Rafael Grande-Aztatzi

Structural evolution of small gold clusters doped by one and two boron atoms.

The potential energy surfaces (PES) of a series of gold–boron clusters with formula AunB (n = 1–8) and AumB2 (m = 1–7) have been explored using a modified stochastic search algorithm. Despite the complexity of the PES of these clusters, there are well‐defined growth patterns. The bonding of these clusters is analyzed using the adaptive natural density partitioning and the natural bonding orbital analyses. Reactivity is studied in terms of the molecular electrostatic potential.

Planar pentacoordinate carbons in CBe5(4-) derivatives.

The potential energy surfaces of a series of clusters with formula CBe5Lin(n-4) (n = 1 to 5) have been systematically explored. Our computations show that the lithium cations preserve the CBe5(4-) pentagon, such that the global minimum structure for these series of clusters has a planar pentacoordinate carbon (ppC) atom. The systems are primarily connected via a network of multicenter σ-bonds, in which the C atom acts as σ-acceptor and this acceptance of charge is balanced by the donation of the 2pz electrons to the π-cloud. The induced magnetic field analysis suggests that the clusters with formula CBe5Lin(n-4) (n = 1 to 5) are fully delocalized. The fact that these ppC-containing clusters are the lowest-energy forms on the corresponding potential energy surfaces raises expectations that these species can be prepared experimentally in the gas phase.

Aluminum's preferential binding site in proteins: Sidechain of amino acids versus backbone interactions

Abstract The interaction of aluminum ion Al(III) with polypeptides is a subject of paramount importance, since it is a central feature to understand its deleterious effects in biological systems. Various drastic effects have been attributed to aluminum in its interaction with polypeptides and proteins. These interactions are thought to be established mainly through the binding of aluminum to phosphorylated and non-phosphorylated amino acid sidechains. However, a new structural paradigm has recently been proposed, in which aluminum interacts directly with the backbone of the proteins, provoking drastic changes in their secondary structure and leading ultimately to their denaturation. In the present paper, we use computational methods to discuss the possibility of aluminum to interact with the backbone of peptides and compare it with the known ability of aluminum to interact with amino acid sidechains. To do so, we compare the thermodynamics of formation of prototype aluminum-backbone structures with prototype aluminum-sidechain structures, and compare these results with previous data generated in our group in which aluminum interacts with various types of polypeptides and known aluminum biochelators. Our results clearly points to a preference of aluminum towards amino acid sidechains, rather than towards the peptide backbone. Thus, structures in which aluminum is interacting with the carbonyl group are only slightly exothermic, and they become even less favorable if the interaction implies additionally the peptide nitrogen. However, structures in which aluminum is interacting with negatively-charged sidechains like aspartic acid, or phosphorylated serines are highly favored thermodynamically.

Structural and optical properties of the naked and passivated Al5Au5 bimetallic nanoclusters

The structural and optical properties of both the naked and passivated bimetallic Al5Au5 nanoclusters have been analyzed based on data obtained from ab initio density functional theory and quantum molecular dynamics simulations. It has been found that the Al5Au5 nanocluster possesses a hollow shaped minimum energy structure with segregated Al and Au layered domains, the former representing the electrophilic domain and the latter the nucleophilic domain. In particular, it has been shown that alkali metal cations attach in the nucleophilic domain and hop from one Au site to the next one in the picoseconds time scale, while anions are bound tightly to the Al atoms of the electrophilic domain. Simulating annealing studies are very suggestive of the proneness of the nanocluster towards coalescence into large cluster units, when the cluster is left unprotected by appropriate ligands. Further passivation studies with NaF salt suggest, nonetheless, the possibility of the isolation of the Al5Au5 cluster in molten salts or ionic liquids.

Oxidation of Acid, Base, and Amide Side-Chain Amino Acid Derivatives via Hydroxyl Radical

Hydroxyl radical (•OH) is known to be highly reactive. Herein, we analyze the oxidation of acid (Asp and Glu), base (Arg and Lys), and amide (Asn and Gln) containing amino acid derivatives by the consecutive attack of two •OH. In this work, we study the reaction pathway by means of density functional theory. The oxidation mechanism is divided into two steps: (1) the first •OH can abstract a H atom or an electron, leading to a radical amino acid derivative, which is the intermediate of the reaction and (2) the second •OH can abstract another H atom or add itself to the formed radical, rendering the final oxidized products. The studied second attack of •OH is applicable to situations where high concentration of •OH is found, e.g., in vitro. Carbonyls are the best known oxidation products for these reactions. This work includes solvent dielectric and confirmations effects of the reaction, showing that both are negligible. Overall, the most favored intermediates of the oxidation process at the side chain correspond to the secondary radicals stabilized by hyperconjugation. Intermediates show to be more stable in those cases where the spin density of the unpaired electron is lowered. Alcohols formed at the side chains are the most favored products, followed by the double-bond-containing ones. Interestingly, Arg and Lys side-chain scission leads to the most favored carbonyl-containing oxidation products, in line with experimental results.