Clarifications on statements in Badía et al. (2013), Geoderma 193-194, 13-21

2 Pags. The definitive version is available at: http://www.sciencedirect.com/science/journal/00167061Both fragmental scientific quotations and misquotations can contribute to the spread of mistakes and cast confusion upon future research. We discuss several erroneous or conflictive statements and some misquotations found in an article published in GEODERMA. Many of the flaws are related with the occurrence of gypsum in soils and with the use of the term ‘equivalent’ in the designation of analytical results. Our reading of the subject article raises concerns about its validity, with practical implications on the future use of the concepts and data.Peer reviewe

Automatic characterization of drug/amino acid interactions by energy decomposition analysis

The computational study of drug/protein interactions is fundamental to understand the mode of action of drugs and design new ones. In this study, we have developed a python code aimed at characterizing the nature of drug/amino acids interactions in an accurate and automatic way. Specifically, the code is interfaced with different software packages to compute the interaction energy quantum mechanically, and obtain its different contributions, namely, Pauli repulsion, electrostatic and polarisation terms, by an energy decomposition analysis based on one-electron and two-electron deformation densities. The code was tested by investigating the nature of the interaction between the glycine amino acid and 250 drugs. An energy-structure relationship analysis reveals that the strength of the electrostatic and polarisation contributions is related with the presence of small and large size heteroatoms, respectively, in the structure of the drugLR and JJN acknowledge the Comunidad de Madrid for funding through the Attraction of Talent Program (Grant ref 2018-T1/BMD-10261) and the Spanish Ministry of Science and Innovation (Project PID2020-117806GA-I00). MM thanks Xunta de Galicia for fnancial support through the project GRC2019/2

Nociones de educación, formas, sistemas y métodos de enseñanza, expuestas en 50 lecciones ...

54 páxinas; 22 cmExemplar procedente da Biblioteca da Real Sociedad Económica de Amigos del País (Santiago de Compostela, Galicia

Effect of the QM size, basis set, and polarization on QM/MM interaction energy decomposition analysis

Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) including atomic charges and dipoles is applied to assess the effect of the QM region size on the convergence of the different interaction energy components, namely, electrostatic, Pauli, and polarization, for cationic, anionic, and neutral systems interacting with a strong polar environment (water). Significant improvements are found when the bulk solvent environment is described by a MM potential in the EDA scheme as compared to pure QM calculations that neglect bulk solvation. The predominant electrostatic interaction requires sizable QM regions. The results reported here show that it is necessary to include a surprisingly large number of water molecules in the QM region to obtain converged values for this energy term, contrary to most cluster models often employed in the literature. Both the improvement of the QM wave function by means of a larger basis set and the introduction of polarization into the MM region through a polarizable force field do not translate to a faster convergence with the QM region size, but they lead to better results for the different interaction energy components. The results obtained in this work provide insight into the effect of each energy component on the convergence of the solute−solvent interaction energy with the QM region size. This information can be used to improve the MM FFs and embedding schemes employed in QM/MM calculations of solvated systems.Agencia Estatal de Investigación | Ref. PID2020-117806GA-I00Comunidad de Madrid | Ref. 2018-T1/BMD-10261Xunta de Galicia | Ref. GRC2019/24Universidade de Vigo/CISU

Nódulos y Concreciones

Torrijo, F.; Mandado Collado, JMA. (2010). Nódulos y Concreciones. Investigación y Ciencia: Edición Española de Scientific American. (409):76-83. http://hdl.handle.net/10251/65237S768340

Paragénesis yeso-sílex en el Sector Aragonés de la Cuenca Terciaria del Ebro

En este trabajo se estudia la asociación litológica existente entre el yeso y el sílex en las zonas del Sector Aragonés de la Cuenca Terciaria del Ebro donde se tienen evidencias. El sílex aparece casi exclusivamente en el cuadrante noroccidental del Sector Aragonés, extensamente asociado a las litofacies yesíferas del Mioceno inferior. En los yesos de Borja-Ablitas–Monteagudo, localizados muy próximos a la Cordillera Ibérica, las silicificaciones están presentes de forma masiva, formando nódulos y estratos potentes y continuos, con contactos bruscos con los niveles yesíferos con los que se asocian. Sin embargo, en las extensas áreas yesíferas de la Fm. Zaragoza, situadas en el centro de la cuenca, las silicificaciones son microscópicas y están dispersas entre las distintas subunidades. La textura de las silicificaciones es sobretodo esferulítica, formada por un núcleo opalino y una envuelta fibroso-radiada de cuarcina-lutecita. En menor proporción, también están presentes el cuarzo microcristalino y megacuarzo. La textura de los yesos es secundaria alabastrina en los yesos de la Fm. Zaragoza, y primaria lenticular en los yesos de Borja-Ablitas-Monteagudo. Mediante el trabajo de campo y el estudio de lámina delgada, se comprueba que el sílex se encuentra reemplazando al yeso, y que el proceso de removilización, transporte y precipitación se tuvieron que producir durante la diagénesis. Los flujos con la sílice disuelta provenientes del área fuente, llegando a la cuenca evaporítica favorecidos por un pH básico, donde se produciría la precipitación de la sílice por un descenso brusco del pH debido a la influencia de materia orgánica. Mediante estas interpretaciones, y a partir del contexto geológico de la evolución evaporítica terciaria de la Cuenca del Ebro, hemos podido discutir la posible área fuente de la sílice y su momento de emplazamiento

Depósitos silexíticos en el terciario continental de la Cuenca de Calatayud: Caracterización y génesis

The tertiary Calatayud Basin is a NW-SE elongated depression, extending from Calatayud (Zaragoza) to Montalbán (Teruel) and whose dimensions are approximately 130 km long and 20 km wide. This basin consists of two distinct sub-basins separated by the Daroca High (Calatayud Basin in the northern sector and Montalbán Basin in the sourthern sector). These Basins present a quite similar sedimentary evolution of the Neogene evaporitic and carbonatic lacustrine systems, that generally ocuppy central locations in both basins. Three main sedimentary units (Lower, Intermediate and Upper units) divided by two main sedimentary breaks are traditionally described in the Calatayud Basin. The lower and the Intermediate units have evaporitic sedimentation, whilst the Upper Unit is typically freshwater fluvio-lacustrine sedimentation. This work focuses on the study of carbonatic materials placed in the Cristo de Ribota hermitage area, which is localized in the Intermediate Unit of Calatayud Basin, to the Northern of Sierra de Armantes. The interest of this area lies in the presence of silexitic levels, whose thickness can be metric, exceptional in the geologic record and that it raises interesting troubles at the time of establishing a hypothesis on the possible origin of the silica that generates these sílex deposits, as well as in the establishment of a genetic model. The sílex levels in the Cristo de Ribota series appear mainly in carbonate rocks. Petrographic studies of the samples taken in this area show a replacement of silica by carbonate, as well as a silica cementation in karts cavities generated by epidiagenetic karts processes. These cavities acted as conduits for fluids saturated in silica which resulted in silex deposits. The fluids should necessarily have an episodic character and the fact that karstic cavities can be filled with silica or carbonate is an evidence of it. For the silica precipitation, not only the low temperature and a less than 9 pH are necessary, but also there must exist a lot of silica-supersatured water, as well as a high permeability. The source of silica deposits in this area is probably diagenetic, but also it would be necessary to consider a thermal origin corresponding to the contribution of silica by hydrothermal fluids

Dispersión de metales pesados en los suelos del término municipal de Zaragoza

Desde la década de los 80 existe una normativa medioambiental que asegura una buena práctica industrial, pero, las fábricas en los años anteriores vertían en su entorno los productos residuales fruto de su actividad, tal y como ocurría en la ciudad de Zaragoza.El crecimiento de Zaragoza supuso que las industrias situadas en las inmediaciones del centro de la ciudad se desplazasen hacia zonas más periféricas dejando un sustrato potencialmente contaminado en metales pesados, por ejemplo, arsénico, cadmio, cobalto, cromo, cobre, mercurio, molibdeno, plomo y zinc, cuyo riesgo para la salud y el medioambiente es ampliamente conocido.Este informe aporta información sobre aspectos relevantes como la concentración de metales pesados en los suelos de la ciudad, los factores que han podido influir en su dispersión o las causas de su origen.<br /

Travertines associated with the Alhama-Jaraba thermal waters (NE, Spain): Genesis and geochemistry

Freshwater carbonates are interesting archives in palaeoenvironmental reconstructions. However, more studies of those systems are needed to fully understand past environments. In this work the actively-forming travertines of the Alhama-Jaraba thermal system were studied for the first time in order to evaluate the relationship between the geochemical and mineralogical composition and the environmental conditions during their formation. With that aim, a combination of petrographical, mineralogical, geochemical and stable isotope analyses were carried out. These carbonates provide a natural laboratory for the study of the effect of different variables (natural and anthropogenic) on carbonate precipitation. The results showed that there is a close relationship between the mineralogy of the solid precipitates and the formation temperature, and only the samples formed from overheated waters (40–60 °C) show significant concentrations of aragonite. Aragonite-bearing samples show higher concentrations in Sr, Ba and U while calcitic solids are enriched in Mg. These differences could be attributed to mineralogy, temperature or different precipitation rates. The geochemical evaluation of the chemistry of both the solids and their parental waters suggests that differences in the rate of CO2-degassing and, in some cases, evaporation are the primary environmental controls on isotopic compositions. In addition, the results show that, if strong evaporation and CO2-degassing are involved, calcite precipitation occurs under conditions of isotopic disequilibrium with its parental water. The results of our study are useful to interpret old depositional environments and palaeotemperatures

MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch caseSpanish Ministry of Science and Innovation; MCIN/AEI, Grant/Award Numbers: PID2020-117806GA-I00, PID2019-110091GB-I00; María de Maeztu, Grant/Award Number: CEX2018-000805-M; Comunidad de Madrid, Grant/Award Number: 2018-T1/BMD-10261; Xunta de Galicia, Grant/Award Number: GRC2019/24; the European Social Fund; Spanish Ministry of Education and Vocational Training, Grant/Award Number: FPU19/02292; Universidade de Vigo, Grant/Award Number: PREUVIGO-21; Universidad Autonoma de Madri