Progress in High-Resolution Atomic Force Microscopy (AFM) Imaging

Topics Covered

Description of Alkanes
AFM Imaging of Alkane Layers on Graphite
Imaging in AM and FM Modes
About Agilent Technologies


High-resolution imaging has been the primary feature that attracts researchers’ attention to scanning probe microscopy (SPM), yet there are still a number of outstanding questions regarding this function of scanning tunneling microscopes (STM) and atomic force microscopes (AFM). A few related issues, starting with AFM imaging of alkane layers on graphite, will be addressed here.

Description of Alkanes

Normal alkanes (chemical formula: CnH2n+2) are linear molecules with a preferential zigzag conformation of -CH2- groups. Their terminal -CH3 groups are slightly larger than their - CH2- groups, but more mobile. At ambient conditions, alkanes with n=18 and higher are solid crystals (the melting temperature of C18H38 is 28° C) with chains oriented practically vertical in respect to the larger faces of the crystals. Contact mode AFM images of such a surface of a C36H74 crystal (which is formed of -CH3 groups) have revealed the periodical arrangement of these groups [1].

It has long been known that on the surface of graphite the alkane molecules are assembled in flat-lying lamellar structures in which the fully extended molecules are oriented along three main graphite directions (see Figure 1). This molecular order is characterized by a number of periodicities: 0.13nm spacing between neighboring carbon atoms, 0.25nm spacing between -CH2- groups along the chain in the zigzag conformation, 0.5nm interchain distance inside the lamellae, and the lamellar width — the length of the extended CnH2n+2 molecule. The latter varies from 2.3 nm for C18H38 to 49.5 nm for C390H782 (the longest alkane synthesized).

Figure 1. Sketch showing lamellar and molecular order of normal alkane on graphite.

AFM Imaging of Alkane Layers on Graphite

Alkane adsorbates on graphite were first examined with STM [2]. In such experiments, a droplet of saturated alkane solution is deposited on a graphite surface. A metallic tip penetrates this droplet, as well as a molecular adsorbate at the liquid-solid interface, until it detects a tunneling current. At these conditions, the tip is scanning over the ordered molecular layer in the immediate vicinity of the substrate. STM images of normal alkanes on graphite (such as the one reproduced from [3] and presented in Figure 2) clearly demonstrate the fine details of the molecular arrangement, such as lamellar edges, individual chains inside the lamellae, and the zigzag conformation of the alkane chains.

Figure 2. STM image of C36H74 alkanes on graphite.

In STM imaging at the liquid-solid interface, the probe is surrounded by alkane-saturated solution. Any instability of the imaging and the use of low tunneling gap resistance will cause mechanical damage to the alkane order, and the probe might record an image of the underlying graphite. If the gap is increased again, the alkane order will be restored due to a pool of alkane molecules. It is practically impossible to obtain STM images of “dry” alkane layers on graphite because occasional damage to the layers is non-repairable.

Studies of dry alkane layers on graphite can be performed with AFM, but thus far the “STM” resolution of the lamellae arrangement has not been achieved. Initially, lamellar adsorbates of C60H122 on graphite were examined in amplitude modulation mode and spacing of 7.6 nm on different lamellar planes and multilayered structures could clearly be seen in resultant images [4]. In the absence of standards for the “few nanometers” range, these periodical structures can be employed for X- and Y-axis calibration of scanners. Although formerly used as a way to prove the high-resolution imaging capabilities of a particular scanning probe microscope, visualization of the 7.6nm strips is no longer considered challenging. Today, the ability to obtain images of smaller lamellar structures (e.g., C36H74 with 4.5nm spacing, C18H38 with 2.3nm spacing) provides a better gauge of microscope performance and operator experience.

Typical AFM images of C18H38, C36H74, and C60H122 lamellae on graphite obtained with an Agilent 5500 atomic force microscope are shown in Figure 3. The lamellar edges are clearly resolved in these images. The origin of the contrast is the difference between the effective stiffness of the lamellar core (-CH2- sequences) and its edges (-CH3 and nearby -CH2- groups). The complex pattern of C36H74 lamellae seen in the “350 nm” image is caused by the grains of the substrate as well as the peculiarities of the chain order inside the lamellae. In some sample preparations, neighboring chains are shifted to better accommodate the bulky -CH3 end groups, leading to the chains’ tilt in respect to the lamellar edges. Therefore, individual lamellar widths might be smaller than the length of the alkane chains.

Figure 3. AFM images of normal alkanes on graphite obtained in amplitude modulation mode.

Keeping in mind the STM images of normal alkanes on graphite, it is rather interesting to speculate as to whether such resolution can be achieved via AFM, either in contact or oscillatory (amplitude modulation, frequency modulation) modes. There has been definite progress in this respect, as demonstrated by AFM images of three different alkanes (C18H38, C242H486, and C390H782) on graphite obtained in contact mode (see Figures 4 and 5). The spacing, which is related to the lamellae and the individual chains, is discernable in the image of C18H38 lamellae (Figure 4). The zigzag pattern along the closely packed alkane chains is seen in the image of the ultralong alkane, C390H782 (Figure 4). Several slightly twisted lamellae were detected in the images of C242H486 (Figure 5). In the “100 nm” image, a number of linear defects caused by missing chains or their parts are distinguishable. Individual alkane chains, which are extended between the edges of the lamellae, are also visible in the “55 nm” image.

Figure 4. AFM images of C18H38 and C390H782 lamellae on graphite obtained in contact mode.

Figure 5. AFM images of C242H486 lamellae on graphite obtained in contact mode.

A high-density image containing a number of pixels from 1k to 4k must be collected in order to observe the lamellar edges and individual chains of long alkanes within the same image. Such imaging takes time and requires an instrument with low thermal drift. The demonstrated visualization of molecular spacing down to 0.25 nm in contact mode offers hope that similar observations can be achieved in oscillatory amplitude modulation (AM) and oscillatory frequency modulation (FM) modes when applied in ambient conditions or under liquid. Visualization with 0.25nm resolution of the molecular structure of pentacene has already been achieved in FM experiments in UHV and at low temperatures [5].

Imaging in AM and FM Modes

For a number of years, progress in AFM has been in some part related to the developments and applications of FM mode. This technique, which was originally employed in UHV as an alternative to AM mode for the detection of tip-sample force interactions and scanning, is now also used for high-resolution imaging in air and under liquid. High-resolution images of mica, self-assemblies of alkanethiols, and polydiacetylene (PDA) crystals have been recorded with FM mode using “homemade” setups [6, 7]. These periodical structures are characterized by spacing greater than 0.5 nm. In some cases, molecular-scale individual defects have been observed. Similar findings have been reported utilizing AM mode [8]. Several high-resolution images obtained in AM mode with an Agilent 5500 atomic force microscope are shown in Figures 6–8.

Using AM mode in air, a number of molecular-resolution images have been obtained of the surface of a PDA crystal. After a crystal is cleaved, its largest atomically smooth face (with few linear defects) is the most suitable for molecular-scale imaging (see Figure 6, top right). At higher magnification, the periodical pattern mimicking the crystalline structure of the bc-plane can be obtained (Figure 6, top right and bottom).

Figure 6. AFM images of a polydiacetylene crystal obtained in amplitude modulation mode in air. A red rectangle indicates the crystallographic lattice on the bc-plane of this crystal.

This lattice, with orthogonal spacing of 0.5 nm (the repeat distance along the c-axis) and 0.7 nm (half of the repeat distance along the b-axis), was also detected using different probes (see Figure 7). Despite the similarity of the image patterns obtained with different probes, image variations are noticeable. There is definitely a lack of high resolution of fine atomic-scale features. This is a common characteristic of images obtained in AM and FM modes in air and under liquid, where spacing less than 0.5 nm is poorly resolved.

Figure 7. AFM images of a polydiacetylene crystal obtained in amplitude modulation mode in air. This probe was different from the one used in the experiment that yielded the images shown in Figure 6.

The situation is only slightly better for images in contact mode, where in addition to visualization of a mica surface, the lattices of MoS2 and graphite can be observed. Contact mode images of these layered materials are shown in Figure 8.

Figure 8. Top row: topography images of three layered crystals obtained in contact AFM mode. Topography contours along these images are presented directly below them, in the middle row. Bottom row: 3D representations of the crystallographic surface structure of carbon, Se, and potassium atoms.

The original images are quite noisy, but the periodical lattices can be enhanced via an FFT procedure that leads to perfect hexagonal patterns (embedded in the top portion of the images). Topography traces along the images are presented directly below them; these traces show that the surface corrugations increase from 40 pm (graphite) to 300 pm (mica). Therefore, molecular-scale imaging of mica is less demanding due to its larger corrugations and interatomic separations, as depicted in 3D sketches of the atomic surface structure of the crystals (Figure 8, bottom row).


In summary, the current status of atomic-scale imaging in AFM is not satisfactory — there is room for further improvement. The progress of high-resolution imaging in AM and FM modes is particularly desirable; both oscillatory modes can be applied to a much broader range of materials (including soft objects) as compared with contact mode AFM. Future progress relies on instrumental improvements such as better signal-to-noise characteristics, lower thermal drift, and improved detection and control of tip-sample forces, as well as the use of sharp probes.

Another critical issue is related to gaining a better understanding of the nature of atomic-scale resolution in AFM, a topic that has been under discussion since the first successful visualization of atomic- and molecular-scale lattices in contact mode. Single atomic-scale defects have never been practically recorded in contact mode. Therefore, such imaging provides only lattice resolution — in contrast to true atomic resolution where the detection of such defects is expected. Imaging of periodical lattices with defects has been demonstrated in FM and AM images (first in UHV and later in ambient conditions), but the results of computer simulation have revealed that visualization of the defects does not necessarily mean that the surrounding molecular order is correctly reproduced in the images [9, 10]. These findings emphasize a need for comprehensive interplay between experiment and theory in the analysis of atomic-scale data.


[1] W. Stocker et al., Polym. Bull. 1991, 26, 215–222.

[2] G.C. McGonigal, R.H. Bernhardt, and D.J. Thomson, Appl. Phys. Lett. 1990, 57, 28.

[3] W. Liang et al., Adv. Mater. 1993, 5, 817–821.

[4] S.N. Magonov and N.A. Yerina, Langmuir 2003, 19, 500–504.

[5] L. Gross et al., Science 2009, 324, 142.

[6] T. Fukuma et al., Appl. Phys. Lett. 2005, 86, 193108.

[7] T. Fukuma et al., Appl. Phys. Lett. 2005, 86, 034103.

[8] D. Klinov and S. Magonov, Appl. Phys. Lett. 2004, 84, 2697.

[9] S. Belikov and S. Magonov, Jap. Jour. Appl. Phys. 2006, 45, 2158.

[10] S. Belikov and S. Magonov, Proc. Amer. Control Soc., St. Louis, 2009, 979.

About Agilent Technologies

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Date Added: May 11, 2011 | Updated: Jun 11, 2013
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