The 2-pyridone/2-hydroxypyridine tautomerism in gas phase: An excited state roaming reaction.

Multiconfigurational methods (CASSCF and CASPT2) were employed to gain a new understanding of the mechanism of the gas-phase phototautomerization of 2-pyridone/2-hydroxypyridine. Potential energy curves and crossing points of the low-lying excited states were analyzed. The results show that the tautomerization only occurs from 2-pyridone to 2-hydroxypyridine after electronic excitation to the S1 (ππ*) state. From this state, the system would be able to reach a conical intersection between S1 and the dissociative S2 (πσ*) due to vibrational effects. Then, it can evolve to the hydroxy form in its ground state by reaching an intersection seam between the S0 and the πσ* states. For this to happen, a roaming process responsible for the hydrogen atom migration would be required; otherwise, the system would revert to the 2-pyridone tautomer. The unfeasibility of the reverse process after optical excitation from the lactim to the lactam form is explained by the great amount of energy needed to reach the conical intersection between the ππ* and πσ* states. These findings would provide new insights into the understanding of the photophysics and photochemistry of a primordial heterocycle, considered a prebiotic model known to be found in interstellar clouds.

Trans-cinnamaldehyde-related overproduction of benzoic acid and oxidative stress on Arabidopsis thaliana.

Introduction: Trans-cinnamaldehyde is a specialised metabolite that naturally occurs in plants of the Lauraceae family. This study focused on the phytotoxic effects of this compound on the morphology and metabolism of Arabidopsis thaliana seedlings. Material and methods: To evaluate the phytotoxicity of trans-cinnamaldehyde, a dose-response curve was first performed for the root growth process in order to calculate the reference inhibitory concentrations IC50 and IC80 (trans-cinnamaldehyde concentrations inducing a 50% and 80% inhibition, respectively). Subsequently, the structure and ultrastructure of the roots treated with the compound were analysed by light and electron microscopy. Based on these results, the following assays were carried out to in depth study the possible mode of action of the compound: antiauxinic PCIB reversion bioassay, determination of mitochondrial membrane potential, ROS detection, lipid peroxidation content, hormone quantification, in silico studies and gene expression of ALDH enzymes. Results: Trans-cinnamaldehyde IC50 and IC80 values were as low as 46 and 87 µM, reducing the root growth and inducing the occurrence of adventitious roots. At the ultrastructural level, the compound caused alterations to the mitochondria, which were confirmed by detection of the mitochondrial membrane potential. The morphology observed after the treatment (i.e., appearance of adventitious roots) suggested a possible hormonal mismatch at the auxin level, which was confirmed after PCIB bioassay and hormone quantification by GC-MS. The addition of the compound caused an increase in benzoic, salicylic and indoleacetic acid content, which was related to the increased gene expression of the aldehyde dehydrogenase enzymes that can drive the conversion of trans-cinnamaldehyde to cinnamic acid. Also, an increase of ROS was also observed in treated roots. The enzyme-compound interaction was shown to be stable over time by docking and molecular dynamics assays. Discussion: The aldehyde dehydrogenases could drive the conversion of trans-cinnamaldehyde to cinnamic acid, increasing the levels of benzoic, salicylic and indoleacetic acids and causing the oxidative stress symptoms observed in the treated seedlings. This would result into growth and development inhibition of the trans-cinnamaldehyde-treated seedlings and ultimately in their programmed-cell-death.

Molecular Design of Interfaces of Model Food Nanoemulsions: A Combined Experimental and Theoretical Approach.

The composition and structure of the interfacial region of emulsions frequently determine its functionality and practical applications. In this work, we have integrated theory and experiments to enable a detailed description of the location and orientation of antioxidants in the interfacial region of olive-oil-in-water nanoemulsions (O/W) loaded with the model gallic acid (GA) antioxidant. For the purpose, we determined the distribution of GA in the intact emulsions by employing the well-developed pseudophase kinetic model, as well as their oxidative stability. We also determined, by employing an in silico design, the radial distribution functions of GA to gain insights on its insertion depth and on its orientation in the interfacial region. Both theoretical and experimental methods provide comparable and complementary results, indicating that most GA is located in the interfacial region (~81.2%) with a small fraction in the aqueous (~18.82%). Thus, GA is an effective antioxidant to inhibit lipid oxidation in emulsions not only because of the energy required for its reaction with peroxyl radical is much lower than that between the peroxyl radical and the unsaturated lipid but also because its effective concentration in the interfacial region is much higher than the stoichiometric concentration. The results demonstrate that the hybrid approach of experiments and simulations constitutes a complementary and useful pathway to design new, tailored, functionalized emulsions to minimize lipid oxidation.

A Highly Efficient Neutral Anion Receptor in Polar Environments by Synergy of Anion-π Interactions and Hydrogen Bonding.

Herein, it is shown how anion recognition in highly polar solvents by neutral metal-free receptors is feasible when multiple hydrogen bonding and anion-π interactions are suitably combined. A neutral aromatic molecular tweezer functionalized with azo groups is shown to merge these two kinds of interactions in a unique system and its efficiency as an anion catcher in water is evaluated using first-principles quantum methods. Theoretical calculations unequivocally prove the high thermodynamic stability in water of a model anion, bromide, captured within the tweezer's cavity. Thus, static calculations indicate anion-tweezer interaction energies within the range of covalent or ionic bonds and stability constants in water of more than 10 orders of magnitude. First-principles molecular dynamics calculations also corroborate the stability through the time of the anion-tweezer complex in water. It shows that the anion is always found within the tweezer's cavity due to the combination of the tweezer-anion interactions plus a hydrogen bond between the anion and a water molecule that is inside the tweezer's cavity.

Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model.

The effects of charge overlap, or charge penetration, are neglected in most force fields and interaction terms in QM/MM methods. The effects are however significant at intermolecular distances near the van der Waals minimum. In the present study, we propose a method to evaluate the intermolecular Coloumb interaction using Slater-type functions, thus explicitly modeling the charge overlap. The computational cost of the method is low, which allows it to be used in large systems with most force fields as well as in QM/MM schemes. The charge distribution is modeled as a distributed multipole expansion up to quadrupole and Slater-type functions of angular momentum up to L = 1. The exponents of the Slater-type functions are obtained using a divide-and-conquer method to avoid the curse of dimensionality that otherwise is present for large nonlinear optimizations. A Levenberg-Marquardt algorithm is applied in the fitting process. A set of parameters is obtained for each molecule, and the process is fully automated. Calculations have been performed in the carbon monoxide and the water dimers to illustrate the model. Results show a very good accuracy of the model with relative errors in the electrostatic potential lower than 3% over all reasonable separations. At very short distances where the charge overlaps is the most significant, errors are lower than 8% and lower than 3.5% at distances near the van der Waals minimum.

Theoretical vibrational Raman and surface-enhanced Raman scattering spectra of water interacting with silver clusters.

In this study, we analyzed the Raman spectrum of a water molecule adsorbed on a cluster of 20 silver atoms, and the plasmonic electromagnetic effect of the silver surface was also considered to give a theoretical prediction of the surface-enhanced Raman scattering spectrum. The calculations were performed at the density functional theory (DFT) level by using both frozen and unfrozen silver clusters. Two different models were used to consider the plasmonic enhancement; one of them was a modified classical (dipole) model and the other was the coupled perturbed Hartree-Fock method with excitation frequencies obtained from time-dependent DFT calculations and with proper detuning of these frequencies. The importance of small geometrical distortions of the silver surface in the orientation of the adsorbed water was shown. Moreover, it was shown how the symmetry of the transition dipole moment and the symmetry of the vibrational modes influence the Raman intensities of the SERS spectrum.

Theoretical design of molecular grippers for anion recognition based on subporphyrazines and subphthalocyanines.

Subphthalocyanines (SubPcs) are 14 π-electron aromatic macrocycles containing three 1,3-diiminoisoindol units N-fused around a central boron atom. Their particular concave π-extended structure makes them potentially useful in fields related to optoelectronics and molecular electronics. Also, their structure makes them potential receptors of complementary convex-shaped molecules. Inspired by the properties of subphthalocyanines and by previous studies about the possibility of obtaining neutral receptors composed of aromatic rings that can bind anions, we performed a theoretical study to analyze the ability of subphthalocyanines and some SubPc analogues to capture anions by non-covalent interactions. This may be relevant, since they can produce a variety of chromogenic reagents for anion detection that are not destroyed in the detection process, since the non-covalent interactions are weak enough to reverse the procedure. We characterized complexes formed between several SubPc derivatives and different anions, and also studied the influence of this process on the optical properties of these molecules. The stabilization trend reflected by the energetic results and the changes shown in the absorption wavelengths of the host molecule under complexation confirm our hypothesis about the possibility of these kinds of molecules being used as chromogenic reagents for anion capture, even in solvents with a large dielectric constant like water.

A computational study of the protonation of simple amines in water clusters.

The microsolvation study of a group of amines with a variable number of water molecules was performed by conducting a theoretical analysis of the properties of the clusters formed by the amines with up to seven molecules of water. We describe the microsolvation of several amines focusing on the dissociation of a water molecule that transfers a proton to the amine and forms a hydroxide ion. Ab initio calculations were performed on these clusters employing the DFT/B3LYP and MP2 methods with the 6-311++G(2d,p) basis set. Several stationary points for each cluster were thus located and characterized as minima from frequency calculations. Intermolecular BSSE corrected interaction energies were obtained. The protonation mechanism of the amines was examined in terms of some parameters that include the lengths of the bonds involved in the process of proton transfer and the frequencies associated with certain O-H and N-H stretching modes. On the basis of the calculations, all studied amines present similar behavior but trimethylamine, whose limitations to be integrated in the water hydrogen bond network cause the instability of some of their complexes. The cyclic configurations are the most stable structures up to five water molecules due to the presence of cooperative effects associated with the hydrogen bonds of water molecules. However, when the number of water molecules increases the spatial forms become the most stable configurations. The dissociated forms were not found to have the most stable configuration in any of the studied systems but energetic differences between the dissociated and non-dissociated forms decrease with the number of water molecules.

Analysis of the SERS spectrum by theoretical methodology: evaluating a classical dipole model and the detuning of the excitation frequency.

Surface-enhanced Raman scattering (SERS) spectroscopy is gaining prominence as one of the most powerful ultradetection techniques. The SERS outcome is essentially a complicated pattern of vibrational bands that allows multiplex analysis but, at the same time, makes difficult the interpretation of unknown analytes or known substances in the presence of complex unknown chemical environments. Herein, we show two computational methods to reproduce the spectral shape of the SERS spectra. The first, based in the modification of the classical dipole model, reproduces with a notable similarity the experimental spectrum excited far to the red of the localized surface plasmon resonance (LSPR). This light and time-efficient model is of great interest to elucidate the orientation of the target on the plasmonic surface or even to accurately identify suspected unknown targets in real samples. However, the experimental SERS spectrum in resonance with the LSPR is also modeled by using a more classical CPHF approach. This method provides also good agreement with the experiment but at the expense of much more computational time.

Anion-π aromatic neutral tweezers complexes: are they stable in polar solvents?

The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.

SERS chiral recognition and quantification of enantiomers through cyclodextrin supramolecular complexation.

We introduce here a simple approach in which a cyclodextrin, functionalized with thiols in the narrower rim, is assembled onto the silver surface of a SERS platform composed of polystyrene beads coated with silver nanoparticles. Trapping properties of the fabricated sensor are demonstrated through the retention of different enantiomers (R,R or/and S,S) of hydrobenzoin (HBZ), a molecule that has not been reported before in SERS because it has no affinity for coinage metal surfaces. Further, selective recognition of each enantiomer and semiquantification of its proportion in a racemic mixture are provided by the analysis of the SERS spectra of the HBZ-cyclodextrin complex, in full agreement with the surface selection rules.

Electron Density Based Partitioning Scheme of Interaction Energies.

In this paper, a new partitioning of the complex interaction energy is proposed. This new partitioning is based on the decomposition of the one-electron and exchange-correlation densities into unperturbed and deformation densities. Thus, the proposed energy fragmentation can be applied at the SCF level and post-SCF levels as long as the corresponding density matrices have been evaluated previously. It provides the typical description of the complex interaction as a summation of electrostatic, exchange-repulsion, and polarization terms. However, the new method allows splitting up the exchange-repulsion into exchange and Pauli-repulsion energies. A full theoretical description of the method is presented, and some examples of its application to small complexes are discussed. A comparison with results obtained using perturbation methods is also carried out, showing that the first order terms obtained from symmetry adapted perturbation theories are perfectly reproduced with the new method. A clear bridge between qualitative deformation density plots and quantitative measures of the interaction energy components can be established within the framework of this new partitioning scheme, giving rise to a graphical and very intuitive interpretation of the complex formation.

Enhancing the interactions between neutral molecular tweezers and anions.

Several structural modifications to the original molecular tweezers of the Klärner's group were made with the aim of improving its binding capacity towards anions. The proposed modifications raise the molecular electrostatic potential inside the cavity and provide more conformational flexibility. The complexes of these new molecules with the halide anions Cl(-), Br(-), I(-) were optimized at the MPW1B95/6-31+G* level of theory. The molecular interactions were analyzed by single point density fitted local second-order Møller-Plesset perturbation theory (DF-LMP2) and DF-LMP2 spin-component-scaled MP2 (SCS-MP2), calculations were performed with the cc-pVTZ basis set. In view of the large magnitude of the interaction energies computed and the stability of the complexes in different solvents, this kind of molecule is a good candidate as molecular host for anion recognition.

Towards the design of neutral molecular tweezers for anion recognition.

Molecular tweezers are simple molecular receptors that can be characterized by the presence of two flat pincers separated by a more or less rigid tether. They have the ability to form complexes with a substrate molecule by gripping the substrate between the tips of the tweezers in a similar manner to that of mechanical tweezers. Klärner et al. synthesized one of the structurally simplest molecular tweezers, which is reported to bind electrodeficient aromatic and aliphatic substrates as well as organic cations. Complexes between these molecular tweezers and electron-rich aromatic, aliphatic, or anionic substrates have not been observed. Inspired by several recent reports that describe the interaction of hexafluorobenzene with electron-rich sites of molecules, we conducted a theoretical study to show the possibility of building molecular tweezers, based on those synthesized by Klärner, which were able to bind to anions and thus increase their potential as molecular receptors. We characterized complexes formed between several fluorinated derivatives of simple tweezers and an iodine anion, and analyzed the nature of the intermolecular interactions as well as the energetics for the process of complexation. The stabilization trend reflected by the energetic results when fluorine substituents were added to benzene rings confirms our hypothesis about the possibility of obtaining neutral tweezers composed of aromatic rings that can bind anions.

Blue-shifting hydrogen bond in the benzene-benzene and benzene-naphthalene complexes.

Ab initio complete optimizations at MP2/6-31++G** level have been performed in the T-shaped geometry of the benzene-benzene and benzene-naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue-shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems.

A density functional theory study on the electrocyclization of 1,2,4,6-heptatetraene analogues: converting a pericyclic to a pseudopericyclic reaction.

A comprehensive B3LYP/6-31+G* study on the electrocyclization of 1,2,4,6-heptatetraene analogues was conducted. Starting from the cyclization of (2Z)-2,4,5-hexatrienal, a pericyclic disrotatory process favored by the assistance of a electron lone pair, we incorporated small modifications in its molecular structure to obtain a truly pseudopericyclic process. To this purpose electronegative atoms (fluorine and nitrogen) were added to give a more electrophilic character on the carbon atom which is attacked by the electron lone pair of the oxygen atom. The complete pathway for each reaction was determined, and changes in magnetic properties were monitored with a view to estimating the aromatization associated with each process. This information, together with the energetic and structural results, allowed us to classify the reactions as pseudopericyclic or pericyclic. Among all studied reactions only one was a truly pseudopericyclic process and another was a borderline case. The features of this unequivocally pseudopericyclic case were analyzed in depth.

Theoretical characterization of structures and energies of benzene-(H2S)n and (H2S)n (n=1-4) clusters.

An ab initio study was performed in clusters up to four H(2)S molecules and benzene using calculations at MP26-31+G(*) and MP2/aug-cc-pVDZ levels. Differences between both sets of calculations show the importance of using large basis sets to describe the intermolecular interactions in this system. The obtained binding energies reflect that benzene has not the same behavior in H(2)S as in water, pointing to a higher solubility of this molecule in H(2)S than in water. The Bz-cluster binding energy was fitted to an asymptotic representation with a maximum value of the energy of -8.00 kcal/mol that converges in a cluster with 12 H(2)S molecules. The obtained intermolecular distance in the Bz-H(2)S dimer is similar to the experimental value; however, the difference is much larger for the angles defining the orientation. The influence of benzene produces a distortion of the (H(2)S)(n) clusters, so the intermolecular distances change with regard to the (H(2)S)(n) isolated clusters. Frequency shifts are larger in clusters with benzene than without it. In the smallest clusters the shift associated to the stretching of the S-H bonded to benzene is the largest one, but for the cluster with three H(2)S molecules this stretching is combined with the other S-H stretching of the molecule so the resulting shift is not the largest one.

Are electrocyclization reactions of (3Z)-1,3,5-hexatrienone and nitrogen derivatives pseudopericyclic? A DFT study.

[reactions: see text] Electrocyclization reactions of (3Z)-1,3,5-hexatrienone and nitrogen derivatives were studied by performing density functional theory (DFT) calculations together with the 6-31+G* basis set. Reactants, products, and transition states for each reaction were localized and the IRC connecting reactants and products was also obtained. Magnetic properties were evaluated along the reaction path to elucidate the characteristics of the reactions studied. As obtained from the calculations, electrocyclization of (3Z)-1,3,5-hexatrienone is a pericyclic process, as indicated by a variety of indexes, such as Nucleus Independent Chemical Shift (NICS), anisotropy of the magnetic susceptibility, or anisotropy of the current-induced density (ACID). This reaction presents characteristics of pericyclic reactions despite the activation energy lowering relative to the electrocyclization of (4Z)-1,2,4,6-heptatetraene, and the relatively small NICS values observed in the transition state. Magnetic properties indicate that an enhancement of the aromaticity relative to reactants and products occurs revealing the absence of orbital disconnections on the cyclic loop of interacting orbitals. Only two reactions among those studied exhibit pseudopericyclic character due to the in-plane attack of the lone pair on nitrogen. In these cases, the reactions showed no barrier for the electrocyclization process, and no aromaticity enhancement was observed.

A DFT study of the pericyclic/pseudopericyclic character of cycloaddition reactions of ethylene and formaldehyde to buta-1,3-dien-1-one and derivatives.

Cycloaddition reactions of ethylene and formaldehyde to buta-1,3-dien-1-one and derivatives were studied by performing a density functional theory study with the 6-31+G* basis set. Reactants, products, and transition states for each reaction were localized, and the path connecting reactants and products was also obtained. Magnetic properties were evaluated along the reaction path to elucidate the characteristics of the reactions studied. Also, a natural bond orbital analysis was performed to study the orbital interactions in the transition states. Calculations indicate that all reactions are pericyclic except three cases, which are pseudopericyclic reactions. In the latter, transition states are almost planar, and magnetic properties do not reveal aromatization enhancement in their transition states. Also, though the participation of lone pairs diminish the pericyclic character of the reactions, sometimes this participation is not enough to generate a change to a pseudopericyclic path. Overall, magnetic properties reveal as a good criterion to elucidate the characteristics of the reactions studied, though a combined application of several criteria is recommended.

DFT study of pericyclic and pseudopericyclic thermal cheletropic decarbonylations. Evaluation of magnetic properties.

A comprehensive B3LYP/6-31G** study of various thermal cheletropic decarbonylations was conducted. The complete pathway for each reaction was determined, and changes in magnetic susceptibility and its anisotropy were monitored with a view to estimating the aromatization associated to each process. This information, together with the energy and structural results, allowed us to clarify cases that are not clearly pseudopericyclic or pericyclic from previous work. Also, our results reveal that pericyclic reactions involve no disconnection in the cyclic array of overlapping orbitals. Therefore, a pseudopericyclic reaction involves at least one such disconnection. In any case, pseudopericyclic reactions involving two disconnections exhibit much clearer features, which facilitates their classification.