Magnetic Properties of Monomer and Dimer Tetrahedral VOx Entities Dispersed on Amorphous Silica-based Materials: Prediction of EPR Parameters from Relativistic DFT Calculations and Broken Symmetry Approach to Exchange Couplings

Molecular structures of the isolated tetrahedral oxovanadium(IV) and bridged μ-oxo-divanadium(IV) complexes hosted by the clusters mimicking surfaces of amorphous silica-based materials were investigated using density functional theory (DFT) calculations. Principal values of the g and A tensors for the monomer vanadyl species were obtained using the coupled-perturbed DFT level of theory and the spin–orbit mean-field approximation (SOMF). Magnetic exchange interaction for the μ-oxo bridged vanadium(IV) dimer was investigated within the broken symmetry approach. An antiferromagnetic coupling of the individual magnetic moments of the vanadium(IV) centers in the [VO–O–VO]2+ bridges was revealed and discussed in detail. The coupling explains pronounced decrease of the electron paramagnetic resonance signal (EPR) intensity, observed for the reduced VOx/SiO2 samples with the increasing coverage of vanadia, in terms of transformation of the paramagnetic monomer species into the dimers with S = 0 ground state

Molecular dynamics simulations of non-equilibrium systems

Peer reviewe

Integrins as therapeutic targets: lessons and opportunities.

The integrins are a large family of cell adhesion molecules that are essential for the regulation of cell growth and function. The identification of key roles for integrins in a diverse range of diseases, including cancer, infection, thrombosis and autoimmune disorders, has revealed their substantial potential as therapeutic targets. However, so far, pharmacological inhibitors for only three integrins have received marketing approval. This article discusses the structure and function of integrins, their roles in disease and the chequered history of the approved integrin antagonists. Recent advances in the understanding of integrin function, ligand interaction and signalling pathways suggest novel strategies for inhibiting integrin function that could help harness their full potential as therapeutic targets

The structure of sodium trisilicate glass via molecular dynamics employing three-body potentials

ABSTRACT Molecular dynamics simulations (MD) employing multibody potentials were used to simulate sodium trisilicate glass (Na2O·3SiO2). A multibody term has been added to a pair potential in order to incorporate the bond directionality which is expected for the partially covalent silicate structure. The structure of the glass was analyzed and results were compared to those found using two-body potentials and molecular statics, as well as to experimental results found using x-ray diffraction, XPS, NMR, and EXAFS. Current results compared favorably to experiment and showed improvement over results obtained using two-body potentials. Nearest neighbor distances and coordination numbers agreed well with published data. Although two-body potentials normally show overcoordinated silicon (>4.3) and broad O–Si–O tetrahedral angle distributions, in this study all silicon exhibited tetrahedral coordination (4.0) and the O–Si–O bond angle distribution was markedly sharpened. The number of nonbridging oxygens was shown to be nearly equal to the number of sodium ions present, and a reasonable distribution of Qc species was found. The overall structure closely resembled the modified network structure of glass proposed experimentally, with silicon tetrahedra remaining intact and sodium ions breaking up the network through the creation of nonbridging oxygens

Template-based combinatorial enumeration of virtual compound libraries for lipids

Abstract A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.</p

Permanent modifications in silica produced by ion-induced high electronic excitation: experiments and atomistic simulations

The irradiation of silica with ions of specific energy larger than ~0.1 MeV/u produces very high electronic excitations that induce permanent changes in the physical, chemical and structural properties and give rise to defects (colour centres), responsible for the loss of sample transparency at specific bands. This type of irradiation leads to the generation of nanometer-sized tracks around the ion trajectory. In situ optical reflection measurements during systematic irradiation of silica samples allowed us to monitor the irradiation-induced compaction, whereas ex situ optical absorption measurements provide information on colour centre generation. In order to analyse the results, we have developed and validated an atomistic model able to quantitatively explain the experimental results. Thus, we are able to provide a consistent explanation for the size of the nanotracks, the velocity and thresholding effects for track formation, as well as, the colour centre yield per ion and the colour centre saturation density. In this work we will discuss the different processes involved in the permanent modification of silica: collective atomic motion, bond breaking, pressure-driven atom rearrangement and ultra-fast cooling. Despite the sudden lattice energy rise is the triggering and dominant step, all these processes are important for the final atomic configuration.The authors acknowledge the computer resources and technical assistance provided by CESVIMA (UPM), funding by Spanish MINECO through project ENE2015-70300-C3-3-R, funding by EUROfusion Consortium through project AWP15-ENR-01/CEA-02 and funding by Madrid Region (CAM) through project Technofusion (II)-CM (S2013/MAE-2745). E.M.B. thanks support from PICT-2014-0696 (ANPCyT), and SeCTyP-UNCuyo grant 2016-0003