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International audience; The physics of Fe-C surface interactions is of fundamental importance to phenomena such as corrosion, catalysis, synthesis of graphene, new steels, etc. To better understand this question, we perform an extensive characterization of the energy landscape for carbon diffusion from bulk to surfaces for bcc iron at low C concentration. C diffusion mechanisms over the three main Fe-surfaces - (100), (110) and (111) - are studied computationally using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo algorithm. Migration and adsorption energies on surfaces as well as absorption energies into the subsurfaces are predicted and then compared to density functional theory (DFT) and experiment. The energy landscape along C-diffusion pathways from bulk to surface is constructed allowing a more extensive characterization of the diffusion pathways between surface and subsurface. In particular, effective migration energies from (100), (110) and (111) surfaces, to the bulk octahedral site are found to be around similar to 1.6 eV, similar to 1.2 eV and similar to 13 eV respectively suggesting that C insertion into the bulk cannot take place in pure crystalline Fe, irrespective of the exposed surface.

Complex magnetic domain structures and the energy barriers between them are responsible for pseudo‐single domain phenomena in rock magnetism, and contribute significantly to the magnetic remanence of paleomagnetic samples. This article introduces MERRILL, an open source software package for three‐dimensional micromagnetics optimised and designed for the calculation of such complex structures. MERRILL has a simple scripting user interface that requires little computational knowledge to use, but provides research strength algorithms to model complex, inhomogeneous domain structures in magnetic materials. It uses a finite‐element/boundary‐element numerical method, optimally suited for calculating magnetization structures of local energy minima (LEM) in irregular grain geometries that are of interest to the rock and paleomagnetic community. MERRILL is able to simulate the magnetic characteristics of LEM states in both single grains, and small assemblies of interacting grains, including saddle‐point paths between nearby LEMs. Here, the numerical model is briefly described, and an overview of the scripting language and available commands is provided. The open source nature of the code encourages future development of the model by the scientific community.

The effects of hole injection in amorphous-IGZO is analyzed by means of first-principles calculations. The injection of holes in the valence band tail states leads to their capture as a polaron, with high self-trapping energies (from 0.44 to 1.15 eV). Once formed, they mediate the formation of peroxides and remain localized close to the hole injection source due to the presence of a large diffusion energy barrier (of at least 0.6eV). Their diffusion mechanism can be mediated by the presence of hydrogen. The capture of these holes is correlated with the low off-current observed for a-IGZO transistors, as well as, with the difficulty to obtain a p-type conductivity. The results further support the formation of peroxides as being the root cause of Negative bias illumination stress (NBIS). The strong self-trapping substantially reduces the injection of holes from the contact and limits the creation of peroxides from a direct hole injection. In presence of light, the concentration of holes substantially rises and mediates the creation of peroxides, responsible for NBIS., Comment: 8 pages, 8 figures, to be published in Journal of Applied Physics

Human rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We study here a mathematical model for the structural transition between the native particle of human rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e. a sequence of metastable states with decreasing energy connected by minimum energy paths. We explore several transition pathways and discuss their implications for the RNA exit process.

The kinetic studies of the H-abstraction reaction of CF3CH(OH) CF3 with the OH radical, which is predicted to have two classes of possible reaction channels, were carried out. The minimum energy path and energetics were calculated at M062X/6-31+G (d,p) method. The rate coefficients for each reaction channels were evaluated by canonical variational transition state theory (CVT) with the small-curvature tunneling correction (SCT) and zero-curvature tunneling over the wide range of temperature of 200-3000 K. The temperature-dependent rate expression for the title reaction is obtained to be k(Total) = 2.60 � 10-22T3.04 exp(372.45/T) cm3 molecule-1 s-1; with k (298) = 3.54 � 10-14 cm3 molecule -1 s-1. The global warming potentials (GWPs) and atmospheric lifetimes of CF3CH(OH)CF3 are computed in the present investigation. The atmospheric implications and the degradation mechanism of CF3CH(OH)CF3 are discussed. It is concluded that this compound can be suggested as an acceptable substitute to HFCs in terms of its atmospheric lifetime and GWPs. � 2013 American Chemical Society.

The Fischer-Tropsch reaction is initiated by direct CO dissociation for Iron catalyst even though a H-assisted mechanism may be easier on other metals. In the gas phase, the CO dissociation is only favorable for Fe-clusters composed by more than 11 atoms. We show here the remarkable effect of the support TiO 2 (1 1 0), making this dissociation exothermic for Fe 4 and Fe 5 clusters. The main factor for the CO activation is the electron transfer to the reducible support. The role of the TiO 2 (1 1 0) support is to transform the neutral cluster into a positively charged one for which CO dissociation is easier.

Identification of radiation-induced radicals in relatively simple molecules is a prerequisite for the understanding of reaction pathways of the radiation chemistry of complex systems. Sucrose presents an additional practical interest as a versatile radiation dosimetric system. In this work, we present a periodic density functional theory study aimed to identify the fourth stable radical species in this carbohydrate. The proposed model is a fragment suspended in the lattice by hydrogen bonds with an unpaired electron at the original C5’ carbon of the fructose unit. It requires a double scission of the ring accompanied by substantial chemical and geometric reorganization.

This study reports the density functional theory (DFT) and classical molecular dynamics (MD) study of the lattice dynamical, mechanical and anionic transport behaviours of ThO2 in the superionic state. DFT calculations of phonon frequencies were performed at different levels of approximation as a function of isotropic dilation (ε) in the lattice parameter. With the expansion of the lattice parameter, there is a softening of B1u and Eu phonon modes at the X symmetry point of the Brillouin zone. As a result of the nonlinear decrease at the X point, the B1u and Eu phonon modes cross each other at ε = 0.03, which is associated with a sharp increase in the narrow peak of the phonon density of states, signifying a higher occupation and hence a higher coupling of these modes at high temperatures. The mode crossing also indicates anionic conductivity in the 〈001〉 direction leading to occupation of interstitial sites. Moreover, MD and nudged elastic band calculated diffusion barriers indicate that 〈001〉 is the easy direction for anion migration in the normal and superionic states. With a further increase in the lattice parameter, the B1u mode continues to soften and becomes imaginary at a strain (ε) of 0.036 corresponding to a temperature of 3430 K. The calculated temperature variation of single crystal elastic constants shows that the fluorite phase of ThO2 remains elastically stable up to the superionic regime, though the B1u phonon mode is imaginary in that state. This leads to anionic disorder at elevated temperatures. Tracking of anion positions in the superionic state as a function of time in MD simulations suggests a hopping model in which the oxygen ions migrate from one tetrahedral site to another via octahedral interstitial sites.

Atomic layer deposition (ALD) has been recognized as a promising method to deposit conformal and uniform thin film of copper for future electronic devices. However, many aspects of the reaction mechanism and the surface chemistry of copper ALD remain unclear. In this paper, we employ plane wave density functional theory (DFT) to study the transmetalation ALD reaction of copper dimethylamino-2-propoxide [Cu(dmap)2] and diethylzinc [Et2Zn] that was realized experimentally by Lee et al. [ Angew. Chem., Int. Ed. 2009, 48, 4536−4539]. We find that the Cu(dmap)2 molecule adsorbs and dissociates through the scission of one or two Cu–O bonds into surface-bound dmap and Cu(dmap) fragments during the copper pulse. As Et2Zn adsorbs on the surface covered with Cu(dmap) and dmap fragments, butane formation and desorption was found to be facilitated by the surrounding ligands, which leads to one reaction mechanism, while the migration of ethyl groups to the surface leads to another reaction mechanism. During both reaction mechanisms, ligand diffusion and reordering are generally endothermic processes, which may result in residual ligands blocking the surface sites at the end of the Et2Zn pulse, and in residual Zn being reduced and incorporated as an impurity. We also find that the nearby ligands play a cooperative role in lowering the activation energy for formation and desorption of byproducts, which explains the advantage of using organometallic precursors and reducing agents in Cu ALD. The ALD growth rate estimated for the mechanism is consistent with the experimental value of 0.2 Å/cycle. The proposed reaction mechanisms provide insight into ALD processes for copper and other transition metals.

A new approach is reported for tailoring the pore geometry in five series of multivariate metal-organic frameworks (MOFs) based on the structure [Zn-2(bdc)(2)(dabco)] (bdc = 1,4-benzenedicarboxylate, dabco = 1,8-diazabicyclooctane), DMOF-1. A doping procedure has been adopted to form series of MOFs containing varying linker ratios. The series under investigation are [Zn-2(bdc)(2-x)(bdc-Br)(x)(dabco)]center dot nDMF 1 (bdc-Br = 2-bromo-1,4-benzenedicarboxylate), [Zn-2(bdc)(2-x)(bdc-I)(x)(dabco)]center dot nDMF 2 (bdc-I = 2-iodo-1,4-benzenedicarboxylate), [Zn-2(bdc)(2-x)(bdc-NO2)(x)(dabco)]center dot nDMF 3 (bdc-NO2 = 2-nitro-1,4-benzenedicarboxylate), [Zn-2(bdc)(2-x)(bdc-NH2)(x)(dabco)]center dot nDMF 4 (bdc-NH2 = 2-amino-1,4-benzenedicarboxylate) and [Zn-2(bdc-Br)(2-x)(bdc-I)(x)(dabco)] nDMF 5. Series 1-3 demonstrate a functionality-dependent pore geometry transition from the square, open pores of DMOF-1 to rhomboidal, narrow pores with increasing proportion of the 2-substituted bdc linker, with the rhomboidal-pore MOFs also showing a temperature-dependent phase change. In contrast, all members of series 4 and 5 have uniform pore geometries. In series 4 this is a square pore topology, whilst series 5 exhibits the rhomboidal pore form. Computational analyses reveal that the pore size and shape in systems 1 and 2 is altered through non-covalent interactions between the organic linkers within the framework, and that this can be controlled by the ligand functionality and ratio. This approach affords the potential to tailor pore geometry and shape within MOFs through judicious choice of ligand ratios.

We present a comprehensive set of first-principles electronic structure calculations of the properties of substitutional transition metal solutes and point defects in austenite (face-centered cubic, paramagnetic Fe). Clear trends were observed in these quantities across the transition metal series, with solute-defect interactions strongly related to atomic size, and only weakly related to more subtle details of magnetic or electronic structure. Oversized solutes act as strong traps for both vacancy and self-interstitial defects and as nucleation sites for the development of protovoids and small self-interstitial loops. The consequent reduction in defect mobility and net defect concentrations in the matrix explains the observation of reduced swelling and radiation-induced segregation. Our analysis of vacancy-mediated solute diffusion demonstrates that below about 400 K Ni and Co will be dragged by vacancies and their concentrations should be enhanced at defect sinks. Cr and Cu showopposite behavior and are depleted at defect sinks. The stable configuration of some oversized solutes is neither interstitial nor substitutional; rather they occupy two adjacent lattice sites. The diffusion of these solutes proceeds by a novel mechanism, which has important implications for the nucleation and growth of complex oxide nanoparticles contained in oxide dispersion strengthened steels. Interstitial-mediated solute diffusion is negligible for all except the magnetic solutes (Cr, Mn, Co, and Ni). Our results are consistent across several antiferromagnetic states and surprising qualitative similarities with ferromagnetic (body-centered cubic) Fe were observed; this implies that our conclusions will be valid for paramagnetic iron.

The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple “for-loop” construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The structural changes throughout the entire reductive radiation-induced pathway of L-alpha-alanine are solved on an atomistic level with the aid of periodic DFT and nudged elastic band (NEB) simulations. This yields unprecedented information on the conformational changes taking place, including the protonation state of the carboxyl group in the "unstable'' and "stable'' alanine radicals and the internal transformation converting these two radical variants at temperatures above 220 K. The structures of all stable radicals were verified by calculating EPR properties and comparing those with experimental data. The variation of the energy throughout the full radiochemical process provides crucial insight into the reason why these structural changes and rearrangements occur. Starting from electron capture, the excess electron quickly localizes on the carbon of a carboxyl group, which pyramidalizes and receives a proton from the amino group of a neighboring alanine molecule, forming a first stable radical species (up to 150 K). In the temperature interval 150-220 K, this radical deaminates and deprotonates at the carboxyl group, the detached amino group undergoes inversion and its methyl group sustains an internal rotation. This yields the so-called "unstable alanine radical''. Above 220 K, triggered by the attachment of an additional proton on the detached amino group, the radical then undergoes an internal rotation in the reverse direction, giving rise to the "stable alanine radical'', which is the final stage in the reductive radiation-induced decay of alanine.

We used density functional theory to characterize various crystalline phases of NiTi alloys: (i) high-temperature austenite phase B2; (ii) orthorhombic B19; (iii) the monoclinic martensite phase B19′; and (iv) a body-centered orthorhombic phase (BCO), theoretically predicted to be the ground state. We also investigated possible transition pathways between the various phases and the energetics involved. We found B19 to be metastable with a 1 meV energy barrier separating it from B19′. Interestingly, we predicted a new phase of NiTi, denoted B19′′, that is involved in the transition between B19′ and BCO. B19′′ is monoclinic and can exhibit shape memory; furthermore, its presence reduces the internal stress required to stabilize the experimentally observed B19′ structure, and it consequently plays a key role in NiTi’s properties.

We applied density functional theory based on ultrasoft pseudopotentials to study the structural properties of Ir-4 clusters both in the gas phase and adsorbed on a MgO(100) surface. To resolve the discrepancy between experimental data which suggest a tetrahedral structure for Ir-4 and theoretical results which show a strong preference for the square isomer, we investigated the effect of several adsorbates on the equilibrium atomic structure of the clusters. Calculated binding energies of a single H, C, or O atom, as well as one CO or OH molecule, to three stable Ir-4 isomers indicate that C or CO adsorption significantly influences the relative stability of Ir-4 isomers. For MgO(100)-supported Ir-4, atomic carbon is able to change the isomer preference from the square to the tetrahedral geometry.

We present a combined experimental and theoretical study of the CO2 interaction with the Ni(110) surface. Photoelectron spectroscopy, temperature-programmed desorption, and high-resolution electron energy loss spectroscopy measurements are performed at different coverages and for increasing surface temperature after adsorption at 90 K with the aim to study the competing processes of CO2 dissociation and desorption. Simulations are performed within the framework of density functional theory using ab initio pseudopotentials, focusing on selected chemisorption geometries, determining the energetics and the structural and vibrational properties. Both experimental and theoretical vibrational frequencies yield consistent indications about two inequivalent adsorption sites that can be simultaneously populated at low temperature: short-bridge site with the molecular plane perpendicular to the surface and hollow site with the molecular plane inclined with respect to the surface. In both sites, the molecule has pure carbon or mixed oxygen-carbon coordination with the metal and is negatively charged and bent. Predicted energy barriers for adsorption and diffusion on the surface suggest a preferential adsorption path through the short-bridge site to the hollow site, which is compatible with the experimental findings. Theoretical results qualitatively support literature data concerning the increase of the work function upon chemisorption.

The dissociation of molecular hydrogen on a Mgs0001d surface and the subsequent diffusion of atomic hydrogen into the magnesium substrate is investigated using Density Functional Theory (DFT) calculations and rate theory. The minimum energy path and corresponding transition states are located using the nudged elastic band method, and rates of the activated processes are calculated within the harmonic approximation to transition state rate theory, using both classical and quantum partition functions based atomic vibrational frequencies calculated by DFT. The dissociation/recombination of H2 is found to be rate-limiting for the ab- and desorption of hydrogen, respectively. Zero-point energy contributions are found to be substantial for the diffusion of atomic hydrogen, but classical rates are still found to be within an order of magnitude at room temperature.

The main discharge product at the cathode of non-aqueous Li-air batteries is insulating Li2O2 and its poor electronic conduction is a main limiting factor in the battery performance. Here, we apply density functional theory calculations (DFT) to investigate the potential of circumventing this passivation by controlling the morphological growth directions of Li2O2 using directed poisoning of specific nucleation sites and steps. We show SO2 to bind preferentially on steps and kinks on the (1-00) facet and to effectively lower the discharge potential by 0.4 V, yielding a more facile discharge on the (0001) surface facet. Addition of a few percent SO2 in the O-2 stream may be used to control and limit growth of Li2O2 in specific directions and increase the electronic conduction through formation of interfaces between Li2O2 and Li-2(SO2)-type inclusions, which may ultimately lead to an increased accessible battery capacity at the expense of a limited increase in the overpotentials.