Investigation of the Stability Mechanisms of Eight-Atom Binary Metal Clusters Using DFT Calculations and k-means Clustering Algorithm.

Here, we report density functional theory calculations combined with the k-means clustering algorithm and the Spearman rank correlation analysis to investigate the stability mechanisms of eight-atom binary metal AB clusters, where A and B are Fe, Co, Ni, Cu, Ga, Al, and Zn (7 unary and 21 binary clusters). Based on the excess energy analysis, the six most stable binary clusters are NiAl, NiGa, CoAl, FeNi, NiZn, and FeAl, and except for FeNi, their highest energetic stabilities can be explained by the hybridization of the d- and sp-states, which is maximized at the 50% composition, i.e., A4B4. Based on the Spearman correlation analysis, the energetic stability of the binary clusters increases with an increase in the highest occupied molecule orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy separation, which can be considered as a global descriptor. Furthermore, reducing the total magnetic moment values increases the stability for binary clusters without the Fe, Co, and Ni species, while the binary FeB, CoB, and NiB clusters increase their energetic stability with a decrease in the cluster radius, respectively, i.e., an energetic preference for compact structures.

Ab initio investigation of the role of the d-states occupation on the adsorption properties of H2, CO, CH4 and CH3OH on the Fe13, Co13, Ni13 and Cu13 clusters.

Here, we report a theoretical investigation, based on density functional theory calculations, into the role of the occupation d-states on the adsorption properties of CH4, CO, H2 and CH3OH on 3d 13-atom transition-metal (TM13) clusters (TM = Fe, Co, Ni, Cu). Except for Cu13, a gradual increase in the occupation of the d-states, i.e., from Fe13 to Ni13, increases the magnitude of the adsorption energy almost linearly for the H2/TM13 and CO/TM13 systems, which can be explained by the enhancement of the sp-d hybridization due to the shift of the d-states towards the highest occupied molecular orbital (HOMO). For Cu13, the d-states are located well below the HOMO, which reduces the sp-d hybridization, and hence, a smaller adsorption energy is obtained. However, this picture does not hold for CH4/TM13 and CH3OH/TM13, where the adsorption energy has nearly the same value for all TM13 clusters, which can be explained by electrostatic effects such as local polarization of the molecules and nearby TM atoms, and hence, the basic features of physisorption systems. Based on the electron density difference, the polarization effects are slightly larger for systems with empty d-states.

A hybrid-DFT investigation of the Ce oxidation state upon adsorption of F, Na, Ni, Pd and Pt on the (CeO2)6 cluster.

The formation of small polarons in CeO2-x compounds has been investigated mainly on solids, compact surfaces, and large nanoparticles. However, those findings cannot be easily transferred to small ceria clusters, where size effects might play a crucial role. In this work, we report a hybrid density functional theory investigation within the Heyd-Scuseria-Ernzerhof functional to elucidate the response of the Ce oxidation state upon the adsorption of F, Na, Ni, Pd, and Pt on the (CeO2)6 cluster. Among the selected species, only the Na and Ni adatoms contribute to the formation of a single small-polaron neighboring the CeIII+ cation (i.e., change from CeIV+ to CeIII+) accompanied by a local distortion in the cluster structure, which can be explained by the large magnitude of the charge transfer from the adatoms to the cluster and change in the nature of the Ce f-states (delocalized to localized). The same effect is also obtained by adding a single electron to the (CeO2)6 cluster. The Pd and Pt adatoms yield only small charge transfer to the (CeO2)6 cluster, which is not enough to affect the Ce oxidation state. As expected, F binds to the cationic Ce sites and leads to the same effects as obtained by removing a single electron from the cluster, which implies the formation of a localized hole with O p-character above the highest occupied molecular orbital accompanied also by a local structural distortion; however, it does not affect the Ce oxidation state.

Ab initio insights into the structural, energetic, electronic, and stability properties of mixed CenZr15-nO30 nanoclusters.

Mixed CeO2-ZrO2 nanoclusters have the potential to play a crucial role in nanocatalysis, however, the atomistic understanding of those nanoclusters is far from satisfactory. In this work, we report a density functional theory investigation combined with Spearman rank correlation analysis of the energetic, structural and electronic properties of mixed CenZr15-nO30 nanoclusters as a function of the composition (n = 0, 1,…,14, 15). For instance, we found a negative excess energy for all putative global minimum CenZr15-nO30 configurations with a minimum at about n = 6 (i.e., nearly 40% Ce), in which both the oxygen anion surroundings and cation radii play a crucial role in the stability and distribution of the chemical species. We found a strong energetic preference of Zr4+ cations to occupy larger coordination number sites, i.e., the nanocluster core region, while the Ce4+ cations are located near vacuum exposed O-rich regions. As expected, we obtained an almost linear decrease of the average bond lengths by replacing Ce4+ by Zr4+ cations in the (ZrO2)15 nanoclusters towards the formation of mixed CenZr15-nO30 nanoclusters, which resulted in a shift towards higher vibrational frequencies. Besides, we also observed that the relative stability of the mixed oxides is directly correlated with the increase (decrease) of the Zr d-state (Ce f-state) contribution to the highest occupied molecular orbital with the increase of the Zr content, hence driving the gap energy towards higher values.

Understanding the interplay between π-π and cation-π interactions in [janusene-Ag]+ host-guest systems: a computational approach.

Janusene is a symmetrical molecule that contains four benzene rings, with two of them forced to be in a vertical quasi-parallel face-to-face alignment. The unique physical nature of the transannular interactions and the electronic features of the region between the enforced parallel rings was tested with the complexation of Ag+ ion as a probe to evaluate the interplay between π-stacking and cation-π non-bonded interactions. The janusene framework and the [janusene-Ag]+ host-guest (H-G) system were analyzed through the introduction of substituent groups with different chemical natures and in different parts of the host framework. The janusenes were used to tune both π-stacking and cation-π interactions. Three modes of substitution (facial, lateral, and facial plus lateral) were explored to gain insight into the effects of such scaffold modifications on the dual non-bonded interactions. Our findings suggest that the η2:η2 silver coordination is the most stable interaction mode between the silver ion and the janusene parallel rings. The cation-π interaction in the host structure is stabilized by electron donating groups and destabilized by electron withdrawing groups. The stabilization effect is highlighted with substitutions on the facial and facial plus lateral modes, with the latter being due to additive cooperation between the substituent groups. The bonding analysis indicates that [janusene-Ag]+ complexes containing electron withdrawing groups in the facial and facial plus lateral substitution schemes are more stabilized by orbital interactions. Complexes with electron donating groups and the complexes with substituent groups in the lateral position are mainly stabilized by electrostatic interactions, although in all cases orbital and dispersive interactions are also essential to describe the bonding situation. We envisage that these results will guide the development of new systems with increased cation-π interaction capability.

Shedding Light on the Hydrolysis Mechanism of cis, trans-[Ru(dmso)4Cl2] Complexes and Their Interactions with DNA-A Computational Perspective.

Using several computational tools such as density functional theory analysis, docking, and MD simulations, we performed a study on cis, trans-[Ru(II)(dmso)4Cl2] complexes, which have therapeutic potential as antimetastatic agents, and their association with DNA. Kohn-Sham energy decomposition analysis reveals that dmso ligands have much smaller interaction energies compared to the chlorido ligands, and their substitution by aquo ligands induces an extra stabilization of the other metal-ligand bonds. Once the complex is hydrolyzed, the aquo ligands have the weakest interactions to the metallic center and therefore are more labile for substitution by a DNA atom. Molecular docking and molecular dynamics were employed to understand the complex preassociation to DNA, pointing to a higher affinity of the hydrolyzed complexes, as well as showing spontaneous binding events during the simulations. Our results are consistent with the experimentally available data that suggest a mechanism in which the complexes are quickly hydrolyzed in solution, before forming cross-links with the DNA molecule. We present a set of methods that could be used to optimize these complexes computationally, aiding in the development of new drugs based on transition metals.

In vivo and in silico anti-inflammatory mechanism of action of the semisynthetic (-)-cubebin derivatives (-)-hinokinin and (-)-O-benzylcubebin.

(-)-Cubebin (CUB), isolated from seeds of Piper cubeba, was used as starting material to obtain the derivatives (-)-hinokinin (HK) and (-)-O-benzyl cubebin (OBZ). Using paw edema as the experimental model and different chemical mediators (prostaglandin and dextran), it was observed that both derivatives were active in comparison with both negative (5% Tween® 80 in saline) and positive (indomethacin) controls. The highest reduction in the prostaglandin-induced edema was achieved by OBZ (66.0%), while HK caused a 59.2% reduction. Nonetheless, the dextran-induced paw edema was not significantly reduced by either of the derivatives (HK or OBZ), which inhibited edema formation by 18.3% and 3.5%, respectively, in contrast with the positive control, cyproheptadine, which reduced the edema by 56.0%. The docking analysis showed that OBZ presented the most stable ligand-receptor (COX-2 - cyclooxygenase-2) interaction in comparison with CUB and HK.

Synthesis and Solvatochromism of Substituted 4-(Nitrostyryl)phenolate Dyes.

4-(Nitrostyryl)phenols 2a-9a were synthesized, and by deprotonation in solution, the solvatochromic phenolates 2b-9b were formed. Their absorption bands in the vis region of the spectra are due to π-π* electronic transitions, of an intramolecular charge-transfer nature, from the electron-donor phenolate toward the electron-acceptor nitroarene moiety. The frontier molecular orbitals and natural bond orbitals were analyzed for the protonated and deprotonated forms. The calculated geometries are in agreement with X-ray structures observed for 4a, 6a, and 8a. The HOMO-LUMO energy gaps suggest that, after their deprotonation, an increase in the electron delocalization is observed. In the protonated compounds, the HOMO is primarily localized over the phenol ring and the C═C bridge. After deprotonation, it extends toward the entire molecule, including the NO2 groups. The solvatochromism of each dye was studied in 28 organic solvents, and it was found that all compounds exhibit a reversal in solvatochromism, which is interpreted in terms of the ability of the media to stabilize their electronic ground and excited states to different extents. The Catalán multiparameter equation is used in the interpretation of the solvatochromic data, revealing that the most important contribution to the solute/solvent interaction is the hydrogen-bond donor acidity of the solvent.