One-dimensional structures of three quinone molecules on Au(111)
Min Hui Chang a, Won Jun Jang b, Min Wook Lee a, Seungwu Han c, Se-Jong Kahng a,*
a Department of Physics, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea b Samsung Advanced Institute of Technology, Samsung Electronics, Suwon, Gyeonggi-do 16678, South Korea c Department of Materials Science and Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
Quinone molecules form self-assembled structures in biological systems playing a key role in charge transport. Here, we report on the self-assembled chain structures of three quinone molecules, anthraquinone (AQ), naphthacenequinone (NQ), and pentacenequinone (PQ) on Au(111) studied using scanning tunneling micro-scopy. They all formed one-dimensional chain structures confined to herringbone structures of Au(111) at the low-coverage limit. The observed structures were explained with O•••H hydrogen bonds, as revealed by our density functional theory calculations.
1. Introduction
Intramolecular charge distributions within neutral molecules are major driving forces for their intermolecular interactions. A part of positive electrostatic potential attracts that of negative counterpart of a neighboring molecule to form an intermolecular bond such as hydrogen (H) bond, dipole-dipole interaction, van der Waals interaction, and halogen bond [1–13]. With these, molecules form various self-assembled structures, providing a key mechanism to construct large-scale biological systems such as membranes, DNAs, and protein folding enzymes. The self-assembled structures are also useful in nano-technology, for example, well-ordered porous networks can be con-structed for molecular recognition and storage. On crystal surfaces, molecules form various two-dimensional structures such as rectangular, honeycomb, windmill, and lamella structures as revealed by scanning tunneling microscopy (STM) studies [14–34]. They also form one-dimensional (1D) chain structures, with rod-like molecules such as quinones [2,3,27,35]. Quinones form self-assembled structures in bio-logical systems, to serve as acceptors in charge transport [36–40]. We have previously studied self-assembled structures of anthraquinone (AQ) and dichloroanthraquinone on Au(111) in focus of two-dimensional structures made of hydrogen bonds and van der Waals interactions [29,32]. However, studies on the 1D self-assembled struc-tures of quinone molecules are not available in literatures.
Here, we report on 1D chain structures of three quinone molecules, anthraquinone, naphthacenequinone (NQ), and pentacenequinone (PQ)
on Au(111) studied using STM. We observed chain structures for all the three molecules that could be explained with O•••H hydrogen bonds as reproduced by our density functional theory (DFT) calculations. Different from the other two molecules, NQ forms straight chains because of its asymmetric molecular structure.
2. Experimental methods
The experiments were performed using a home-built STM housed in an ultrahigh vacuum (UHV) chamber with a base pressure below 1 ×10− 10 torr. The Au(111) surface was prepared from a thin film (200 nm thick) of Au on mica that was exposed to several cycles of Ne-ion sput-tering and annealing at 800 K over the course of 1 hr. The surface cleanliness of the Au(111) was checked by observing typical herring-bone structures on the terraces in the STM images. Commercially available AQ, NQ, and PQ molecules (Tokyo Chemical Industry, Japan) were thermally evaporated onto the surface at submonolayer coverage from an alumina-coated crucible, keeping the substrate temperature at 150 K. The molecular sources were outgassed for several hours prior to deposition. The prepared sample was transferred to the STM, and measurement was performed at 80 K using Pt-Rh alloy tip.
3. Theoretical calculations
Density functional theory calculations were performed using the VASP code [41,42]. Interaction between ions and electrons was
approximated by the projector-augmented wave (PAW) potential [43]. The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) functional is used to describe the exchange-correlation energies between electrons [44]. The energy cut-off for the plane wave basis was set to 500 eV. To include non-bonding interactions between the molecules, especially of the van der Waals type, the dispersion corrected DFT-D2 method proposed by Grimme was adopted [45–47]. Parallelepiped simulation cells containing two AQ, NQ and PQ molecules were adopted to form the periodic structures. The side length L (or lattice constants) and the angle θ of a parallelogram parallel to the molecular plane were varied to find the most stable structure. The height of the simulation cell perpendicular to the mo-lecular plane was fixed at 30 Å, while the lateral cell parameters L and θ were optimized such that the residual stress was reduced under 6.2 meV/Å3.
4. Results and discussion
Fig. 1(a) shows the ball and stick models of AQ, NQ, and PQ mole-cules. Fig. 1(b)–(d) show STM images after depositing the molecule on Au(111). The coverages estimated from STM images and our models were less than 0.1 monolayer. All the three STM images show well- known herringbone structures of Au(111) as well as 1D chains of mol-ecules. Molecules tend to form chains confined to the face-centered cubic (fcc) regions of herringbone structures. When the molecules arrived at the surface, they had enough kinetic energy to overcome the diffusion barriers made by the ridges of herringbone structures. One molecule met another molecule or existing chain to participate in a chain. The fcc regions of herringbone structures provide more active adsorption sites for various atoms and molecules on Au(111) because of their low surface-atom density than those in hexagonal close-packed (hcp) regions and dislocation ridges [48− 51].
Fig. 2(a), (c) and (e) show higher resolution (compared to Fig. 1) STM images. It was easy to recognize a single molecule in STM images,
because the three molecules commonly showed rod-like shapes. Mo-lecular models are superimposed over the STM images of (b) AQ, (d) NQ and (f) PQ that are magnified from the squared regions of (a), (c), and (e), respectively. Three neighboring AQ molecules form two different configurations, straight and staggered, as described by the molecular models in Fig. 2(b). Three neighboring PQ molecules also form the two configurations, as in Fig. 2(f). In contrast, three neighboring NQ mole-cules form only staggered configuration as shown in Fig. 2(d). No straight structure made of three NQ molecules was observed in our ex-periments. Because of this, the chain structures of NQ molecules looked straighter than those of AQ and PQ. The chain structures of NQ bend when the herringbone structures bend, simply following the shape of herringbone structures. Rarely, the chain structures of NQ bend where the herringbone structures did not. In such cases, impurity molecules such as AQ were inserted at kink locations as denoted with arrows in Fig. 2(c) (and also in Fig. S1 of supporting material).
To consider possible intermolecular interactions in the models pro-posed from our experiments, we calculated intramolecular electrostatic potential distributions for isolated molecules using first principles methods based on GGA. Fig. 3(a), (c) and (e) show the electrostatic
Fig. 1. (a) Ball and stick models of Anthraquinone (AQ), Naphthacenequinone (NQ) and Pentacenequinone (PQ) molecules. (b)–(d) Typical STM images of one-dimensional structures of AQ, NQ and PQ molecules on Au(111) surface, respectively. The sizes of STM images: (b) 68 × 68 nm2, (c) 70 × 70 nm2 and (d) 58 × 58 nm2. Tunneling current: IT = 0.1 nA. Sample voltage: (b) VS = 1.05 V, (c) VS = - 0.16 V, and (d) VS = -1.02 V.
Fig. 2. High resolution (compared to Fig. 1) STM images of (a) AQ, (c) NQ and (e) PQ molecules on Au(111) surface. Molecular models of (b) AQ, (d) NQ and (f) PQ from Fig. 1(a) are superimposed over the STM images that are magnified from the squared regions in (a), (c) and (e), respectively. Three AQ and PQ molecules can form both straight and staggered configurations, whereas three NQ can form staggered configuration only. The sizes of STM images: (a) 19 ×19 nm2, (c) 13 × 13 nm2 and (e) 17 × 17 nm2. Tunneling current: IT = 0.1 nA. Sample voltage: (a) VS = 0.75 V, (c) VS = 1.03 V and (e) VS = 0.78 V.
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potential mapped on the iso-surfaces of 0.003 e/Bohr3. H and O atoms show positive and negative electrostatic potential, due to their large electro-negativity difference (H: 2.20, O: 3.44). From these, the exper-imental models of Fig. 2 can be explained with the models shown in Fig. 3(b), (d) and (f). The two neighboring molecules have 2, 4, and 4 O•••H interactions in the molecular models of AQ, NQ, and PQ, respectively. Differences in energies can be used to explained why NQ always shows staggered configuration but not straight one. If NQ takes a straight configuration, the number of O•••H interactions between two molecules would be reduced from 4 to 3, significantly (25%) lowering the intermolecular formation energy [See supporting material Fig. S2]. Thus NQ molecules energetically prefer staggered configurations. In contrast, because both straight and staggered configurations of AQ have the same number of O•••H interactions, 2, there is no reason why staggered is preferred over straight, or the opposite way for AQ mole-cules. Similarly, straight and staggered configurations should be equal for PQ molecules. In the case of NQ, therefore, the number of O•••H interactions is the microscopic origin that explains how molecular asymmetry affects the configurations of intermolecular structures.
To explain the detailed intermolecular structures, we performed DFT calculations for staggered configurations of three molecules. In our calculations, we considered free molecules. It has been reported that planar organic molecules had numerous adsorption sites on fcc metal surfaces, and in particular on Au(111) the variation of adsorption energy was relatively modest considering the energy gains of intermolecular interactions [52]. More profound understanding would be possible by including substrate. Parallelogram unit cells containing two AQ, PQ, and
NQ molecules as bases, were adopted to construct the periodic structures as depicted in Fig. 3(a). We considered a side length L and an angle θ of a parallelogram as two independent parameters. The calculated formation energy is displayed in color code as functions of both L and θ as shown in Fig. 4(b), (d) and (f). The energy zero corresponds to that of the isolated molecule. Stable intermolecular structures were obtained for each molecule. The L and θ of the most stable structures obtained from cal-culations are marked in Fig. 4(b), (d) and (f). It turned out that all the three molecules showed the stable structures at the L around 1.4 nm and the θ around 30◦. The calculation results show reasonable agreement with those obtained from experiments as summarized in Table 1.
Because the computational results well-reproduce the models in Fig. 2, the distances of O•••H interactions in Fig. 2(b), (d) and (f) are extracted from the minimum-energy structures. The two O•••H in-teractions in AQ show an identical distance 0.255 nm. The four hydrogen bonds in NQ show two different distances 0.232 and 0.246 nm as depicted in Fig. 4(c). This means that the three atoms H, O, and H participating in O•••H interactions do not form an isosceles triangle. If there are only three atoms that form O•••H interactions between two molecules, it may be natural for them to have isosceles triangle config-urations. However, when there is another set of three H, O, and H as in NQ, there is no way for them to form two isosceles triangles at the same time. Similarly, the four hydrogen bonds in PQ show two distances 0.246 and 0.235 nm as depicted in Fig. 4(f). Still, the two distances of hydrogen bonds in NQ and those of PQ obtained from calculation results were different, showing how symmetry and length of molecules affect the details of intermolecular interactions. From our DFT calculations, we obtained the energy gains of 221, 317, and 339 meV per molecule in AQ, NQ, and PQ, respectively. Thus each O•••H interaction carries energy gain between 110 and 80 meV. In our calculation scheme, the portions of van der Waals corrections were about 50 % of binding energies, as shown in Table 2. Besides the staggered configurations shown in Fig. 4 (a), we also performed the DFT calculations for straight configurations. It was confirmed that the two configurations shared about the same binding energies for AQ and PQ as shown in Table S1 of supporting material, but for NQ, the binding energy of straight configuration was 60 % of that of staggered one. Thus our DFT calculations also tell us that staggered configuration is preferred to straight configuration for NQ. Our calculations were performed only with free molecules. More pro-found understanding would be possible by including substrate.
We observed that the single molecule in staggered configurations showed asymmetric shapes. Fig. 5(a)–(c) show cross sections along the long axes of two neighboring molecules in a chain. It is clear that the heights of two ends of each molecule are unequal and that the height profiles of two neighboring molecules show seesaw-like antisymmetric arrangement. These can be explained with tilted molecular structures with antisymmetric arrangement to adopt the geometrical environment provided by the fcc region of herringbone structures as depicted in Fig. 5 (d). The height differences between the two ends of NQ, and PQ mole-cules were similar to each other, but much larger than that of an AQ molecule. It is natural that molecules whose lengths are close to the half width of a basin would feel larger height difference made by the basin structures of fcc region. It was estimated that the half width of a basin made by fcc would be 1.23 nm, and the length of AQ, NQ, and PQ were 0.91, 1.15, and 1.39 nm, respectively. These numbers explain why NQ and PQ have similar height differences that are larger than that of AQ. We also were able to estimate the tilt angles to be 0.01◦, 0.25◦, and 0.23◦
in AQ, NQ, and PQ, respectively. We tried to include the effect of tilting in our calculations, but could not have noticeable effect because angles were too small. Although our experimental observations could be reasonably explained with the tilted molecular model, we could not rule out the possibility that the asymmetric rod shape originated from elec-tronic effect. For example, the end that is closer to the Au surface may appear brighter in the STM, due to the stronger electronic arrangement of the molecule to the conducting substrate and the resulting increased density of electrons.
Fig. 3. Calculated electrostatic potential distributions of (a) AQ, (c) NQ and (e) PQ molecules at isodensity surfaces. Schematic illustrations for two nearest neighbor (b) AQ, (d) NQ and (f) PQ molecules. The positive and negative po-tentials are colored in red and blue, respectively. The dotted lines indicate possible O•••H interactions. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.).
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5. Conclusions
We studied the 1D chain structures of AQ, NQ, and PQ on Au(111) using STM and DFT at the low-coverage limit. All the three molecules
formed 1D chains confined to fcc regions of herringbone structures. AQ and PQ molecules can form both straight and staggered configurations, whereas NQ can form only staggered configuration because of difference in binding energies. Detailed molecular structures were explained with O•••H interactions as reproduced with our density functional theory calculations.
CRediT authorship contribution statement
Min Hui Chang: Investigation, Formal analysis, Writing – review & editing. Won Jun Jang: Investigation. Min Wook Lee: Investigation. Seungwu Han: Resources. Se-Jong Kahng: Conceptualization, Writing – original draft, Project administration.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper
Fig. 4. The calculated results for relaxed 1D structures of (a) AQ, (c) NQ and (e) PQ molecules from density functional theory calculations. The energy gains per molecule as functions of lattice parameters and angles for (b) AQ, (d) NQ and (f) PQ molecules, respectively.
Table 1 Experimental and calculated lattice parameters and angles.
Table 2 Contribution of Van der Waals interaction on binding energies.
With vdW interaction Without vdW interaction AQ 221 meV 109 meV NQ 317 meV 149 meV PQ 339 meV 162 meV
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Acknowledgment
The authors gratefully acknowledge financial support from the Na-tional Research Foundation of Korea (Grants No. 2021R1A2C1012526, No. 2021R111A1A01053172, and No. 2018R1A4A1024157), and Korea University Grants. This work was supported by the Supercomputing Center/Korea Institute of Science and Technology Information with supercomputing resources including technical support (KSC-2018-C1- 0005).
Supplementary materials
Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.susc.2021.121911.
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Fig. 5. Height profiles along the long axes of two neighboring (a) AQ, (b) NQ and (c) PQ molecules. (d) Schematic illustrations of geometrical structures of molecules and herringbone fcc structures.
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