Functional Extrapolations to Tame Unbound Anions in Density-Functional Theory Calculations
Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densitie…
Interaction of Mo(CO) 6 and its derivative fragments with the Cu(001) surface: Influence on the decomposition process
A theoretical study on the adsorption and decomposition of molybdenum carbonyl on the copper (001) surface is reported. The adsorption structures and energies of Mo(CO)n molecules (n = 1 … 6) are computed systematically using density functional theory with Van der Waals corrections. By analyzing the energies of the various conformations, the main factors that determine the stable adsorption geometry are identified. Insight into the thermodynamics of decomposition is gained by calculating the reaction energy for dissociation of Mo(CO)n into Mo(CO)n−1 and CO. In the gas phase, this reaction is highly endothermic for all n. On the Cu surface, however, removal of the first CO group (n = 6) beco…
Theoretical investigation of the platinum substrate influence on BaTiO 3 thin film polarisation
Density functional theory calculations are performed to study the out-of-plane polarisation in BaTiO3 (BTO) thin films epitaxially grown on platinum. Prior to any polarisation calculation, the stability of the Pt(001)/BaTiO3(001) structure is thoroughly discussed. In particular, the nature of the Pt/BTO and BTO/vacuum interfaces is characterised. The growth of BTO is shown to start with a TiO2 layer while the nature of the surface termination does not broadly modify the stability. Therefore both upper terminations are considered when describing the ferroelectric behaviour in Pt/BTO interfaces. The geometric and electronic effects of the substrate on the polarisation are investigated. To iso…
EPHA7 haploinsufficiency is associated with a neurodevelopmental disorder
International audience; Ephrin receptor and their ligands, the ephrins, are widely expressed in the developing brain. They are implicated in several developmental processes that are crucial for brain development. Deletions in genes encoding for members of the Eph/ephrin receptor family were reported in several neurodevelopmental disorders. The ephrin receptor A7 gene (EPHA7) encodes a member of ephrin receptor subfamily of the protein-tyrosine kinase family. EPHA7 plays a role in corticogenesis processes, determines brain size and shape, and is involved in development of the central nervous system. One patient only was reported so far with a de novo deletion encompassing EPHA7 in 6q16.1. We…
Ferroelectric polarization switching induced from water adsorption in BaTiO 3 ultrathin films
The influence of water on the out-of-plane polarization of ${\mathrm{BaTiO}}_{3}$ (BTO) ultrathin films is studied by means of density functional theory calculations. The adsorption is investigated for different coverages on both terminations of BTO with, for each case, all possible states of polarization, namely, paraelectric, polarized upward, and polarized downward. We thus demonstrate different behavior as a function of the termination. While ${\mathrm{H}}_{2}\mathrm{O}$ adsorbs only dissociatively on the BaO termination, with a reinforced interaction compared to BTO without out-of-plane polarization, only molecular adsorption is observed on the ${\mathrm{TiO}}_{2}$ termination. In addi…
Self-consistent continuum solvation (SCCS): the case of charged systems.
The recently developed self-consistent continuum solvation model (SCCS) [O. Andreussi, I. Dabo, and N. Marzari, J. Chem. Phys. 136, 064102 (2012)] is applied here to charged species in aqueous solutions. Describing ions in solution represents a great challenge because of the large electrostatic interactions between the solute and the solvent. The SCCS model is tested over 106 monocharged species, both cations and anions, and we demonstrate its flexibility, notwithstanding its much reduced set of parameters, to describe charged species in solution. Remarkably low mean absolute errors are obtained with values of 2.27 and 5.54 kcal/mol for cations and anions, respectively. These results are co…
Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with developmental disorders
BackgroundBalanced chromosomal rearrangements associated with abnormal phenotype are rare events, but may be challenging for genetic counselling, since molecular characterisation of breakpoints is not performed routinely. We used next-generation sequencing to characterise breakpoints of balanced chromosomal rearrangements at the molecular level in patients with intellectual disability and/or congenital anomalies.MethodsBreakpoints were characterised by a paired-end low depth whole genome sequencing (WGS) strategy and validated by Sanger sequencing. Expression study of disrupted and neighbouring genes was performed by RT-qPCR from blood or lymphoblastoid cell line RNA.ResultsAmong the 55 pat…
Incomplete penetrance and phenotypic variability of 6q16 deletions including SIM1.
International audience; 6q16 deletions have been described in patients with a Prader-Willi-like (PWS-like) phenotype. Recent studies have shown that certain rare single-minded 1 (SIM1) loss-of-function variants were associated with a high intra-familial risk for obesity with or without features of PWS-like syndrome. Although SIM1 seems to have a key role in the phenotype of patients carrying 6q16 deletions, some data support a contribution of other genes, such as GRIK2, to explain associated behavioural problems. We describe 15 new patients in whom de novo 6q16 deletions were characterised by comparative genomic hybridisation or single-nucleotide polymorphism (SNP) array analysis, including…