Theoretical study of the adsorption of benzene on coinage metals

Long and oriented graphene nanoribbon synthesis from well-ordered 10,10'-dibromo-9,9'-bianthracene monolayer on crystalline Au surfaces

Bottom-up synthesis on metal surfaces has attracted attention for the fabrication of graphene nanoribbons (GNRs) with atomically-precise chemical structures to realize novel electronic devices. However, control of length and orientation on surfaces during GNR synthesis is difficult, thus, achieving longer and aligned GNR growth is a significant challenge. Herein, we report GNR synthesis from a well-ordered dense monolayer on Au crystalline surfaces for long and oriented GNR growth. Scanning tunneling microscopy showed that 10,10'-dibromo-9,9'-bianthracene (DBBA) precursors deposited on Au(111) at room temperature self-assembled into a well-ordered dense monolayer, and the straight molecular wire structure was formed where Br atoms in each precursor were adjacent along the wire axis. The DBBAs in the monolayer were found to be hardly desorbed from the surface under subsequent heating and efficiently polymerize along with the molecular arrangement, resulting in more long and oriented GNR growth compared to the conventional growth method. The result is attributed to be suppression of random diffusion and desorption of the DBBAs on the Au surface during polymerization due to the densely-packed DBBA structure. Additionally, an investigation of the effect of the Au crystalline plane on the GNR growth revealed further anisotropic GNR growth on Au(100) compared to Au(111) due to the stronger interactions of DBBA with Au(100). These findings provide fundamental knowledge for controlling GNR growth from a well-ordered precursor monolayer to achieve more long and oriented GNRs.

How Accurate Are Approximate Density Functionals for Noncovalent Interaction of Very Large Molecular Systems?

Noncovalent intermolecular interactions are very important in many research areas. Therefore, it is vital to understand the extent to which approximate density functionals give a proper description of noncovalent interactions. Previous research has demonstrated that some approximate density functionals can predict usefully accurate interaction energies for many noncovalent systems; however, most of that work is limited to small and moderate-sized molecules. Very recently though, accurate benchmarks have become available for some very large molecules. The present work applies 21 approximate density functionals to compute the binding energies of seven large molecular systems that have a number of atoms ranging from 200 to 910. The results are judged by comparison to the recently published CIM-DLPNO-CCSD(T) results, which are assumed to provide a reliable benchmark. The five most accurate methods among those tested are found to be PW6B95-D4, PW6B95-D3(BJ), revM11, M06-L, and MN15.

Tuning Single-Molecule Conductance by Controlled Electric Field-Induced trans-to-cis Isomerisation

External electric fields (EEFs) have proven to be very efficient in catalysing chemical reactions, even those inaccessible via wet-chemical synthesis. At the single-molecule level, oriented EEFs have been successfully used to promote in situ single-molecule reactions in the absence of chemical catalysts. Here, we elucidate the effect of an EEFs on the structure and conductance of a molecular junction. Employing scanning tunnelling microscopy break junction (STM-BJ) experiments, we form and electrically characterize single-molecule junctions of two tetramethyl carotene isomers. Two discrete conductance signatures show up more prominently at low and high applied voltages which are univocally ascribed to the trans and cis isomers of the carotenoid, respectively. The difference in conductance between both cis-/trans- isomers is in concordance with previous predictions considering π-quantum interference due to the presence of a single gauche defect in the trans isomer. Electronic structure calculations suggest that the electric field polarizes the molecule and mixes the excited states. The mixed states have a (spectroscopically) allowed transition and, therefore, can both promote the cis-isomerization of the molecule and participate in electron transport. Our work opens new routes for the in situ control of isomerisation reactions in single-molecule contacts.

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.

Computational Investigations of Dispersion Interactions between Small Molecules and Graphene-like Flakes

We investigate dispersion interactions in a selection of atomic, molecular, and molecule-surface systems, comparing high-level correlated methods with empirically corrected density functional theory (DFT). We assess the efficacy of functionals commonly used for surface-based calculations, with and without the D3 correction of Grimme. We find that the inclusion of the correction is essential to get meaningful results, but there is otherwise little to distinguish between the functionals. We also present coupled-cluster quality interaction curves for H₂, NO₂, H₂O, and Ar interacting with large carbon flakes, acting as models for graphene surfaces, using novel absolutely localized molecular orbital based methods. These calculations demonstrate that the problems with empirically corrected DFT when investigating dispersion appear to compound as the system size increases, with important implications for future computational studies of molecule-surface interactions.

Influence of Electronic Structure Modeling and Junction Structure on First-Principles Chiral Induced Spin Selectivity

We have carried out a comprehensive study of the influence of electronic structure modeling and junction structure description on the first-principles calculation of the spin polarization in molecular junctions caused by the chiral induced spin selectivity (CISS) effect. We explore the limits and the sensitivity to modeling decisions of a Landauer/Green's function/two-component density functional theory approach to CISS. We find that although the CISS effect is entirely attributed in the literature to molecular spin filtering, spin-orbit coupling being partially inherited from the metal electrodes plays an important role in our calculations on ideal carbon helices, even though this effect cannot explain the experimental conductance results. Its magnitude depends considerably on the shape, size, and material of the metal clusters modeling the electrodes. Also, a pronounced dependence on the specific description of exchange interaction and spin-orbit coupling is manifest in our approach. This is important because the interplay between exchange effects and spin-orbit coupling may play an important role in the description of the junction magnetic response. Our calculations are relevant for the whole field of spin-polarized electron transport and electron transfer, because there is still an open discussion in the literature about the detailed underlying mechanism and the magnitude of physical parameters that need to be included to achieve a consistent description of the CISS effect: seemingly good quantitative agreement between simulation and the experiment can be caused by error compensation, because spin polarization as contained in a Landauer/Green's function/two-component density functional theory approach depends strongly on computational and structural parameters.

Reproducibility of potential energy surfaces of organic/metal interfaces on the example of PTCDA on Ag(111)

Molecular adsorption at organic/metal interfaces depends on a range of mechanisms: covalent bonds, charge transfer, Pauli repulsion, and van der Waals (vdW) interactions shape the potential energy surface (PES), making it key to understanding organic/metal interfaces. Describing such interfaces with density functional theory requires carefully selecting the exchange correlation (XC) functional and vdW correction scheme. To explore the reproducibility of the PES with respect to the choice of method, we present a benchmark of common local, semi-local, and non-local XC functionals in combination with various vdW corrections. We benchmark these methods using perylene-tetracarboxylic dianhydride on Ag(111), one of the most frequently studied organic/metal interfaces. For each method, we determine the PES using a Gaussian process regression algorithm, which requires only about 50 density functional theory calculations as input. This allows a detailed analysis of the PESs' features, such as the positions and energies of minima and saddle points. Comparing the results from different combinations of XC functionals and vdW corrections enables us to identify trends and differences between the approaches. PESs for different computation methods are in qualitative agreement but also display significant quantitative differences. In particular, the lateral positions of adsorption geometries agree well with experiment, while adsorption heights, energies, and barriers show larger discrepancies.

Next-Generation Nonlocal van der Waals Density Functional

The fundamental ideas for a nonlocal density functional theory-capable of reliably capturing van der Waals interactions-were already conceived in the 1990s. In 2004, a seminal paper introduced the first practical nonlocal exchange-correlation functional called vdW-DF, which has become widely successful and laid the foundation for much further research. However, since then, the functional form of vdW-DF has remained unchanged. Several successful modifications paired the original functional with different (local) exchange functionals to improve performance, and the successor vdW-DF2 also updated one internal parameter. Bringing together different insights from almost 2 decades of development and testing, we present the next-generation nonlocal correlation functional called vdW-DF3, in which we change the functional form while staying true to the original design philosophy. Although many popular functionals show good performance around the binding separation of van der Waals complexes, they often result in significant errors at larger separations. With vdW-DF3, we address this problem by taking advantage of a recently uncovered and largely unconstrained degree of freedom within the vdW-DF framework that can be constrained through empirical input, making our functional semiempirical. For two different parameterizations, we benchmark vdW-DF3 against a large set of well-studied test cases and compare our results with the most popular functionals, finding good performance in general for a wide array of systems and a significant improvement in accuracy at larger separations. Finally, we discuss the achievable performance within the current vdW-DF framework, the flexibility in functional design offered by vdW-DF3, as well as possible future directions for nonlocal van der Waals density functional theory.

Ab initio investigation of the role of transition-metal dopants in the adsorption properties of ethylene glycol on doped Pt(100) surfaces

Ethylene glycol (EG) has been considered as a promising alcohol for direct alcohol fuel cells, however, our atomistic understanding of its interaction with doped transition-metal (TM) substrates is not well established. Here, we employed density functional theory calculations within the additive van der Waals D3 correction to improve our atomistic understanding of the role of TM dopants on the adsorption properties of EG on undoped and doped Pt(100) surfaces, namely, Pt₈TM₁/Pt₉/Pt(100) and Pt₉/Pt₈TM₁/Pt(100), where substitutional TM dopants (Fe, Co, Ni, Ru, Rh and Pd) are located within the topmost or subsurface Pt(100) layers, respectively. Except for Pd, all the studied TM dopants showed strong energetic preference for the subsurface layer, which can be explained by the segregation energy and charge effects, and it is not affected by the EG adsorption. In the lowest energy configurations of the undoped and doped substrates, EG binds via one OH group, with the anionic O atom located close to the on-top cationic TM site and the H atom parallel to the surface and pointing towards the bridge site. However, at slightly higher energy configurations, EG adsorbs via one OH with the C-C bond almost perpendicular to the surface, or via both OH groups. As expected, the adsorption is stronger on Pt₈TM₁/Pt₉/Pt(100) with EG (OH group) bound to the cationic TM site and a O-TM distance of about 2 Å. Furthermore, doping enhanced the adsorption energy, and hence, decreased the distance between EG and the surface. For all substrates, adsorption induces a reduction of the work function, which is larger for the adsorption of EG via two OH groups.

Structural Phase Transitions of Molecular Self-Assembly Driven by Nonbonded Metal Adatoms

The involvement of metal atoms in molecular assemblies has enriched the structural and functional diversity of two-dimensional supramolecular networks, where metal atoms are incorporated into the architecture via coordination or ionic bonding. Here we present a temperature-variable study of the self-assembly of the 1,3,5-tribromobenzene (TriBB) molecule on Cu(111) that reveals the involvement of nonbonded adatoms in the molecular matrix. By means of scanning tunneling microscopy and noncontact atomic force microscopy, we demonstrate the molecular-level details of a phase transition of TriBB assembly from the close-packed to porous honeycomb structures at 78 K. This is an unexpected transformation because the close-packed phase is thermodynamically favored in view of its higher molecular density and more intermolecular bonds as compared to the honeycomb lattice. A comprehensive density functional theory calculation suggests that Cu adatoms should be involved in the formation of the honeycomb network, where the Cu adatoms help stabilize the molecular assembly via enhanced van der Waals interactions between TriBB molecules and the underlying substrate. Both calculation and experimental results suggest no chemical bonding or direct charge transfer between the adatoms and the molecules, thus the electronic characteristics of the Cu adatoms trapped in the molecular confinement are close to the intrinsic ones on a clean metal surface and different from those in the traditional coordination-bonded framework. The nonbonded metal adatoms embedded self-assemblies may complement the metal-organic coordination system and can be used to tailor the chemical reactivity and electronic properties of supramolecular structures.

Cooperativity and coverage dependent molecular desorption in self-assembled monolayers: computational case study with coronene on Au(111) and HOPG

One of the common practices in the literature of molecular desorption is the comparison of theoretically (mostly using DFT) calculated single molecule adsorption energies with experimental desorption energies from studies like temperature programmed desorption (TPD) etc. Comparisons like those do not consider that the experimental desorption energies are obtained via ensemble techniques while theoretical values are calculated at the single molecule level. Theoretical values are generally based upon desorption of a single molecule from a clean surface, or upon desorption of an entire monolayer. On the other hand, coverage dependent molecule-molecule interactions add to and modify molecule-substrate interactions that contribute to the experimentally determined desorption energies. In this work, we explore the suitability of an additive nearest neighbor model for determining general coverage dependent single molecule desorption energies in non-covalent self-assembled monolayers (SAMs). These coverage dependent values serve as essential input to any model attempting to reproduce coverage dependent desorption or for understanding the time dependent desorption from a partially covered surface. This method is tested using a case study of coronene adsorbed on Au(111) and HOPG substrates with periodic DFT calculations. Calculations show that coronene exhibits coverage and substrate dependence in molecular desorption. We found that intermolecular contact energies in the coronene monolayer are not strongly influenced by the HOPG substrate, while coronene desorption on Au(111) exhibits strong cooperativity where the additive model fails.

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.

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.

Quantitative Understanding of van der Waals Interactions by Analyzing the Adsorption Structure and Low-Frequency Vibrational Modes of Single Benzene Molecules on Silver

The combination of a sub-Kelvin scanning tunneling microscope and density functional calculations incorporating van der Waals (vdW) corrections has been used successfully to probe the adsorption structure and low-frequency vibrational modes of single benzene molecules on Ag(110). The inclusion of optimized vdW functionals and improved C6-based vdW dispersion schemes in density functional theory is crucial for obtaining the correct adsorption structure and low-energy vibrational modes. These results demonstrate the emerging capability to quantitatively probe the van der Waals interactions between a physisorbed molecule and an inert substrate.

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.

Competition between Hexagonal and Tetragonal Hexabromobenzene Packing on Au(111)

Low-temperature scanning tunneling microscope investigations reveal that hexabromobenzene (HBB) molecules arrange in either hexagonally closely packed (hcp) [Formula: see text] or tetragonal [Formula: see text] structure on Au(111) dependent on a small substrate temperature difference around 300 K. The underlying mechanism is investigated by density functional theory calculations, which reveal that substrate-mediated intermolecular noncovalent C-Br···Br-C attractions induce hcp HBB islands, keeping the well-known Au(111)-22×√3 reconstruction intact. Upon deposition at 330 K, HBB molecules trap freely diffusing Au adatoms to form tetragonal islands. This enhances the attraction between HBB and Au(111) but partially reduces the intermolecular C-Br···Br-C attractions, altering the Au(111)-22×√3 reconstruction. In both cases, the HBB molecule adsorbs on a bridge site, forming a ∼15° angle between the C-Br direction and [112̅]Au, indicating the site-specific molecule-substrate interactions. We show that the competition between intermolecular and molecule-substrate interactions determines molecule packing at the subnanometer scale, which will be helpful for crystal engineering, functional materials, and organic electronics.

Quasi one-dimensional band dispersion and surface metallization in long-range ordered polymeric wires

On-surface covalent self-assembly of organic molecules is a very promising bottom-up approach for producing atomically controlled nanostructures. Due to their highly tuneable properties, these structures may be used as building blocks in electronic carbon-based molecular devices. Following this idea, here we report on the electronic structure of an ordered array of poly(para-phenylene) nanowires produced by surface-catalysed dehalogenative reaction. By scanning tunnelling spectroscopy we follow the quantization of unoccupied molecular states as a function of oligomer length, with Fermi level crossing observed for long chains. Angle-resolved photoelectron spectroscopy reveals a quasi-1D valence band as well as a direct gap of 1.15 eV, as the conduction band is partially filled through adsorption on the surface. Tight-binding modelling and ab initio density functional theory calculations lead to a full description of the band structure, including the gap size and charge transfer mechanisms, highlighting a strong substrate-molecule interaction that drives the system into a metallic behaviour.

Vibrational Signature of a Single Water Molecule Adsorbed on Pt(111): Toward a Reliable Anharmonic Description

In this study, we present a thorough benchmarking of our direct anharmonic vibrational variation-perturbation approach for adsorbed molecules on surfaces. We then use our method to describe the vibrational structure of a water molecule adsorbed on a Pt(111) surface and compare our results with the available experimental data. By using an explicitly correlated hybrid method to describe the molecule-surface interaction, we improve on the initial periodic PBE/DZP potential energy landscape and obtain vibrational frequencies that are of near-experimental accuracy. We introduce an implementation of anharmonic z-polarized IR intensity calculation and explain the absence of antisymmetric O-H stretch in the experimental data for the adsorbed water molecule, while the symmetric O-H stretch is predicted to be visible.