Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

Water models with realistic physical-chemical properties are essential to study a variety of biomedical processes or engineering technologies involving molecules or nanomaterials. Atomistic models of water are constrained by the feasible computational capacity, but calibrated coarse-grained (CG) ones can go beyond these limits. Here, we compare three popular atomistic water models with their corresponding CG model built using finite-size particles such as ellipsoids. Differently from previous approaches, short-range interactions are accounted for with the generalized Gay-Berne potential, while electrostatic and long-range interactions are computed from virtual charges inside the ellipsoids. Such an approach leads to a quantitative agreement between the original atomistic models and their CG counterparts. Results show that a timestep of up to 10 fs can be achieved to integrate the equations of motion without significant degradation of the physical observables extracted from the computed trajectories, thus unlocking a significant acceleration of water-based mesoscopic simulations at a given accuracy

Computational prediction of L_{3} EXAFS spectra of gold nanoparticles from classical molecular dynamics simulations

We present a computational approach for the simulation of extended x-ray absorption fine structure (EXAFS) spectra of nanoparticles directly from molecular dynamics simulations without fitting any of the structural parameters of the nanoparticle to experimental data. The calculation consists of two stages. First, a molecular dynamics simulation of the nanoparticle is performed and then the EXAFS spectrum is computed from “snapshots” of structures extracted from the simulation. A probability distribution function approach calculated directly from the molecular dynamics simulations is used to ensure a balanced sampling of photoabsorbing atoms and their surrounding scattering atoms while keeping the number of EXAFS calculations that need to be performed to a manageable level. The average spectrum from all configurations and photoabsorbing atoms is computed as an Au L3-edge EXAFS spectrum with the FEFF 8.4 package, which includes the self-consistent calculation of atomic potentials. We validate and apply this approach in simulations of EXAFS spectra of gold nanoparticles with sizes between 20 and 60 Å. We investigate the effect of size, structural anisotropy, and thermal motion on the gold nanoparticle EXAFS spectra and we find that our simulations closely reproduce the experimentally determined spectra

Host dependence of the electron affinity of molecular dopants

International audienceCharge carriers energetics is key in electron transfer processes such as those that enable the electrical doping of organic semiconductors. In this study, we take advantage of the quantitative accuracy of embedded GW calculations to perform a series of virtual experiments that allow measuring the electron affinity of p-type dopants in different host solids. Our calculations show that the energy levels of a molecular impurity strongly depend on the host environment as a result of electrostatic intermolecular interactions. In particular, the electron affinity of a dopant impurity in a given semiconductor is found to be up to 1 eV lower than that of the pure dopant crystal. This result questions the pertinence of the electron affinity measured for pure dopants in order to predict doping efficiency in a specific host. The role of the Coulomb electron-hole interaction for the dopant-to-semiconductor charge transfer and for the release of doping-induced charges is discussed

A computational study of supported rhodium catalysts

In this work, density functional theory (DFT) was used to obtain microscopic structures of heterogeneous catalysts based on rhodium supported on a metal oxide (-Al2O3). Two different methodologies were used. The first methodology uses a periodic model and a plane-wave basis set to solve the Schrödinger equation in the framework of Bloch’s theorem. The optimised structures of RhI(CO)2/ -Al2O3 species obtained at this level of theory have bond lengths in agreement with experimental EXAFS determinations. The weighted linear combination of Rh K-edge XANES spectra computed using the three most dominant structures reproduces well the phase and shape of the oscillations of the experimental XANES spectrum, providing support for the computed structures. The second methodology is based on hybrid quantum mechanical (QM)/molecular mechanical (MM) calculations. Within this scheme the support is described at the MM level of theory while the region of interest, the absorption site where the surface RhI(CO)2 complex lies, is described with a suitable QM approach. These hybrid calculations performed at the PBE/ECP/cc-pVDZ level of theory were used to obtainminimum-energy structures and harmonic stretching frequencies of RhI(CO)2/-Al2O3 species. The computed bond lengths and harmonic stretching frequencies were in good agreement with the experimental evidence and with the results obtained using periodic model

Predicting the Conditions for Homeotropic Anchoring of Liquid Crystals at a Soft Surface. 4-n-Pentyl-4\u2032-cyanobiphenyl on Alkylsilane Self-Assembled Monolayers

We have studied, using atomistic molecular dynamics simulations, the alignment of the nematic liquid-crystal 4-n-pentyl-4\u2032-cyanobiphenyl (5CB) on self-assembled monolayers (SAMs) formed from octadecyl- and/or hexyltrichlorosilane (OTS and HTS) attached to glassy silica. We find a planar alignment on OTS at full coverage and an intermediate situation at partial OTS coverage because of the penetration of 5CB molecules into the monolayer, which also removes the tilt of the OTS SAM. Binary mixtures of HTS and OTS SAMs instead induce homeotropic (i.e., perpendicular) alignment. A comparison with the existing experimental literature is provided

Structural characterisation of supported Rh(CO)2/gam-Al2O3 catalysts by periodic DFT calculations

Microscopic structures of monodispersed rhodium dicarbonyl species chemisorbed on a ceramic metal-oxide support (?-alumina) have been obtained by density functional theory (DFT) calculations with periodic boundary conditions applied. Several minimum energy structures of species were obtained and their relative energies indicate that, in the most energetically stable geometry, the rhodium atom is coordinated in a square-planar environment and forms a four-membered Rh–O–Al–O ring, with one Al atom octahedrally coordinated. Another docking geometry, close lying in energy, also has a square-planar coordination for the rhodium atom and involves a six-membered Rh–O–Al–O–Al–O ring with one Al octahedrally coordinated and one Al tetrahedrally coordinated. Computed bond lengths were found to be in reasonable agreement with experimental bond lengths as determined by EXAFS spectroscopy. Theoretical Rh K-edge XANES spectra suggest that the pre-edge region probes electronic states localized on the RhI(CO)2 unit, while postedge features probe the electronic states arising from the RhI(CO)2 interaction with the support, which partly depends on the docking geometry of the RhI(CO)2 units.<br/

Are Coarse-Grained Structures as Good as Atomistic Ones for Calculating the Electronic Properties of Organic Semiconductors?

International audienceThe quality of amorphous molecular morphologies obtained with a recently introduced coarse-grained model, representing molecules in terms of connected anisotropic beads (Phys. Chem. Chem. Phys. 2019, 21, 26195), is benchmarked against reference atomistic data. Typical smallmolecule organic semiconductors in their pristine and doped forms are chosen as a challenging and technologically relevant case study for our comparison, which includes both structural features and the resulting electronic properties, such as charge carrier energy levels, energetic disorder, and intermolecular charge transfer couplings. Our analysis shows that our accurate coarse-grained model leads to molecular glasses that are very similar to native atomistic samples, with the discrepancy being further reduced upon back-mapping. The electronic properties computed for back-mapped morphologies are almost indistinguishable from the atomistic reference, especially for multibranched poly(hetero)cyclic hydrocarbons usually employed as organic semiconductors. This study provides a proof of principle for highly accurate large-scale simulations of complex molecular systems at a reduced computational cost

Pentacene Crystal Growth on Silica and Layer-Dependent Step-Edge Barrier from Atomistic Simulations

International audienc

Structural characterization of alkylsilane and fluoroalkylsilane self-assembled monolayers on SiO2 by molecular dynamics simulations

We present molecular dynamics simulations of self-assembled monolayers (SAMs) chemisorbed on an atomically flat amorphous silicon dioxide substrate. We model two prototypical SAM-forming alkylsilanes, octadecyltrichlorosilane (OTS) and 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS), that find widespread use in organic electronic applications. Crucially, our model does not rely on an explicit bonding between the alkylsilane and the substrate, thus allowing for the spontaneous organization of molecules into regular structures, which we studied as a function of coverage. By comparing the calculated tilt angle, film thickness, and lattice parameters with experiments, we conclude that the simulated morphologies are quantitatively consistent with the experimental evidence, demonstrating the accuracy of the simulation methodology. We take advantage of the atomistic resolution of the calculations for carrying out a detailed one-to-one comparison between the structure and the electronic properties of the two SAMs. In particular, we find that OTS molecules show a coverage-dependent tilt, while FDTS molecules are always vertically oriented, regardless of the coverage. More importantly for organic electronic applications, we observe that OTS SAMs do not alter the electrostatic potential of silica, while FDTS SAMs induce a negative voltage shift which increases with coverage and saturates at about -2