A first principles study of methanol decomposition on Pd(111): Mechanisms for O-H bond scission and C-O bond scission

There is some dispute as to whether methanol decomposition occurs by O-H bond scission or C-O bond scission. By carrying out density functional theory calculations, we investigate both scenario of the reaction pathways of methanol decomposition on a Pd(111) surface. It is shown that the O-H bond scission pathway is much more energetically favorable than the C-O bond scission pathway. The high reaction barrier in the latter case is found to be due to the poor bonding abilities of CH3 and OH with the surface at the reaction sites. (C) 2001 American Institute of Physics.

Stepwise addition reactions in ammonia synthesis: A first principles study

Catalytic ammonia synthesis is believed to proceed via dissociation of N-2 and H-2 with subsequent stepwise addition reactions from an adsorbed nitrogen atom to NH3. The first step, N-2 dissociation, has been thoroughly studied. However, little is known about the microscopic details of the stepwise addition reactions. To shed light on these stepwise addition reactions, density functional theory calculations with the generalized gradient approximation are employed to investigate NHx (x=1,3) formation on Ru(0001). Transition states and reaction barriers are determined in each elementary step. It is found that the reaction barriers for stepwise addition reactions are rather high, for example, the barrier for NH hydrogenation is calculated to be 1.28 eV, which is comparable with that of N-2 dissociation. In addition, one of the stepwise addition reactions on a stepped surface is also considered. The reaction barrier is found to be much higher than that of N-2 dissociation on the same stepped surface, which indicates the importance of stepwise addition reactions in ammonia synthesis. (C) 2001 American Institute of Physics.

Statistical-mechanical description of classical test-particle dynamics in the presence of an external force field: modelling noise and damping from first principles

Aiming to establish a rigorous link between macroscopic random motion (described e.g. by Langevin-type theories) and microscopic dynamics, we have undertaken a kinetic-theoretical study of the dynamics of a classical test-particle weakly coupled to a large heat-bath in thermal equilibrium. Both subsystems are subject to an external force field. From the (time-non-local) generalized master equation a Fokker-Planck-type equation follows as a "quasi-Markovian" approximation. The kinetic operator thus defined is shown to be ill-defined; in specific, it does not preserve the positivity of the test-particle distribution function f(x, v; t). Adopting an alternative approach, previously introduced for quantum open systems, is proposed to lead to a correct kinetic operator, which yields all the expected properties. A set of explicit expressions for the diffusion and drift coefficients are obtained, allowing for modelling macroscopic diffusion and dynamical friction phenomena, in terms of an external field and intrinsic physical parameters.

Electronic stopping power of H and He in Al and LiF from first principles

Non-linearities in the electronic stopping power of light projectiles in bulk Al and LiF are addressed from first principles using time-evolving time-dependent density functional theory. In the case of Al, the agreement of the calculations with experiments for H and He projectiles is fair, but a recently observed transition for He from one value of the electronic friction coefficient to a higher value at v ~ 0.3 a.u. is not reproduced by the calculations. For LiF, better accuracy is obtained as compared with previously published simulations, albeit the threshold remains overestimated. © 2013 Elsevier B.V.

Protection of DNA against low-energy electrons by amino acids: A first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.

Identifying the trend of reactivity for sp2 materials: an electron delocalization model from first principles calculations

The reactivity of sp² carbon materials is studied using the adsorption and dissociation of O₂ on graphene and graphene oxide as model systems. The reactions on the basal plane, zigzag and armchair edges of graphene and graphene oxide with different oxygen-containing groups are calculated using first principles calculations. Two Brønsted-Evans- Polanyi relationships are identified and an electron delocalization model is suggested to understand the general trend of reactivity for sp² carbon materials.

A first principles study of CH3 dehydrogenation on Ni(111)

Density functional theory with gradient corrections and spin polarization has been used to study the dehydrogenation of CH3 on Ni(111), a crucial step in many important catalytic reactions. The reaction, CH3(ads)--> CH2(ads)+H-(ads), is about 0.5 eV endothermic with an activation energy of more than 1 eV. The overall reaction pathway is rather intriguing. The C moiety translates from a hcp to a fcc site during the course of the reaction. The transition state of the reaction has been identified. The CH3 species is highly distorted, and both C and the active H are centered nearly on top of a row of Ni atoms with a long C-H bond length of 1.80 Angstrom. The local density of states coupled with examination of the real space distribution of individual quantum states has been used to analyze the reaction pathway. (C) 2000 American Institute of Physics. [S0021-9606(00)30218-5].

Strong second harmonic generation in SiC, ZnO, GaN two-dimensional hexagonal crystals from first-principles many-body calculations

The second harmonic generation (SHG) intensity spectrum of SiC, ZnO, GaN two-dimensional hexagonal crystals is calculated by using a real-time first-principles approach based on Green's function theory [Attaccalite et al., Phys. Rev. B: Condens. Matter Mater. Phys. 2013 88, 235113]. This approach allows one to go beyond the independent particle description used in standard first-principles nonlinear optics calculations by including quasiparticle corrections (by means of the GW approximation), crystal local field effects and excitonic effects. Our results show that the SHG spectra obtained using the latter approach differ significantly from their independent particle counterparts. In particular they show strong excitonic resonances at which the SHG intensity is about two times stronger than within the independent particle approximation. All the systems studied (whose stabilities have been predicted theoretically) are transparent and at the same time exhibit a remarkable SHG intensity in the range of frequencies at which Ti:sapphire and Nd:YAG lasers operate; thus they can be of interest for nanoscale nonlinear frequency conversion devices. Specifically the SHG intensity at 800 nm (1.55 eV) ranges from about 40-80 pm V(-1) in ZnO and GaN to 0.6 nm V(-1) in SiC. The latter value in particular is 1 order of magnitude larger than values in standard nonlinear crystals.

Elementary steps in aqueous proton transfer reactions : a first principles molecular dynamics study

La nature des acides dans un environnement aqueux est primordiale dans de nombreux aspects de la chimie et de la biologie. La caractéristique principale d'un acide est sa capacité à transférer un proton vers une molécule d'eau ou vers n'importe quelle base, mais ce procédé n'est pas aussi simple qu'il y paraît. Il peut au contraire être extrêmement complexe et dépendre de manière cruciale de la solvatation des différents intermédiaires de réaction impliqués. Cette thèse décrit les études computationnelles basées sur des simulations de dynamique moléculaire ab initio qui ont pour but d'obtenir une description à l'échelle moléculaire des divers procédés de transferts de proton entre acide et bases dans un milieu aqueux. Pour cela, nous avons étudié une serie de système, dont l'acide hydrofluorique aqueux, l'acide trifluoroacétique aqueux, et un système modèle constitué d'un phénol et d'une entité carboxylate reliés entre eux par une molécule d'eau en solution aqueuse. Deux états intermédiaires ont été identifiés pour le transfert d'un proton depuis un acide. Ces intermédiaires apparaissent stabilisés par un motif local de solvatation via des ponts H. Leurs signatures spectroscopiques ont été caractérisées au moyen de la spectroscopie infrarouge, en utilisant le formalisme de la dynamique moléculaire ab initio, qui inclut l'effet quantique nucléaire de manière explicite. Cette étude a aussi identifié trois chemins de réaction élémentaire, qui sont responsable pour le transfert d'un proton d'un acide à une base, ainsi que leurs échelles de temps caractéristiques. Les conclusions tirées de ces études sont discutées dans les détails, au niveau moléculaire, avec une emphase sur les comparaisons entre les résultats théoriques et les mesures expérimentales obtenues dans a littérature ou via des collaborateurs.

First-principles study of the neutral molecular metal Ni(tmdt)2.

The electronic structure of the molecular solid Ni(tmdt)2, the only well characterized neutral molecular metal to date, has been studied by means of first-principles density functional calculations. It is shown that these calculations correctly describe the metallic vs semiconducting behavior of molecular conductors of this type. The origin of the band overlap leading to the metallic character and the associated Fermi surfaces has been studied.

MgO/Ag(001) interface structure and STM images from first principles

The interface of MgO/Ag(001) has been studied with density functional theory applied to slabs. We have found that regular MgO films show a small adhesion to the silver substrate, the binding can be increased in off-stoichiometric regimes, either by the presence of O vacancies at the oxide film or by a small excess of O atoms at the interface between the ceramic to the metal. By means of theoretical methods, the scanning tunneling microscopy signatures of these films is also analyzed in some detail. For defect free deposits containing 1 or 2 ML and at low voltages, tunnelling takes place from the surface Ag substrate, and at large positive voltages Mg atoms are imaged. If defects, oxygen vacancies, are present on the surface of the oxide they introduce much easier channels for tunnelling resulting in big protrusions and controlling the shape of the image, the extra O stored at the interface can also be detected for very thin films.