Second-Row Transition-Metal Doping of (Zn i S i ), i = 12, 16 Nanoclusters: Structural and Magnetic Properties

Abstract: TM@Zn i S i nanoclusters have been characterized by means of the Density Functional Theory, in which Transition Metal (TM) stands from Y to Cd, and i = 12 and 16. These two nanoclusters have been chosen owing to their highly spheroidal shape which allow for favored endohedral structures as compared to other nanoclusters. Doping with TM is chosen due to their magnetic properties. In similar cluster-assembled materials, these magnetic properties are related to the Transition Metal-Transition Metal (TM-TM) distances. At this point, endohedral doping presents a clear advantage over substitutional or exohedral doping, since in the cluster-assembled materials, these TM would occupy the well-fixed center of the cluster, providing in this way a better TM-TM distance control to experimentalists. In addition to endohedral compounds, surface structures and the TS's connecting both isomers have been characterized. In this way the kinetic and thermal stability of endohedral nanoclusters is predicted. We anticipate that silver and cadmium endohedrally doped nanoclusters have the longest life-times. This is due to the weak interaction of these metals with the cage, in contrast to the remaining cases where the TM covalently bond to a region of the cage. The open-shell electronic structure of Ag provides magnetic properties to Ag@Zn i S i clusters. Therefore, we have further characterized (Ag@Zn 12 S 12 ) 2 and (Ag@Zn 16 S 16 ) 2 dimers both in the ferromagnetic and antiferromagnetic state, in order to calculate the corresponding magnetic exchange coupling constant, J

·OH Oxidation Toward S- and OH-Containing Amino Acids

The hydroxyl radical is the most reactive oxygen species, and it is able to attack macromolecules such as proteins. Such oxidation processes are the cause of a number of diseases. Several oxidized products have been experimentally characterized, but the reaction pathways remain unclear. Herein, we present a theoretical study on the attack of hydroxyl radicals on hydroxyl- and sulfur-containing amino acid side chains. Several reaction mechanisms, such as hydrogen abstraction, electron transfer, or ·OH addition have been considered to investigate several reaction mechanisms. Two different dielectric values (4 and 80) have been used to model the effect of different protein environments. In addition, different alternative conformations of the amino acid backbone have been considered. Overall, the results indicate that the thermodynamics is the main factor driving the reaction pathway preference and, to a great extent, explains the formation of the experimental oxidized produts. Sulfur-containing amino acids would be oxidized more easily than OH-containing amino acids, which confirms the experimental evidence. This is determined by the stability of the sulfur radical intermediates. These results are not dramatically affected by either different dielectrics or backbone conformations

Stability and aromaticity of B i N i rings and fullerenes

B i N i clusters have been studied using the hybrid B3LYP density functional and diffusion quantum Monte Carlo (DMC) methods. Different cluster families have been characterized for each cluster size using B3LYP, and the energy differences have been compared with those obtained within DMC. The DMC results predict that the global minimum energy structures are rings for i = 2 9, a three-ring structure for i = 10 and spheroids for i 11. The aromaticity of the ring structures has been studied using the Nuclear Independent Chemical Shifts (NICS) criterion. According to this criterion, rings with an odd number of BN units are aromatic. Aromatic structures are thought to be the most stable, and the DMC results for the most stable structures are consistent with this hypothesis, but in some cases the B3LYP results are not

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 confirmation’s 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

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 confirmation’s 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

Plasmonic Resonances in the Al₁₃^– Cluster: Quantification and Origin of Exciton Collectivity

Recently, plasmonic resonances in molecules, clusters, and nanostructures have gathered a lot of attention for their potential range of applicability. Unlike other metal nanostructures, a wide variety of aluminum nanostructures show very promising plasmonic properties. Theoretical and computational investigations helped to understand the nature of collective excitations in such finite systems. However, such theoretical investigations are based on qualitative approaches rather than accurate quantitative methods. In the present work, the collectivity of the low-lying states of Al₁₃^– are investigated within the time-dependent density functional theory and analyzed through different computational tools. A novel tool, which provides a quantitative index of the collective nature of the electronic excitations, has been introduced, the so-called transition inverse participation ratio (TIPR) index. The obtained results suggest the presence of plasmonic-like transitions in the Al₁₃^– cluster and that these transitions are linked to the icosahedral symmetry of the cluster, allowing the rationalization by the simple jellium model. We believe that the present work opens the opportunity for the study and applicability of this type of electronic transition in aluminum clusters and in other related nanostructures

Quantum Monte Carlo study of the ground state and low-lying excited states of the scandium dimer

A large set of electronic states of scandium dimer has been calculated using high-level theoretical methods such as quantum diffusion Monte Carlo (DMC), complete active space perturbation theory as implemented in GAMESS-US, coupled-cluster singles, doubles, and triples, and density functional theory (DFT). The 3Sigmau and 5Sigmau states are calculated to be close in energy in all cases, but whereas DFT predicts the 5Sigmau state to be the ground state by 0.08 eV, DMC and CASPT2 calculations predict the 3Sigmau to be more stable by 0.17 and 0.16 eV, respectively. The experimental data available are in agreement with the calculated frequencies and dissociation energies of both states, and therefore we conclude that the correct ground state of scandium dimer is the 3Sigmau state, which breaks with the assumption of a 5Sigmau ground state for scandium dimer, believed throughout the past decades