Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy

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Science  01 Nov 2013:
Vol. 342, Issue 6158, pp. 611-614
DOI: 10.1126/science.1242603

Imaging Hydrogen Bonds

The decoration of atomic force microscope tips with terminal CO molecules has afforded much higher resolution of the bonding of adsorbed molecules. Zhang et al. (p. 611, published online 26 September) show that this method, in combination with density function theory calculations, can image and characterize hydrogen-bonding contacts formed between 8-hydroxyquinoline molecules adsorbed on the (111) surface of copper under cryogenic conditions. At room temperature, a different bonding configuration was revealed that was the result of the molecules dehydrogenating on the copper surface and coordinating with surface copper atoms.


We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Intermolecular bonding has been experimentally characterized mainly through crystallography via x-ray and electron diffractions, as well as through infrared, Raman, nuclear magnetic resonance, and near-edge extended absorption fine-structure spectroscopy (1, 2). At the single-molecule level, state-of-the-art scanning tunneling microscopy (STM) is a technique widely used to elucidate the molecular structure and chemical specificity of surface-immobilized species (35). The bonding interactions between molecules in self-assemblies were also evidenced in scanning tunneling hydrogen microscopy (6). Nevertheless, most of the characterization techniques are, thus far, more sensitive to the covalent structures of the molecules, and in many cases, theoretical calculations of intermolecular interaction are also not as precise as those for covalently bound species.

Recently, noncontact atomic force microscopy (NC-AFM) has achieved superior resolution in real-space that has enabled the identification of the chemical structure, adsorption configurations, and chemical transformation of individual molecules (710). For example, the difference in bond order in aromatic molecules was distinguished via electron-density–dependent Pauli repulsion with CO-functionalized NC-AFM tips (11), and AFM tomography revealed the angular symmetry of a chemical bond on surface (12). Herein, we used NC-AFM to investigate the intermolecular interactions in 8-hydroxyquinoline (8-hq) (Fig. 1A) molecular assemblies formed on Cu(111) at liquid helium (LHe) and room temperatures (RTs). The hydrogen bonds (H bonds) formed between 8-hq molecules were characterized by high-resolution AFM images, and the local bonding configuration was determined with the atomic precision. We also observe the coordination complex composed of dehydrogenated 8-hq and Cu adatoms. The observations were validated with ab initio density functional theory (DFT) calculations.

Fig. 1 STM and AFM measurements and DFT calculations of single 8-hq on Cu(111).

(A) Chemical structure of 8-hq. (B) DFT-calculated molecular electron density maps at a distance of 150 pm above the molecule. (C) Constant-current STM topography image (voltage V = –100 mV, current I = 100 pA) with a CO-functionalized tip. (D to F) Constant-height AFM frequency shift images (V = 0 V, amplitude A = 100 pm) at different tip heights. The tip height Δz was set with respect to a reference height given by the STM set point above (–100 mV, 100 pA) the bare Cu(111) substrate in the vicinity of the molecule. The plus (or minus) sign denotes the increase (or decrease) of tip height. (D) Δz = +30 pm; (E) Δz = +10 pm; (F) Δz = 0 pm. The size of all images is 1.3 by 1.0 nm.

The 8-hq molecules deposited on Cu(111) at LHe temperature appeared as individual molecules or randomly assembled aggregates (fig. S1) (13). For the single 8-hq molecules, DFT calculations suggest that the molecular plane is slightly tilted with respect to the substrate because of the weak interactions between the OH group and the N atom of 8-hq and Cu(111) surface. Compared with the calculated total electron density of the molecule shown in Fig. 1B, the STM image (Fig. 1C) exhibits no internal features of the heterocycle because the tunneling current is primarily sensitive to the local density of states near the Fermi level. In contrast, the AFM images with a CO-functionalized tip revealed the submolecular structure of 8-hq through the short-range Pauli repulsive force (Fig. 1, D to F). The calculated electron density map (Fig. 1B) qualitatively reproduces the observed contrast in frequency shift (Δf) in the AFM image. Here, the AFM sensor measured the total force of three components (7, 14): (i) the long-range attractive electrostatic forces, responsible for the overall negative Δf background in the images; (ii) the attractive van der Waals force, which contributed to the dark halo surrounding the molecule without atomic corrugation; and (iii) the short-range Pauli repulsion, which contributed to the atomic contrast of molecular structure with respect to the metal substrate. When the tip height was decreased (Fig. 1, D to F), the increasing proportion of Pauli repulsion in the total force enhanced contrast in the AFM images. Although a quantitative understanding of the AFM imaging mechanism is nontrivial, a direct correlation between the AFM images and the chemical structure of a molecule can still be rationalized. In our case, the heterocyclic skeleton and the hydroxyl group of 8-hq were readily distinguished. The pyridine ring in the heterocycle is slightly pronounced, which may be caused by tilting of the molecular plane on the substrate. A further interpretation of the topography need also take into account the difference in electron density of the phenol ring and the pyridine ring.

The AFM images of the 8-hq molecular aggregates (Fig. 2, A and B) reveal bonding-like features between adjacent molecules in the assemblies that were reproduced in all of the observations, whereas these features were not observed in the corresponding STM images at the same regions [see fig. S3 and (13)]. A close examination of the position and orientation of the bonding-like structures indicated that they coincide very well with the expected locations of H bonds formed between 8-hq molecules (Fig. 2, C and D). The results from recent theoretical and experimental investigations suggest that the H bond has both an electrostatic origin and a partly covalent character (15, 16). Despite extensive studies of H bonding in supramolecular and biological systems using various techniques, direct identification of the bonding configuration of the H bond in real-space is elusive (17).

Fig. 2 AFM measurements of 8-hq assembled clusters on Cu(111).

(A and B) Constant-height frequency shift images of typical molecule-assembled clusters and their corresponding structure models (C and D). Imaging parameters: V = 0 V, A = 100 pm, Δz = +10 pm. Image size: (A) 2.3 by 2.0 nm; (B) 2.5 by 1.8 nm. The dashed lines in (C) and (D) indicate likely H bonds between 8-hq molecules. Green, carbon; blue, nitrogen; red, oxygen; white, hydrogen.

The formation of covalent bonds in unimolecular reactions has recently been reported (10). The bond contrast in the AFM images has been qualitatively compared with the bond order, where the higher local electron density leads to stronger Pauli repulsion exerted on the tip (10, 11). In our observations, the Δf contrast of these intermolecular bonds is comparable to that of intramolecular covalent bonds in the constant-height images, as also evident in the force spectroscopy measurements (fig. S4) (13). Given the clearly identified bonding sites, we could perform a detailed analysis of the H bond configurations (18). The apparent bond lengths of the intermolecular H bonds were measured, as summarized in fig. S5 (13), and can be used as a reference for data acquired through other characterization methods to understand the effect of the substrate on H bonding (19).

Our study also revealed differences in the H bond configurations in the 8-hq self-assemblies on surface and those in the bulk crystal. In addition to the conventional H bond, which involves only the OH group and N atom of 8-hq, we also observed H bond formation between the aromatic rings and the OH group or N atom. These results provide direct evidence for the influence of substrate on the intermolecular bonding characteristics (1, 20).

We performed DFT calculations on two types of molecular clusters to further understand the origin of the contrast of intermolecular H bonds in our observation. In Fig. 3A, the paired 8-hq molecules were bonded by two H bonds of O-H···N, as illustrated by the black dotted lines in Fig. 3B (21). The calculated total electron density plotted in Fig. 3C shows a bright spot at the position of the O atom and a protrusion toward the adjacent molecule around the position of the N atom. The in-plane plot of the differential charge density (Fig. 3D), which is defined as Embedded Image (where Embedded Image is the electron density of 8-hq adsorbed on the Cu substrate, Embedded Image is the electron density of the Cu substrate, and Embedded Image is the electron density of 8-hq), reflects the charge redistribution after the bond forms between two 8-hq molecules and indicates that covalent-like characteristics developed from charge reductions near the H and N atoms that led to charge accumulation between them. As expected, the enhanced charge density at N and O is consistent with the charge transfer from H to N and O atoms, whereas the charge accumulation offers an additional repulsive force to the tip at the region along the H bonding direction. Thus, the observed line feature between the two 8-hq molecules in the AFM image is attributed to a joint effect that results from both the covalent charge in H···N and the charge transferred from H to N and O. The above interpretation is primarily based on the simplified mechanism of tip-to-sample Pauli repulsion (22). A quantitative understanding of the image contrast of an H bond may require further consideration of the relaxation of the CO molecule attached on the tip apex (11). In another configuration (Fig. 3, E to H), DFT calculations also concluded electron density redistribution in the proximity of the newly formed bond. In this unconventional C-H···N hydrogen bond, the effect of charge accumulation between N and H atoms is much weaker compared with that in the O-H···N hydrogen bond (1, 15).

Fig. 3 AFM measurements and DFT calculations of 8-hq dimers on Cu(111).

Constant-height frequency shift image of the O-H···N dimer (A) and the N···H-Ph dimer (Ph, phenyl) (E) and their corresponding DFT-calculated structure models (B and F), electron density maps (C and G), and charge difference maps (D and H). Imaging parameters: V = 0 V, A = 100 pm, Δz = +50 pm (A), Δz = +10 pm (E). Image size: (A) 1.6 by 1.6 nm; (E) 1.5 by 2.0 nm. The dashed frames in (B) and (F) indicate the calculation regions in (D) and (H).

When 8-hq was deposited onto Cu(111) at RT, the molecules formed highly ordered dimers and trimers, which are distinct from the H-bonded aggregates formed at the LHe temperature. No internal structures of these dimers and trimers could be resolved in the high-resolution STM images (fig. S8). The size of these molecular aggregates did not correspond to those of the H-bonded clusters from DFT calculations. The AFM images of the dimers and trimers (Fig. 4, A and B) allowed the identification of the outer edge of the molecules corresponding to the positions of H or C atoms, but the inner edge was blurred.

Fig. 4 AFM measurements and DFT calculations of coordination complexes (dehydrogenated 8-hq and copper adatoms) on Cu(111).

Constant-height AFM frequency shift images (A and B), the corresponding DFT-calculated structure models (C and D), and electron localization function maps (E and F) of dimer (Cuq2) and trimer (Cu3q3) complexes (q, dehydrogenated 8-hq). Imaging parameters: (A) V = 0 V, A = 100 pm, Δz = +100 pm, 2.0 by 2.0 nm; (B) V = 0 V, A = 100 pm, Δz = +80 pm, 2.4 by 2.4 nm. The tip height Δz was set with respect to a reference height given by the STM set point (–30 mV, 100 pA) above the bare Cu(111) substrate. The dashed lines in (C) and (D) refer to the H bonds formed in the complexes. The complexes were formed by depositing 8-hq on Cu(111) at RT. Orange spheres represent Cu adatoms.

The dehydrogenation of the hydroxyl group on Cu(111) at RT has been widely reported (23). Our experimental and theoretical calculation results also suggest that the individual 8-hq molecules exist as radical species that are weakly bound to the substrate by O and N atoms in a tilted orientation (fig. S7). Alternatively, the highly mobile 8-hq radicals coordinate with Cu adatoms on surface to form an organometallic complex (24). The proposed chemical structures of a dimer and trimer, respectively, in which the dehydrogenated 8-hq is assembled via an O(N)-Cu bond, are shown in Fig. 4, C and D. The calculated geometric sizes of these 8-hq complexes agree well with the AFM observations.

When the AFM is operated in the Pauli repulsion regime, the repulsive force from the outermost-shell valence electrons is also relevant to Embedded Image, which is in the form of kinetic energy. Here, Embedded Image is the electron wave function of the nth eigenstate of the sample. The kinetic energy reflects the localization property of electrons, which can be estimated by the electron localization function (ELF) (25). The ELF of the dimer and trimer exhibited strongly localized electron density donation from N to Cu, whereas the electrons between the Cu-Cu bonding are rather delocalized (Fig. 4, E and F). We attributed the bonding features in the central regions of the dimer and trimer to N-Cu coordination bonding, similar to the observed formation of the metal-organic coordinate bond excited by inelastic electrons (9, 26). According to the ELF, the O-Cu bond is strongly polarized, and the most shared electrons of the bond are localized around O; thus, the AFM signal is negligible. The C-H···O hydrogen bonds formed in the dimer and trimer were detectable in AFM because of the localized electrons around O and H.

Structural details—including the molecular conformation, the bond configuration, and the interacting sites on the functional groups—acquired from high-resolution noncontact AFM images provided useful insights into the mechanisms of molecular assembly and recognition. Because the H bond is ubiquitous in nature and central to biological functions, the present technique may provide an important and complementary characterization method for unraveling the fundamental aspects of molecular interactions at the single-molecule level. The observation of H bonding in real-space may also stimulate theoretical discussion about the nature of this intermolecular interaction.

Supplementary Materials

Materials and Methods

Figs. S1 to S9

References (2832)

References and Notes

  1. Supplementary materials are available on Science Online.
  2. The observation of an intramolecular hydrogen bond was tentatively proposed by Gross et al. in the study of the organic compound cephalandole A (8).
  3. The measured bond length may involve the amplification effect of CO on the tip apex, as discussed in (11). It should also be noted that the expected bending of X−H···Y was not resolved in all of the hydrogen bonds shown in Fig. 2, A and B. The exact mechanism was not understood.
  4. We found that it is difficult to obtain a high-resolution AFM image on this specific type of 8-hq dimer compared with single molecules or other molecular aggregates. These dimers often accidentally dislocate during AFM imaging, indicating a weaker interactions between the molecules and the substrate. We suggested that the formation of two hydrogen bonds in the dimer weaken the binding interaction of -OH and N of 8-hq to the metal substrate. Note that the optimal imaging parameters for this dimer (see the Fig. 3A legend) are different from those used for other molecular clusters.
  5. We conducted a further calculation (13) following the method proposed in (27).
  6. Acknowledgments: This project is partially supported by the Ministry of Science and Technology of China (grants 2012CB933001 and 2012CB932704), the Natural Science Foundation of China (grants 21173058, 21203038, 11274308, and 11004244), the Beijing Natural Science Foundation (grant 2112019), and the Basic Research Funds in Renmin University of China from the Central Government (grant no. 12XNLJ03). W.J. was supported by the Program for New Century Excellent Talents in Universities. Calculations were performed at the Physics Lab for High-Performance Computing of Renmin University of China and Shanghai Supercomputer Center. We thank W. Ho, P. Grutter, and L. Gross for valuable discussion and technical advice.
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