Molecular adsorption on coinage metal subnanoclusters: A DFT+D3 investigation.

Gold and silver subnanoclusters with few atoms are prominent candidates for catalysis-related applications, primarily because of the large fraction of lower-coordinated atoms exposed and ready to interact with external chemical species. However, an in-depth energetic analysis is necessary to characterize the relevant terms within the molecular adsorption process that can frame the interactions within the Sabatier principle. Herein, we investigate the interaction between Agn and Aun subnanoclusters (clu, n = 2-7) and N2 , NO, CO, and O2 molecules, using scalar-relativistic density functional theory calculations within van der Waals D3 corrections. The onefold top site is preferred for all chemisorption cases, with a predominance of linear (≈180°) and bent (≈120°) molecular geometries. A larger magnitude of adsorption energy is correlated with smaller distances between molecules and clusters and with the weakening of the adsorbates bond strength represented by the increase of the equilibrium distances and decrease of molecular stretching frequencies. From the energetic decomposition, the interaction energy term was established as an excellent descriptor to classify subnanoclusters in the adsorption/desorption process concomitant with the Sabatier principle. The limiting cases: (i) weak molecular adsorption on the subnanoclusters, which may compromise the reaction activation, where an interaction energy magnitude close to 0 eV is observed (e.g., physisorption in N2 /Ag6 ); and (ii) strong molecular interactions with the subnanoclusters, given the interaction energy magnitude is larger than at least one of the individual fragment binding energies (e.g., strong chemisorption in CO/Au4 and NO/Au4 ), conferring a decrease in the desorption rate and an increase in the possible poisoning rate. However, the intermediate cases are promising by involving interaction energy magnitudes between zero and fragment binding energies. Following the molecular closed-shell (open-shell) electronic configuration, we find a predominant electrostatic (covalent) nature of the physical interactions for N2 ⋯clu and CO ⋯clu (O2 ⋯clu and NO⋯clu), except in the physisorption case (N2 /Ag6 ) where dispersive interaction is dominant. Our results clarify questions about the molecular adsorption on subnanoclusters as a relevant mechanistic step present in nanocatalytic reactions.

The effect of different energy portions on the 2D/3D stability swapping for 13-atom metal clusters.

The complexity of Cu13, Ag13, and Au13 coinage-metal clusters was investigated through their energy contributions via a density functional theory study, considering improvements in the PBE functional, such as van der Waals (vdW) corrections, spin-orbit coupling (SOC), Hubbard term (+U), and their combinations. Investigating two-dimensional (planar 2D) and three-dimensional (distorted 3D, CUB - cuboctahedral, and ICO - icosahedral) configurations, we found that vdW corrections are dominant in modulating the stability swapping between 2D and ICO (3D) for Ag13 (Au13), whereas for Cu13 its role is increasing the relative stability between 2D (least stable) and 3D (most stable), setting ICO as the reference. Among the energy portions that constitute the relative total energy, the dimensionality difference correlates with the magnitude of the relative dispersion energy (large for 2D/ICO and small for 3D/ICO) as the causal factor responsible for an eventual stability swapping. For instance, empirical vdW corrections may favor Ag13 as ICO, while semi empirical ones tend to swap the stability by favoring 2D. The same tendency is observed for Au13, except when SOC is included, which enlarges the stability of 3D over 2D. Energy decomposition analysis combined with the natural orbitals for the chemical valence approach confirmed the correlations between the dimensionality difference and the magnitude of the relative dispersion energies. Our structural analysis protocol was able to capture the local distortion effects (or even their absence) through the quantification of the Hausdorff chirality measure. Here, ICO, CUB, and 2D are achiral configurations for all coinage-metal clusters, whereas Cu13 as 3D presents a slight chirality when vdW correction based on many body dispersion is used, at the same time Ag13 as 3D turned out to be chiral for all calculation protocols as evidence of the role of the chemical composition.

Stability Changes in Iridium Nanoclusters via Monoxide Adsorption: A DFT Study within the van der Waals Corrections.

Small iridium nanoclusters are prominent subnanometric systems for catalysis-related applications, mainly because of a large surface-to-volume ratio, noncoalescence feature, and tunable properties, which are completely influenced by the number of atoms, geometry, and molecular interaction with the chemical environment. Herein, we investigate the interaction between Irn nanoclusters (n = 2-7) and polluting molecules, CO, NO, and SO, using van der Waals D3 corrected density functional theory calculations. Starting from a representative structural set, we determine the growth pattern of the lowest energy unprotected Irn nanoclusters, which is based on open structural motifs, and from the adsorption of a XO (X = C, N, and S) molecule, the preferred high-symmetric adsorption sites were determined, dominated by the onefold top site. For protected systems, 4XO/Ir4 and 6XO/Ir6, we found a reduction in the total magnetic moment, while the equilibrium bonds of the nanoclusters expanded (contracted) due to mCO and mNO (mSO) adsorption, with exceptions for systems with large structural distortions (4SO/Ir4 and 6NO/Ir6). Meanwhile, the C-O and N-O (S-O) bond strength decreases (increases) following an increase (decrease) in the C-O and N-O (S-O) distances upon adsorption. We show, through energetic analysis, that for the different chemical environments, relative stability changes occur from the most stable unprotected nanoclusters, planar square (Ir4), and prism (Ir6) to higher energy isomers. The change in the stability order between the two competing protected systems is feasible if the balance between the interaction energy (additive term) and distortion energies (nonadditive terms) compensates for the relative total energies of the unprotected configurations. For all systems, the interaction energy is the main reason responsible for stability alterations, except for 4SO/Ir4, where the main contribution is from a small penalty due to Ir4 distortions upon adsorption, and for 4NO/Ir4, where the energetic effects from the adsorption do not overcome the difference between the binding energies of the unprotected nanoclusters. Finally, from energy decomposition and Hirshfeld charge analysis, we find a predominant covalent nature of the physical contributions in mOX···Irn interactions with a cationic core (Irn) and an anionic shell (XO coverage).

The usefulness of energy decomposition schemes to rationalize host-guest interactions.

This perspective focuses on the crucial role that energy decomposition schemes play in elucidating the physical nature of non-covalent interactions in supramolecular systems, particularly from the point of view of host-guest systems stabilized by non-covalent interactions, which are fundamental to molecular recognition. The findings reported here reveal the robustness and practical application of methods such as EDA-NOCV in rationalizing molecular recognition situations in systems such as calixarenes, cyclophanes and other box-shaped hosts, capable of incorporating different chemical species as anions and PAHs. We expect that the discussed cases in this perspective can be viewed as an initial assessment for the multidimensional nature of the weak interactions underlying supramolecular aggregations, which can be recognized in a plethora of different structures constantly synthesized and characterized by chemists around the world.

What is the driving force behind molecular triangles and their guests? A quantum chemical perspective about host-guest interactions.

The physical nature of host-guest (HG) interactions occurring between molecular triangles and linear anions was explored using density functional theory (DFT) calculations combined with energy decomposition analyses (EDA), nuclear independent chemical shift (NICS), and non-covalent interaction index (NCI). We demonstrate that: (i) in addition to the host being significantly rigid, the strain energies are not negligible, especially for host 2; (ii) halogen anions interact mainly by electrostatic forces (ΔEelst > ΔE > ΔEdisp), meanwhile; (iii) trihalogen anions interact mostly by dispersion forces (ΔEdisp > ΔEelst≈ΔE). The NICS and NCI calculations corroborate the idea that HG interactions are considerably mediated through dispersion terms, and also indicate an antiaromatic character inside the host walls.

CO, NO, and SO adsorption on Ni nanoclusters: a DFT investigation.

Nickel nanoclusters are very promising for catalysis-related applications, especially involving chemical reactions with polluting molecules, such as carbon, nitrogen, and sulfur monoxides, which are directly or indirectly involved in serious environmental pollution problems. Therefore, it is of utmost importance to improve the understanding of the interaction between Ni nanoclusters and diatomic molecules, such as CO, NO, and SO, to provide insights into real subnano catalysts. Thus, here, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties of CO, NO, and SO on Ni nanoclusters. From energetic and electronic criteria applied to Nin nanoclusters (n = 2-15), we selected Ni6 (octahedron) and Ni10 (triangular pyramid) nanoclusters as supports. According to our analyses, the molecular adsorption increases the stability of Ni nanoclusters, especially for Ni6 systems. The interaction intensity is larger for SO than for NO and CO in adsorbed systems, and the strong OS-Ni interaction is responsible for the well-known sulfur poisoning on transition-metal systems. The lowest energy adsorption sites are onefold for CO/Ni6, NO/Ni6, and CO/Ni10; twofold for NO/Ni10; and threefold for SO/Ni6 and CO/Ni10, where CO and NO molecules sustain linear and perpendicular geometries, while SO geometry changes to a bent configuration resulting from a sideways adsorption. The equilibrium bond lengths of the molecules expand upon adsorption, from 0.9% (NO/Ni6/10) to 11.3% (SO/Ni6/10), consequently, the internal molecular bond strengths decrease, since there is a reduction in the molecular stretching frequencies. This result occurs most strongly for SO followed by NO and CO systems, which was confirmed by an estimation of the energetic contribution of the distortion after the adsorption process. Thus, the strong S-Ni interaction, given by SO chemisorption on hollow sites with a sideways interaction, implies an energetic decrease and, consequently, a part of the energy gained from the SO-Ni interaction is from the SO and nanocluster distortions. Ultimately, using the energy decomposition analysis (from SAPT0) for XO/Ni6 systems, we improved the understanding of the CO and NO (SO) singlet (doublet) spin multiplicities' interaction with Ni6 nanoclusters.

A theoretical indicator of transition-metal nanoclusters applied in the carbon nanotube nucleation process: a DFT study.

Knowledge about the appropriate indicators to point out the best components in a catalytic process is a basic prerequisite for obtaining insights into optimized reactions as, for example, in the chemical vapour deposition method, which enables the growth of carbon nanotubes. In this work, we report a density functional theory study of 13-atom transition-metal nanoclusters interacting with (5,0) zigzag and (3,3) armchair carbon nanotube fragments, considering all transition-metal species from the periodic table as possible candidates for the chemical vapour deposition method. The icosahedral configuration was found to be a good model to simulate the seed of nucleation in the case of the short carbon nanotube fragments that are initially formed during the growth process. From full geometric optimizations, without any constraints, we found that the energetic and structural nanocluster properties change as a function of the occupation of the bonding and anti-bonding d-states. The center of gravity of the occupied d-states for nanoclusters is found to be a good indicator to reveal the best candidates for the interaction with the carbon nanotubes, namely, Sc-Cu, Y-Nb, Pd, Lu, Hf, and Pt. The interaction between all transition-metal nanoclusters with both armchair and zigzag segments is favorable in terms of the adhesion energy, where the adhesion is larger for systems with smaller occupation of the d-states. The bond strength is more pronounced for systems with zigzag fragments than those with armchair fragments, which is confirmed by the smaller average bond length between the metal atoms of the nanocluster and the C atoms of the zigzag segment. Our prediction about the best 13-atom transition-metal candidates is reinforced by the linear relationship between the adhesion energy and the center of gravity of the occupied d-states. Thus, the adhesion energy presents increased intensity for the interaction between carbon nanotube fragments and nanoclusters in relation to the smaller occupation of the d-states. Consequently, our model is able to provide a good descriptor for indicating the best 13-atom transition-metal candidates in the chemical vapour deposition process.

Bare versus protected tetrairidium clusters by density functional theory.

The tetrairidium (Ir4) clusters are subnanometric systems vastly applied in catalysis, especially, because of the higher activity than mononuclear Ir complexes, intrinsic and controllable stability in relation to supports, and non-coalescence properties. The main catalytic properties of nanoclusters (activity and selectivity) are directly associated with their size, shape, and interactions with the environment, whose understanding requires study at the atomistic level. Here, the Ir4 clusters are studied considering the energetic stability for different chemical environments, bare versus protected, using density functional theory calculations within the generalized gradient approximation with van der Waals corrections and spin-orbit coupling, employing the all-electron projected augmented wave method. The square planar isomer is confirmed for the bare case as the lowest energy configuration considering semilocal and non-local exchange-correlation functionals, however, for different chemical environments (Ir4 protected by CO, O2, PH3, and SH2 ligands) the energy stability scenario is different; for CO, O2, and PH3 ligands the tetrahedron is the most stable isomer, in agreement with experimental insights, while for SH2 ligands the square motif is the most stable isomer. To improve the understanding of these systems, structural and electronic analysis were performed, in addition to energy decomposition analysis, to explore the bonding situation in Ir4 compounds. Our results showed an important relationship between the geometrical behavior and the nature and magnitude of Ir2Ir2 interactions, showing how the chemical environment affects the Ir4 nanoclusters. In general, the compounds with tetrahedron motifs showed a weakening of the σ and π bonds in relation to the square ones.

In vitro cytotoxicity and structure-activity relationship approaches of ent-kaurenoic acid derivatives against human breast carcinoma cell line.

In this study, ent-kaurenoic acid derivatives were obtained by microbial transformation methodologies and tested against breast cancer cell lines (MCF-7). A multivariate quantitative-structure activity relationship (QSAR) analysis was performed taking into account both microbial transformation derivatives and other analogues previously reported in literature to give some insight into the main features behind the cytotoxic activity displayed by kaurane-type diterpenes against MCF-7 cells. The partial least square regression (PLS) method was employed in the training set and the best PLS model was built with a factor describing 69.92% of variance and three descriptors (logP, εHOMO and εHOMO-1) selected by the Ordered Predictors Selection (OPS) algorithm. The QSAR model provided reasonable regression (Q2 = 0.64, R2 = 0.72, SEC = 0.29 and SEV = 0.33). The model was validated by leave-N-out cross-validation, y-randomization and external validation (R2pred = 0.89 and SEP = 0.27). The selected descriptors indicated that the activity was mainly related to electronic parameters (HOMO and HOMO-1 molecular orbital energies), as well as to logP. These findings suggest that higher activity values are directly related with both higher logP and frontier orbital energy values. The positive relationship between these orbitals and the activity suggests that the ent-kaurenoic acid analogues interaction with the target involves charge displacement, which is entirely consistent with the literature. Based on these findings, three compounds were proposed and one of them was synthesized and tested. The experimental result confirmed the activity predicted by the model.

Copaifera duckei Oleoresin and Its Main Nonvolatile Terpenes: In Vitro Schistosomicidal Properties.

In this article, the in vitro schistosomicidal effects of three Brazilian Copaifera oleoresins (C. duckei, C. langsdorffii, and C. reticulata) are reported. From these botanical sources, the oleoresin of C. duckei (OCd) demonstrated to be the most promising, displaying LC50 values of 75.8, 50.6, and 47.2 µg/ml at 24, 48, and 72 h of incubation, respectively, against adult worms of Schistosoma mansoni, with a selectivity index of 10.26. Therefore, the major compounds from OCd were isolated, and the diterpene, (-)-polyalthic acid (PA), showed to be active (LC50 values of 41.7, 36.2, and 33.4 µg/ml, respectively, at 24, 48, and 72 h of incubation). Moreover, OCd and PA affected the production and development of eggs, and OCd modified the functionality of the tegument of S. mansoni. Possible synergistic and/or additive effects of this balsam were also verified when a mixture of the two of its main compounds (PA and ent-labd-8(17)-en-15,18-dioic acid) in the specific proportion of 3:1 (w/w) was tested. The obtained results indicate that PA should be considered for further investigations against S. mansoni, such as, synergistic (combination with praziquantel (PZQ)) and in vivo studies. It also shows that diterpenes are an important class of natural compounds for the investigation of agents capable of fighting the parasite responsible for human schistosomiasis.