Juan Jesús López-González

Measurement and ab initio modeling of the inelastic neutron scattering of solid melamine: Evidence of the anisotropy in the external modes spectrum

Abstract The inelastic neutron scattering spectrum of melamine has been measured and a normal coordinates analysis has been performed in order to interpret the vibrational dynamics. This study reveals the anisotropy in the external mode spectrum and its important role in the internal modes region. Thus, the Debye–Waller factor has taken a value for the out-of-plane vibrations four times greater than that for the in-plane vibrations. A molecular force field refinement has been carried out in independent symmetry coordinates (D 3h ) in order to confirm the vibrational assignments. The final force field is free of redundancies and therefore the corresponding force constants are unambiguous.

Carbohydrates in the gas phase: conformational preference of D-ribose and 2-deoxy-D-ribose

A full exploration of the conformational landscape of D-ribose and 2-deoxy-D-ribose monosaccharides in the gas phase has been performed using DFT methods (B3LYP and M06-2X). Open-chain, furanose and pyranose configurations have been examined. Up to 954 and 668 stable structures have been obtained for D-ribose and 2-deoxy-D-ribose. Among these structures, up to 35 and 22 have relative energies smaller than 5 kJ mol−1 with respect to the absolute minimum of each molecule, respectively. For D-ribose, pyranose in α- and β-forms is the most populated according to both functionals, the β-diastereoisomer being the most populated. For 2-deoxy-D-ribose, the α-pyranose form is in majority. The β/α relationship of pyranose forms presents different results for both functionals: for M06-2X it increases in D-ribose and decreases in 2-deoxy-D-ribose at 0 K with respect to the room temperature results, the opposite case occurring in B3LYP. Intramolecular weak interactions have been characterized using the AIM and NBO methodologies.

Chiral recognition of amino acid enantiomers by a crown ether: chiroptical IR-VCD response and computational study.

We report on a combined experimental and computational study of the chiral recognition of the amino acid serine in protonated form (L/D-SerH(+)), by the crown ether (all-S)-(18-crown-6)-2,3,11,12-tetracarboxylic acid (S-18c6H4). Infrared and vibrational circular dichroism spectroscopies (IR-VCD) are employed to characterize the chiroptical response of the complexes formed by S-18c6H4 with the L-SerH(+) and D-SerH(+) enantiomers in dried thin films obtained from aqueous solutions. The study focuses on vibrational modes directly related to the intermolecular hydrogen bonds between the crown ether derivative and serine, responsible for crown-serine binding, namely, the C═O and C-O stretching modes, and on the C-O-H bending mode, which yield intense IR and VCD signals in the range of wavenumbers 900-2000 cm(-1). The experimental spectra are analyzed in combination with a computational structural survey and optimization at different levels of density functional theory. The conformational landscape of the complexes is found to be primarily governed by a bowl-like structure of the crown ether host and a tripodal coordination of the protonated R-NH3(+) group of serine with the oxygen atoms of the central ether ring. Additionally, one or two of the carboxylic side groups of the crown ether interact with the -COH and -COOH groups of serine. Chiral selectivity is probed by recording the IR and VCD spectra of dried thin films obtained from aqueous solutions with equimolar concentrations of the two serine enantiomers and the macrocycle. The results demonstrate a marked chiral recognition of L-SerH(+) relative to D-SerH(+) by the S-18c6H4 substrate, which arises from the favorable host-guest coordination through H-bonds at optimum distances and collinear orientations, also involving a limited distortion of the crown ether backbone.

Vibrational analysis of the inelastic neutron scattering spectrum of pyridine

Abstract A vibrational analysis of the pyridine molecule has been performed by combining inelastic neutron scattering (INS) data and quantum mechanical calculations at the RHF, MP2 and B3LYP levels, with the 6-31G** and 6-311G** basis sets. Firstly, in order to test which level of theory is the best in reproducing the INS profile, this was calculated from the atomic displacement matrix of the pyridine molecule. DFT proved to be the most suitable option reproducing the above-mentioned spectrum, for both wave numbers and intensities. Secondly, in order to approximate the calculated spectrum to the observed one, the initial force constants matrix calculated at the B3LYP/6-311G** level was symmetrized using a set of independent symmetry coordinates (C2v). All the diagonal and some off-diagonal force constants were fitted until the difference between observed and calculated spectra was minimized. Good agreement between both calculated and experimental INS spectra supports the validity of our ‘empirical’ (or effective) force field.

Conformational Preference and Chiroptical Response of Carbohydrates D‑Ribose and 2‑Deoxy‑D‑ribose in Aqueous and Solid Phases

This work targets the structural preferences of D-ribose and 2-deoxy-D-ribose in water solution and solid phase. A theoretical DFT (B3LYP and M06-2X) and MP2 study has been undertaken considering the five possible configurations (open-chain, α-furanose, β-furanose, α-pyranose, and β-pyranose) of these two carbohydrates with a comparison of the solvent treatment using only a continuum solvation model (PCM) and the PCM plus one explicit water molecule. In addition, experimental vibrational studies using both nonchiroptical (IR-Raman) and chiroptical (VCD) techniques have been carried out. The theoretical and experimental results show that α- and β-pyranose forms are the dominant configurations for both compounds. Moreover, it has been found that 2-deoxy-D-ribose presents a non-negligible percentage of open-chain forms in aqueous solution, while in solid phase this configuration is absent.

Calculation of internal valence force constants for XY6(Oh) octahedral molecules

Abstract The valence force constants have been calculated in terms of simple dependent rectilinear internal co-ordinates for a series of XY 6 octahedral molecules that have been amply studied from a vibrational point of view, i.e. the hexafluorides of sulphur, selenium, molybdenum, tungsten and uranium. The calculations have been carried out using the most recent force constants in symmetry co-ordinates to appear in the literature and following Kuczeras treatment, according to which the indetermination of the internal valence force constants involved in redundancies can be solved by using the transformation F * R = W T WF R W T W , which he calls the pure vibrational force field. The results show that the eleven F R dependent constants are reduced to seven F * R independent constants, the same number as the F S independent force constants. This is because of the zero value of the ƒ′* dα constants and the relationships ƒ* dα = −ƒ″* dα ƒ* αα = −ƒ″* αα ƒ* α =−2ƒ′* αα −ƒ′″* αα that are obtained from the combination of the above mentioned F * R transformation and the sum rule in Kuczeras treatment. These latter relationships can be obtained from the interactions between the displacement coordinates with which they are associated. This has allowed individual values to be assigned to the bending, bending—bending and stretching—bending constants for the above mentioned molecules without the need for recourse to any model whatsoever.

Understanding the Aldo‐Enediolate Tautomerism of Glycolaldehyde in Basic Aqueous Solutions

The biochemically important interconversion process between aldoses and ketoses is assumed to take place via 1,2-enediol or 1,2-enediolate intermediates, but such intermediates have never been isolated. The current work was undertaken in an attempt to detect the presence of the 1,2-enediol structure of glycolaldehyde in alkaline medium, actually a 1,2-enediolate, and to try to clarify the scarce data existing about both the formation of deprotonated enediol and the aldo-enediolate equilibrium. The Raman spectra of neutral and basic solutions were recorded as a function of time for eleven days. Several bands associated with the presence of the enediolate were observed in alkaline medium. Glycolaldehyde exists as three different structures in aqueous solution at neutral pH, that is, hydrated aldehydes, aldehydes and dimers, with a respective ratio of approximately 4:0.25:1. Additionally, the formation of Z-enediolate forms takes place at basic pH, together with an increase in the concentration of aldehyde species, such as 2-oxoethan-1-olate, and a decrease in the concentrations of the hydrated aldehyde and dimeric forms. The theoretical ratio of ≈1.5:1 for aldehyde:Z-enediolate reproduces the experimental Raman spectrum in basic medium, with an additional contribution of the previously mentioned ratio between the hydrated aldehyde and dimeric forms. Finally, Raman spectroscopy allowed us to monitor the enolization of this carbohydrate model and conclude that aldo-enediol tautomerism-formally aldo-enediolate-happens when a suitable amount of basic species is added.

Deducing the molecular properties of zwitterionic, protonated, deprotonated, and double-deprotonated forms of L-cysteine from vibrational spectroscopy (IR, Raman, VCD) and quantum chemical calculations

AbstractThe behavior of L-cysteine (C3H7NO2S, (2R)-2-amino-3-sulfanylpropanoic acid) in water at different pH values was analyzed both experimentally and theoretically. The behavior was studied at pH values of 5.21 (at this pH, L-cysteine is a zwitterionic species), 1.00 (protonated species), 8.84 (monodeprotonated species), and 13.00 (dideprotonated species). We carried out a vibrational study using nonchiroptical (IR–Raman) and chiroptical (VCD) techniques complemented by quantum chemical calculations. We adopted a dual strategy, as follows. (i) The hybrid density functionals B3LYP and M062X and the ab initio MP2 method were employed, with the same 6-311++G (d,p) basis set, in order to characterize the relative energies and structures of an extensive set of conformers of L-cysteine. The presence of water was included by utilizing the IEF-PCM implicit solvation model. (ii) The vibrational analysis was made using a chirality-sensitive using a chirality-sensitive technique (VCD) and chirality-insensitive techniques (IR, including MIR and FIR, and Raman), especially in aqueous solution. The results obtained theoretically and experimentally were compared in order to deduce the most stable structures at each pH. Moreover, for the first time, the monodeprotonated anion of L-cysteine was detected in aqueous solution by means of IR, Raman and vibrational circular dichroism (VCD). Finally, analysis of the low-frequency region using the IR and Raman techniques was shown to be a very important way to understanding the conformational preference of the zwitterionic species. FigureConformational stability and chiroptical properties of L-Cys at different pH values

A Topological Geometric Method for the Obtention of Symmetry-Adapted Functions for Point Groups IV. The Dihedral Groups

Abstract Symmetry-adapted icosahedral harmonics have been obtained by using a new method based on the geometrical and topological properties of icosaedral spatial arrangements of charged particles. This study has allowed us to show that especially for groups of high symmetry, our method proved to be more simple and advantageous than others existing in the literature, as for instance the projection operator classical method.

Conformational Flexibility of Limonene Oxide Studied By Microwave Spectroscopy

Monoterpenoids are biogenic volatile organic compounds that play a major role in atmospheric chemistry by participating in the formation of aerosols. In this work, the monoterpenoid (R)-(+)-limonene oxide (C10 H16 O) was characterized in the gas phase by Fourier-transform microwave spectroscopy in a supersonic jet. Five conformers of limonene oxide, four equatorial and one axial considering the configuration of the isopropenyl group, were unambiguously identified from analysis of the rotational spectrum. The observed conformers include cis and trans forms, which are stabilized by a subtle balance of hydrogen bonds, dispersive interactions, and steric effects. Estimated conformational relative abundances surprisingly reveal that the abundance of the axial conformer is similar to that of some of the equatorial conformers. In addition, the potential energy surface was extensively explored by using density functional theory and ab initio methods.