Enhancing DFT-based energy landscape exploration by coupling quantum mechanics and static modes.

Unravelling the atomic scale diffusion that can occur at the surface, at the interface or into the bulk is challenging: multi-scale modelling approaches usually require intensive prospective calculations and moreover huge human investment. In this article, the Static Mode (SM) approach is coupled with Quantum Mechanics (QM) calculations in order to guide the exploration of the energy landscape, by optimizing the choice of events that are significant for the evolution of the system. SM enable the determination of the strain field of a set of atoms submitted to external and localized stresses, like atomic displacements. Here, we present a workflow based on the systematic SM exploration, with the objective to reduce both exploration time and human load when used with ab initio level calculations. The QMSM coupling allows the screening, scoring and selection of relevant directions that are further used to initiate and study diffusion in atomic systems. The most relevant deformations are then refined and relaxed with DFT calculations. In this paper, the overall QMSM approach is described and we discuss its use for the identification of atomic diffusion in two different systems of interest: grafting of a molecule on an oxide surface and studying the dynamical behavior of a point-defect in a bulk crystalline material.

IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns.

We propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm Iteratively suggests Rotated atom-centered reference frames and Assignments (iterative rotations and assignments (IRA)). The frame for which a permutationally invariant set-set distance, namely, the Hausdorff distance, returns a minimal value is chosen as the solution of the matching problem. IRA is able to find rigid rotations, reflections, translations, and permutations between structures with different numbers of atoms, for any atomic arrangement and pattern, periodic or not. When distortions are present between the structures, optimal rotation and translation are found by further applying a standard singular value decomposition-based method. To compute the atomic assignments under the one-to-one assignment constraint, we develop our own algorithm, constrained shortest distance assignments (CShDA). The overall approach is extensively tested on several structures, including distorted structural fragments. The efficiency of the proposed algorithm is shown as a benchmark comparison against two other shape matching algorithms. We discuss the use of our approach for the identification and comparison of structures and structural fragments through two examples: a replica-exchange trajectory of a cyanine molecule, in which we show how our approach could aid the exploration of relevant collective coordinates for clustering the data, and a SiO2 amorphous model, in which we compute distortion scores, and compare them with a classical strain-based potential. The source code and benchmark data are available at https://github.com/mammasmias/IterativeRotationsAssignments.

Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics.

Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly focus on water reorganization around GTP, which appears to be crucial to evaluate favorable and unfavorable hydration sites for hydrolysis. The NRas-GTP complex is analyzed using a hybrid quantum mechanics/molecular mechanics approach, treating for the first time to our knowledge transient water molecules at the ab initio level and leading to results that account for the electrostatic coupling between the protein complex and the solvent. We show that for the wild-type protein, water molecules are found around the GTP γ-phosphate group, forming an arch extended from residues 12 to 35. Two density peaks are observed, supporting previous results that suggest the presence of two water molecules in the active site, one in the vicinity of residue 35 and a second one stabilized by hydrogen bonds formed with nitrogen backbone atoms of residues 12 and 60. The structural changes observed in NRas Gln 61 mutants result in the drastic delocalization of water molecules that we discuss. In mutants Q61H and Q61K, for which water distribution is overlocalized next to residue 60, the second density peak supports the hypothesis of a second water molecule. We also conclude that Gly 60 indirectly participates in GTP hydrolysis by correctly positioning transient water molecules in the protein complex and that Gln 61 has an indirect steric effect in stabilizing the preorganized catalytic site.

A perfect wetting of Mg monolayer on Ag(111) under atomic scale investigation: First principles calculations, scanning tunneling microscopy, and Auger spectroscopy.

First principles calculations, scanning tunneling microscopy, and Auger spectroscopy experiments of the adsorption of Mg on Ag(111) substrate are conducted. This detailed study reveals that an atomic scale controlled deposition of a metallic Mg monolayer perfectly wets the silver substrate without any alloy formation at the interface at room temperature. A liquid-like behavior of the Mg species on the Ag substrate is highlighted as no dot formation is observed when coverage increases. Finally a layer-by-layer growth mode of Mg on Ag(111) can be predicted, thanks to density functional theory calculations as observed experimentally.

Diaminoethane adsorption and water substitution on hydrated TiO2: a thermochemical study based on first-principles calculations.

Epoxy-amines are used as structural adhesives deposited on Ti. The amine adhesion to a Ti surface depends highly on the surface state (oxidation, hydroxylation). Amines may adsorb above preadsorbed water molecules or substitute them to bind directly to surface Ti(4+) Lewis acid sites. The adsorption of a model amine molecule, diaminoethane (DAE), on a model surface, hydrated TiO2-anatase (101) surface, is investigated using Density Functional Theory including Dispersive forces (DFT-D) calculations. DAE adsorption and water substitution by DAE are exothermic processes and turn nearly isoenergetic at high coverage with adsorption-substitution energies around -0.3 eV (including dispersion forces and ZPE). Complementary ab initio molecular dynamics studies also suggest that the formation of an amine-water interaction induces water desorption from the surface at room temperature, a preliminary step towards the amine-Ti bond formation. An atomistic thermodynamic approach is developed to evaluate the interfacial free energy balance of both processes (adsorption and substitution). The main contributions to the energetic balance are dispersive interactions between molecules and the surface on the exergonic side, translational and rotational entropic contributions on the endergonic one. The substitution process is stabilized by 0.55 eV versus the adsorption one when free solvation, rotational and vibrational energies are considered. The main contribution to this free energy gain is due to water solvation. The calculations suggest that in toluene solvent with a water concentration of 10(-4) M or less, a full DAE layer replaces a preadsorbed water layer for a threshold concentration of DAE ≥ 0.1 M.

Deep Levels and Electron Paramagnetic Resonance Parameters of Substitutional Nitrogen in Silicon from First Principles.

Nitrogen is commonly implanted in silicon to suppress the diffusion of self-interstitials and the formation of voids through the creation of nitrogen-vacancy complexes and nitrogen-nitrogen pairs. Yet, identifying a specific N-related defect via spectroscopic means has proven to be non-trivial. Activation energies obtained from deep-level transient spectroscopy are often assigned to a subset of possible defects that include non-equivalent atomic structures, such as the substitutional nitrogen and the nitrogen-vacancy complex. Paramagnetic N-related defects were the object of several electron paramagnetic spectroscopy investigations which assigned the so-called SL5 signal to the presence of substitutional nitrogen (NSi). Nevertheless, its behaviour at finite temperatures has been imprecisely linked to the metastability of the NSi center. In this work, we build upon the robust identification of the SL5 signature and we establish a theoretical picture of the substitutional nitrogen. Through an understanding of its symmetry-breaking mechanism, we provide a model of its fundamental physical properties (e.g., its energy landscape) based on ab initio calculations. Moreover by including more refined density functional theory-based approaches, we calculate EPR parameters (↔g and ↔A tensors), elucidating the debate on the metastability of NSi. Finally, by computing thermodynamic charge transition levels within the GW method, we present reference values for the donor and acceptor levels of NSi.

A computational chemist approach to gas sensors: modeling the response of SnO2 to CO, O2, and H2O gases.

A general bottom-up modeling strategy for gas sensor response to CO, O(2), H(2)O, and related mixtures exposure is demonstrated. In a first stage, we present first principles calculations that aimed at giving an unprecedented review of basic chemical mechanisms taking place at the sensor surface. Then, simulations of an operating gas sensor are performed via a mesoscopic model derived from calculated density functional theory data into a set of differential equations. Significant presence of catalytic oxidation reaction is highlighted.

Density Functional Investigation on α-MoO3 (100): Amines Adsorption and Surface Chemistry.

The (100) surface of α-MoO3 should possess overwhelmingly more exposed Mo atoms than the (010), and the exposed Mo has been extensively considered as an active site for amine adsorption. However, α-MoO3 (100) has drawn little attention concerning the amine sensing mechanism. In this research, adsorption of ammonia (NH3), monomethylamine (MMA), dimethylamine (DMA), and trimethylamine (TMA) is systematically investigated by density functional theory (DFT). All four of these molecules have high affinity to α-MoO3 (100) through interaction between the N and the exposed Mo, and the affinity is mainly influenced by both the characteristics of the molecules and the geometric environment of the surface active site. Adsorption and dissociation of water and oxygen molecule on stoichiometric and defective α-MoO3 (100) surfaces are then simulated to fully understand the surface chemistry of α-MoO3 (100) in practical conditions. At low temperature, α-MoO3 (100) must be covered with a large number of water molecules; the water can desorb or dissociate into hydroxyl groups at high temperature. Oxygen vacancy (VO) can be generated through the annealing process during sensor device fabrication; VO must be filled with an O2 molecule, which can further interact with adsorbed water nearby to form hydroxyl groups. According to this research, α-MoO3 (100) must be the active surface for amine sensing and its surface chemistry is well understood. In the near future, further reaction and interaction will be simulated at α-MoO3 (100), and much more attention should be paid to α-MoO3 (100) not only theoretically but also experimentally.

Finding Reaction Pathways and Transition States: r-ARTn and d-ARTn as an Efficient and Versatile Alternative to String Approaches.

Finding transition states and diffusion pathways is essential to understand the evolution of materials and chemical reactions. Such characterization is hampered by the heavy computation costs associated with exploring energy landscapes at ab initio accuracy. Here, we revisit the activation-relaxation technique (ARTn) to considerably reduce its costs when used with the density functional theory and propose three adapted versions of the algorithm to efficiently (i) explore the energy landscape of complex materials with the knowledge of a single minimum (ARTn); (ii) identify a transition state when two minima or a guess transition state is given (refining ART or r-ART); and (iii) reconstruct complex pathways between two given states (directed ART or d-ART). We show the application of these three variants on benchmark examples and on various complex defects in silicon. For the latter, the presented improvements to ART lead to much more precise transition states while being 2 to 6 times faster than the commonly used string methods such as the climbing image nudged elastic band method (CI-NEB).

Elementary surface chemistry during CuO/Al nanolaminate-thermite synthesis: copper and oxygen deposition on aluminum (111) surfaces.

The surface chemistry associated with the synthesis of energetic nanolaminates controls the formation of the critical interfacial layers that dominate the performances of nanothermites. For instance, the interaction of Al with CuO films or CuO with Al films needs to be understood to optimize Al/CuO nanolaminates. To that end, the chemical mechanisms occurring during early stages of molecular CuO adsorption onto crystalline Al(111) surfaces are investigated using density functional theory (DFT) calculations, leading to the systematic determination of their reaction enthalpies and associated activation energies. We show that CuO undergoes dissociative chemisorption on Al(111) surfaces, whereby the Cu and O atoms tend to separate from each other. Both Cu and O atoms form islands with different properties. Copper islanding fosters Cu insertion (via surface site exchange mechanism) into the subsurface, while oxygen islands remain stable at the surface. Above a critical local oxygen coverage, aluminum atoms are extracted from the Al surface, leading to oxygen-aluminum intermixing and the formation of aluminum oxide (γ-alumina). For Cu and O co-deposition, copper promotes oxygen-aluminum interaction by oxygen segregation and separates the resulting oxide from the Al substrate by insertion into Al and stabilization below the oxide front, preventing full mixing of Al, Cu, and O species.

Synthesis, structural studies, theoretical calculations, and linear and nonlinear optical properties of terpyridyl lanthanide complexes: new evidence for the contribution of f electrons to the NLO activity.

The synthesis and structural, photophysical, and second-order nonlinear optical (NLO) properties of a novel lanthanide terpyridyl-like complex family LLn(NO(3))(3) (Ln = La, Gd, Dy, Yb, and Y) are reported. The isostructural character of this series in solution and in the solid state has been established on the basis of X-ray diffraction analysis in the cases of yttrium and gadolinium complexes, theoretical optimization of geometry (DFT), and NMR spectroscopy. The absorption, emission, and solvatochromic properties of the free terpyridyl-like ligand L were thoroughly investigated, and the twist intramolecular charge transfer (TICT) character of the lowest energy transition was confirmed by theoretical calculation (TDDFT and CIS). The similar ionochromic effect of the different lanthanide ions was evidenced by the similar UV-visible spectra of the complete family of complexes. On the other hand, the quadratic hyperpolarizability coefficient beta, measured by the harmonic light scattering (HLS) technique, is clearly dependent on the nature of the metal, and a careful examination of the particular case of yttrium unambiguously confirms the contribution of metal f electrons to the NLO activity.