Evolucion y perspectivas del sector vitivinicola

Peer Reviewe

Extracting dimer structures from simulations of organic-based materials using QM/MM methods

The functionality of weakly bound organic materials, either in Nanoelectronics or in Materials Science, is known to be strongly affected by their morphology. Theoretical predictions of the underlying structure–property relationships are frequently based on calculations performed on isolated dimers, but the optimized structure of the latter may significantly differ from experimental data even when dispersion-corrected methods are used for it. Here, we address this problem on two organic crystals, namely coronene and 5,6,11,12-tetrachlorotetracene, concluding that it is caused by the absence of the surrounding monomers present in the crystal, and that it can be efficiently cured when the dimer is embedded into a general Quantum Mechanics/Molecular Mechanics (QM/MM) geometry optimization scheme. We also investigate how the size of the MM region affects the results. These findings may be helpful for the simulation of the morphology of active materials in crystalline or glassy samples.This work is supported by the “Ministerio de Economía y Competitividad” of Spain and the “European Regional Development Fund” through project CTQ2014–55073-P

Theoretical study of stability and charge-transport properties of coronene molecule and some of its halogenated derivatives: A path to ambipolar organic-based materials?

We have carefully investigated the structural and electronic properties of coronene and some of its fluorinated and chlorinated derivatives, including full periphery substitution, as well as the preferred orientation of the non-covalent dimer structures subsequently formed. We have paid particular attention to a set of methodological details, to first obtain single-molecule magnitudes as accurately as possible, including next the use of modern dispersion-corrected methods to tackle the corresponding non-covalently bound dimers. Generally speaking, this class of compounds is expected to self-assembly in neighboring π-stacks with dimer stabilization energies ranging from –20 to –30 kcal mol−1 at close distances around 3.0–3.3 Å. Then, in a further step, we have also calculated hole and electron transfer rates of some suitable candidates for ambipolar materials, and corresponding charge mobility values, which are known to critically depend on the supramolecular organization of the samples. For coronene and per-fluorinated coronene, we have found high values for their hopping rates, although slightly smaller for the latter due to an increase (decrease) of the reorganization energies (electronic couplings).This work is supported by the “Ministerio de Educación y Ciencia” of Spain and the “European Regional Development Fund” through Project No. CTQ2011-27253

Theoretical Insights for Materials Properties of Cyclic Organic Nanorings

The synthesis of new carbon nanoforms with remarkable and fine‐tuned bulk properties still represents a formidable challenge, with cyclic organic nanorings emerging in recent years for the template‐driven design of this kind of systems. The design and engineering of these materials can be first controlled at the molecular scale, to further induce their specific self‐assembly toward tailored properties at the nanoscale. Theoretical studies have lately contributed to the understanding of the underlying physical effects, the development of synthetic strategies, and the rationalization of novel materials properties, employing a variety of methods ranging from accurate calculations of isolated molecules to atomistic molecular dynamics simulations of a large sample of molecules in realistic conditions, which will be reviewed here with a focus on the transition from single‐molecule to supramolecular properties.Computational resources were provided along the years by projects CTQ2014-55073-P and PID2019-106114GB-I00 (“Ministerio de Ciencia e Innovación”) and AICO/2018/175 (“Generalitat Valenciana”)

Use of quadrupole time-of-flight mass spectrometry for proposal of transformation products of the herbicide bromacil after water chlorination

The herbicide bromacil has been extensively used in the Spanish Mediterranean region, and although plant protection products containing bromacil have been withdrawn by the European Union, this compound is still frequently detected in surface and ground water of this area. However, the fast and complete disappearance of this compound has been observed in water intended for human consumption, after it has been subjected to chlorination. There is a concern about the possible degradation products formed, since they might be present in drinking water and might be hazardous. In this work, the sensitive full-spectrum acquisition, high resolution and exact mass capabilities of hybrid quadrupole time-of-flight (QTOF) mass spectrometry have allowed the discovery and proposal of structures of transformation products (TPs) of bromacil in water subjected to chlorination. Different ground water samples spiked at 0.5 µg/mL were subjected to the conventional chlorination procedure applied to drinking waters, sampling 2-mL aliquots at different time intervals (1, 10 and 30 min). The corresponding non-spiked water was used as control sample in each experiment. Afterwards, 50 μL of the water was directly injected into an ultra-high-pressure liquid chromatography (UHPLC)/electrospray ionization (ESI)-(Q)TOF system. The QTOF instrument enabled the simultaneous recording of two acquisition functions at different collision energies (MSE approach): the low-energy (LE) function, fixed at 4 eV, and the high-energy (HE) function, with a collision energy ramp from 15 to 40 eV. This approach enables the simultaneous acquisition of both parent (deprotonated and protonated molecules) and fragment ions in a single injection. The low mass errors observed for the deprotonated and protonated molecules (detected in LE function) allowed the assignment of a highly probable molecular formula. Fragment ions and neutral losses were investigated in both LE and HE spectra to elucidate the structures of the TPs found. For those compounds that displayed poor fragmentation, product ion scan (MS/MS) experiments were also performed. On processing the data with specialized software (MetaboLynx), four bromacil TPs were detected and their structures were elucidated. To our knowledge, two of them had not previously been reported

Determining the cohesive energy of coronene by dispersion-corrected DFT methods: Periodic boundary conditions vs. molecular pairs

We investigate the cohesive energy of crystalline coronene by the dispersion-corrected methods DFT-D2, DFT-D3, and DFT-NL. For that purpose, we first employ bulk periodic boundary conditions and carefully analyze next all the interacting pairs of molecules within the crystalline structure. Our calculations reveal the nature and importance of the binding forces in every molecular pair tackled and provide revised estimates of the effects of two- and three-body terms, leading to accurate results in close agreement with experimental (sublimation enthalpies) reference values.Financial support by the “Ministerio de Economía y Competitividad” of Spain and the “European Regional Development Fund” through Project No. CTQ2011-27253. The work in Mons was supported by the “Programme d’Excellence de la Région Wallonne” (OPTI2MAT project) and FNRS-FRFC

Analysis of Stratosphere-troposphere exchange processes associated to the Northern Subtropical Jet Stream

Informe técnico que recoge la contribución del INM y el INTA al proyecto TRACAS (Transport of Chemical species Across the Subtropical tropopause) (ENV4-CT97-0546).An intensive campaign of 41 ozonesoundings was conducted from February 1st to April 23rd 1999 at Tenerife (28ºN, 16ºW). The Subtropical Jet Stream (STJ) is located close to the Canary Islands in this period. A case analysis (March 25th and 26th) is presented to describe in detail the STE processes associated to the STJ, using both, meteorological analysis and information provided by the ozone soundings. Ozone sonde statistical analysis assess the significant role played by the STJ in the intrusions of subtropical upper tropospheric air masses into the midlatitude lower stratosphere

Molecular Dynamics Simulations for Genetic Interpretation in Protein Coding Regions: Where we Are, Where to Go and When

The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants