Interplay between Halogen and Hydrogen Bonds in 2D Self-Assembly

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Interplay Between Halogen and Hydrogen Bonds in 2D SelfAssembly on Gold Surface: A First-Principles Investigation Yunxiang Lu, Shaoze Zhang, Changjun Peng, and Honglai Liu J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.7b09325 • Publication Date (Web): 24 Oct 2017 Downloaded from http://pubs.acs.org on October 25, 2017

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The Journal of Physical Chemistry

Interplay between Halogen and Hydrogen Bonds in 2D Self-Assembly on Gold Surface: A First-Principles Investigation

Yunxiang Lu,*,# Shaoze Zhang,# Changjun Peng, and Honglai Liu

Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.

Abstract: The interplay between halogen bonding and hydrogen bonding has arisen recent interest in the formation of 2D self-assembled molecular arrays on solid surfaces. Herein we present a first-principles density functional theory study of the self-assemblies of two brominated anthraquione molecules on Au(111) and Au(110). The possible binding sites of these two compounds on the facets were firstly explored, and then various self-assembled patterns involving different halogen and hydrogen bonds were examined both in gas phase and on gold surface. To visually investigate the nature of lateral adsorbate-adsorbate and vertical adsorbate-substrate interactions, the atoms in molecules, noncovalent interaction index, and electron density difference analyses were undertaken. The molecules tend to be self-assembled by means of triangular binding motifs with simultaneous halogen and hydrogen bonds. Upon the formation of the dimers in gas phase as well as on gold surface, significant band shifts around Fermi energy take place, due to intermolecular orbital hybridization. The simulated scan tunneling microscopy images via the Tersoff-Hamann approach are in good agreement with those determined experimentally. The results reported in this work should be of fundamental importance in the simultaneous application of these two parallel noncovalent interactions in molecular self-assembly on surfaces.

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Introduction Molecular self-assembly, which refers to the spontaneous association of precursor molecules into large and ordered structures, has been widely used in the engineering of nanomaterials and molecular devices.1-5 Self-assembly of functional molecules on solid surfaces is also an important tool to fabricate novel two-dimensional (2D) materials with applications on molecular electronics.6 In general, the self-assembly process and resulting patterns on surfaces are controlled by the delicate balance between molecule-molecule and molecule-substrate interactions.7 Hydrogen

bonding is the most frequently used

intermolecular forces in molecular self-assembly, because of its directionality, strength, and high selectivity.8-16 A particular example of the formation of well-ordered 2D supramolecular networks mediated by hydrogen bonding is carboxylic acids.17 Carboxylic moieties exhibit combined hydrogen bond donor and acceptor character, thereby facilitating the self-assembly on solid surfaces. In recent years, another directional interaction, in which halogen atoms behave as electrophilic species, has become a promising driven force in the self-assembly of extended structures.18-27 This interaction has been termed as halogen bonding by analogy to classical hydrogen bonding.28-30 It is well known that covalently-bonded halogen atoms exhibit positive electrostatic potential (ESP), so-called σ-hole, on the extension of the R−X bonds.31-34 Therefore, electronegative atoms or groups prefer to approach the σ-hole, giving rise to strong, specific, and directional halogen bonding. Kahng et al. firstly studied the self-assemblies of two brominated rod-like molecules on Au(111) and Ag(111) via scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, and they revealed that porous 2D supramolecular networks are mediated by Br···Br interactions.35,36 Subsequently, the influence of the position and number of bromine substituents on the formation of highly-ordered self-assembled structures of pyrene derivatives was investigated under ultra-high vacuum conditions.37 It was found that the molecular networks on Au(111) are mainly stabilized by H···Br···Br triangular binding motifs. Very recently, the group of Wang and Wan has demonstrated the formation of halogen bond-driven open porous networks on highly oriented pyrolytic graphite (HOPG) using ethynylpyridine and aryl-halide-based building blocks.38 2


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To further govern 2D molecular structures, the simultaneous use of two different intermolecular forces has become an attractive tool in molecular self-assembly on surfaces. Murakoshi and co-works recently reported the cooperative effect of hydrogen bonding and halogen bonding in the 2D molecular arrangement of two brominated terephthalic acids on HOPG, and they pointed out that the coexistence of halogen substituents and some oxygen-containing functional moieties, such as hydroxyl, carbonyl, and carboxyl groups, in the molecules could produce desirable 2D molecular structures.39 Then, the cooperation and competition of Br···O/Br···S/Br···Br halogen bonds, H···Br/H···O hydrogen bonds, and interchain van der Waals (vdW) interactions in the self-assembled monolayers of π-conjugated thienophenanthrene derivatives were explored via STM experiments and DFT calculations.40-42 Particularly, Kahng et al. have detected rigid triangular structures consisting of simultaneous halogen and hydrogen bonds in the self-assembled supramolecular structures of 1,5- and 2,6-dibromoanthraquinones on Au(111).43,44 They also proposed molecular models that were well reproduced by first-principles calculations. Despite these attempts, the interplay between halogen and hydrogen bonds in the self-assembly processes and its influence on the resulting patterns remain largely unclear. Although the cooperativity and competition of halogen bonding and hydrogen bonding were thoroughly studied in the fields of crystal engineering, molecular recognition, and biological systems,45-55 this topic has received much less attention in surface-based 2D self-assembly. Furthermore, all previous DFT calculations of these two parallel interactions coexisting in molecular self-assembly were performed without considering the substrate effects, and the nature of intermolecular forces and molecule-substrate interactions was not fully understood yet. In this work, the interplay between halogen and hydrogen bonds in the self-assemblies of two functional molecules, 1,5-dibromoanthraquinone (1) and 2,6-dibromoanthraquinone (2), on both Au(111) and Au(110) facets was studied via first-principles DFT calculations. These two compounds contain two Br substituents at different positions and two carbonyl groups, which are capable of forming multiple intermolecular interactions, such as Br···O/Br···Br and H···Br/H···O bonds. Ten binding patterns involving different halogen and hydrogen bonds were proposed and calculated in gas phase as well as on gold surface. With a view to gaining 3



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deeper insight into the nature of molecule-molecular and molecule-substrate interactions, the atoms in molecules (AIM),56 noncovalent interaction index (NCI),57 and electron density difference (EDD) methods were used. This work will be of vital importance in 2D self-assembly of functional molecules on surfaces and opens up opportunities for the design of target building blocks.

Computational methodology All periodic calculations were performed by means of the Vienna Ab initio Simulation Package (VASP, version 5.3.5)58-61 using plane-wave DFT (PW-DFT) within the projector augmented wave (PAW) potentials method.62 The generalized gradient approximation (GGA) with the parametrization of Perdew-Burke-Ernzerhof (PBE) was used to describe the interaction energy of exchange-correlation.63 The DFT-D3 method,64 developed by the group of Grimme, was applied to correct the dispersion calculations, and the Becke-Johnson damping65 with the most recent damping function66 was employed to avoid the vanishing forces at short distances. The electron wave functions in the regions between the cores were expanded in a plane-wave-basis setup to a cutoff energy of 400 eV. The optimization was performed at a 2 2 1 k-point mesh for Brillouin zone integration, which was generated by Monkhorst-Pack method with Gamma centered.67 The conjugate gradient algorithm was chosen to determine the movement of ions, and the ionic relaxations were performed until the Hellmann-Feynman forces acting on each ion were below 0.05 eV/Å. All structures were relaxed until the energy changed by less than 1 10-5 eV. To unravel the nature of molecule-molecule and molecule-substrate interactions, a series of binding patterns showing different halogen and hydrogen bonds were calculated both in vacuum and on the noble metal surface. A slab model containing three atomic layers was utilized for Au(110), while a simple two-layer slab model was employed for Au(111) due to the large computational cost. In both models the topmost layer was free to relax during the optimization, while the lower layers were kept frozen at the optimized bulk positions. To avoid the effect of neighboring dimers generated due to the periodical condition, the sufficient slab was used a p(4 × 4) supercell, resulting in 96 and 128 Au atoms for Au(110) and Au(111), 4


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respectively. Moreover, a vacuum of 18 Å was introduced to c orientation for creating a more realistic slab structure. A cubic box of 35 Å × 35 Å × 35 Å was used to optimize isolated molecules and the dimers in gas phase, which were placed at the center of the box. The lattice parameters for modeling the isolated molecules, slab, and self-assembly systems are listed in Table S1. The adsorption energy (Eads) was evaluated as Eads = Esystem – EM – Esurface

(1)

where Esystem is the energy of the optimized substrate-adsorbate system; EM and Esurface are the total electronic energies of the molecules and the gold surface, respectively, after separate geometry optimizations. We also computed the interaction energy (Eint) and cohesion energy (Ecohe) to assess substrate-molecule and molecule-molecule interactions, which were defined as Eint = Esystem – Edimer – Esurface*

(2)

Ecohe = Edimer – 2EM

(3)

where Edimer and Esurface* are the energies of the dimer and clean gold surface, respectively, which kept in the same structure as that in the optimized self-assembly systems.

RESULTS AND DISCUSSION The ESP results of the two molecules under study. The three-dimensional real space function, electrostatic potential V(r),68 measures the electrostatic interaction between a unit point charge placed at r and the position of interest (expect for the positions RA of the nuclei) as follows: VESP ( r ) = Vnuc ( r ) + Vele ( r ) = ∑ A

ZA ρ ( r ') −∫ dr ' r − RA r−r'

(4)

The sign of V(r) indicates whether the position of interest is dominated by nuclear (positive) or electronic (negative) charges. In general, V(r) is performed on the ρ(r) = 0.001 a.u. isosurface as molecular vdW surface, because this definition reflects specific electron structure features of a molecule.69 Based on the analysis of ESP on vdW surface, the strength and orientation of noncovalent interactions can be predicted and explained by examining the positions and magnitude of maxima and minima on the surface. 5



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The ESP surfaces of the two compounds 1 and 2, together with the most positive surface ESP (Vs,max) for the Br and H atoms as well as the most negative ESP (Vs,min) for the O atom, are shown in Figure 1. Owing to the negative ESP values, the outer regions of the O atoms are dominated by electronic charges. Furthermore, the O atom in 1 possesses a slightly more negative Vs,max than that in 2 (-30.77 kcal/mol vs -27.00 kcal/mol), which can be ascribed to the conjugation between the π electrons of the carbonyl group and the lone pair of the neighboring Br atom in 1. In contrast, the Br and H atoms behave as electrophilic centers, because of the positive ESP values. As a result of the effect of the p-π conjugation, the Br atom in 1 has a smaller Vs,max than that in 2 (13.81 kcal/mol vs 18.90 kcal/mol). Additionally, the largest Vs,max is predicted for the H atom instead of the Br atom, thus implying the favorable hydrogen-bond-donor positions. Here it is worth noting that the Br atoms also have slightly negative ESP perpendicular to the C−Br bonds, which indicates that these atoms can also act as hydrogen bond acceptors. Hence, during the process of self-assembly of the two compounds on gold surface, halogen bonds and hydrogen bonds can be simultaneously formed between the molecules. Figure 1 Monomolecular Adsorption on Gold Surface. To discuss the probable adsorption positions for isolated molecules on Au(111) facet, the sites on the atop of gold atoms, on the center of the unit cell of facet, and on the bridge site of adjacent gold atoms were defined as the top, hollow, and bridge sites, respectively (see Figure S1). Due to the geometric characteristics of the anthraquinones, a Br atom and an O atom in 1 and 2 can be simultaneously put on these sites. For Au(110) facet, nonetheless, two different bridge sites, i.e., the bridge sites across or adjacent to the neighbor Au atoms, were taken into account, and two Br or O atoms in 1 and 2 can concurrently be placed on these sites. The optimized structures for various adsorption sites on two metal facets are displayed in Figures S2 and S3, and the corresponding geometric and energetic data are presented in Table S2. On Au(111) facet, the stability for the adsorption of 1 on the top site is slightly superior to the hollow and bridge sites, while the total electronic energies for the adsorption of 2 on the three sites are quite similar to each other. This can be explained by the fact that although two Br and O atoms in the molecules occupy the hollow or bridge site, other two Br and O atoms 6


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seem to reside on the top of the Au atoms. On Au(110) cleavage plane, the molecule 1 prefers to be adsorbed on the top site, while the most stable adoption site for 2 is the O hollow site. Notably, the computed adsorptions energies at different sites vary significantly so that the molecules have the preference to be located at certain specific sites on the sparse packing facet. Compared with the systems of Au(111), the adsorption energies for the most stable structures of the Au(110) systems are calculated to be larger in absolute value, in line with the shorter distances between the adsorbents and the Au(110) facet. Binding geometries, Energies and Topologies for Self-Assembly Systems. Based on the ESP results and the STM experiments,43,44 we proposed ten molecular models (1a-1e and 2a-2e) for the dimers of 1 and 2 (cf. Figure 2). These dimer structures were firstly optimized in gas phase. To investigate the interplay between hydrogen and halogen bonds in detail, the AIM theory of Bader was employed herein. In this topology analysis, the points at where gradient norm of function value is zero (except at infinity) are called as critical points (CPs), which can be classified into four types: nuclear critical point (NCP), bond critical point (BCP), ring critical point (RCP), and cage critical point (CCP), according to how many eigenvalues of Hessian matrix of function are negative. In the molecular graphs, the NCPs, in which three eigenvalues of Hessian matrix of function are negative, namely the local maximum, were displaced by the specific atoms due to the almost equal positions. The BCPs, the second-order saddle points, in which two eigenvalues of Hessian matrix of function are negative, are labeled as red dots and appear between attractive atom pairs in the graph. The RCPs (blue dots), which are usually located at the center of ring system and display steric effect, only have one negative eigenvalue of Hessian matrix of function. The CCPs, nevertheless, were not detected in present systems due to the planarity of the dimers. Once the CPs are searched, the so-called bond path can be generated to link the BCP and associated two local maxima of density. The cohesive energies, geometric parameters, and electron densities (ρ) at the BCPs for the dimers are listed in Table 1, and other topological properties at the BCPs are given in Table S3. The cohesive energies for the dimers of 1 are predicted to range from -84.5 eV to -217.3 eV, and the experimental geometry 1a appears to be the lowest energy structure. In this 7



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configuration, three hydrogen bond CPs (HBCPs) and one halogen bond CP (XBCP) were identified, as shown in Figure 2. A Br atom in one molecule simultaneously establishes a Br···Br bond and a Br···H bond with the other, leading to a rigid triangular structure. This Br···Br interaction can be viewed as the attractive electrophile-nucleophile pairing type II contact, that is, the positive ESP of a Br atom points towards the negative part of the other Br atom.30, 70-71 An O atom also forms a similar triangular structure with two O···Br bonds. These triangular structures involving different halogen and hydrogen bonds provide an efficient way to form supramolecular structures. In other four configurations, only hydrogen bonds or halogen bonds are found by the topological analysis. Albeit five hydrogen bonds are detected in 1b, the cohesive energy is computed to be much less negative than that for 1a, which signifies the complementary nature of halogen and hydrogen bonds in 2D self-assemblies. Table 1 Figure 2 Here it should be pointed out that two BCPs between the Br and O atoms and two RCPs at the center of the five-membered rings were also identified for every molecule 1 in the dimers, thus suggesting intramolecular Br···O interactions. Particularly, ρ at the BCPs for these intramolecular bonds is calculated greater than that for intermolecular hydrogen and halogen bonds. Therefore, intramolecular Br···O interactions are much stronger in strength and should play an important role in determining the conformations of 1 on surfaces, which has been totally ignored in previous studies.43 For the dimers of 2, the most stable configuration 2a (the experimental geometry)44 is stabilized by four triangular structures that consist of Br···O and Br···H/O···H bonds (see Figure 2). Each two triangles share a Br···O bond, resulting in an acute angle around the Br and O atoms. Similarly, the hydrogen-bonded structures 2d (another experimental structure)43 and 2e are predicted to be energetically less favorable, further implying the cooperative effect between hydrogen and halogen bonds. The potential energy density (V) at BCP has been shown to be highly correlated with bond energies:72 1 EB = V 2

(5)

8


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The bond energy is an intuitive tool for assessing the strength of every single interaction by extracted it from the whole cohesive energy. In the most stable configuration 1a, the C−H···O interaction with HBCP2 plays a dominant role in stabilizing this structure, while the same type of hydrogen bond with HBCP1 is much weaker, consistent with the longer intermolecular distance and the deviation from linearity. Although five HBCPs are searched for 1b, these hydrogen bonds are very weak in strength. In the halogen-bonded structure 1c, the C−Br···O bond is estimated to be much stronger than the C−Br···Br bond. The lowest energy structure 2a is mainly stabilized by two C−H···O hydrogen bonds, while in 2b and 2c the cohesive energies are mainly contributed by C−Br···O halogen bonds. Subsequently, the optimized configurations of the dimers were put on the gold surface, and one of the molecules was located at the adsorption sites as those in monomolecular adsorption. The relaxed optimizations were then performed on these systems. The most stable configurations for the dimers on both facets are graphically depicted in Figure 3, and other optimized structures are shown in Figures S4 and S5. The energetic data for the most stable configurations are listed in Table 2, and the corresponding data for other optimized structures are given in Table S4. Note that all triangular structures formed by different halogen and hydrogen bonds are preserved on gold surface.

Figure 3 Table 2 In the lowest energy configurations for the dimers of 1 on Au(111) facet, one molecule is always adsorbed on the top site, similar to that in monomolecular adsorption. However, the most stable sites for the dimers of 2 on Au(111) are changed depending upon different binding patterns. From Table 2, it can be seen that for all the Au(111) systems the adsorption energies (Eads) are calculated to be more negative than the interaction energies (Eint), which indicates that the distortion of the adsorbates and the substrate in the self-assembly process reduces the attraction between the molecules and the surface. In addition, the cohesion energies (Ecohe) for the dimers on Au(111) are almost equal to or even more negative than those in the gas phase. For example, a more negative Ecohe is predicted for the most stable configuration of 1b on Au(111) compared with that in the gas phase (-234.5 meV vs -169.8 meV), thereby suggesting much stronger intermolecular interactions on Au(111) facet. 9



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In comparison, only two dimer structures extracted from the experimental STM images were selected to investigate on Au(110).43 Once the most stable sites were determined, other binding patterns were optimized on these positions. The most stable sites for the dimers of 1 and 2 are the top sites of the Br atoms and the hollow sites of the O atoms, respectively. Similar to that in monomolecular adsorption, the total electronic energies vary remarkably at different sites on Au(110). Surprisingly, for most of the Au(110) systems Eads is calculated to be less negative than Eint, which means that the deformation of the adsorbates and the adsorbents enhances the interactions between the molecules and the surface. In addition, Ecohe for the dimers on Au(110) is computed to be considerably smaller in absolute value than that in gas phase, thus suggesting much weaker intermolecular interactions on Au(110) facet. Clearly, the deformation of the adsorbents and the deviation from the planarity of the dimers lead to longer intermolecular distances or less linear interactions on Au(110), and moreover the adsorption behaviors (distances, angles and strengths) of the two molecules in the dimers are very different on the less densely packing facet. Albeit the interactions between the molecules and Au(110) are predicted to be stronger than those in the Au(111) systems, the self-assembly process seems to be more feasible on the Au(111) facet, on account of stronger intermolecular interactions between the adsorbates. The 2D configurations can be well formed on Au(111), because the more densely packing substrate is capable of adsorbing molecules with similar strength on different adsorption sites.

NCI Analysis. The noncovalent interaction (NCI) index, recently developed by the Yang’s group, has been employed as a topological method for the visualization of noncovalent interactions. Based on the electron density and its derivatives, the reduced density gradient (s or RDG) was determined as follows:

s=

1 2(3π )

2 1/3

∇ρ

(6)

ρ 4/3

It is able to identify noncovalent interactions with spikes in the low density region of the plot of s(ρ). To distinguish the interaction types, another density derivative, i.e. the sign of the Laplacian of the density (∇2ρ), was also introduced.73 However, this derivative cannot be utilized to discriminate noncovalent interactions directly, because the Laplacian is dominated by the principle axis of vitiation and appears to be positive for all closed-shell interactions. 10


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Usually, the Laplacian is decomposed into three contributions along the maximal variation axes, that is, ∇2ρ = λ1 + λ2 + λ3, (λ1 < λ2 < λ3). Within the NCI approach, the perpendicular plan, the sign of second eigenvalue λ2, is adopted to detach the attraction from repulsion interaction. Modified by diagraming sign(λ2)ρ as the abscissa, the interactions can be categorized into three main types: the spike lying at negative value corresponds to strong attractive interaction, nearly zero value to vdW interaction, and positive value to steric repulsion. Additionally, the 2D data can be inputted to construct 3D plots constituted of s isosurfaces, and a RGB coloring scheme thus can be applied to rank interactions, where blue for stabilizing interactions, green for delocalized weak interactions, and red for destabilizing interactions. For large self-assembly systems, however, the reproduction of the electron density by DFT is very expensive. Therefore, promolecular density has been used in the NCI scheme, which is obtained by superimposing spherical neutral atomic densities centered at the atomic position

ρ pro = ∑ i ρ iat

(7)

where ρiat is pre-fitted spherically averaged electron density of atom i. Promolecular density obtained from simple exponential atomic pieces is able to predict low-density, low-reduced-gradient regions similar to density-functional results. The free atomic densities used in these calculations consist of one Slater-type function for each electron shell, fit to closely reproduce spherically averaged, density-functional atomic densities. The 2D scatter plots and 3D color-dyed isosurface graphs for the experimental pattern (1a and 2a) on Au(111) and Au(110) are depicted in the Figures 4 and S6. In the system of

1a-Au(111), the blue isosurface between the Br and O atoms indicates the intramolecular Br···O interaction, consistent with the identification of a BCP between the two atoms within the AIM analysis. In addition, the red region in close proximity to the Br···O isosurface implies the conformation locking role of such interaction, in line with the existence of a RCP in the AIM graph. Not expectedly, the first negative spike (approximately -0.02 a.u.) corresponds to this blue Br···O isosurface, thereby suggesting much stronger intramolecular Br···O bonds. The second spike corresponds to the light blue isosurfaces between the Br atoms and the surface Au atoms (top site), which indicates covalent dative interactions 11



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between these atoms. The neighboring O atoms also establish dative bonds with the surface Au atoms. The next continuous spikes, spanning from -0.015 a.u. to -0.005 a.u., correspond to the green isosurfaces between the molecules as well as between the adsorbates and the substrate. Consequently, intermolecular Br···Br, Br···H, and O···H bonds are weak electrostatic interactions, and the interactions between the benzene rings and the surface are mainly dispersive. The brown isosurfaces between the molecules and the metal surface are indicative of the long-range electrostatic repulsion.74

Figure 4 Similarly, in the 2a-Au(111) system, the interactions between the benzene rings and the substrate are primarily dispersive, and the Br and O atoms forms covalent dative interactions with the surface Au atoms. The most negative spike, nonetheless, corresponds to the two intermolecular O···H bonds that exhibit shorter O···H distances and a better linearity than those in 1a-Au(111). The next negative spike indicates the Br···Au interactions, likely because the Br atoms are located beyond the top of the surface Au atoms. As shown in Figure S6, intramolecular Br···O interactions also take place in the system of

1a-Au(110). However, the molecule-substrate interactions in this system show some discrete characteristics: (1) the isosurfaces between the molecules and the surface are considerably smaller in volume, due to the much less densely packed Au(110); (2) the interactions of the atoms in 1 with the Au atoms become much stronger, as a result of the shorter interatomic distances. The most negative spike lying at approximately -0.04 a.u. corresponds to the round blue isosurface between the Br and Au atoms at the top site, concordant with the much shorter Br···Au distance (about 2.8 Å). The next few negative spikes in blue bracket indicate strong C···Au and O···Au interactions, and the less negative spikes in green bracket correspond to weak intermolecular Br···Br, Br···H, and O···H bonds. Overall, covalent dative interactions between the Br and O atoms in the molecules and the surface Au atoms play a crucial role in determining the binding sites of the molecules on the gold surface. Albeit the molecule-substrate interactions in the self-assembly systems of Au(110) are much stronger than those in the Au(111) systems, the close-packed plane could provide a smooth self-assembling environment due to the continuous isosurfaces between the molecules and the Au(111) surface. Intermolecular halogen and hydrogen bonds with 12


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different strength belong to weak electrostatic interactions.

EDD Analysis. To understand the changes of electron density distribution between the molecules as well as between the adsorbates and the substrate during the process of self-assembly, we mapped the EDD plots for two self-assembly patterns (1a and 2a) on the gold facets. The EDD was defined as

∆ρ (r ) = ρ (r ) − ∑ ρi (r )

(8)

i

where ρ is the total density of the whole system and ρi is the electronic density of each molecule and the slab within the geometry of the system. The red and blue isosurfaces represent the regions in which electron density is increased and decreased after the molecules assembled on the surfaces. From Figure 5, it is seen that in the 1a-Au(111) system, electron density is shifted from the backside of O in one molecule toward the two H atoms in the other, thus implying the triangular structure formed by two C–H···O hydrogen bonds. The C–H···Br bond is indicated by the concentrated region of density around the Br atom toward the H atom. The formation of the Br···Br bond does not perturb the electron density distribution remarkably, because only a slightly increased region occurs around the Br atom. In addition, concentrated regions are observed on the top of some surface Au atoms right underneath the C/H atoms in the benzene rings, which suggests the charge transfer from the substrate to the molecules. However, the charge tends to be shifted from the Br and O atoms to the surface Au atoms, due to the depleted electron density of these Au atoms. Particularly, a region of increased electron density is also found on the top site of the surface Au atom below the Br atom, as a consequence of the polarization effect.75 The 2a-Au(111) system possesses similar EDD characteristics to those of 1a-Au(111), and evident charge transfer take place in the region along the donor or acceptor for both hydrogen and halogen bonds.

Figure 5 In the self-assembly system of Au(110), surprisingly, the changes of electron density distribution are not observed for intermolecular H···Br and Br···Br interactions (cf. Figure S7), which can be attributed to the distorted structure arising from the very strong Br···Au interactions. Furthermore, the electron density is shifted markedly between the surface Au

13



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atoms and the atoms in the molecules, in harmony with the much stronger adsorbate-substrate interactions as demonstrated above. Notably, the polarization of electron density is detected not only between the Br/O atoms and the surface Au atoms but also between the C/H atoms and the Au atoms.

Density of States (DOS). In solid-state and condensed matter physics, the density of states (DOS) of a system describes the number of states per interval of energy at each energy level available to be occupied. In this work, DOS of isolated molecules, monomolecular adsorption, and self-assembly process were calculated and compared to analyze the electronic structure, intermolecular interactions, and substrate effects. The calculated Fermi energy was set to zero (eV) for all DOS curves. The computed DOS and projected DOS (the contributions of atomic orbitals to the DOS of the corresponding atoms) for isolated molecules 1 and 2 are depicted in Figure S8. In the case of 1, the band gap is about 1.0 eV. The top of the valence band has two overlapped bands: the first band (~-0.4 eV to ~-1.7 eV) is mostly populated by oxygen px orbital followed by bromine px with some carbon px and py orbitals; the second band (~-1.2 eV to ~-2.0 eV) is mainly contributed by the pz orbitals of bromine and carbon with minor contributions from oxygen pz orbital. The bottom of the conduction band is dominated by the pz orbitals of carbon and oxygen. Particularly, in the energy level (~-0.4 to ~-1.7 eV) at the top of valence band, two shoulder peaks, assigning to the O px and Br px orbitals, are depicted as a significant orbital hybridization, which should be aroused from two strong intramolecular Br···O interactions in this molecule. However, this hybridization is not detected in the DOS curves of 2 that exhibit the band gap slightly broader than 1. The top of the valence band of 2 is mainly occupied by oxygen px orbital and the pz orbitals of Br and C, and some contributions from other carbon orbitals are also seen in this energy span. The contributions for the bottom of the conduction band of 2 hold a remarkable similarity to those for 1. Density of states for the monolayers of 1 and 2 on the two facets are plotted in Figures S9 and S10. When the molecule 1 adsorbs on the Au(111) surface, the position of peaks does not change remarkably, but the relative magnitude (peak height/area under curve) of some orbitals appears to be different from that in isolated 1. Above the Fermi energy, some additional states with partial occupancy (< 1e-) are observed from -0.53 eV to 0.52 eV, due to the broadenings 14


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of the pz orbitals of bromine and carbon. These states could be metal-induced-gap-states, which are absent in the DOS of isolated 1. In addition, the band broadenings also change the original states. For example, the second band of the top of the valence band, which is populated by the pz orbitals of bromine, carbon and oxygen, merges into the neighboring peaks. Furthermore, the carbon and oxygen pz orbitals also merge into the downward energy band, while the bromine pz orbital shows an upward shift to the original first band of the top of the valence band. For the 1-Au(110) system, the resulting additional states and band broadenings become more pronounced so that the orbital hybridizations between the molecule and the metal surface are enhanced. All the peaks in the Au(110) system show the downward shifts, on account of the increased Fermi energy after adsorption. Particularly, in the top of the valence band of 1-Au(110) the oxygen py orbital contributes significantly, whereas this characteristic peak is not obvious in 1-Au(111). Owing to the strong band spread aroused from the substrate effect, the third band before the top of the valence band of isolated 1 tends to be diminished in both 1-Au(111) and 1-Au(110). In addition, the bottom of the conduction band and the following energy level alignments in the Au(111) system remain almost unaltered, whereas the third band strongly hybridizes with the fourth band in the Au(110) system due to the upgraded carbon orbitals. When 2 adsorbs on the Au(111) and Au(110) facets, similar band spread and additional bands are also disclosed around the top of valence band and the bottom of the conduction band. All in all, the band broadenings and the additional states in the energy level alignments can be the result of the orbital hybridizations between the C, Br and O atoms in the molecules and different metal substrates in the adsorption processes. We also calculated the DOS of the experimental pattern 1a in the vacuum as well as on Au(111) and Au(110). Due to the orbital hybridization between the two molecules, the band gap of the dimer narrows more than 0.3 eV, as shown in Figure 6. When the self-assembly process occurs on the Au(111) surface, the height and broadening for the carbon orbitals in the DOS curves are declined to a greater degree with respect to the bromine and oxygen contributions, which implies that more carbon orbitals hybridize with the metal orbitals. This agrees well with the large volume of NCI isosurfaces between the metal surface and benzene 15



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rings. Similar to that in monomolecular adsorption, some additional metal-induced-gap-states are also observed around the Fermi energy.76-78 Notably, the DOS curves of the two molecules (1 and 1’) in the dimer are somewhat similar to each other both in the vacuum and on the Au(111) surface.

Figure 6 The downward shift is also found for all the energy level alignments in the 1a-Au(110) system (see Figure S11). However, in the energy level spanning from -2 eV to -4 eV, the DOS curves of 1 and 1’ show notable dissimilarities. Although the DOS of 1 (red) holds a significant resemblance with that in the Au(111) system, an additional band contributed mainly by carbon orbitals is detected for 1’ (blue) in the energy level from -2 eV to -3 eV, and a trivial band at the energy level of -4 eV appears to be vanished in the DOS of 1’. Furthermore, at the bottom of the conduction band and the next two bands, the DOS curve of

1’ spreads to a greater extent with respect to 1, as a result of the stronger orbital hybridizations aroused from substrate effect. These alterations of DOS alignments illustrate that the electronic structures are quite different for each molecule self-assembled on the less densely packing due to the dissimilar adsorption sites. The more densely packing surface should provide a more parallel adsorption environment for the synthon, which may be suitable for the formation of 2D supramolecular structures.

Simulated scanning tunneling microscopy (STM) images. To further investigate the whole process of self-assembly, we optimized the experimental patterns in the vacuum using the lattice parameters found by Kahng et al. to reproduce the real configurations.43 Then, the simulated STM images were obtained using the Tersoff-Hamann approximation.79-80 Under this approximation the tunneling current is supposed to be proportional to the local density of states (LDOS) at the center of the STM tip. During the experiments, the constant current STM images just involve the surface states that locate around the tip (< 2 Å) as it scans the surface. However, the simulated current STM images include the charge densities of the whole system as the partial charge was computed in a given widow energy. Accordingly, it is not logical to compare the experimental results with the simulated images without any modification. To achieve a rational comparison, the STM images were obtained at a height above the surface of 16


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approximately 5 Å. Additionally, the self-assembly pattern images were simulated under the experimental conditions, i.e., the negative (-1.5 V and -1.8 V) and positive (+0.5 V) bias. The positive value implies current flow into unoccupied surface states (electrons move from tip to surface), while the negative value indicates current flow into occupied surface states (electrons move from surface to tip).

Figure 7 As shown in Figures 7 and S12, a square pattern was obtained for 1, while a V-type pattern and a chevron structure were obtained for 2, in good agreement with the experimental STM images.43,44 For the self-assembly of 1, the Br···Br interactions play a crucial role in the formation of the square pattern. In the V-type self-assembly pattern of 2, multiple hydrogen bonds are formed to stabilize this configuration, and the Br···O halogen bonds are of vital importance in the formation of the chevron structure. Current simulated STM images elucidate that a theoretical self-assembly configuration has an electronic structure compatible with experimental appearance, and they can also aid the identification for experimental images. Specifically, during the scans of metal tip, the molecular morphologies would suffer non-negligible perturbations due to the field of tip.81 However, the STM images of self-assembly process can be qualitatively predicted here without the external destabilization.

Conclusions In the present work, the self-assemblies of two brominated anthraquione molecules on gold surface were studied using first-principles DFT calculations. Many theoretical frameworks, such as AIM, NCI, EDD, DOS, and stimulated STM image, were employed to provide a fundamental understanding of the interplay between halogen and hydrogen bonds in 2D molecular self-assembly. Different triangular binding motifs consisting of Br···Br/Br···O bonds and H···Br/H···O bonds were found both in gas phase and on gold surface. These triangular structures were also frequently observed in the crystals of small molecular systems and protein-ligand complexes. Therefore, these specific motifs provide an effective way to construct robust supramolecular structures in different dimensions. Particularly, halogen bonds and hydrogen bonds exhibit the complementary character in 2D self-assemblies, as revealed by our calculations. 17



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The adsorption behaviors of the molecules, such as distances, angles and strengths, on less densely packing facet are quite different from each other. In contrast, the more densely surface provides a more parallel adsorption environment for the adsorbates, which may be suitable for the formation of 2D supramolecular self-assemblies. We hope that the results reported in this work will assist in the engineering of the self-assemblies with simultaneous halogen and hydrogen bonds on different densely packing metal surfaces.

ASSOCIATED CONSTENT Supporting Information The Supporting Information is available free of charge on the ACS Publications website at DOI:. Calculated results of monomolecular adsorptions on gold surface and the NCI, EDD, DOS, and SIM diagrams of the dimers on Au(110).

AUTHOR INFORMATION Corresponding Author *(Y.L.) E-mail: [email protected].

Author Contributions #

Y.L. and S.Z. contributed equally to this article.

Notes The authors declare no competing financial interest.

ACKNOWLEDGEMENT This work was supported by the National Natural Science Foundation of China (21473054 and 21776069) and the National Basic Research Program of China (2015CB251401).

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23



Page 24 of 33

Table 1. Geometric, Energetic and AIM Data for All the Bonding Patterns under Studya 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

1a

Ecohe -210.5

1b

-169.8

1c

-164.0

1d

-85.6

1e

-83.5

2a

-221.2

2b

-195.8

2c

-157.5

2d

-152.2

2e

-82.9

a

CP HBCP 1 HBCP 2 HBCP 3 XBCP 1 XBCP 2 RCP HBCP 1 HBCP 2 OBCP HBCP 3 HBCP 4 HBCP 5 XBCP 1 XBCP 2 XBCP 3 HBCP 1 HBCP 2 XBCP 1 XBCP 2 HBCP 1 XBCP 1 HBCP 2 HBCP 3 XBCP 2 HBCP 4 XBCP 1 HBCP 1 HBCP 2 XBCP 2 HBCP 1 HBCP 2 XBCP 1 HBCP 1 HBCP 2 HBCP 1 HBCP 2

Interaction C-H⋅⋅⋅O C-H⋅⋅⋅O C-H⋅⋅⋅Br C-Br⋅⋅⋅Br C-Br⋅⋅⋅O C-Br⋅⋅⋅O-C C-H⋅⋅⋅Br C-H⋅⋅⋅O C-O⋅⋅⋅O C-H⋅⋅⋅O C-H⋅⋅⋅Br C-H⋅⋅⋅Br C-Br⋅⋅⋅O C-Br⋅⋅⋅Br C-Br⋅⋅⋅O C-H⋅⋅⋅Br C-H⋅⋅⋅O C-Br⋅⋅⋅O C-Br⋅⋅⋅O C-H⋅⋅⋅Br C-Br⋅⋅⋅O C-H⋅⋅⋅O C-H⋅⋅⋅O C-Br⋅⋅⋅O C-H⋅⋅⋅Br C-Br⋅⋅⋅O C-H⋅⋅⋅Br C-H⋅⋅⋅Br C-Br⋅⋅⋅O C-H⋅⋅⋅Br C-H⋅⋅⋅Br C-Br⋅⋅⋅O C-H⋅⋅⋅O C-H⋅⋅⋅Br C-H⋅⋅⋅Br C-H⋅⋅⋅Br

d 2.904 2.339 2.703 3.523 2.921

angle 112.0 135.1 154.0 171.8 71.5

3.603 2.877 3.545 2.834 3.636 3.461 3.051 4.008 3.026 2.516 3.090 3.531 3.583 3.218 3.554 2.247 2.240 3.543 3.189 3.055 2.843 2.813 2.995 3.435 2.713 2.937 2.714 2.891 3.090 2.635

131.4 176.3 141.6 173.7 123.8 132.1 166.1 121.2 166.8 154.1 153.8 148.4 147.3 172.1 85.1 156.1 155.9 85.2 171.7 154.7 165.5 164.0 156.0 176.7 164.2 170.8 172.2 137.3 172.8 151.9

102ρ 0.414 1.105 1.077 0.956 1.773 1.354 0.165 0.271 0.223 0.302 0.194 0.218 0.987 0.432 1.036 1.336 0.184 0.382 0.425 0.376 0.533 1.248 1.266 0.545 0.399 1.107 0.846 0.898 1.235 0.264 1.051 1.331 0.458 0.846 0.544 1.314

EB -35.4 -114.4 -85.4 -64.9 -176.6 -10.1 -22.9 -17.8 -26.0 -11.5 -13.9 -95.1 -28.0 -100.5 -117.6 -13.3 -30.2 -34.0 -23.8 -40.1 -125.2 -127.2 -41.2 -25.5 -102.3 -60.9 -65.5 -117.2 -14.8 -80.1 -130.5 -39.5 -60.2 -35.0 -102.3

Energies are given in meV, distances in angstroms, angles in degrees, and electron density in a.u. The CPs are labeled in Figure 2.

24


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Table 2. The adsorption energy, interaction energy, and the dimers self-assembled on the surfaces.a Eads Eint Ecohe Au(111)-1 111-1a-top -3999.7 -3790.6 -211.0 111-1b-top -4021.9 -3795.0 -234.5 111-1c-top -4009.1 -3858.9 -157.5 111-1d-top -3868.9 -3765.1 -107.6 -3937.3 -3830.3 -110.2 111-1e-top Au(110)-1 110-1a-top-Br -4373.3 -4404.3 -52.6 -4289.9 -4253.8 -83.0 110-1b-top-Br 110-1c-top-Br -4502.1 -4561.7 0.9 110-1d-top-Br -4143.6 -4286.9 78.8 110-1e-top-Br -4364.1 -4496.2 60.4

cohesion energy for the most stable configurations of

Au(111)-2 111-2a-top 111-2b-bridge 111-2c-top 111-2d-bridge 111-2e-hollow Au(110)-2 110-2a-hollow-O 110-2b-hollow-O 110-2c-hollow-O 110-2d-hollow-O 110-2e-hollow-O

a

The energetic data are given in meV.

25


Eads

Eint

Ecohe

-3919.4 -3909.3 -3837.1 -3854.1 -3809.5

-3712.0 -3700.2 -3669.8 -3704.0 -3727.3

-209.0 -211.3 -165.7 -152.3 -84.4

-4131.1 -4190.9 -4277.9 -4207.0 -4146.0

-4026.4 -4110.8 -4343.7 -4241.0 -4272.4

-139.6 -135.7 1.4 -33.7 67.0


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Figure 1. The ESP on the vdW surface (isosurface = 0.001 au) of 1 and 2, together with Vs,max for the Br and H atoms as well as Vs,min for the O atoms. The filled color varies from red (negative) to yellow (neutral) and to blue (positive).

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Figure 2. The molecular graphs for different bonding patterns of the dimers. The intermolecular halogen bond paths are shown in red, the intramolecular halogen bond paths in purple, and the hydrogen bond paths in blue. The red and blue dots represent the BCPs and RCPs, respectively. 27



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Figure 3. The most stable configurations of the dimers self-assembled on Au(111) and Au(110). Halogen bonds are shown in red, hydrogen bonds in blue, and the molecule-substrate interactions in purple. Only the topmost layers are displayed in the aerial views for simplicity.

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Figure 4. NCI dyed-isosurfaces and scatter plots of spro versus ρpro(r) multiplied by sign(λ2(r)) by utilizing promolecular density for two self-assembly systems.

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Figure 5. Difference of electron density for the experimental patterns on Au(111). The surfaces correspond to density differences of ±0.001au (opaque) and ±0.0004 au (transparent). The red and blue areas indicate increased and reduced electron densities in the self-assembly system.

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Figure 6. Density of states (DOS) for the self-assembly of 1 in the vacuum (upper) as well as on Au(111) (lower). 31



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Figure 7. Simulated STM images for three experimental self-assembly systems 1a, and 2a. 32


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TOC Graphic

33


Interplay between Halogen and Hydrogen Bonds in 2D Self-Assembly

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