29 research outputs found
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 (<sup>•</sup>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 <sup>•</sup>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 <sup>•</sup>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 <sup>•</sup>OH can abstract
another H atom or add itself to the formed radical, rendering the
final oxidized products. The studied second attack of <sup>•</sup>OH is applicable to situations where high concentration of <sup>•</sup>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 (<sup>•</sup>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 <sup>•</sup>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 <sup>•</sup>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 <sup>•</sup>OH can abstract
another H atom or add itself to the formed radical, rendering the
final oxidized products. The studied second attack of <sup>•</sup>OH is applicable to situations where high concentration of <sup>•</sup>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 Al<sub>13</sub><sup>–</sup> 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 Al<sub>13</sub><sup>–</sup> 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 Al<sub>13</sub><sup>–</sup> 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
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