QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Mechanism of H2 production by the [FeFe]H subcluster of di-iron hydrogenases: implications for abiotic catalysts.

To explore the possibility that the active center of the di-iron hydrogenases, the [FeFe] H subcluster, can serve by itself as an efficient hydrogen-producing catalyst, we perform comprehensive calculations of the catalytic properties of the subcluster in vacuo using first principles density functional theory. For completeness, we examine all nine possible geometrical isomers of the Fe(II)Fe(I) active-ready state and report in detail on the relevant ones that lead to the production of H 2. These calculations, carried out at the generalized gradient approximation level, indicate that the most efficient catalytic site in the isolated [FeFe] H subcluster is the Fe d center distal (d) to the [4Fe-4S] H cluster; the other iron center site, the proximal Fe p, also considered in this study, has much higher energy barriers. The pathways with the most favorable kinetics (lowest energy barrier to reaction) proceed along configurations with a CO ligand in a bridging position. The most favorable of these CO-bridging pathways start from isomers where the distal CN (-) ligand is in up position, the vacancy V in down position, and the remaining distal CO is either cis or trans with respect to the proximal CO. These isomers, not observed in the available enzyme X-ray structures, are only marginally less stable than the most stable nonbridging Fe d-CO-terminal isomer. Our calculations indicate that this CO-bridging CN-up isomer has a small barrier to production of H 2 that is compatible with the observed rate for the enzyme. These results suggest that catalysis of H 2 production could proceed on this stereochemically modified [FeFe] H subcluster alone, thus offering a promising target for functional bioinspired catalyst design.

Methane dehydrogenation on Rh@Cu(111): a first-principles study of a model catalyst.

The issue of tuning the relative height of the first two dehydrogenation barriers of methane (CH(4) --> CH(3) + H and CH(3) --> CH(2) + H) is addressed using density-functional theory. It is shown that the combination of a very active reaction center-such as Rh-with a more inert substrate-such as Cu(111)-may hinder the second dehydrogenation step with respect to the first, thus resulting in the reverse of the natural order of the two barriers' heights.

Orbital energetics and molecular recognition.

We present preliminary data demonstrating that orbital eigenenergy fluctuation recorded in the course of ab initio molecular dynamics calculations may contain information relevant in determining molecular behavior and recognition. A simple scheme is presented that maps these data to molecular descriptors. Using computational drug design as the context, these descriptors are compared with previous electronic eigenvalue descriptor methods with encouraging results.

Hydrophobic-hydrophilic interactions of water with alkanethiolate chains from first-principles calculations.

The interaction of water with alkanethiolate chains is studied from first principles. A detailed analysis is performed by optimizing the structure of small water clusters, one-dimensional water chains, and ordered and disordered thin water layers adsorbed on hydroxyl(OH)- and methyl(CH3)-terminated alkanethiol monolayers. The hydrophilic/hydrophobic character of these two different substrates is investigated by means of an energetic analysis combined with hydrogen-bond counting. On the hydrophilic OH-terminated alkanethiol surface, zigzag, one-dimensional water chains and disordered thin water layers are the energetically favored structures. The ab initio results can be used to determine the optimal value of the empirical parameters characterizing a suitable force field to be used in classic molecular dynamics simulations.

Energetically driven reorganization of a modified catalytic surface under reaction conditions.

The compositional and structural rearrangements at the catalyst surface during chemical reactions are issues of great importance for understanding and modeling the catalytic processes. Low-energy electron microscopy and photoelectron spectromicroscopy studies of the real-space structure and composition of a Au-modified Rh(110) surface during water formation reveal reorganization processes due to Au mass transport triggered by the propagating reaction fronts. The temporal evolution of the surface reaction results in a 'patterned' surface consisting of separated Au-rich and Au-poor phases with different oxygen coverage, Rh surface structure, and reactivity. The experimental results are complemented by ab initio electronic-structure calculations of the O and Au adsorption phases, which demonstrate that the reorganization of the Au adlayer by the propagating reaction fronts is an energetically driven process. Our findings suggest that reaction-induced spatial inhomogeneity in the surface composition and structure is a common feature of metal catalysts modified with adatoms which become mobile under reaction conditions.

Engineering the reactivity of metal catalysts: a model study of methane dehydrogenation on Rh(111).

The first two steps of methane dissociation on Rh(111) have been investigated using density-functional theory, focusing on the dependence of the catalyst's reactivity on the atomic coordination of the active metal site. We find that, although the barrier for the dehydrogenation of methane (CH4 --> CH3 + H) decreases as expected with the coordination of the binding site, the dehydrogenation of methyl (CH3 --> CH2 + H) is hindered at an ad-atom defect, where the first reaction is instead most favored. Our findings indicate that, if it were possible to let the dissociation occur selectively at ad-atom defects, the reaction could be blocked after the first dehydrogenation step, a result of high potential interest for many dream reactions such as, for example, the direct conversion of methane to methanol.

Adsorption of 3-pyrroline on Si(100) from first principles.

The chemisorption of 3-pyrroline (C(4)H(7)N) on Si(100) is studied from first principles. Three different structures can be realized for which, depending on the temperature, the chemisorption process is facile (for two of them it is essentially barrierless); among these configurations the most favored one, from a thermodynamical point of view, is a dissociated structure obtained through an exothermic reaction characterized by the formation of a N-Si bond and a H-Si bond in which the H atom is detached from the molecule. Several other chemisorption structures are possible which, however, require overcoming a significant energy barrier and often breaking multiple bonds. A number of reaction paths going from one stable structure to another have been investigated. We have also generated, for the two basic adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements, and we propose a possible reaction mechanism for nitrogen incorporation.