effect, while NBO analysis reveals that the sulphur atom is responsible for the higher hyperconjugative stabilising energy.