Adsorption of small aromatic molecules on gold: a DFT localized basis set study including van der Waals effects

A theoretical study of the oxidation of benzene by manganese oxide clusters: formation of quinone intermediates

Manganese oxides (MnxOy) have been widely applied in various chemical industrial processes owing to their long lifetime, low cost and high abundance. They have been used as co-reactants for the elimination of volatile organic compounds (VOCs); however, their oxidation mechanism is not clearly established. In this theoretical study, interaction capacities between benzene (C6H6) and MnxOy clusters, which were modeled with MnO2 and Mn2O3 molecules, were investigated by quantum chemical computations using density functional theory (DFT) with the PBE-D3 functional. The interaction capacity between C6H6 and MnxOy was evaluated, and the probing of the initial stage of the C6H6 oxidation at a molecular level offers an in-depth oxidation reaction path. Interaction energies computed in several spin states, along with the analysis of the electron distribution using the quantum theory of atoms in molecules, natural bond orbital and Wiberg bond index techniques as well as local softness values and MO energies of fragments, point out that the interaction between C6H6 and Mn2O3 is stronger than that with MnO2, amounting to -43 and -35 kcal mol-1, respectively, and the metal atom is identified as the primary active site. During the oxide cluster-assisted oxidation, benzene firstly undergoes an oxidation reaction by active oxygen to generate intermediates such as hydroquinone and benzoquinone. The pathway involving p-benzoquinone as the product (noted as PR1) is the most energetically favored one through a transition structure lying at 19 kcal mol-1, below the energy reference of the reactants, leading to an energy barrier significantly lower than that of 36 kcal mol-1 found for the gas phase oxidation reaction with molecular oxygen without the assistance of the oxide clusters. Potential energy profiles illustrating the reaction paths and molecular mechanisms were described in detail.

Boron-rich hybrid BCN nanoribbons for highly ambient uptake of H2S, HF, NH3, CO, CO2 toxic gases

Nanomaterials-based gas sensors are widely applied for the monitoring and fast detection of hazardous gases owing to their sensitivity and selectivity. Hydrogen sulfide (H2S), hydrogen fluoride (HF), ammonia (NH3), and carbon monoxide/dioxide (CO/CO2) produced from petroleum fields, sewage, mines, and gasoline are harmful for both human life and environment. With an increase in the emission of these toxic compounds, their real-time monitoring and efficient adsorbent application and storage are very necessary. To this end, we investigated the adsorption characteristic and sensitivity factor of these five toxic gases on armchair and zigzag hybrid boron-carbon-nitride (BCN) nanoribbons with/without boron-rich (B-rich) defects using first principle calculation, where 25%, 33%, and 50% carbon concentration were considered. Our findings reveal that B-rich nanoribbons have strong adsorption energy, charge transfer, and structural deformation owing to the double acceptor of B-rich defects. Moreover, the zigzag and armchair forms of these hybrid BCN nanoribbons show physical adsorption, altering their band gap and phase transition after adsorbing these toxic gases, where B-rich nanoribbons possess high sensitivity to NH3 and CO among other gases. Furthermore, B-rich hybrid nanoribbons have higher CO2 adsorption energy than the standard free energy of CO2 at room temperature. This study suggests that hybrid BCN nanoribbons and B-rich defected structures can be good candidates for the uptake and storage of toxic gases, helping experimental groups to design efficient ambient gas sensors.

Exploring adsorption behavior of sulfur and nitrogen compounds on transition metal-doped Cu(100) surfaces: insights from DFT and MD simulations

We conducted an extensive investigation using density functional theory (DFT) calculations and ReaxFF molecular dynamics (MD) simulations to elucidate the mechanisms of desulfurization and denitrogenation on Cu(100) surfaces. This study encompassed both pristine surfaces and those modified with Pt or Rh transition metals. Our primary objective was to gain a deep understanding of the adsorption behavior of thiophene (C4H4S) and pyridine (C5H5N) molecules on stepped Cu(100) surfaces, which serve as models for sulfur and nitrogen compounds. We systematically explored the interplay among water, adsorption efficiency, and surface regeneration capabilities. Using DFT, we thoroughly examined various aspects, including interaction energies, charge transfers, changes in electron density, and alterations in work function upon molecule adsorption. Notably, we observed a decrease in the interaction energy of thiophene, whereas that of pyridine increased when adsorbed on Pt/Rh-doped surfaces compared to pristine ones. Thiophene adsorption reduced the work function, potentially enhancing detectability, without causing inhibitory effects on any surface. Stepped Cu(100) surfaces demonstrated a strong affinity for thiophene, exhibiting an energy difference of approximately 86 kJ mol-1. However, this trend reversed on doped surfaces, where pyridine displayed stronger adsorption than thiophene, resulting in energy differences of around 123 kJ mol-1 and 62 kJ mol-1 on Pt-Cu and Rh-Cu surfaces, respectively. Moreover, our investigation highlighted the regeneration capacity of these surfaces, indicating that all surfaces can be considered promising candidates for desulfurization, while only Cu and Pt-Cu surfaces were found to be suitable for denitrogenation. Furthermore, results from MD simulations in combination with potential of mean force (PMF) simulations at 300 K, aligned with DFT calculations, confirmed the adsorption configurations of pyridine and thiophene. This analysis demonstrated the competitive advantage of thiophene over pyridine in adsorption and highlighted the inhibitory effect of water on pyridine adsorption on the Cu(100) surface.

First principles study on the potential of functionalized porous silicon to capture adverse agents to human health: The role played by the interface interactions

Porous Silicon (PSi) is an ideal material to build biosensors due to its large surface area and biocompatibility. However, it lacks of selectivity. By adhering bilayer lipids, active sites are added for vital biochemical processes. Such processes are promoted by different proteins, which aid to detect pollutants and drugs, among other. The present work is a systematic theoretical study at the density functional theory level on PSi models, functionalized with H and OH. Several concentrations of such functional groups were assessed at the pores to elucidate the reactivity via Fukui indexes of electrophilic and nucleophilic attack. The 1,2-dimyristoyl-sn-glycero-3-phosphocholine(DMPC) lipid was used as a probe system to interact with the PSi. The attraction was evaluated as electrostatic with a van der Waals contribution. The adsorption was highly selective to the degree of functionalization at the pore. The PSi facets (100) and (001) showed different mechanisms of interaction with the DMPC lipid. The theoretical absorption spectra addressed that the DMPC lipid could be identified with intensity variations coming from the degree of functionalization at the pore, which may be further rationalized experimentally. The present methodology may aid to tailor novel materials to capture and identify adverse agents present in the environment.

Enhanced H2 Storage Capacity of Bilayer Hexagonal Boron Nitride (h-BN) Incorporating van der Waals Interaction under an Applied External Electric Field

Lightweight two-dimensional materials are being studied for hydrogen storage applications due to their large surface area. The characteristics of hydrogen adsorption on the h-BN bilayer under the applied electric field were investigated. The overall storage capacity of the bilayer is 6.7 wt % from our theoretical calculation with E _ads of 0.223 eV/H₂. The desorption temperature to remove the adsorbed H₂ molecules from the surface of the h-BN bilayer system in the absence of an external electric field is found to be ∼176 K. With the introduction of an external electric field, the E _ads lies in the range of 0.223-0.846 eV/H₂ and the desorption temperature is from 176 to 668 K. Our results show that the external electric field enhances the average adsorption energy as well as the desorption temperature and thus makes the h-BN bilayer a promising candidate for hydrogen storage.

Interaction of Aromatic Molecules with Forsterite: Accuracy of the Periodic DFT-D4 Method

Density functional theory (DFT) has provided deep atomic-level insights into the adsorption behavior of aromatic molecules on solid surfaces. However, modeling the surface phenomena of large molecules on mineral surfaces with accurate plane wave methods (PW) can be orders of magnitude more computationally expensive than localized atomic orbitals (LCAO) methods. In the present work, we propose a less costly approach based on the DFT-D4 method (PBE-D4), using LCAO, to study the interactions of aromatic molecules with the {010} forsterite (Mg2SiO4) surface for their relevance in astrochemistry. We studied the interaction of benzene with the pristine {010} forsterite surface and with transition-metal cations (Fe2+ and Ni2+) using PBE-D4 and a vdW-inclusive density functional (Dion, Rydberg, Schröder, Langreth, and Lundqvist (DRSLL)) with LCAO methods. PBE-D4 shows good agreement with coupled-cluster methods (CCSD(T)) for the binding energy trend of cation complexes and with PW methods for the binding energy of benzene on the forsterite surface with a difference of about 0.03 eV. The basis set superposition error (BSSE) correction is shown to be essential to ensure a correct estimation of the binding energies even when large basis sets are employed for single-point calculations of the optimized structures with smaller basis sets. We also studied the interaction of naphthalene and benzocoronene on pristine and transition-metal-doped {010} forsterite surfaces as a test case for PBE-D4. Yielding results that are in good agreement with the plane wave methods with a difference of about 0.02-0.17 eV, the PBE-D4 method is demonstrated to be effective in unraveling the binding structures and the energetic trends of aromatic molecules on pristine and transition-metal-doped forsterite mineral surfaces. Furthermore, PBE-D4 results are in good agreement with its predecessor PBE-D3(BJM) and with the vdW-inclusive density functionals, as long as transition metals are not involved. Hence, PBE-D4/CP-DZP has been proven to be a robust theory level to study the interaction of aromatic molecules on mineral surfaces.

Bonding of Gold Nanoclusters on Graphene with and without Point Defects

Hybrid nanostructures of size-selected nanoparticles (NPs) and 2D materials exhibit striking physical and chemical properties and are attractive for many technology applications. A major issue for the performance of these applications is device stability. In this work, we investigate the bonding of cuboctahedral, decahedral and icosahedral Au NPs comprising 561 atoms on graphene sheets via 103-atom scale ab initio spin-polarized calculations. Two distinct cases we considered: (i) the Au NPs sit with their (111) facets on graphene and (ii) the NPs are oriented with a vertex on graphene. In both cases, we compare the binding energies with and without a graphene vacancy under the NP. We find that in all cases, the presence of the graphene vacancy enhances the bonding of the NPs. Significantly, in the vertex-on-graphene case, the binding energy is considerably increased by several eVs and becomes similar to the (111) facet-on-graphene case. The strain in the NPs is found to be minimal and the displacement of the carbon atoms in the immediate neighborhood of the vacancy is on the 0.1 Å scale. The work suggests the creation of stable NP-graphene systems for a variety of electronic, chemical and photonic applications.

The effect of translation on the binding energy for transition-metal porphyrines adsorbed on Ag(111) surface

The characteristics of interaction between six transition-metal porphyrines and the Ag(111) surface are detailed here as resulted from DFT calculations. Van der Waals interactions as well as the strong correlation in 3d orbitals of transition metals were taken into account in all calculations, including the structural relaxation. For each system we investigate four relative positions of the metallic atom on top the surface. We show that the interaction between the transition metal and silver is the result of a combination between the dispersion interaction, charge transfer and weak chemical interaction. The detailed analysis of the physical properties, such as dipolar and magnetic moments and the molecule-surface charge transfer, analyzed for different geometric configurations allows us to propose qualitative models, relevant for the understanding of the self-assembly processes and related phenomena.

Translation of metal-phthalocyanines adsorbed on Au(111): from van der Waals interaction to strong electronic correlation

Using first-principles calculations, we investigate the binding energy for six transition metal - phthalocyanine molecules adsorbed on Au(111). We focus on the effect of translation on molecule - surface physical properties; van der Waals interactions as well as the strong correlation in d orbitals of transition metals are taken into account in all calculations. We found that dispersion interaction and charge transfer have the dominant role in the molecule-surface interaction, while the interaction between the transition metal and gold has a rather indirect influence over the physics of the molecule-surface system. A detailed analysis of the physical properties of the adsorbates at different geometric configurations allows us to propose qualitative models to account for all values of interface dipole charge transfer and magnetic moment of metal-phthalocyanines adsorbed on Au(111).

Hierarchical self-assembly of enantiopure and racemic helicenes at the liquid/solid interface: from 2D to 3D

The performance of organic nanostructures is closely related to the organization of the functional molecules. Frequently, molecular chirality plays a central role in the way molecules assemble at the supramolecular level. Herein we report the hierarchical self-assembly of benzo-fused tetrathia[7]helicenes on solid surfaces, from a single surface-bound molecule to well-defined microstructures, using a combination of various characterization techniques assisted by molecular modeling simulations. Similarities as well as discrepancies are revealed between homochiral and heterochiral aggregations by monitoring the hierarchical nucleation of helicenes on surfaces, where the impact of enantiopurity, concentration and adsorbate-substrate interaction on molecular organization are disclosed.

DFT computational correlations on conformational barriers of Zn2+ and Ni2+ chiral meso-(α,β-unsaturated)- porphyrins

Correlations between DFT and experimental measurements on Zn²⁺ and Ni²⁺ chiral meso-(α,β-unsaturated)- porphyrins were performed using Kohn-Sham methodology. The exchange-correlation Becke88-Perdew86 functional was used in conjunction with double-zeta Slater basis sets. An accurate description of the electronic processes depending on the metal ion (Zn, Ni) or ligand (perilaldehyde and myrtenal) was made, confirming experimental results in terms of structural and electronic modifications. Moreover, this theoretical study provides a stronger knowledge and interpretation of the dynamical conformational features of the free base, Zn and Ni structures. Fundamental links between the central metallic atom and distortions of the porphyrinic core and ligands were demonstrated, in agreement with experimental data. We observed that the core in ZnPeriP and ZnMyrtP species is almost flat, in comparison with the Ni porphyrinic core, which appeared much more distorted. The type of distortion differs between PeriP and MyrtP ligands, with a combined saddled-ruffled characteristic with the former and a pronounced ruffled twisting for the latter. Finally, conformational energy barriers were extracted by spinning one of the arms in steps of 20° in a 360° dihedral angle. The resulted conformational barriers for NiPeriP or NiMyrtP are lower in energy than for ZnPeriP or ZnMyrtP, in agreement with experimental data.

The gold/ampicillin interface at the atomic scale

In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs have been thus reported to overcome highly ampicillin-resistant bacteria. However, the structure at the atomic scale of these hybrid systems remains misunderstood. In this paper, the structure of the interface between an ampicillin molecule AMP and three flat gold facets Au(111), Au(110) and Au(100) has been investigated with numerical simulations (dispersion-corrected DFT). Adsorption energies, bond distances and electron densities indicate that the adsorption of AMP on these facets goes through multiple partially covalent bonding. The stability of the AuNP/AMP nanoconjugates is explained by large adsorption energies and their potential antibacterial activity is discussed on the basis of the constrained spatial orientation of the grafted antibiotic.

Adsorption-induced conformational isomerization of alkyl-substituted thiophene oligomers on Au(111): impact on the interfacial electronic structure

Alkyl-substituted quaterthiophenes on Au(111) form dimers linked by their alkyl substituents and, instead of adopting the trans conformation found in bulk oligothiophene crystals, assume cis conformations. Surprisingly, the impact of the conformation is not decisive in determining the lowest unoccupied molecular orbital energy. Scanning tunneling microscopy and spectroscopy of the adsorption geometries and electronic structures of alkyl-substituted quaterthiophenes show that the orbital energies vary substantially because of local variations in the Au(111) surface reactivity. These results demonstrate that interfacial oligothiophene conformations and electronic structures may differ substantially from those expected based on the band structures of bulk oligothiophene crystals.