Steering Two-Dimensional Porous Networks with Ï-Hole Interactions

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Steering Two-Dimensional Porous Networks with #-Hole Interactions of Br···S and Br···Br Lingbo Xing, Wei Jiang, Zhichao Huang, Jing Liu, Huanjun Song, Wenhui Zhao, Jingxin Dai, Hao Zhu, Zhaohui Wang, Paul S. Weiss, and Kai Wu Chem. Mater., Just Accepted Manuscript • DOI: 10.1021/acs.chemmater.9b01126 • Publication Date (Web): 22 Mar 2019 Downloaded from http://pubs.acs.org on March 23, 2019

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Chemistry of Materials

Steering Two-Dimensional Porous Networks with σ-Hole Interactions of BrS and BrBr Lingbo Xing,1 Wei Jiang, 2 Zhichao Huang, 1 Jing Liu,1 Huanjun Song,1,4 Wenhui Zhao,1 Jingxin Dai, 1 Hao Zhu,1 Zhaohui Wang,2 Paul S. Weiss,3,* and Kai Wu1,*

1BNLMS,

College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China

2CAS

Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China

3California

NanoSystems Institute, Department of Chemistry and Biochemistry, and Department

of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States 4Research

Institute of Aerospace Special Materials and Processing Technology, Beijing, 100074, China

ACS Paragon Plus Environment

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E-mail: [email protected], [email protected]

ABSTRACT

The self-assembly of 3,10-dibromo-perylo[1,12-b,c,d]thiophene (DBPET) on Ag(111) leads to three types of ordered porous networks – honeycomb PN1, Kagome PN2, and hybrid PN3. Detailed experimental and theoretical analyses confirm the thermal stability order of the three constructed porous networks. High-resolution scanning tunnelling microscopy images indicate the importance of two σ-hole interactions of BrS and BrBr in steering two-dimensional molecular assembly on metal surfaces.


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On-surface two-dimensional porous supramolecular networks have attracted tremendous interest1-4 due to their potential applications in secondary molecular templating,5 molecular recognition,6 molecular devices,7 information storage,8,9 and heterogeneous catalysis.10 Various weak interactions such as hydrogen bonding,11,12 metal-ligand coordination,13,14 dipolar coupling,15 - stacking,16 van der Waals forces,17 substrate-mediated interactions18-20 and the like have been exploited to assemble molecular building blocks into ordered networks on surfaces. Recently, noncovalent interactions were explored, involving σ-holes located at covalently bound atoms of Groups IV–VII and a lone pair of electrons associated with a Lewis base or an anion.21-24 σ-hole refers to the region with positive electrostatic potential, which stems from anisotropic charge distributions. As a typical example of the σ-hole interactions, halogen bonding is not only crucial in biological system for drug design,25-27 but also widely utilized to construct novel assembly structures.28-35 Other σ-hole interactions involving various types of atoms such as chalcogens, pnicogens and tetrels have also attracted great attention. For instance, Wang et al. showed that SS interaction plays important role in


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directing the 2D self-assembly of a fused thiophene derivative trans-1,2-(dithieno[2,3-

b:3',2'-d]thiophene)ethene (TDT).36 Ignacio and coworkers achieved double-walled networks of [3,9-dibromodinaphtho[2,3-b:2',3-d]furan (Br-DNF) driven by BrO interactions.37 Despite extensive computer modelling and studies of biomolecules,38-40 sulfur···halogen interaction has barely been reported for surface assemblies.

Herein, the self-assembly of 3,10-dibromo-perylo[1,12-b,c,d]thiophene (DBPET) on Ag(111) was systematically investigated by combined scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. As one of the hetero-annulated perylene derivatives, DBPET is a p-type semiconductor in various organic electronic devices like organic field-effect transistors, as we previously reported.41 Here, the experimental results revealed three types of nanoporous networks, based on the interplay of the σ-hole interactions of BrS and BrBr. To the best of our knowledge, this is the first observation that the sulfur···halogen electrostatic interaction can be utilized to steer supramolecular assembly with high complexity on metal surfaces.


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RESULTS Figure 1a shows a representative STM image of the DBPET molecules on Ag(111) with proposed chemical structure superimposed. An individual DBPET molecule possesses a C2v symmetry and appears like a Chinese gold ingot. Both ends of the molecule are terminated by bromine, while a sulphur atom sits atop the aromatic backbone. The longitude of the molecule was measured to be 1.1 ± 0.1 nm, in good agreement with the calculated value of the DBPET backbone, ~1.06 nm, according to first-principles calculations based on m062x/6-311++G(d,p). The calculated spatial distribution of the electrostatic potential (ESP) for DBPET is shown in Fig. 1b where blue and red colors indicate the positive and negative potentials, respectively. A molecular model is superimposed where Br atoms are shown in red, S in yellow, H in white, and C in grey. The ESP map illustrates the characteristic positive σ-holes and the negatively charged equatorial zone on the bromine atoms, induced by the connecting aromatic core. Lone pairs on the sulphur atom appear perpendicular to the DBPET molecular plane in red, and the covalently bonded hydrogen atoms hold a positive potential. Fig. 1c depicts a large-scale STM image of three co-existing self-assembled porous networks (labelled as


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PN1, PN2, and PN3) formed by thermally evaporated DBPET molecules on Ag(111) held at ~100 K. The black dashed lines show the boundaries of three assembly phases and the fuzzy zones at the domain boundaries are due to the mobile molecules at 77 K.42 The inset of high-resolution STM image of the lattice structure shows the three-fold symmetry of Ag(111) surface.

Fig. 1 (a) Scanning tunneling microscope (STM) image of an individual 3,10-dibromoperylo[1,12-b,c,d]thiophene (DBPET) molecule on Ag(111). The molecular structure of DBPET is superimposed and its measured length is marked by white arrow. Imaging


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conditions: Sample bias = 100 mV, current = 100 pA, imaging temperature = 4.2 K. (b) Calculated molecular electrostatic potential distribution of the DBPET molecule at the isodensity surface shown in blue (positive) and red (negative). (c) A large-scale STM topographic image (100 mV, 100 pA, 77 K) showing three types of porous networks (PN1, PN2, and PN3) after deposition of the DBPET molecules on Ag(111) held at 100 K. The black dashed lines indicate the boundaries between the three assembly phases. Inset: High-resolution STM image of the Ag(111) surface lattice structure (10 mV, 100 pA, 4.2 K).

Figure 2a shows a high-resolution STM image of the honeycomb PN1. Each rhombus unit cell contains three molecules with the lattice parameters a = 2.6 ± 0.1 nm, b = 2.6 ± 0.1 nm and α = 60 ± 2°. Therefore, the DBPET surface molecular density (DM) is 0.512 nm-2. Each black T-shaped pattern in Fig. 2b represents one DBPET in which the Br atoms are simplified by two solid circles and the S atom, by a solid square, for the sake of clarity. The Br terminals appear as protrusions (displayed as brighter) among three molecules form typical cyclic halogen bonds, which originate from the σ-hole electrostatic attraction at each trimeric node. The substrate lattice has three-fold symmetry matching


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the three-fold cyclic nodes. Such BrBr interactions (black dotted arrows in Fig. 2c) are accompanied by the weak synergistic BrH hydrogen bonding between the Br atom in one DBPET molecule and the α-H atom in another adjacent DBPET molecule (blue dashed lines in Fig. 2c), which have been reported previously in many molecular assemblies.29,43-48 The BrBr bond (D1) length is 4.19 Å and the C-BrBr angle is 180°. The BrH distance, D2, is 4.94 Å. Although DBPET is an achiral molecule, the cyclic node is chiral, either CW or CCW, due to the directionality of halogen bonds. The black dotted arrows in Fig. 2c indicate the CW chirality of PN1 in Fig. 2a and the homochiral domains with different orientations appear stochastic on surfaces (shown in figure S4). Note that the orientation of the sulphur atoms influences the interactions of neighboring DBPET molecules because of the HH repulsion and BrH attraction, and the S atoms orient slightly differently.


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Fig. 2 (a) High-resolution scanning tunneling microscope images (10 mV, 100 pA, 4.2 K) of the honeycomb PN1. Molecular models are superimposed and the unit cell is marked by the white parallelogram. The white arrows mark the directions of the Ag(111) substrate derived from the substrate lattice. (b) Proposed structural models are given for PN1, where the DBPET molecule is represented by a T-shaped symbol. The red dashed line highlight nine DBPET molecules which will be mentioned below. (c) BrBr interactions are indicated by black dashed arrows and possible BrH interactions are highlighted by


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blue dashed lines in the enlarged models of PN1. D1 and D2 refer to the lengths of the BrBr and BrH bonds, respectively.

In the PN2 structure shown in Fig. 3a, the DBPET molecules assemble into an ordered two-dimensional Kagome lattice. There are six monomers in each unit cell with the lattice parameters as a = 3.3 ± 0.1 nm, b = 3.3 ± 0.1 nm, α = 60 ± 2°. Its DM is 0.636 nm-2, higher than that in PN1. The proposed structural model in Fig. 3b is in good agreement with the observed STM images, which illustrates the hierarchical self-assembly process.49-53 Three neighboring DBPET molecules stay together to form a propeller-shaped trimer unit where each molecule takes a symmetric arrangement of 120°. Thus, six DBPET trimers rotate by 60° with respect to each other to form a hexagonal ring that includes 18 DBPET molecules and extends along two surface directions to form a 2D Kagome porous network. Similar to the ternary cyclic halogen bonds in PN1, the high-resolution picture (Fig. 3a) as well as the proposed molecular model (Fig. 3c) indicate that the dominant driving force for the propeller-shaped trimer is the BrS interactions, highlighted by red dashed arrows, together with the weak BrH interactions marked by the light blue dashed


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lines. The BrS interactions are established by docking the lone-pair electrons on S to the positively charged σ-hole on Br. The BrS bond (D3) is 3.79 Å in length, shorter than the BrBr bond in PN1, and the C-BrS angle (θ) is 164°. The length of the weak BrH hydrogen bond, D4, is 4.70 Å. In Fig. S5, the complexation energy of the trimer unit is 1.38 kcal/mol for PN1 driven by the BrBr interaction and -0.74 kcal/mol for PN2 driven by BrS interaction, respectively. Such a DFT calculation shows that the BrBr interaction is stronger than the BrS one, in agreement with the higher electronegativity of the Br atom. In addition, the Br···H interactions (dark blue dashed lines in Fig. 3c) and van der Waals interactions co-play an important role in connecting two neighboring trimer units and finally rise to the Kagome network. The Br···H bond (D5) is measured to be 3.08 Å in length, implying that it is relatively stronger than D4. The trimer unit is chiral due to the directionality of BrS bond and the red dotted arrows in Fig. 3c indicate the CW chirality. Chirality is transferred to the hexagonal ring and amplified in the whole Kagome porous network,54-58 so that PN2 exhibits two homochiral domains of CW and CCW in Fig. S6.


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Fig. 3 (a) High-resolution scanning tunneling microscope images (10 mV, 100 pA, 4.2 K) of PN2 porous networks. Molecular models are superimposed and the unit cell is marked by the white parallelogram. (b) Proposed structural models for the hierarchical selfassembly of PN2. (c) The enlarged models of the unit cell. The propeller-shaped trimer is driven by the BrS interactions, highlighted by red dashed arrows, together with the weak BrH interactions marked by the light blue dashed lines. BrH interactions marked by the dark blue dashed lines play key roles to connect two neighboring trimer units. D3, D4, and D5 refer to the lengths of the BrS, weak BrH, and strong BrH bonds, respectively. θ is the C-BrS angle.


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Fig. 4a shows the complicated hybrid self-assembled structure of PN3. Amazingly, the unit cell consists of up to 36 molecules with lattice parameters a = 8.2 ± 0.1 nm, b = 8.2 ± 0.1 nm, α = 60 ± 2°. Hence, the molecular density of PN3 (0.618 nm-2) falls in between those for PN1 and PN2. In Fig. 4b, the STM topographic image at a higher bias (2 V, 100 pA, 77 K) show the magical periodicity of the PN3 structure. The region circled by dark blue hexagon is analyzed with a detailed model shown in Fig. 4c. According to the superimposed structural model in Fig. 4c, PN3 is actually a combination of hexagons mentioned in PN2 and dendrimers (nine DBPET molecules circled by the red dashed line in Fig. 2b) abstracted from PN1. Each hexagon is surrounded by six dendrimers and each dendrimer, by three hexagons and three dendrimers. As a result, the σ-hole interactions of both BrBr and BrS are of great importance for stabilization of the PN3 assembly. Beyond that, the neighboring dendrimers and hexagons are connected by the strong Br···H interactions as well as by van der Waals forces.


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Fig. 4 (a) High-resolution STM images (10 mV, 100 pA, 4.2 K) of the hybrid PN3 network. Molecular models are superimposed and the unit cell is marked by the white parallelogram. (b) STM topographic image (2 V, 100 pA, 77 K) showing the complex periodicity of PN3. The region circled by dark blue hexagon is further analyzed in Fig. 4c. (c) Proposed structural models are given for PN3 which consist of red hexagons in PN2 and black dendrimers in PN1.


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DISCUSSION Temperature plays a vital role in tuning both the thermodynamics and kinetics for the network formation. The kinetically metastable network can be transformed into a thermodynamically favored one by thermal annealing.59-62 After deposition of DBPET on Ag(111) held at ~100 K, three phases co-exist on the surface (Fig. 5a). Experimental statistics are conducted on large areas of the sampling surface and the relative ratios of PN1:PN2:PN3 is 19:69:12 (see the statistic histograms in Fig. 5d), respectively. The fuzzy zones at the domain boundaries are caused by the thermal motion of the molecules at 77 K.42 After annealed at room temperature for 10 min, the PN1 phases disappear and the occupancy of the PN3 structures (dashed black circles in Fig. 5b) decreases from 12% down to 6% while the PN2 coverage increases to 94%. A further increase in the annealing time by 15 min leads to that the Ag(111) surface is fully covered by the PN2 structures (Fig. 5c) and the domain areas can be as large as 200 × 200 nm2. We note that the disordered areas consisting of the mobile molecules also increase. These experimental


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results demonstrate that PN2 is the most thermodynamically stable phase, and PN1, the least stable one.

Fig. 5 Large-scale scanning tunneling microscope images (1 V, 30 pA, 77 K) of the DBPET porous networks after annealing of the sample at room temperature for (a) 0, (b) 10, and (c) 15 min. The black dashed circle indicates the PN3 structures. (d) Statistic histograms of the relative occupancy of PN1 (blue bars), PN2 (red bars), and PN3 (green bars) upon increase of the annealing time.


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Molecular coverage is also an important factor for the formation and regulation of onsurface self-assembled supramolecular architectures.63,64 Fig. 6a shows the large-scale STM image after deposition of 0.3 ML DBPET on Ag(111) held at ~100 K. PN2 is the only ordered phase at this low coverage with many mobile molecules. In Fig. 6b, PN3 appears when the DBPET molecules are re-deposited on the sample and PN1 finally shows up with more DBPET molecules added (Fig. 6c). As the molecular coverage increases, the molecular assemblies appear in the order of PN2 > PN3 > PN1, which is opposite to molecular density in the three phases mentioned above. If the assembled phases are envisioned as a 2D crystal phase, and the mobile molecules as the corresponding liquid phase, the "assembly-disassembly" quasi-phase equilibrium is actually established at liquid nitrogen temperatures.42 At low coverage, the mobility of the precursors is large enough to form a more stable PN2 phase.


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Fig. 6 (a) Large-scale scanning tunneling microscope image of exclusively PN2 structures after dosing 0.3 ML DBPET on Ag(111) held at ~100 K. (b) Large-scale STM images of co-existing PN2 and PN3 phases after redepositing more DBPET molecules. (c) Coexistence of the three phases by adding more precursors on the surface. Imaging conditions: Sample bias = 100 mV, current = 100 pA, imaging temperature = 77 K.

Density functional theory calculations were carried out to compare the energetics of the two phases whose molecular models (Fig. 7a, c) are constructed according to the measured distances and angles between the molecules acquired in Fig. 2a and Fig. 3a. Taking PN1 in Fig. 7b for example, the M0 molecule marked by the red circle is set to be fragment 1 and M1 - M4 molecules marked by the blue, fragment 2. Such a model ignores


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the interactions of the M0 molecules with other molecules except for fragment 2. M062x/6311++G (d,p) method is employed to calculate the energy variation by restriction of all molecules in the same plane. The energy change is given by the following formula:

Ec = E(M0 - M4) - E(M0) - E(M1 - M4) + E(BSSE) where E(M0 - M4), E(M0), and E(M1 - M4) correspond to the energy of the whole system, fragment 1, and fragment 2. E(BSSE) is the energy correction of basis set superposition errors. Note that the calculation does not include the interaction between DBPET and Ag(111) due to its tremendous computational complexity. The calculation process for PN2 is similar to PN1 except that M1-M5 are set to be fragment 2. It turns out that the Ec value for PN1 is -1.75 kcal/mol for PN1 and -2.97 kcal/mol for PN2, indicating that the interactions between the DBPET molecules in the PN2 structure are larger than those in PN1. As mentioned above, the PN3 structures are actually built up by the segments of PN1 and PN2, so the Ec value for PN3 is estimated to be in the range of –1.75 to -2.97 kcal/mol. Therefore, the thermal stability sequence follows PN2 > PN3 > PN1, which is consistent with the structural transformations shown in Figs. 5 and 6.


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Fig. 7 Calculated energy variations based on the models for (a) PN1 and (c) PN2. (b) Molecules used in the calculations for PN1 where M0 is highlighted by a red oval and M1M4 by blue ovals. (d) Molecules used in the calculations for PN2 where M0 is highlighted by the red oval and M1-M5 by blue ovals. Ec refers to the complexation energy.

Given that the calculated energy of the trimer unit for PN2 (-0.74 kcal/mol) is higher than that for PN1 (-1.38 kcal/mol), one can safely conclude that multiple interactions (including the Br···H interaction and van der Waals force) contribute to stabilize the PN2 structure, which is the most thermally stable phase. In Fig. S7a, deposited DBPET on


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Au(111) at 100 K forms the same PN2 structure as on Ag(111) (Fig. 6a) except for that the unassembled molecules are preferably adsorbed in the fcc region of the reconstructed herringbone structure on Au(111). Due to the low mobility and stronger moleculesubstrate interaction on Cu(111), DBPET only forms a close-packed phase with a zig-zag feature (Fig. S7b). Both high-resolution STM image and corresponding molecular model in Fig. S7c suggest that the relatively strong BrH bonds (highlighted by the dark blue dashed lines) are the driving force. Although the BrS σ-hole interaction is relatively weaker than the BrBr and strong BrH interactions, it does serve as an indispensable one to steer the PN2 and PN3 structures.

CONCLUSIONS AND PROSPECTS Three types of ordered porous 2D networks have been successfully prepared via thermal deposition of the DBPET precursors on a cryogenic Ag(111) surface. Annealing experiments and DFT calculations have shown that the PN2 structure is the most thermally stable phase. High-resolution STM images as well as molecular modelling demonstrate that the BrBr halogen bond stabilizes the honeycomb-like PN1 assembling


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structure and the BrS interaction is an indispensable driving force for the formations of the Kagome PN2 and complicated hybrid PN3 structures. The directional BrS interaction is actually the electrostatic attraction between the positively charged σ-hole on Br and the lone-pair electrons on S, resulting in chiral DBPET aggregation on surface. Compared with BrBr halogen bond, the BrS σ-hole interaction is weaker in strength due to the lower electronegativity of the S atom. However, the BrS bond can indeed serve as an additional intermolecular force to efficiently steer 2D selfassemblies on metal surfaces. Our experimental results indicate that multiple intermolecular interactions via rational design of the assembling precursors hold the promise to construct hierarchical, complex and functional molecular assemblies, which may lead to applications in biomaterials, molecular devices, and catalysis.


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EXPERIMENTS AND CALCULATIONS All experiments were conducted on an ultrahigh vacuum (UHV) -STM (USM-1200S) with a base pressure of < 2 × 10-10 mbar. The Ag(111) sample (MaTecK GmbH) was cleaned by repeated circles of Ar+ sputtering and subsequent annealing at 733 K. The DBPET (SI) was thermally deposited onto the the clean Ag(111) surface via a custom tantalum boat at about 100 K. The coverage of the molecules was measured with a quartz balance. The samples were subsequently annealed by taking out them from the STM chamber to the preparation chamber at room temperature for different durations, as noted. The STM tip was made out of an electrochemically etched W wire (Ø 0.25 mm) and was prepared by electron-beam heating in UHV. All STM images presented here were acquired at at 77 K or 4.2 K, as noted, in constant-current mode and processed with WSxM software.65

SUPPORTING INFORMATION


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Synthetic procedure and characterization of DBPET. Extended analysis of the assembly chirality. The calculated complexation energy of the trimer units in PN1 and PN2. The substrate eﬀect on the assembly. The Supporting Information is available free of charge on the ACS Publications website at TDK.

AUTHOR INFORMATION Corresponding Author *E-mail: [email protected] *E-mail: [email protected]. ORCID Lingbo Xing: 0000-0002-8734-5241 Wei Jiang: 0000-0002-0153-7796 Jing Liu: 0000-0002-8120-7147 Huanjun Song: 0000-0003-1814-8604 Wenhui Zhao: 0000-0002-2948-5035


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Zhaohui Wang: 0000-0001-5786-5660 Paul S. Weiss: 0000-0001-5527-6248 Kai Wu: 0000-0002-5016-0251 Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

Funding Sources This work is jointly supported by the Ministry of Science and Technology (2017YFA0204702) and the National Science Foundation China (21333001, 91527303), China.

REFERENCES (1) Kudernac, T.; Lei, S.; Elemans, J. A.; De Feyter, S. Two-Dimensional Supramolecular SelfAssembly: Nanoporous Networks on Surfaces. Chem. Soc. Rev. 2009, 38, 402-421. (2) Liang, H.; He, Y.; Ye, Y.; Xu, X.; Cheng, F.; Sun, W.; Shao, X.; Wang, Y.; Li, J.; Wu, K. TwoDimensional Molecular Porous Networks Constructed by Surface Assembling. Coord. Chem. Rev. 2009, 253, 2959-2979.


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Steering Two-Dimensional Porous Networks with Ï-Hole Interactions

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Steering Two-Dimensional Porous Networks with Ï-Hole Interactions