Pelargonic acid's interaction with the auxin transporter PIN1: A potential mechanism behind its phytotoxic effects on plant metabolism.

Pelargonic acid (PA) is a saturated fatty acid commonly found in several organisms, that is known for its phytotoxic effect and its use as bioherbicide for sustainable weed management. Although PA is already commercialised as bioherbicide, its molecular targets and mode of action is unknown according to the Herbicide Resistance Action Committee. Therefore, the aim of this work was focusing on the way this natural active substance impacts the plant metabolism of the model species Arabidopsis thaliana.

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.

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

Introduction: -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 seedlings.

Material And Methods: To evaluate the phytotoxicity of -cinnamaldehyde, a dose-response curve was first performed for the root growth process in order to calculate the reference inhibitory concentrations IC50 and IC80 (-cinnamaldehyde concentrations inducing a 50% and 80% inhibition, respectively).

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.

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.

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.

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.

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.

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.

Simultaneous SERS detection of copper and cobalt at ultratrace levels.

We report a SERS-based method for the simultaneous and independent determination of two environmental metallic pollutants, Cu(ii) and Co(ii). This was achieved by exploiting the coordination-sensitive Raman bands of a terpyridine (TPY) derivative for detecting transition metal ions. Changes in the vibrational SERS spectra of dithiocarbamate anchored terpyridine (TPY-DTC) were correlated as a function of each metal ion concentration, with limits of detection comparable to those of several conventional analytical methods.

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.

Ultrafast ring-opening/closing and deactivation channels for a model spiropyran-merocyanine system.

The photochemistry of a model merocyanine-spiropyran system was analyzed theoretically at the MS-CASPT2//SA-CASSCF(14,12) level. Several excited singlet states were studied in both the closed spiropyran and open merocyanine forms, and the paths to the different S(1)/S(0) conical intersections found were analyzed. After absorption of UV light from the spiropyran form, there are two possible ultrafast routes to efficient conversion to the ground state; one involves the rupture of the C(spiro)-O bond leading to the open form and the other involves the lengthening of the C(spiro)-N bond with no photoreaction.

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.

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.

Calculation of the molecular and atomic properties of selected anions in water.

The polarizability and other properties have been studied for F(-), Cl(-), Br(-), and HCOO(-) in water using a combined quantum chemical statistical mechanics simulation model that explicitly takes into account the Pauli repulsion as well as the electrostatic coupling between the QM system and the classical surroundings. It is shown that the surrounding molecules significantly reduce both the polarizability and the size of the anions. For the formate ions, local properties have been computed.

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.

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.

Planar or nonplanar: what is the structure of urea in aqueous solution?

A combined quantum chemical statistical mechanical method has been used to study the solvation of urea in water, with emphasis on the structure of urea. The model system consists of three parts: a Hartree-Fock quantum chemical core, 99 water molecules described with a polarizable force-field, and a dielectric continuum. A free-energy profile along the transition of urea from planar to a nonplanar structure is calculated.

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.

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.

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.

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.

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.

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.

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.