Accurate Ab Initio Simulations Research Articles

Ab initio self-energy embedding for the photoemission spectra of NiO and MnO

The accurate ab-initio simulation of periodic solids with strong correlations is one of the grand challenges of condensed matter. While mature methods exist for weakly correlated solids, the ab-initio description of strongly correlated systems is an active field of research. In this work, we show results for the single particle spectral function of the two correlated $d$-electron solids NiO and MnO from self-energy embedding theory. Unlike earlier work, the theory does not use any adjustable parameters and is fully ab-initio, while being able to treat both the strong correlation and the non-local screening physics of these materials. We derive the method, discuss aspects of the embedding and choices of physically important orbitals, and compare our results to x-ray and angle-resolved photoemission spectroscopy as well as bremsstrahlung-isochromat spectroscopy.

Multiwavelength Raman spectroscopy of ultranarrow nanoribbons made by solution-mediated bottom-up approach

Here we present a combined experimental and theoretical study of graphene nanoribbons (GNRs), where detailed multi-wavelength Raman measurements are integrated by accurate ab initio simulations. Our study covers several ultra-narrow GNRs, obtained by means of solution-based bottom-up synthetic approach, allowing to rationalize the effect of edge morphology, position and type of functional groups as well as the length on the GNR Raman spectrum. We show that the low-energy region, especially in presence of bulky functional groups is populated by several modes, and a single radial breathing-like mode cannot be identified. In the Raman optical region, we find that, except for the fully-brominated case, all GNRs functionalized at the edges with different side groups show a characteristic dispersion of the D peak (8-22 cm-1/eV). This has been attributed to the internal degrees of freedom of these functional groups, which act as dispersion-activating defects. The G peak shows small to negligible dispersion in most of the cases, with larger values only in presence of poor control of the edges functionalization, exceeding the values reported for highly defected graphene. In conclusion, we have shown that the characteristic dispersion of the G and D peaks offer further insight on the GNR structure and functionalization, by making Raman spectroscopy an important tool for the characterization of GNRs.

Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra.

The capability of the multiconfigurational restricted active space approach to identify electronic structure from spectral fingerprints is explored by applying it to iron L-edge X-ray absorption spectroscopy (XAS) of three heme systems that represent the limiting descriptions of iron in the Fe-O2 bond, ferrous and ferric [Fe(P)(ImH)2]0/1+ (P = porphine, ImH = imidazole), and FeII(P). The level of agreement between experimental and simulated spectral shapes is calculated using the cosine similarity, which gives a quantitative and unbiased assignment. Further dimensions in fingerprinting are obtained from the L-edge branching ratio, the integrated absorption intensity, and the edge position. The results show how accurate ab initio simulations of metal L-edge XAS can complement calculations of relative energies to identify unknown species in chemical reactions.

High pressure elastic properties of minerals from ab initio simulations: The case of pyrope, grossular and andradite silicate garnets

A computational strategy is devised for the accurate ab initio simulation of elastic properties of crystalline materials under pressure. The proposed scheme, based on the evaluation of the analytical stress tensor and on the automated computation of pressure-dependent elastic stiffness constants, is implemented in the CRYSTAL solid state quantum-chemical program. Elastic constants and related properties (bulk, shear and Young moduli, directional seismic wave velocities, elastic anisotropy index, Poisson's ratio, etc.) can be computed for crystals of any space group of symmetry. We apply such a technique to the study of high-pressure elastic properties of three silicate garnet end-members (namely, pyrope, grossular, and andradite) which are of great geophysical interest, being among the most important rock-forming minerals. The reliability of this theoretical approach is proved by comparing with available experimental measurements. The description of high-pressure properties provided by several equations of state is also critically discussed.

Low-temperature phase of BaTiO3: Piezoelectric, dielectric, elastic, and photoelastic properties fromab initiosimulations

A complete theoretical characterization of dielectric, elastic, photoelastic, and piezoelectric tensors of the low-temperature rhombohedral phase of BaTiO${}_{3}$ was performed by accurate ab initio simulations within periodic boundary conditions, using one-electron Hamiltonians and atom-centered Gaussian-type-function basis sets as in the crystal program. Because this phase is stable only at very low temperature, experimental characterization is difficult, and none of such tensorial properties have been measured. For this reason, we validated our method by comparing structural, electronic, and vibrational properties of the other three phases of BaTiO${}_{3}$ (cubic, tetragonal, and orthorhombic) with available experimental data. The effect of the adopted one-electron Hamiltonian on the considered tensorial properties, beyond the simple local density approximation and the dependence on the electric field frequency of dielectric and photoelastic constants, is explicitly investigated.

Erratum to: Elastic properties of six silicate garnet end members from accurate ab initio simulations

The online version of the original article can be found under doi:10.1007/s00269-013-0630-4.A. Erba (*) · A. Mahmoud · R. Orlando · R. Dovesi Dipartimento di Chimica and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Universita di Torino, via Giuria 5, 10125 Torino, Italye-mail: alessandro.erba@unito.it

Elastic properties of six silicate garnet end members from accurate ab initio simulations

The elastic properties of six silicate garnet end members, among the most important rock-forming minerals, are investigated here for the first time via accurate ab initio theoretical simulations. The Crystal program is used, which works within periodic boundary conditions and allows for all-electron basis sets to be adopted. From the computed elastic tensor, Christoffel’s equation is solved along a set of crystallographic directions in order to fully characterize the seismic wave velocity anisotropy in such materials. Polycrystalline isotropic aggregate elastic properties are derived from the computed single-crystal data via the Voigt-Reuss-Hill averaging procedure. Transferability of the elastic properties from end members to their solid solutions with different chemical compositions is also addressed.

Two-stage Folding of HP-35 from Ab Initio Simulations

Accurate ab initio simulation of protein folding is a critical step toward elucidation of protein-folding mechanisms. Here, we demonstrate highly accurate folding of the 35 residue villin headpiece subdomain (HP35) by all-atom molecular dynamics simulations using AMBER FF03 and the generalized-Born solvation model. In a set of 20 μs long simulations, the protein folded to the native state in multiple trajectories, with the lowest C α RMSD being 0.39 Å for residues 2–34 (excluding residues 1 and 35). The native state had the highest population among all sampled conformations, and the center of most populated cluster had a C α RMSD of 1.63 Å. Folding of this protein can be described as a two-stage process that followed a well-defined pathway. In the first stage, formation of helices II and III as a folding intermediate constituted the rate-limiting step and was initiated at a folding nucleus around residues Phe17 and Pro21. The folding intermediate further acted as a template that facilitated the folding and docking of helix I in the second stage. Detailed descriptions of the folding kinetics and the roles of key residues are presented.

Ab initio molecular dynamics in adaptive coordinates.

We present a formulation of ab initio molecular dynamics that exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a molecular-dynamics simulation of the ${\mathrm{CO}}_{2}$ molecule, and allows the reproduction of detailed features of its vibrational spectrum such as the splitting of the Raman ${\mathrm{\ensuremath{\sigma}}}_{\mathit{g}}^{+}$ mode caused by Fermi resonance. This approach opens the way to highly accurate ab initio simulations of organic compounds.

Plastic softening by hydrogen plasma charging in pure iron

Atomistic simulations are a powerful complement to experimental probes for understanding the nanoscale processes associated with the effects of hydrogen (H) on plasticity and fracture that are the underlying causes of hydrogen embrittlement (HE). Current experimental techniques provide quantitative measures of the macroscopic effects of H on plastic flow and fracture but are unable to determine the nanoscale distribution of H atoms in equilibrium nor, more importantly, as a function of time. Conversely, atomistic simulations can provide information on the nanoscale distribution of H around important lattice defects (vacancies, dislocations, grain boundaries, cracks) and probe the mechanical behavior of these defects in the presence and absence of H. Thus, in principle, atomistic simulations can test fundamental theories and conjectures that arise in attempting to rationalize experimental features of HE. However, atomistic simulations have a range of limitations that must be well-recognized. Accurate ab initio simulations are limited to small numbers of atoms and cannot capture necessary time evolution. Molecular simulations using semi-empirical interatomic potentials can handle more atoms and longer time scales, but are limited by accuracy of the potentials and time scales that remain far smaller than experimental time scales. The value of atomistic simulations thus lies primarily in creating targeted simulations to assess the energetics of specific configurations or specific mechanisms of deformation or fracture, along with theoretical models to estimate realistic time scales that remain inaccessible in simulations. Because of their limitations, atomistic simulations may not be definitive, but they nonetheless provide considerable insight by supporting or contradicting conjectures and concepts proposed to rationalize experiments. Here, the above issues are discussed in more detail and several examples, mainly from the work of the current authors, and including previously-unpublished studies on the effects of H on the bowout of the edge dislocations in α-Iron and predictions of solute-drag by H in nickel, serve to demonstrate how atomistic simulations can be used to reveal important features of the behavior of H in metals.