Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Density functional theory study of H and H2 interacting with NiAl(110)

We present results of extensive density functional theory (DFT) calculations for H and H2 interacting with NiAl(110). Continuous representations of the full dimensional potential energy surface (PES) for the H/NiAl(110) and H2/NiAl(110) systems are obtained by interpolation of the DFT results using the corrugation reducing procedure. We find a minimum activation energy barrier of approximately 300 meV for dissociative adsorption of H2, which is consistent with the energy threshold obtained in molecular beam experiments for H2 (nu=0). We explain vibrational enhancement observed in experiments as the consequence of vibrational softening in the entrance channel over the most reactive surface site. The H2/NiAl(110) PES shows a high surface site selectivity: for energies up to 0.1 eV above threshold, H2 adsorption can only take place around top-Ni sites (within a circle of radius approximately 0.3 A). A strong energetic corrugation is observed: energy barriers for dissociation vary by more than 1 eV between the most and the least reactive sites. In contrast, geometric corrugation is much less pronounced and comparable to that of low index single metal surfaces like Cu or Pt.     

Dissociative adsorption of N2 on W(1 1 0): Theoretical study of the dependence on the incidence angle

The dissociative adsorption of N₂ on W(1 1 0) is studied using classical dynamics on a six-dimensional potential energy surface obtained from density functional theory calculations. Two distinct channels are identified in the dissociation process: a direct one and an indirect one. It is shown that the direct channel is inhibited for low energy molecules (E_i < 400 meV) and low incidence angles. The indirect channel includes long-lasting dynamic trapping of the molecule at the surface before dissociation. The dependence of the sticking coefficient on the initial incidence angle is analyzed. The theoretical results compare well with values measured using molecular beam techniques.     

Dry Reforming of Methane on a Highly‐Active Ni‐CeO2 Catalyst: Effects of Metal‐Support Interactions on C−H Bond Breaking

Ni‐CeO₂ is a highly efficient, stable and non‐expensive catalyst for methane dry reforming at relative low temperatures (700 K). The active phase of the catalyst consists of small nanoparticles of nickel dispersed on partially reduced ceria. Experiments of ambient pressure XPS indicate that methane dissociates on Ni/CeO₂ at temperatures as low as 300 K, generating CH_x and CO_x species on the surface of the catalyst. Strong metal–support interactions activate Ni for the dissociation of methane. The results of density‐functional calculations show a drop in the effective barrier for methane activation from 0.9 eV on Ni(111) to only 0.15 eV on Ni/CeO_2?x(111). At 700 K, under methane dry reforming conditions, no signals for adsorbed CH_x or C species are detected in the C 1s XPS region. The reforming of methane proceeds in a clean and efficient way.     

Eley–Rideal reaction dynamics between O atoms on β-cristobalite (1 0 0) surface: A new interpolated potential energy surface and classical trajectory study

We present a theoretical study of the collisions of atomic oxygen with O-precovered β-cristobalite (1 0 0) surface. We have constructed a multidimensional potential energy surface for the O₂/β-cristobalite (1 0 0) system based mainly on a dense grid of density functional theory points by using the interpolation corrugation-reducing procedure. Classical trajectories have been computed for quasithermal (100–1500 K) and state-specific (e.g., collision energies between 0.01 and 4 eV) conditions of reactants for different O incident angles (θ_v). Atomic sticking and O_2(adsorbed) formation are the main processes, although atomic reflection and Eley–Rideal (ER) reaction (i.e., O₂ gas) are also significant, depending their reaction probabilities on the O incident angle. ER reaction is enhanced by temperature increase, with an activation energy derived from the atomic recombination coefficient (γ_O(θ_v = 0°, T)) equal to 0.24 ± 0.02 eV within the 500–1500 K range, in close agreement with experimental data. Calculated γ_O(θ_v = 0°, T) values compare quite well with available experimental γ_O(T) although a more accurate calculation is proposed. Chemical energy accommodation coefficient β_O(T) is also discussed as a function of ER and other competitive contributions.     

Low sticking probability in the nonactivated dissociation of N2 molecules on W(110)

The six-dimensional potential energy surface for the dissociation of N2 molecules on the W(110) surface has been determined by density functional calculations and interpolated using the corrugation reducing procedure. Examination of the resulting six-dimensional potential energy surface shows that nonactivated paths are available for dissociation. In spite of this, the dissociation probability goes to a very small value when the impact energy goes to zero and increases with increasing energy, a behavior usually associated with activated systems. Statistics on the dynamics indicate that this unconventional result is a consequence of the characteristics of the potential energy surface at long distances. Furthermore, two distinct channels are identified in the dissociation process, namely, a direct one and an indirect one. The former is responsible for dissociation at high energies. The latter, which includes long-lasting dynamic trapping in the vicinity of a potential well above the W top position, is the leading mechanism at low and intermediate energies.     

Lowering Energy Barriers in Surface Reactions through Concerted Reaction Mechanisms

Any technologically important chemical reaction typically involves a number of different elementary reaction steps consisting of bond‐breaking and bond‐making processes. Usually, one assumes that such complex chemical reactions occur in a step‐wise fashion where one single bond is made or broken at a time. Using first‐principles calculations based on density functional theory we show that the barriers of rate‐limiting steps for technologically relevant surface reactions are significantly reduced if concerted reaction mechanisms are taken into account.     

H2 dissociation on individual Pd atoms deposited on Cu(111)

We present a Molecular Dynamics (MD) study based on Density Functional Theory (DFT) calculations for H(2) interacting with a Pd-Cu(111) surface alloy for low Pd coverages, Θ(Pd). Our results show, in line with recent experimental data, that single isolated Pd atoms evaporated on Cu(111) significantly increase the reactivity of the otherwise inert pure Cu surface. On top of substitutional Pd atoms in the Pd-Cu(111) surface alloy, the activation energy barrier for H(2) dissociation is smaller than the lowest one found on Cu(111) by a factor of two: 0.25 eV vs. 0.46 eV. Also in agreement with experiments, our DFT-MD calculations show that a large fraction of the dissociating H atoms efficiently spillover from Pd (i.e. the active sites), thanks to their extra kinetic energy due to the ~0.50 eV chemisorption exothermicity. Still, our DFT-MD calculations predict a dissociative sticking probability for low energy H(2) molecules that is much smaller than the estimated value from scanning tunneling microscopy experiments. Thus, further theoretical and experimental investigations are required for a complete understanding of H(2) dissociation on low-Θ(Pd) Pd-Cu(111) surface alloys.     

A classical dynamics method for H2 diffraction from metal surfaces

We present a discretization method that allows one to interpret measurements on diffraction of diatomic molecules from solid surfaces using six-dimensional (6D) classical trajectory calculations. It has been applied to the D2NiAl(110) and H2Pd(111) systems (which are models for activated and nonactivated dissociative chemisorption, respectively) using realistic potential energy surfaces obtained from first principles. Comparisons with experimental results and 6D quantum dynamical calculations show that, in general, the method is able to predict the relative intensity of the most important diffraction peaks. We therefore conclude that classical mechanics can be an efficient guide for experimentalists in the search for the most significant diffraction channels.     

Theoretical study of the structure of self-assembled monolayers of short alkylthiolates on Au(111) and Ag(111): the role of induced substrate reconstruction and chain-chain interactions

We compare the stability of various structures of high coverage self-assembled monolayers (SAMs) of short alkylthiolates, S(CH(2))(n-1)CH(3) (= C(n)), on Ag(111) and Au(111). We employ: (i) the ab initio thermodynamics approach based on density functional theory (DFT) calculations, to compare the stability of SAMs of C(1) (with coverages Θ = 3/7 and 1/3) on both substrates, and (ii) a set of pairwise interatomic potentials derived from second-order M?ller-Plesset (MP2) perturbation theory calculations, to estimate the role of chain-chain (Ch-Ch) interactions in the structure and stability of SAMs of longer chain alkylthiolates. For C(1)/Ag(111) (C(1)/Au(111)) the SAM with Θ = 3/7 is more (less) stable than for Θ = 1/3 in a wide range of temperatures and pressures in line with experiments. In addition, for the molecular densities of SAMs corresponding to Θ = 3/7 and 1/3, the MP2-based Ch-Ch interaction potential also predicts the different chain orientations observed experimentally in SAMs of alkylthiolates on Ag(111) and Au(111). Thus, for short length alkylthiolates, a simple model based on first principles calculations that separately accounts for molecule-surface (M-S) and Ch-Ch interactions succeeds in predicting the main structural differences between the full coverage SAMs usually observed experimentally on Ag(111) and Au(111).