Adsorption of small aromatic molecules on the (111) surfaces of noble metals: A density functional theory study with semiempirical corrections for dispersion effects

Exploring the Conformational Space of a Sulfonyl-Based Ionic Liquid on Platinum-Based Mono and Bimetallic Surfaces

Understanding the arrangement of ionic liquids at the interface and their interactions with the surface is crucial for enhancing selectivity in heterogeneous reactions for practical applications. In this study, we investigate the nature of the adsorption and structural orientations of a sulfonyl-based ionic liquid on platinum-based mono- and bimetallic (111) surfaces employing replica exchange molecular dynamics and first-principles density functional theory calculations. More than 30 confirmations of the ionic liquid are identified on both monometallic and bimetallic surfaces. In addition to adsorption energies, factors such as dynamics of ionic liquids, molecule-surface distances, and charge transfer analyses are found to be important indicators for understanding adsorption phenomena. The sulfonyl anion exhibits contrasting behavior on the two surfaces, showing a preference for chemisorption on the monometallic surface, while the pyrrolidinium cation is physisorbed on both metal surfaces. Both metal surfaces are negatively charged primarily because of charge transfer from the sulfonyl anion. The analysis of the orientational preference reveals a nearly flat orientation of the cation on the monometallic surface, while a tilted orientation is observed on the bimetallic surface.

Assessing plasmon-induced reactions by a combined quantum chemical-quantum/classical hybrid approach

Plasmon-driven reactions on metal nanoparticles feature rich and complex mechanistic contributions, involving a manifold of electronic states, near-field enhancement, and heat, among others. Although localized surface plasmon resonances are believed to initiate these reactions, the complex reactivity demands deeper exploration. This computational study investigates factors influencing chemical processes on plasmonic nanoparticles, exemplified by protonation of 4-mercaptopyridine (4-MPY) on silver nanoparticles. We examine the impact of molecular binding modes and molecule-molecule interactions on the nanoparticle's surface, near-field electromagnetic effects, and charge-transfer phenomena. Two proton sources were considered at ambient conditions, molecular hydrogen and water. Our findings reveal that the substrate's binding mode significantly affects not only the energy barriers governing the thermodynamics and kinetics of the reaction but also determine the directionality of light-driven charge-transfer at the 4-MPY-Ag interface, pivotal in the chemical contribution involved in the reaction mechanism. In addition, significant field enhancement surrounding the adsorbed molecule is observed (eletromagnetic contribution) which was found insufficient to modify the ground state thermodynamics. Instead, it initiates and amplifies light-driven charge-transfer and thus modulates the excited states' reactivity in the plasmonic-molecular hybrid system. This research elucidates protonation mechanisms on silver surfaces, highlighting the role of molecular-surface and molecule-molecule-surface orientation in plasmon-catalysis.

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.

Pyridine interaction with γ-CuI: synergy between molecular dynamics and molecular orbital approaches to molecule/surface interactions

We have used a synergistic computational approach merging Molecular Dynamics (MD) simulations with density functional theory (DFT) to investigate the mechanistic aspects of chemisorption of pyridine (Py) molecules on copper iodide. The presence of both positive and negative ions at the metal halide surface presents a chemical environment in which pyridine molecules may act as charge donors and/or acceptors. Computational results reveal that Py molecules interact with the γ-CuI(111) surface owing to a combination of noncovalent Cu⋯N, Cu/I⋯π/π*, and hydrogen bonding interactions as determined via Natural Bonding Orbitals (NBO). Introduction of surface defect sites alters the interaction dynamics, resulting in a "localizing effect" in which the Py molecules clump together within the defect site. Significant enhancement of hydrogen bonding between C-H σ* and I 6p orbitals results in more tightly surface-bound Py molecules. Our findings provide a platform for understanding the interaction between Py and Py-derivative vapors and metal-based surfaces that contain both electron acceptor and donor atoms.

Facile preparation, catalytic performance and reaction mechanism of MnxCo1-xOδ/3DOM-m Ti0.7Si0.2W0.1Oy catalysts for the simultaneous removal of soot and NOx

In this work, three-dimensionally ordered macroporous-mesoporous Ti0.7Si0.2W0.1Oy (3DOM-m TiSiWO) supported MnxCo1-xOδ catalysts with different x values were prepared using the colloidal crystal template method and incipient wetness impregnation method. The...

Describing adsorption of benzene, thiophene, and xenon on coinage metals by using the Zaremba-Kohn theory-based model

Semilocal (SL) density functional approximations (DFAs) are widely applied but have limitations due to their inability to incorporate long-range van der Waals (vdW) interaction. Non-local functionals (vdW-DF, VV10, and rVV10) or empirical methods (DFT+D, DFT+vdW, and DFT+MBD) are used with SL-DFAs to account for such missing interaction. The physisorption of a molecule on the surface of the coinage metals (Cu, Ag, and Au) is a typical example of systems where vdW interaction is significant. However, it is difficult to find a general method that reasonably describes both adsorption energy and geometry of even the simple prototypes of cyclic and heterocyclic aromatic molecules such as benzene (C₆H₆) and thiophene (C₄H₄S), respectively, with reasonable accuracy. In this work, we present an alternative scheme based on Zaremba-Kohn theory, called DFT+vdW-dZK. We show that unlike other popular methods, DFT+vdW-dZK and particularly SCAN+vdW-dZK give an accurate description of the physisorption of a rare-gas atom (xenon) and two small albeit diverse prototype organic molecules on the (111) surfaces of the coinage metals.

Ultrafast Dynamics of Electronic Resonances in Molecules Adsorbed on Metal Surfaces: A Wave Packet Propagation Approach

We present a wave packet propagation-based method to study the electron dynamics in molecular species in the gas phase and adsorbed on metal surfaces. It is a very general method that can be employed to any system where the electron dynamics is dominated by an active electron and the coupling between the discrete and continuum electronic states is of importance. As an example, one can consider resonant molecule-surface electron transfer or molecular photoionization. Our approach is based on a computational strategy allowing incorporating ab initio inputs from quantum chemistry methods, such as density functional theory, Hartree-Fock, and coupled cluster. Thus, the electronic structure of the molecule is fully taken into account. The electron wave function is represented on a three-dimensional grid in spatial coordinates, and its temporal evolution is obtained from the solution of the time-dependent Schrödinger equation. We illustrate our method with an example of the electron dynamics of anionic states localized on organic molecules adsorbed on metal surfaces. In particular, we study resonant charge transfer from the π* orbitals of three vinyl derivatives (acrylamide, acrylonitrile, and acrolein) adsorbed on a Cu(100) surface. Electron transfer between these lowest unoccupied molecular orbitals and the metal surface is extremely fast, leading to a decay of the population of the molecular anion on the femtosecond timescale. We detail how to analyze the time-dependent electronic wave function in order to obtain the relevant information on the system: the energies and lifetimes of the molecule-localized quasistationary states, their resonant wavefunctions, and the population decay channels. In particular, we demonstrate the effect of the electronic structure of the substrate on the energy and momentum distribution of the hot electrons injected into the metal by the decaying molecular resonance.

Insight into the mechanism of boron-doping of carbon aerogel for enhancing the activity of low-temperature selective catalytic reduction of NO with NH3

Boron doped carbon aerogel could increase the number of active sites effectively and enhance NO reduction to N₂via NH₃-SCR.

Reply to the ‘Comment on “Quantum interference effects in biphenyl dithiol for gas detection”’ by A. Grigoriev, H. Jafri and K. Leifer, RSC Adv., 2020, , DOI: 10.1039/C9RA00451C

The Comment on our publication [Prasongkit et al., RSC Adv., 2016, 64, 59299] is puzzling since it is well known that biphenyl is fairly non-reactive. Hence, it's not surprising we have low binding energies when the gas molecules were adsorbed on biphenyl dithiol (BPDT). The large binding energy of NO₂ chemisorbed onto BPDT (∼2.04 eV) in the Comment conflicts with existing theoretical and experimental evidence. Grigoriev et al. have attempted to compare their results to our findings, employing different approximation schemes under the density functional theory (DFT) framework. Here, the effect of taking into account van der Waals (vdW) interactions upon the adsorption mechanism of small aromatic molecules has been discussed.

We reply to the Comment by Leifer et al. on our publication [Prasongkit et al., RSC Adv., 2016, 64, 59299]. We maintain that, as biphenyl is non-reactive, low binding energies are expected when gases are adsorbed on biphenyl dithiol.

Atomistic View of Mercury Cycling in Polar Snowpacks: Probing the Role of Hg2+ Adsorption Using Ab Initio Calculations

Photochemical oxidation of atmospheric elemental mercury (Hg0) promotes reactive oxidized Hg (HgII) adsorption on particles and deposition to the polar snowpack. The deposited Hg either returns to the atmosphere via photochemical reduction or remains in the snowpack depending on the strength of adsorption. In this study, we performed ab initio calculations to understand the atomic-level cause of the fate of adsorbed Hg by determining the adsorption affinity for Hg2+, the simplest form of HgII, of barite, halite, muscovite, illite, and ice-Ih as potential adsorbents. The adsorption affinity was estimated by calculating the energy required to dissociate adsorbed Hg2+ from the adsorbents. The results reveal that Hg2+ is stable on the surfaces of the selected adsorbents, except barite, but is prone to photodissociation under solar ultraviolet radiation. This mild adsorption is expected to contribute to the bidirectional exchange of Hg between the atmosphere and the polar snowpack. Thus, this theoretical approach can provide complementary perspectives on polar Hg dynamics beyond the limitations of field and laboratory experiments. Further studies on more complicated and realistic adsorption models with different HgII species and adsorbent surfaces having diverse defective structures are required to better comprehend air–snow Hg cycling in the polar regions.

Functionalization of gold nanoparticles with two aminoalcohol-based quinoxaline derivatives for targeting phosphoinositide 3-kinases (PI3Kα)

Quinoxaline derivatives have attracted considerable attention due to their vast range of applications that includes electroluminescence and biomedicine.

The crucial role of electron transfer from interfacial molecules in the negative potential shift of Au electrode immersed in ionic liquids

Potential of zero charge (PZC) is essential in electrochemistry to understand physical and chemical phenomena at the interface between an electrode and a solution. A negative potential shift from the work function to the PZC has been experimentally observed in a metal/ionic liquid (IL) system, but the mechanism remains unclear and controversial. In this paper we provide valuable insight into the mechanism on the potential shift in the Au/IL (1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide: [BMIM][TFSA]) system using a computational approach combining classical molecular dynamics simulations and first-principles calculations. By separately estimating some contributions to the potential shift, the shift is calculated in an easy-to-understand manner. The resultant PZC is shown to be in good agreement with the experimental one. Among the contributions, the electron redistribution at the Au/IL interface is found to provide the largest negative potential change. This indicates that the redistribution plays a crucial role in determining the potential shift of the Au electrode immersed in the IL. Detailed analyses suggest that the redistribution corresponds to the electron transfer not only from the anionic TFSA but also from the cationic BMIM molecules to the Au electrode surface. This unique observation is understood to originate from the interfacial structure where the IL molecules are in very close proximity to the electrode surface via dispersion interaction.

Tailoring atomic layer growth at the liquid-metal interface

Engineering atomic structures at metal surfaces represents an important step in the development of novel nanomaterials and nanodevices, but relies predominantly on atomic/molecular beam epitaxy under ultrahigh vacuum conditions, where controlling the deposition processes remains challenging. By using solution-borne nanosized gold clusters as a precursor, here we develop a wet deposition protocol to the fabrication of atomically flat gold nanoislands, so as to utilize the dynamic exchange of surface-active molecules at the liquid-metal interface for manipulating the growth kinetics of ultrathin metallic nanostructures. While remarkable shape and size selection of gold nanoislands is observed, our experimental and theoretical investigations provide compelling evidences that organic adsorbates can impart a bias to the island orientation by preferred adsorption and alignment and intervene in the assembly and disassembly of adatom islands by complexing with Au adatoms. This approach offers a simple solution to regulate atomic layer growth of metals at ambient conditions.

Re-evaluating how charge transfer modifies the conformation of adsorbed molecules

The archetypal electron acceptor molecule, TCNQ, is generally believed to become bent into an inverted bowl shape upon adsorption on the coinage metal surfaces on which it becomes negatively charged. New quantitative experimental structural measurements show that this is not the case for TCNQ on Ag(111). DFT calculations show that the inclusion of dispersion force corrections reduces not only the molecule-substrate layer spacing but also the degree of predicted molecular bonding. However, complete agreement between experimentally-determined and theoretically-predicted structural parameters is only achieved with the inclusion of Ag adatoms into the molecular layer, which is also the energetically favoured configuration. The results highlight the need for both experimental and theoretical quantitative structural methods to reliably understand similar metal-organic interfaces and highlight the need to re-evaluate some previously-investigated systems.

Graphene Translucency and Interfacial Interactions in the Gold/Graphene/SiC System

Integration of graphene into electronic circuits through its joining with conventional metal electrodes (i.e., gold) appears to be one of the main technological challenges nowadays. To gain insight into this junction, we have studied the physicochemical interactions between SiC-supported graphene and a drop of molten gold. Using appropriate high-temperature experimental conditions, we perform wetting experiments and determine contact angles for gold drops supported on graphene epitaxially grown on 4H-SiC. The properties of the metal/graphene interface are analyzed using a wide variety of characterization techniques, along with computational simulations based on density functional theory. In contrast with the established literature, our outcomes clearly show that graphene is translucent in the gold/graphene/SiC interface, and therefore its integration into electronic circuits primarily depends on the right choice of the support to produce favorable wetting interactions with liquid gold.

Exploring the driving forces behind the structural assembly of biphenylthiolates on Au(111)

In this contribution, we use dispersion-corrected density functional theory to study inter- and intramolecular interactions in a prototypical self-assembled monolayer (SAM) consisting of biphenylthiolates bonded to Au(111) via thiolate groups. The goal is to identify the nature of the interactions that drive the monolayer into a specific conformation. Particular focus is laid on sampling realistic structures rather than high symmetry model configurations. This is achieved by studying conceptually different local minimum structures of the SAM that are obtained via exploring the potential energy surface from systematically varied starting geometries. The six obtained packing motifs differ in the relative arrangement of the two molecules in the unit cell (co-planar versus herringbone) and in the intramolecular configuration (twisted versus planar rings). We find that van der Waals interactions within the organic adsorbate and between the adsorbate and substrate are the main reason that these molecular assemblies can form stable structures at all. The van der Waals interactions are, however, very similar for all observed motifs; by analyzing various types of interactions in the course of three notional SAM-formation steps, we find that the main driving force stabilizing the actual global minimum structure originates from electrostatic interactions between the molecules.

Thermodynamics of Alkanethiol Self-Assembled Monolayer Assembly on Pd Surfaces

We investigate the structure and binding energy of alkanethiolate self-assembled monolayers (SAMs) on Pd (111), Pd (100), and Pd (110) facets at different coverages. Dispersion-corrected density functional theory calculations are used to correlate the binding energy of alkanethiolates with alkyl chain length and coverage. The equilibrium coverage of thiolate layers strongly prefers 1/3 monolayer (ML) on the Pd (111) surface. The coverage of thiolates varies with chemical potential on Pd (100) and Pd (110), increasing from 1/3 to 1/2 ML on (100) and from 1/4 to 1/2 ML on (110) as the thiol chemical potential is increased. Higher coverages are driven by attractive dispersion interactions between the extended alkyl chains, such that transitions to higher coverages occur at lower thiol chemical potentials for longer chain thiolates. Stronger adsorption to the Pd (100) surface causes the equilibrium Wulff construction of Pd particles to take on a cubic shape upon saturation with thiols. The binding of H, O, and CO adsorbates is weakened as the thiolate coverage is increased, with saturation coverages causing unfavorable binding of O and CO on Pd (100) and weakened binding on other facets. Temperature-dependent CO diffuse reflectance infrared Fourier transform spectroscopy experiments are used to corroborate the weakened binding of CO in the presence of thiolate SAMs of varying surface density. Preliminary results of multiscale modeling efforts on the Pd-thiol system using a reactive force field, ReaxFF, are also discussed.

Joint Experimental and Computational Investigation of the Flexibility of a Diacetylene-Based Mixed-Linker MOF: Revealing the Existence of Two Low-Temperature Phase Transitions and the Presence of Colossal Positive and Giant Negative Thermal Expansions

Solvothermal reaction in N,N-dimethylformamide (DMF) between 1,6-bis(1-imidazolyl)-2,4-hexadiyne monohydrate (L1⋅H₂ O), isophthalic acid (H₂ L2), and Zn(NO₃ )₂ ⋅6 H₂ O gives the diacetylene-based mixed-ligand coordination polymer {[Zn(L1)(L2)](DMF)₂ }_n (UMON-44) in 38 % yield. Combination of DSC with variable-temperature single-crystal X-ray diffraction revealed the occurrence of two phase transitions spanning the ranges 129-144 K and 158-188 K. Furthermore, the three structurally similar phases of UMON-44 show giant negative and/or colossal positive thermal expansions. These unusual phenomena exist without any change in the contents of the unit cell. DFT calculations using the PBE+D3 dispersion scheme were able to distinguish between these polymorphs by accurately reproducing their salient structural features, although corrections in the size of the unit cell turned out to be necessary for the high-temperature phase to account for its large thermal expansion. In addition, the infrared spectra (vibration frequencies and peak intensities) of these theoretical models were calculated, allowing for univocal identification of the corresponding polymorphs. Last, the limits of our computational method were tested by calculating the phase transition temperatures and their associated enthalpies, and the derived figures compare favorably with the values determined experimentally.

The dynamics of benzene on Cu(111): a combined helium spin echo and dispersion-corrected DFT study into the diffusion of physisorbed aromatics on metal surfaces

We use helium spin-echo spectroscopy (HeSE) to investigate the dynamics of the diffusion of benzene adsorbed on Cu(111). The results of these measurements show that benzene moves on the surface through an activated jump-diffusion process between the adsorption sites on a Bravais lattice. Density Functional Theory (DFT) calculations with van der Waals (vdW) corrections help us understand that the molecule diffuses by jumping through non-degenerate hollow sites. The results of the calculations shed light on the nature of the binding interaction between this prototypical aromatic molecule and the metallic surface. The highly accurate HeSE experimental data provide a quantitatively stringent benchmark for the vdW correction schemes applied to the DFT calculations and we compare the performances of several dispersion interaction schemes.

Adsorption of Homotrifunctional 1,2,3-Benzenetriol on a Ge(100)-2 × 1 Surface

The adsorption of the homotrifunctional 1,2,3-benzenetriol on Ge(100)-2 × 1 has been investigated by density functional theory calculations, Fourier transform infrared spectroscopy, and X-ray-photoelectron spectroscopy. The results show that the adsorption can occur through OH dissociation of all three hydroxyl groups, and that all three reaction pathways are kinetically and thermodynamically favorable. A coverage-dependent analysis shows that at low coverage, the molecule reacts to form a mix of trifold and dually bound adsorbates. As the coverage increases, the reactions are limited to dissociative adsorption through single and dual attachments. Calculations on the three possible dually bound configurations further reveals that the dissociative adsorption of the third hydroxyl group is limited by geometrical constraints to only two reaction channels. Finally, the proximity between OH-groups in the molecule favors intra- and intermolecular hydrogen bonding, which stabilizes singly and dually bound adsorbate configurations and limits the reactivity of the functional groups.

Tuning the work function of stepped metal surfaces by adsorption of organic molecules

Understanding the binding mechanisms for aromatic molecules on transition-metal surfaces, especially with defects such as vacancies, steps and kinks, is a major challenge in designing functional interfaces for organic devices. One important parameter in the performance of organic/inorganic devices is the barrier of charge carrier injection. In the case of a metallic electrode, tuning the electronic interface potential or the work function for electronic level alignment is crucial. Here, we use density-functional theory (DFT) calculations with van der Waals (vdW) interactions treated with both screened pairwise (vdW^surf) and many-body dispersion (MBD) methods, to systematically study the interactions of benzene with a variety of stepped surfaces. Our calculations confirm the physisorptive character of Ag(2 1 1), Ag(5 3 3), Ag(3 2 2), Ag(7 5 5) and Ag(5 4 4) surfaces upon the adsorption of benzene. The MBD effects reduce the adsorption energies by about 0.15 eV per molecule compared to the results from the DFT  +  vdW^surf method. In addition, we find that the higher the step density, the larger the reduction of the work function upon the adsorption of benzene. We also study the effect of vdW interactions on the electronic structure using a fully self-consistent implementation of the vdW^surf method in the Kohn-Sham DFT framework. We find that the self-consistent vdW^surf effects increase the work function due to the lowered Fermi level and the increased vacuum level. As a result, the benzene/Ag(2 1 1) system has the lowest work function (3.67 eV) among the five adsorption systems, significantly smaller than the work function of the clean Ag(1 1 1) surface (4.74 eV). Our results provide important insights into the stability and electronic properties of molecules adsorbed on stepped metal surfaces, which could help in designing more appropriate interfaces with low work functions for electron transfer.

First-Principles Models for van der Waals Interactions in Molecules and Materials: Concepts, Theory, and Applications

Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches). Particular attention is paid to the intriguing nature of many-body vdW interactions, whose fundamental relevance has recently been highlighted in several landmark experiments. The performance of these models in predicting binding energetics as well as structural, electronic, and thermodynamic properties is connected with the theoretical concepts and provides a numerical summary of the state-of-the-art in the field. We conclude with a roadmap of the conceptual, methodological, practical, and numerical challenges that remain in obtaining a universally applicable and truly predictive vdW method for realistic molecular systems and materials.

Towards highly active Pd/CeO2 for alkene hydrogenation by tuning Pd dispersion and surface properties of the catalysts

Extensive applications of noble metals as heterogeneous catalysts are limited by their global reserve scarcity and exorbitant price. Identifying the intrinsic active nature of a catalyst benefits the designing of catalysts with trace amounts of noble metals; these catalysts display better or comparable overall catalytic efficiency than their heavily loaded counterparts. Herein, systematic studies on Pd dispersion and surface properties of a series of Pd/CeO₂ catalysts for styrene hydrogenation showed that high Pd dispersion and surface abundant defects of the catalysts are essential to realize superior activity. Highly dispersed subnanometric Pd clusters on porous nanorods of ceria with a large surface Ce³⁺ fraction of 27.4%, high Pd dispersion of 73.6%, and low Pd loading of 0.081 wt% delivered a very large turnover frequency of 103 233 h^-1 based on each exposed Pd atom for styrene hydrogenation at 1.0 MPa H₂ and 30 °C. Experimental data, kinetic analysis, and density functional theory calculations revealed that the highly dispersed Pd shows a low affinity for styrene and provides more exposed Pd sites for hydrogen activation. The surface abundant defects (oxygen vacancy) of Pd/CeO₂ catalysts can enrich the electron density of Pd, improve its capability for H₂ dissociation and lower the affinity of styrene for Pd.

Aromatic molecules on low-index coinage metal surfaces: Many-body dispersion effects

Understanding the binding mechanism for aromatic molecules on transition-metal surfaces in atomic scale is a major challenge in designing functional interfaces for to (opto)electronic devices. Here, we employ the state-of-the-art many-body dispersion (MBD) approach, coupled with density functional theory methods, to study the interactions of benzene with low-index coinage metal surfaces. The many-body effects contribute mostly to the (111) surface, and leastly to the (110) surface. This corresponds to the same sequence of planar atomic density of face-centered-cubic lattices, i.e., (111) > (100) > (110). The binding energy for benzene/Au(110) is even stronger than that for benzene/Ag(110), due to a larger broadening of molecular orbitals in the former case. On the other hand, our calculations show almost identical binding energies for benzene on Ag(111) and Au(111), which contradicts the classic d-band center theory that could well predict the trend in chemisorption energies for various small molecules on a number of metal surfaces. Our results provide important insight into the benchmark adsorption systems with opener surfaces, which could help in designing more complex functional interfaces.

The role of the crystalline face in the ordering of 6-mercaptopurine self-assembled monolayers on gold

Well-ordered molecular films play an important role in nanotechnology, from device fabrication to surface patterning. Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) on the Au(100)-(1 × 1) and Au(111)-(1 × 1) have been used to understand the interplay of molecule-substrate interactions for heterocyclic thiols capable of binding to the surface by two anchors, which spontaneously form a highly disordered film on Au(111). Our results reveal that for the same surface coverage the simple change of the substrate from Au(111)-(1 × 1) to Au(100)-(1 × 1) eliminates molecular disorder and yields well-ordered SAMs. We discuss these findings in terms of differences in the surface mobility of 6MP species on these surfaces, the energetics of the adsorption sites, and the number of degrees of freedom of these substrates for a molecule with reduced surface mobility resulting from its two surface anchors. These results reveal the presence of subtle molecule-substrate interactions involving the heteroatom that drastically alter SAM properties and therefore strongly impact on our ability to control physical properties and to build devices at the nanoscale.

Optimizing the sputter deposition process of polymers for the Storing Matter technique using PMMA

Quantitative analyses in secondary ion mass spectrometry (SIMS) become possible only if ionization processes are controlled. The Storing Matter technique has been developed to circumvent this so-called matrix effect, primarily for inorganic samples, but has also been extended to organic samples. For the latter, it has been applied to polystyrene in order to investigate the extent of damage in the polymer, its fragmentation during the sputter deposition process and the effect of the deposition process on the spectra taken by Time-of-Flight SIMS (ToF-SIMS). In this work, a multi-technique approach, which employs the Storing Matter technique for deposition and ToF-SIMS and X-ray photoelectron spectroscopy for characterization, is used to enhance the control of the deposition process, including the thickness of the deposit, the alteration of the source film and the influence of polymer composition on the Storing Matter process. Poly (methyl methacrylate) (PMMA) is used for this work. More detailed information about the sticking of polymer fragments on the metal collector is obtained by density functional theory calculations. This work allows for the conclusion that a part of the fragments deposited on the collector surface diffuses on the latter, reacts and recombines to form larger fragments. The behaviour observed for PMMA is similar to polystyrene, showing that oxygen has no major influence on the processes occurring during the sputter deposition process. Additionally, we have developed a new methodology using 2D ToF-SIMS images of the deposit to monitor the deposit thickness and to identify surface contaminations. The latter are not only located at the position of the deposit but all over the collector surface. Copyright © 2016 John Wiley & Sons, Ltd.

Surface-enhanced Raman scattering of coumarin 343 on silver colloidal nanoparticles

Surface-enhanced Raman scattering (SERS) of coumarin 343 (C343) adsorbed on silver colloidal nanoparticles reduced by sodium citrate was investigated and the surface adsorption geometry of C343 on Ag was sought by optimizing C343-Ag complexes for neutral and deprotonated C343 molecules in the DFT simulations. The SERS of C343 showed a number of spectral changes upon solution pH change. We found that deprotonated C343 adsorbs on the Ag nanoparticles through the carboxylate group keeping a perpendicular geometry to the surface. When protonated, the adsorption geometry of C343 is changed into more or less flat to the surface as the cyclic ester group becomes a preferred surface adsorption site.

Surface Adsorption from the Exchange-Hole Dipole Moment Dispersion Model

The accurate calculation of intermolecular interaction energies with density functional theory requires methods that include a treatment of long-range, nonlocal dispersion correlation. In this work, we explore the ability of the exchange-hole dipole moment (XDM) dispersion correction to model molecular surface adsorption. Adsorption energies are calculated for six small aromatic molecules (benzene, furan, pyridine, thiophene, thiophenol, and benzenediamine) and the four DNA nucleobases (adenine, thymine, guanine, and cytosine) on the (111) surfaces of the three coinage metals (copper, silver, and gold). For benzene, where the experimental reference data is most precise, the mean absolute error in the computed absorption energies is 0.04 eV. For the other aromatic molecules, the computed binding energies are found to be within 0.09 eV of the available reference data, on average, which is well below the expected experimental uncertainties for temperature-programmed desorption measurements. Unlike other dispersion-corrected functionals, adequate performance does not require changes to the canonical XDM implementation, and the good performance of XDM is explained in terms of the behavior of the exchange hole. Additionally, the base functional employed (B86bPBE) is also optimal for molecular studies, making B86bPBE-XDM an excellent candidate for studying chemistry on material surfaces. Finally, the noncovalent interaction (NCI) plot technique is shown to detect adsorption effects in real space on the order of tenths of an eV.

Real-space visualization of conformation-independent oligothiophene electronic structure

We present scanning tunneling microscopy and spectroscopy (STM/STS) investigations of the electronic structures of different alkyl-substituted oligothiophenes on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes adopted distinct straight and bent conformations. By combining STS maps with STM images, we visualize, in real space, particle-in-a-box-like oligothiophene molecular orbitals. We demonstrate that different planar conformers with significant geometrical distortions of oligothiophene backbones surprisingly exhibit very similar electronic structures, indicating a low degree of conformation-induced electronic disorder. The agreement of these results with gas-phase density functional theory calculations implies that the oligothiophene interaction with the Au(111) surface is generally insensitive to molecular conformation.

Interaction of a Self-Assembled Ionic Liquid Layer with Graphite(0001): A Combined Experimental and Theoretical Study

The interaction between (sub)monolayers of the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide [BMP](+)[TFSA](-) and graphite(0001), which serves as a model for the anode|electolyte interface in Li-ion batteries, was investigated under ultrahigh vacuum conditions in a combined experimental and theoretical approach. High-resolution scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and dispersion-corrected density functional theory (DFT-D) calculations were employed. After vapor deposition at 300 K, XPS indicates molecular adsorbates with a 1:1 ratio of cations/anions. Cool down to ∼100 K leads to the formation of an ordered (2D) crystalline phase, which coexists with a mobile (2D) liquid. DFT-D calculations reveal that adsorbed [BMP](+) and [TFSA](-) species are arranged alternately in a row-like adsorption structure (cation-anion-cation-anion) and that adsorption is dominated by dispersion interactions between adlayer and substrate, on the one hand, and electrostatic interactions between the ions in a row, on the other hand. Simulated STM images of that structure closely resemble the experimental molecular resolved STM images and show that the resolved features mostly stem from the cations.

Oligothiophene wires: impact of torsional conformation on the electronic structure

Different torsional conformations of alkyl-substituted oligothiophenes show nearly identical progressions of particle-in-a-box-like electronic orbitals.

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.

First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets

The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface.

Dispersion corrected RPBE studies of liquid water

The structure of liquid water has been addressed by ab initio molecular dynamics simulations based on density functional theory. Exchange-correlation effects have been described by the popular PBE and RPBE functionals within the generalized gradient approximation as these functionals also yield satisfactory results for metals which is important to model electrochemical interfaces from first principles. In addition, dispersive interactions are included by using dispersion-corrected schemes. It turns out that the dispersion-corrected RPBE functional reproduces liquid water properties quite well in contrast to the PBE functional. This is caused by the replacement of the over-estimated directional hydrogen-bonding in the PBE functional by non-directional dispersive interactions.

Carbon dioxide interaction with isolated imidazole or attached on gold clusters and surface: competition between σ H-bond and π stacking interaction

Using first principle methodologies, we investigate the subtle competition between σ H-bond and π stacking interaction between CO2 and imidazole either isolated, adsorbed on a gold cluster or adsorbed on a gold surface. These computations are performed using MP2 as well as dispersion corrected density functional theory (DFT) techniques. Our results show that the CO2 interaction goes from π-type stacking into σ-type when CO2 interacts with isolated imidazole and Au clusters or surface. The balance between both types of interactions is found when an imidazole is attached to a Au20 gold cluster. Thus, the present study has great significance in understanding and controlling the structures of weakly-bound molecular systems and materials, where hydrogen bonding and van der Waals interactions are competing. The applications are in the fields of the control of CO2 capture and scattering, catalysis and bio- and nanotechnologies.

Chemisorbed oxygen atom on the activation of C–H bond in methane: a Rh model study

The pre-adsorbed oxygen has little effect on the catalytic activity of methane dehydrogenation on Rh-ad-atom catalysts.