Jose M. Mercero

CBe5E− (E = Al, Ga, In, Tl): planar pentacoordinate carbon in heptaatomic clusters

A series of clusters with the general formula CBe(5)E(-) (E = Al, Ga, In, Tl) are theoretically shown to have a planar pentacoordinate carbon atom. The structures show a simple and rigid topological framework-a planar EBe(4) ring surrounding a C center, with one of the ring Be-Be bonds capped in-plane by a fifth Be atom. The system is stabilized by a network of multicenter σ bonds in which the central C atom is the acceptor, and π systems as well by which the C atom donates charge to the Be and E atoms that encircle it.

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.

Quantum mechanical calculations on phosphate hydrolysis reactions

Multiple biological processes are regulated by kinases and phosphatases. This study aims to provide nonenzymatic models for phosphorylation and dephosphorylation of serine, threonine, and tyrosine phosphate using ab initio guantum mechanical calculations. We reduce the problem to methyl phosphate hydrolysis to model serine/threonine, and the hydrolysis of phenyl phosphate to model the tyrosine. HF, B3LYP, and MP2 calculations with a 6‐31+G(d) basis set were employed. The effect of water as a catalyst was also analyzed. As expected, the activation energy barrier is lowered.

The electronic states of Fe2

Abstract The equilibrium bond lengths, harmonic vibrational frequencies, ionization energies and dissociation energies of the iron dimer and its cation were determined by hybrid density functional theory calculations supplemented by single point calculations using coupled cluster theory. Calculations predict correctly the 9 Σ g − state as the ground state of Fe 2 . The ionization and dissociation energies have been found to compare satisfactorily with the experimental values. The ground state of Fe 2 + is found to be 10 Σ g − , corresponding to the 3d 12 4s 3 valence electronic configuration. However, it is worth mentioning that the 8 Σ u + state (3d 13 4s 2 ) is calculated to lie only 0.14 eV higher in energy.

Aluminium in Biological Environments: A Computational Approach

The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far “excluded from biology” metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions to this field, based on computational studies that can yield an understanding of the aluminum biochemistry at a molecular level. Aluminium can interact and be stabilized in biological environments by complexing with both low molecular mass chelants and high molecular mass peptides. The speciation of the metal is, nonetheless, dictated by the hydrolytic species dominant in each case and which vary according to the pH condition of the medium. In blood, citrate and serum transferrin are identified as the main low molecular mass and high molecular mass molecules interacting with aluminium. The complexation of aluminium to citrate and the subsequent changes exerted on the deprotonation pathways of its tritable groups will be discussed along with the mechanisms for the intake and release of aluminium in serum transferrin at two pH conditions, physiological neutral and endosomatic acidic. Aluminium can substitute other metals, in particular magnesium, in protein buried sites and trigger conformational disorder and alteration of the protonation states of the proteins sidechains. A detailed account of the interaction of aluminium with proteic sidechains will be given. Finally, it will be described how alumnium can exert oxidative stress by stabilizing superoxide radicals either as mononuclear aluminium or clustered in boehmite. The possibility of promotion of Fenton reaction, and production of hydroxyl radicals will also be discussed.

Discordant results on the FeO+ + H2 reaction reconciled by quantum Monte Carlo theory

The reaction of the iron oxide cation with the hydrogen molecule is studied in this work using the diffusion quantum Monte Carlo (DMC) method. Previous attempts achieved a qualitative agreement between theory and experiments, but not a satisfactory quantitative explanation which concurs with the experimental facts. The DMC method provides a consistent explanation of the experimental results all along the reaction path. This is due to the fact that DMC accounts for almost all of the correlation energy, which is of vital importance for the correct description of this reaction.

The Electronic Structure of the Al3− Anion: Is it Aromatic?

Multiconfigurational high-level electronic structure calculations show that the Al3(-) ring-like cluster anion has three close low-lying electronic states of different spin, all of them having strong multiconfigurational character. The aromaticity of the cluster has, therefore, been studied by means of total electron delocalization and normalized multicenter electron delocalization indices evaluated from the multiconfigurational wave functions of each state. The lowest-lying singlet and triplet states are found to be highly aromatic, whereas the next lowest-lying state, the quintet state, has much less, though non-negligible, aromatic character.

Sandwich complexes of the metalloaromatic eta(3)-Al3R3 ligand.

Metal sandwich complexes made of metallic Al(3)R(3) aromatic three-membered rings have been characterized, and their structural and electronic properties have been studied using density functional theory. The perfluorinated cyclotrialane ring has been identified as a very stable ligand for sandwichlike complexation, as it bears both large sigma and large pi aromaticities. We have demonstrated that the perfluorocyclotrialane ligand can sandwich metals and metal dimers while retaining its aromaticity upon complexation. Also, we have found that atomic magnetism is preserved upon complexation of magnetic transition-metal atoms. Finally, we have studied the assembly of these sandwichlike complexes into linear polymer-like structures.

Re‐examination of the C6Li6 Structure: To Be, or not To Be Symmetric

The potential energy surface of C6 Li6 was re-examined and a new non-symmetric global minimum was found. The new structure can be described as three C2 (2-) fragments strongly aggregated through lithium bridges. At high temperatures, fluxionality is perceived instead of dissociation. At 600 and 900 K, the BOMD simulations show that the lithium mobility is high, indicating that the cluster behaves in a liquid-like manner (BOMD=Born-Oppenheimer molecular dynamics).

Magnetic Endohedral Transition-Metal-Doped Semiconduncting-Nanoclusters

Endohedral first-row transition-metal-doped TM@Zn(i)S(i) nanoclusters, in which TM stands for the first-row transition-metals from Sc to Zn, and i=12, 16, have been characterized. In these structures the dopant metals are trapped inside spheroidal hollow semiconducting nanoclusters. It is observed that some of the transition metals are trapped in the center of mass of the cluster, whereas others are found to be displaced from that center, leading to structures in which the transition metals display a complex dynamical behavior upon encapsulation. This fact was confirmed by quantum molecular dynamics calculations, which further confirmed the thermal stability of endohedral compounds. In the endohedrally-doped nanoclusters in which the transition-metal atom sits on the center of mass, the host hollow cluster structure remains undistorted after dopant encapsulation. Conversely, if the encapsulated transition-metal atom is displaced from the center of mass, the host hollow cluster structure suffers a very tiny distortion. Additionally, it is found that there is negligible charge transfer between the dopant transition-metal atom and its hollow cluster host and, after encapsulation, the spin densities remain localized on the transition-metal atom. This allows for the atomic-like behavior of the trapped transition-metal atom, which gives rise to their atomic-like magnetic properties. The encapsulation free energies are negative, suggesting that these compounds are thermodynamically stable.