Angeles Peña-Gallego

DFT conformational study of cysteine in gas phase and aqueous solution

Abstract Different conformers of cysteine in gas phase are investigated at the DFT B3LYP/6-31G∗ and B3LYP/6-311++G∗∗ levels. The effect of the solvent is simulated by using the Onsager and polarizable continuum (PCM) models within the self-consistent reaction field method (SCRF) at the B3LYP/6-31G∗ level. Specifically, five neutral forms, two anions and one zwitterion were analysed. Both, in gas phase and solution the most stable normal form has the carboxyl group directed toward the amino group. In accord with the experiment, the PCM model predicts that the most stable structure in solution is a zwitterion, a species that does not exist or has a very small stability in gas phase. A major stabilization in solution is also predicted for the zwitterionic form of anionic cysteine. Thus the PCM model renders correct stability order of the different conformers in solution, while the Onsager model does not, which is due to the underestimation of the electrostatic contributions to the solute–solvent interaction for the zwitterions.

Computational Study on the Characteristics of the Interaction in Naphthalene···(H2X)n=1,2 (X = O, S) Clusters

The characteristics of the interaction between the pi cloud of naphthalene and up to two H2O or H2S molecules were studied. Calculations show that clusters formed by naphthalene and one H2O or H2S molecule have similar geometric features, and also present similar interaction energies. Our best estimates for the interaction energy amount to -2.95 and -2.92 kcal/mol for H2O and H2S, respectively, as obtained with the CCSD(T) method. Calculations at the MP2 level employing large basis sets should be avoided because they produce highly overestimated interaction energies, especially for hydrogen sulfide complexes. The MPWB1K functional, however, provides values pretty similar to those obtained with the CCSD(T) method. Although the magnitude of the interaction is similar with both H2X molecules, its nature is somewhat different: the H2O complex presents electrostatic and dispersion contributions of similar magnitude, whereas for H2S the interaction is dominated by dispersion. In clusters containing two H2X molecules several minima were characterized. In water clusters, the total interaction energy is dominated by the presence of a O-H...O hydrogen bond and, as a consequence, structures where this contact is present are the most stable. However, clusters containing H2S show structures with no interaction between H2S moieties which are as stable as the hydrogen bonded ones, because they allow an optimal H2S...naphthalene interaction, which is stronger than the S-H...S contact. Therefore it is possible that in larger polycycles hydrogen sulfide molecules will be spread onto the surface maximizing S-H...pi interactions rather than aggregated, forming H2S clusters.

Characteristics of the interaction of azulene with water and hydrogen sulfide: A computational study

A computational study was carried out for studying the characteristics of the interaction between azulene and water or hydrogen sulfide. In azulene...water complex the water molecule is located with both hydrogen atoms pointing toward the aromatic cloud but displaced to the five-membered ring. Hydrogen sulfide adopts a similar arrangement but located roughly over the central C-C bond of azulene. Calculations show that hydrogen sulfide interacts with azulene more strongly (-4.19 kcal/mol) than water (-3.76 kcal/mol), although this is only revealed at the highest levels of calculation. The nature of the interaction is electrostatic and dispersive in the same percentage for water cluster, whereas for hydrogen sulfide dispersion is the dominant contribution. Clusters containing two water molecules are controlled by the possibility of establishing an O-H...O hydrogen bond. As a consequence, the most stable structure corresponds to the interaction between a water dimer and azulene, with an interaction energy amounting to -11.77 kcal/mol. Hydrogen sulfide interaction is stronger with azulene than with itself, so structures with S-H...S contact and others, where H(2)S only interacts with azulene, present similar interaction energies (-8.02 kcal/mol for the most stable one).

Effect of microhydration on the guanidinium···benzene interaction.

The effect of microhydration on the interaction of guanidinium cation with benzene has been studied by employing ab initio calculations. Four different structural arrangements were considered for the guanidinium···benzene interaction to which up to six water molecules were added. T-shaped structures are usually the most stable, but as water molecules are included the energy differences with the parallel structures decrease, reaching a point where parallel complexes are even more stable than T-shaped ones. Therefore, the inclusion of water molecules promotes a change in the structure of the cation···π contact. The analysis reveals that these stability changes are more related with the structure of the hydrating water molecules than to a modulation of the cation···π interaction. Already with three water molecules, one water molecule in the T-shaped complex has to be located in the second solvation shell, whereas in parallel structures this occurs with four water molecules. As a consequence energy differences among structures decrease. The calculations show that the nature of the interaction is almost unaffected in T-shaped structures, whereas an important dispersion increment is observed in parallel ones, though its overall effect is small.

Dissociation of ethylene and several deuterated derivatives at 193 and 157 nm by direct classical trajectories

Abstract Several fragmentation reactions of ethylene were investigated by AM1 direct classical trajectories. Product yields were computed for ethylene and several deuterated derivatives at two excitation energies (193 and 157 nm). The atomic elimination channel is favoured as the energy increases, and hydrogen scrambling is found to be an important process at the energies of study, which contrasts with the mechanisms proposed up to date. The computed product yields are in better agreement with experiment than are previous RRKM calculations. The results suggest that the dissociation of ethylene occurs at, on near, the statistical limit, which disagrees with previous conclusions.

Study of the interaction in clusters formed by phenol and CH3X (X=CN,F,Cl) molecules.

The characteristics of the interaction between phenol and acetonitrile, methyl fluoride and methyl chloride were studied. The most stable structures for clusters containing one or two CH3X molecules and one phenol moiety were located by means of ab initio and density functional theory calculations. Phenol-acetonitrile dimer presents two almost equally stable structures; one of them is a typical linearly hydrogen bonded minimum, whereas in the other one, a C-H...pi contact is established accompanied by a distorted O-H...N hydrogen bond. Although the latter minimum presents the larger interaction energy, deformation effects favor the formation of the linear hydrogen bonded one. In complexes with methyl fluoride and methyl chloride, this arrangement is the most stable structure and no linear hydrogen bonded structures were located. Our best estimates for the interaction energies amount to -27.8, -21.6, and -19.7 kJ/mol for clusters of phenol with acetonitrile, methyl fluoride, and methyl chloride, respectively. The main contribution to the stabilization of these clusters is of electrostatic nature, although in structures where a C-H...pi contact is present, the dispersion contribution is also significant. In clusters formed by phenol and two CH3X units, the most stable arrangement corresponds to a head to tail disposal with O-H...X, C-H...X, and C-H...pi contacts forming a cycle. Only for this type of arrangement, three body effects are non-negligible even though they constitute a minor effect. The results also indicate that interactions with methyl fluoride and methyl chloride are of similar intensity, although weaker than with acetonitrile. Significant frequency shifts are predicted for the O-H stretching, which increase when increasing the number of CH3X molecules.

Nonstatistical effects in the unimolecular dissociation of the acetyl radical

Classical trajectory and statistical variational efficient microcanonical sampling transition state theory calculations were carried out to investigate the dissociation dynamics of the acetyl radical. For this purpose, an analytical potential function was developed based on ab initio and experimental data reported in the literature. This potential function reproduces reasonably well the geometries, frequencies, and energies of the stationary points of the ground state potential energy surface. The dynamics of the reaction was shown to be intrinsically non-Rice–Ramsperger–Kassel–Marcus (RRKM) at high energies and particularly at 65.9 kcal/mol, at which experimental work showed evidence for nonstatistical behavior. On the other hand, initial excitations of normal modes 507 (CCO bend), 1079 (CC stretch), 1504 (CH3 umbrella vibration), and 1939 (CO stretch) enhance significantly the rate of reaction; specifically, excitation of the CO stretch gives a rate coefficient an order of magnitude higher than the rate...

Computational study of the interaction of indole-like molecules with water and hydrogen sulfide

The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H···π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH(2) ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.

A MP2 and DFT study of the influence of complexation on the aromatic character of phosphole

This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G* and B3LYP/6-31 + G* study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at both theoretical level and different magnetic properties were evaluated. The main conclusion is the increase of the aromatic character of the phosphole when complexes with Li+, Be2+, and Al3+ are formed.

A MP2 and DFT study of the aromatic character of polyphosphaphospholes. Is the pyramidality the only factor to take into consideration

A comprehensive MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) study of the aromatic character of phospholes, Pn(CH)4-nPH with n = 0-4 was conducted. For this purpose, the structures for these compounds were optimized at both theoretical levels and different magnetic properties (magnetic susceptibility anisotropy, χanis, and the nucleus-independent chemical shifts, NICS) were evaluated. For comparison, these magnetic properties were also calculated in the optimized structures with planarity constraints. We have also applied the ACID (anisotropy of the current-induced density) method in this analysis. The main conclusions are the aromatic character of these compounds, the relationship between aromaticity and planarity and the importance of other factors in this aromaticity.