Mauro Boero

A mechanism of adsorption of β-nicotinamide adenine dinucleotide on graphene sheets: Experiment and theory

Beta-nicotinamide adenine dinucleotide (NAD(+)) and its reduced form (NADH) play major roles in the development of electrochemical enzyme biosensors and biofuel cells. Unfortunately, the oxidation of NADH at carbon electrodes suffers from passivation of the electrodes and a decrease in passing currents. Here, we investigate experimentally and theoretically the reasons for such passivation. High-resolution X-ray photoelectron spectroscopy (HR-XPS), voltammetry, and amperometry show that adsorption occurs on the edges and edge-like defects of graphene sheets. HR-XPS and ab initio molecular dynamics show that the adsorption of NAD(+) molecules on the edges of graphene happens due to interaction with oxygen-containing groups such as carboxylic groups, while graphene edges substituted only with hydrogen are prone to passivation.

Formation of a Covalent Glycosyl–Enzyme Species in a Retaining Glycosyltransferase

Elusive glycosyl-enzyme adduct: Using classical MD simulations and QM/MM metadynamics, the long-time sought glycosyl-enzyme covalent intermediate of a retaining glycosyltransferase, with a putative nucleophile residue in the active site, has been trapped (MD=molecular dynamics; QM/MM=quantum mechanics/molecular mechanics).

Steric and electronic selectivity in the synthesis of Fe-1,2,4,5-tetracyanobenzene (TCNB) complexes on Au(111): From topological confinement to bond formation

A study of the surface assisted self-assembly of 1,2,4,5-tetracyanobenzene (TCNB) acceptor molecules and Fe atoms on an Au(111) surface is presented. While conditions to get the two-dimensional arrays of stable Fe(TCNB)4 complexes are clearly identified, ultrahigh vacuum scanning tunneling microscopy and spectroscopy (STM/STS) coupled with first-principles calculations reveals that situations may occur where Fe and TCNB survive on the surface (as Fe-4TCNB entities) at a higher density than the original molecular monolayer without forming coordination bonds with each other. It is found that the square planar coordination of the Fe(TCNB)4 monomer complexes cannot fully develop in the presence of lateral strain due to growth-induced confinement. A phenomenon similar to steric hindrance involving a strongly modified chirality with a Fe-N-C bond angle of 120° compared to the 180° for the stable complex may then explain why the Fe atom keeps its metallic bond with the surface. The competition between steric and electronic effects, not reported before, may arise elsewhere in surface chemistry involved in the synthesis of new and potentially useful organic nanomaterials.

Origin of structural analogies and differences between the atomic structures of GeSe4 and GeS4 glasses: A first principles study

First-principles molecular dynamics simulations based on density functional theory are employed for a comparative study of structural and bonding properties of two stoichiometrically identical chalcogenide glasses, GeSe4 and GeS4. Two periodic cells of 120 and 480 atoms are adopted. Both glasses feature a coexistence of Ge-centered tetrahedra and Se(S) homopolar connections. Results obtained for N = 480 indicate substantial differences at the level of the Se(S) environment, since Ge-Se-Se connections are more frequent than the corresponding Ge-S-S ones. The presence of a more prominent first sharp diffraction peak in the total neutron structure factor of glassy GeS4 is rationalized in terms of a higher number of large size rings, accounting for extended Ge-Se correlations. Both the electronic density of states and appropriate electronic localization tools provide evidence of a higher ionic character of Ge-S bonds when compared to Ge-Se bonds. An interesting byproduct of these investigations is the occurrence of discernible size effects that affect structural motifs involving next nearest neighbor distances, when 120 or 480 atoms are used.

Reducing the Cost and Preserving the Reactivity in Noble‐Metal‐Based Catalysts: Oxidation of CO by Pt and Al–Pt Alloy Clusters Supported on Graphene

The oxidation mechanisms of CO to CO2 on graphene-supported Pt and Pt-Al alloy clusters are elucidated by reactive dynamical simulations. The general mechanism evidenced is a Langmuir-Hinshelwood (LH) pathway in which O2 is adsorbed on the cluster prior to the CO oxidation. The adsorbed O2 dissociates into two atomic oxygen atoms thus promoting the CO oxidation. Auxiliary simulations on alloy clusters in which other metals (Al, Co, Cr, Cu, Fe, Ni) replace a Pt atom have pointed to the aluminum doped cluster as a special case. In the nanoalloy, the reaction mechanism for CO oxidation is still a LH pathway with an activation barrier sufficiently low to be overcome at room temperature, thus preserving the catalyst efficiency. This provides a generalizable strategy for the design of efficient, yet sustainable, Pt-based catalysts at reduced cost.

Exohedral M–C60 and M2–C60 (M = Pt, Pd) systems as tunable-gap building blocks for nanoarchitecture and nanocatalysis

Transition metal-fullerenes complexes with metal atoms bound on the external surface of C60 are promising building blocks for next-generation fuel cells and catalysts. Yet, at variance with endohedral M@C60, they have received a limited attention. By resorting to first principles simulations, we elucidate structural and electronic properties for the Pd-C60, Pt-C60, PtPd-C60, Pd2-C60, and Pt2-C60 complexes. The most stable structures feature the metal atom located above a high electron density site, namely, the π bond between two adjacent hexagons (π-66 bond). When two metal atoms are added, the most stable configuration is those in which metal atoms still stand on π-66 bonds but tends to clusterize. The electronic structure, rationalized in terms of localized Wannier functions, provides a clear picture of the underlying interactions responsible for the stability or instability of the complexes, showing a strict relationship between structure and electronic gap.

Simple but Efficient Method for Inhibiting Sintering and Aggregation of Catalytic Pt Nanoclusters on Metal-Oxide Supports.

A simple and efficient method to inhibit aggregation of Pt clusters supported on metal oxide was developed, preserving the accessible clusters surface where catalytically active sites are located even at relatively high temperatures up to 700u2005K. The key idea was the inclusion of transition metal atoms such as Ni into the Pt clusters, thus anchoring the clusters through formation of strong chemical bonds with oxygen atoms of the metal-oxide support. To elucidate the efficiency of the method, first-principles molecular dynamics enhanced with free-energy sampling methods were used. These virtual experiments showed how doped Ni atoms, having a stronger affinity to O than Pt, anchor the Pt clusters tightly to the metal-oxide supports and inhibit their tendency to aggregate on the support.

Role of π-Radicals in the Spin Connectivity of Clusters and Networks of Tb Double-Decker Single Molecule Magnets

When single molecule magnets (SMMs) self-assemble into 2D networks on a surface, they interact via the π-electrons of their ligands. This interaction is relevant to the quantum entanglement between molecular qubits, a key issue in quantum computing. Here, we examine the role played by the unpaired radical electron in the top ligand of Tb double-decker SMMs by comparing the spectroscopic features of isolated and 2D assembled entities on surfaces. High-resolution scanning tunneling microscopy (STM) is used to evidence experimentally the Kondo resonance of the unpaired radical spins in clusters and islands and its quenching due to up-pairing at orbital overlaps. The presence or the absence of the Kondo feature in the dI/dV maps turns out to be a good measure of the lateral interaction between molecules in 2D networks. In a 2D cluster of molecules, the π-orbital lobes that are linked through the orbital overlap show paired-up electron wave function (one singly occupied molecular orbital (SOMO) with spin-up and the other with spin-down) and therefore do not experience the Kondo resonance in the experiment. As a result, small clusters built by STM-assisted manipulation of molecules show alternating Kondo features of quantum mechanical origin, from the monomer to the dimer and the trimer. On the other hand, when the TbPc2 molecular clusters grow larger and form extended domains, a geometric rearrangement occurs, leading to the quenching of the Kondo signal on one lobe out of two. The even distribution of overlapping (SOMO) lobes on the perimeter of the molecule is induced by the square symmetry of the semi-infinite lattice and clearly distinguishes the lattice from the clusters.

First-Principles Modeling of Binary Chalcogenides: Recent Accomplishments and New Achievements

This contribution is focussed on a set of first-principles molecular dynamics results obtained over the past fifteen years for disordered chalcogenides. In the first part, we sketch and review the historical premises underlying research efforts devoted to the understanding of structural properties in liquid and glassy Ge(_x)Se(_{1-x}) systems. We stress the importance of selecting well performing exchange-correlation functionals (within density functional theory) to achieve a correct description of short and intermediate range order. In the second part, we provide a specific, comparative example of structural analysis for chalcogenide GeX(_4) systems differing by the chemical identity of the X atom. We are able to demonstrate that the correct account of differences between the coordination environments of the two corresponding glasses requires system sizes substantially larger than (sim )100 atoms. Finally, the role played by the pressure in altering the structural properties of glassy GeSe(_2) is invoked, in light of recent studies devoted to a density-driven structural transformation occurring in this system.

First-Principles Molecular Dynamics Methods: An Overview

This chapter proposes an overview of computational approaches used nowadays in the field of first-principles simulations to model amorphous and liquid materials. The scope is to bring to the attention of the readership advances and (still existing) limitations in the description of the interactions among atoms which, starting in general from an ordered crystallographic structure, undergo significant modifications in the underlying electronic structure for the disordered phases. These subtle details are difficult to capture by resorting on classical model potentials and call for an accurate description of the quantum mechanical description of the intimate constituent of a glassy compound. The heavy computational workload associated can be nowadays overcome in virtue of the increasing computing power of last-generation high performance computers. Also of paramount importance are advances in algorithms and methods capable of providing the required speed-up in terms of both performances and accuracy.