Comparison of the periodic slab approach with the finite cluster description of metal-organic interfaces at the example of PTCDA on Ag(110)

Probing the role of surface termination in the adsorption of azupyrene on copper

The role of the inorganic substrate termination, within the organic-inorganic interface, has been well studied for systems that contain strong localised bonding. However, how varying the substrate termination affects coordination to delocalised electronic states, like that found in aromatic molecules, is an open question. Azupyrene, a non-alternant polycyclic aromatic hydrocarbon, is known to bind strongly to metal surfaces through its delocalised π orbitals, thus yielding an ideal probe into delocalised surface-adsorbate interactions. Normal incidence X-ray standing wave (NIXSW) measurements and density functional theory calculations are reported for the adsorption of azupyrene on the (111), (110) and (100) surface facets of copper to investigate the dependence of the adsorption structure on the substrate termination. Structural models based on hybrid density functional theory calculations with non-local many-body dispersion yield excellent agreement with the experimental NIXSW results. No statistically significant difference in the azupyrene adsorption height was observed between the (111) and (100) surfaces. On the Cu(110) surface, the molecule was found to adsorb 0.06 ± 0.04 Å closer to the substrate than on the other surface facets. The most energetically favoured adsorption site on each surface, as determined by DFT, is subtly different, but in each case involved a configuration where the aromatic rings were centred above a hollow site, consistent with previous reports for the adsorption of small aromatic molecules on metal surfaces.

Unveiling glutamic acid-functionalized LDHs: understanding the Cr(VI) removal mechanism from microscopic and macroscopic view points

Interlayer functionalization modulation is essential for modifying LDHs and improving their selectivity and adsorption capacity for target pollutants. In this work, Glu@NiFe-LDH was synthesized using a simple one-step hydrothermal method and tested for its ability to remove CrO42- from wastewater. The modification significantly increased the composite material's removal ability by 2-3 times, up to 98.36 mg g-1. The behavior of CrO42- adsorption on Glu@NiFe-LDH was further studied by adjusting the affecting factors (i.e., temperature, pH, contact time, initial concentration, and interfering substance), and the adsorption behavior was confirmed as a spontaneous and chemisorption process. And the result was that Glu@NiFe-LDH demonstrated high capacity, efficiency, stability, and selectivity for the adsorption of CrO42- in a single electrolyte and natural water containing competing anions. Furthermore, molecular dynamics simulations (NVT ensemble) were employed to further reveal the mechanism of glutamic acid modification on LDH at the microscopic scale. Additionally, the IRI analysis method revealed the mechanism of weak interaction between glutamic acid molecules and CrO42-. This study provides a detailed understanding of the intercalation mechanism involved in the amino acid modification of LDHs. It explains the adsorption mechanism of metal oxo-acid radicals by amino acid-modified LDHs from a theoretical perspective. The findings offer experiments and a theoretical basis for designing targeted adsorbents in the future.

Investigation of the adsorption performance and mechanism of 2-mercaptoethane sulfonic acid intercalated modified layered double hydroxide on heavy metal ions

In the adsorption process of functionalized layered double hydroxide (LDH) to target pollutants it, is essential to investigate the role of functional groups. In this work, 2‑mercaptoethane sulfonic acid (MS) was used as an intercalation modifier to prepare functionalized NiFe-LDH by solvothermal method. The interfacial interaction between the functional groups and the NiFe-LDH surface was studied via molecular dynamics simulation. During the intercalation process, the more negatively charged sulfonic acid group tends to self-assemble electrostatically with the LDH laminate, while the sulfhydryl group is involved in complexing heavy metal ions. The adsorption experiments showed that the adsorption performance of the adsorbent for the three ions of Cd2+, Mn2+, and Co2+ at 298.15 K was 266.16 mg/g, 175.60 mg/g, and 106.56 mg/g, respectively, which were 10 times, 8.7 times, and 4.9 times higher than that of unmodified NiFe-LDH. Meanwhile, Multiwfn wavefunction analysis combined Visual Molecular Dynamics (VMD) was applied to analyze and visualize the reaction active sites & the interactions between MS and NiFe-LDH, and the complexation of the functional group of MS with metal ions, to insight the role of the functional groups in MS molecule, and to reveal the cause that the adsorption capacity of modified NiFe-LDH for heavy metals greatly improves from the view of atoms.

The role of doped-Mn on enhancing arsenic removal by MgAl-LDHs

To meet the challenges posed by global arsenic water contamination, the MgAlMn-LDHs with extraordinary efficiency of arsenate removal was developed. In order to clarify the enhancement effect of the doped-Mn on the arsenate removal performance of the LDHs, the cluster models of the MgAlMn-LDHs and MgAl-LDHs were established and calculated by using density functional theory (DFT). The results shown that the doped-Mn can significantly change the electronic structure of the LDHs and improve its chemical activity. Compared with the MgAl-LDHs that without the doped-Mn, the HOMO-LUMO gap was smaller after doping. In addition, the -OH and Al on the laminates were also activated to improve the adsorption property of the LDHs. Besides, the doped-Mn existed as a novel active site. On the other hand, the MgAlMn-LDHs with the doped-Mn, the increased of the binding energy, as well as the decreased of the ion exchange energy of interlayer Cl^-, making the ability to arsenate removal had been considerably elevated than the MgAl-LDHs. Furthermore, there is an obvious coordination covalent bond between arsenate and the laminates of the MgAlMn-LDHs that with the doped-Mn.

Coordination of Ethylamine on Small Silver Clusters: Structural and Topological (ELF, QTAIM) Analyses

Amine ligands are expected to drive the organization of metallic centers as well as the chemical reactivity of silver clusters early growing during the very first steps of the synthesis of silver nanoparticles via an organometallic route. Density functional theory (DFT) computational studies have been performed to characterize the structure, the atomic charge distribution, and the planar two-dimensional (2D)/three-dimensional (3D) relative stability of small-size silver clusters (Ag_n, 2 ≤ n ≤ 7), with or without an ethylamine (EA) ligand coordinated to the Ag clusters. The transition from 2D to 3D structures is shifted from n = 7 to 6 in the presence of one EA coordinating ligand, and it is explained from the analysis of the Ag-N and Ag-Ag bond energies. For fully EA saturated silver clusters (Ag_n-EA_n), the effect on the 2D/3D transition is even more pronounced with a shift between n = 4 and 5. Subsequent electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM) topological analyses allow for the fine characterization of the dative Ag-N and metallic Ag-Ag bonds, both in nature and in strength. Electron transfer from ethylamine to the coordinated silver atoms induces an increase of the polarization of the metallic core.

New insights into the capture performance and mechanism of hazardous metals Cr3+ and Cd2+ onto an effective layered double hydroxide based material

The phosphonate functionalized layered double hydroxide constructed through intercalation reaction, and efficiently applied to capture toxicant metal ions. The characterization results indicated that the functionalized composite with many functional groups has adsorption potential to heavy metals. The strong chelation of the phosphonate groups with heavy metal ions proved it an excellent adsorbent leading to a maximum adsorption capacity of 156.95 mg/g (Cr³⁺) and 198.34 mg/g (Cd²⁺) separately. The data of kinetics and isotherm revealed that the chelating adsorption was dominated by chemisorption and monolayer interaction. Notably, the spent adsorbent presented satisfactory reusability after six cycles. Furthermore, the Forcite simulation with the CLAYFF-CVFF force field implied that the critical mechanism for modifiers and the surface sites of the interlayer is electrostatic interaction. Our in-depth exploration in terms of the weak interactions not only demonstrated the strength and nature but also provided a novel way to intuitively capture the type of interactions that occurred around interesting regions. In the end, we made detailed investigations on the chelation mechanism, and the covalent nature played a leading role in the binding interaction. This work provides a valuable strategy for researchers to design novel materials in practice.

In-Depth Study of Heavy Metal Removal by an Etidronic Acid-Functionalized Layered Double Hydroxide

Sorption methodologies play a pivotal role in heavy metal removal to meet the global requirements for uninterrupted access to drinkable water. Standard sorption technologies lack efficiency due to weak adsorbent-metal interaction. To this end, a layered cationic framework material loaded with phosphonate was first fabricated by a facile intercalation method to capture hazardous metals from an aqueous solution. To inquire the removal mechanisms, batch experiments, detection technologies, and simulation calculations were employed to study the interactions at the interface of clay/water. Specifically, the functionalized layered double hydroxide possessed excellent chelation adsorption properties with Zn²⁺ (281.36 mg/g) and Fe³⁺ (206.03 mg/g), in which model fitting results revealed that the adsorption process was chemisorption and monolayer interaction. Further, the interfacial interaction between the phosphonate and clay surface was evaluated by molecular dynamics simulation, and a new concept named the interaction region indicator was used to characterize weak interaction and coordinate bonds. The deep insight into the chelation mechanism was visually presented via the orbital interaction diagram. In addition, the regeneration of the spent adsorbent, adsorption column test, and acute toxicity analysis demonstrated that the synthesized material has immense potential in terms of practical usage for the treatment of toxic pollutants. These results provide a novel path for researchers to properly understand the adsorption behavior.

Trimethyloxonium ion – a zeolite confined mobile and efficient methyl carrier at low temperatures: a DFT study coupled with microkinetic analysis

The reaction network of ethene methylation over H-ZSM-5, including methanol dehydration, ethene methylation, and C3H7+ conversion, is investigated by employing a multiscale approach combining DFT calculations and microkinetic modeling.

Simulations of x-ray absorption spectra for CO desorbing from Ru(0001) with transition-potential and time-dependent density functional theory approaches

The desorption of a carbon monoxide molecule from a Ru(0001) surface was studied by means of X-ray Absorption Spectra (XAS) computed with Transition Potential (TP-DFT) and Time Dependent (TD-DFT) DFT methods. By unraveling the evolution of the CO electronic structure upon desorption, we observed that at 2.3 Å from the surface, the CO molecule has already predominantly gas-phase character. While C 1s XAS is quite insensitive to changes in the C-O bond length, the O 1s excitation is very sensitive with the π* coming down in energy upon CO bond stretching, which competes with the increase in orbital energy due to the repulsive interaction with the metallic surface. We show in a systematic way that the TP-DFT method can describe the XAS rather well at the endpoints (chemisorbed and gas phase) but is affected by artificial charge transfer and/or incorrect spin treatment in the transition region in cases like CO, where there are low-lying π* orbitals and large exchange interactions between the core 1s and valence-acceptor π* orbitals. As an alternative, we demonstrate by comparing with experimental data that a linear response approach using TD-DFT employing common exchange-correlation functionals and finite-size clusters can yield a good description of the spectral evolution of the 1s → π* transition with correct spin and gas-to-chemisorbed chemical shifts in good agreement with experiment.

Local decomposition of hybridization functions: Chemical insight into correlated molecular adsorbates

Hybridization functions are an established tool for investigating the coupling between a correlated subsystem (often a single transition metal atom) and its uncorrelated environment (the substrate and any ligands present). The hybridization function can provide valuable insight into why and how strong correlation features such as the Kondo effect can be chemically controlled in certain molecular adsorbates. To deepen this insight, we introduce a local decomposition of the hybridization function, based on a truncated cluster approach, enabling us to study individual effects on this function coming from specific parts of the systems (e.g., the surface, ligands, or parts of larger ligands). It is shown that a truncated-cluster approach can reproduce the Co 3d and Mn 3d hybridization functions from periodic boundary conditions in Co(CO)₄/Cu(001) and MnPc/Ag(001) qualitatively well. By locally decomposing the hybridization functions, it is demonstrated at which energies the transition metal atoms are mainly hybridized with the substrate or with the ligand. For the Kondo-active 3d_x²-y² orbital in Co(CO)₄/Cu(001), the hybridization function at the Fermi energy is substrate-dominated, so we can assign its enhancement compared with ligand-free Co to an indirect effect of ligand-substrate interactions. In MnPc/Ag(001), the same is true for the Kondo-active orbital, but for two other orbitals, there are both direct and indirect effects of the ligand, together resulting in such strong screening that their potential Kondo activity is suppressed. A local decomposition of hybridization functions could also be useful in other areas, such as analyzing the electrode self-energies in molecular junctions.

Catalyzed Atomic Layer Deposition of Silicon Oxide at Ultralow Temperature Using Alkylamine

We report the catalyzed atomic layer deposition (ALD) of silicon oxide using Si₂Cl₆, H₂O, and various alkylamines. The density functional theory (DFT) calculations using the periodic slab model of the SiO₂ surface were performed for the selection of alternative Lewis base catalysts with high catalytic activities. During the first half-reaction, the catalysts with less steric hindrance such as pyridine would be more effective than bulky alkylamines despite lower nucleophilicity. On the other hand, during the second half-reaction, the catalysts with a high nucleophilicity such as triethylamine (Et₃N) would be more efficient because the steric hindrance is less critical. The in situ process monitoring shows that the calculated atomic charge is a good indicator for expecting the catalyst activity in the ALD reaction. The use of Et₃N in the second half-reaction was essential to improving the growth rate as well as the step coverage of the film because the Et₃N-catalyzed process deposited a SiO₂ film with a step coverage of 98% that is better than 93% of the pyridine-catalyzed process. The adsorption of pyridine, ammonia (NH₃), or trimethylamine (Me₃N) salts was more favorable than that of Et₃N, n-Pr₃N, or ⁱPr₃N salts. Therefore, Et₃N was expected to incorporate less amine salts in the film as compared to pyridine, and the compositional analyses confirmed that the concentrations of Cl and N by the Et₃N-catalyzed process were significantly lower than those by the pyridine-catalyzed process.