Atomic Force Microscopy for Molecular Structure Elucidation.

Topological Defects Induced High-Spin Quartet State in Truxene-Based Molecular Graphenoids

Abstract

Scanning probe microscopy (SPM) can be successfully used in biological investigations1. Scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) are two main SPM techniques and they are capable of imaging biological objects at molecular level under in situ conditions. With this advantage, STM and AFM are applied to study not only the topographical structures of bio-samples in their natural environment, but also their electrochemical properties at liquid-solid interfaces. The electrochemical properties of biomolecules are usually studied by integral electrochemical methods, like cyclic voltammetry. The degree of surface coverage, the surface orientation of enzymes and the activity of a single enzyme remain a question of dispute, however, electrochemical SPM techniques can bring clarification. Electrochemical scanning tunnelling microscopy (EC-STM) and electrochemical atomic force microscopy (EC-AFM) provide visual topological information of biomolecules adsorbed on the electrode surface at single-molecular level. Some experimental issues, such as the requirement of the sample being conductive, potential damage to samples caused by the tunnelling current or tip-sample force, may limit their application. Scanning electrochemical potential microscopy (SECPM), a technique that measures the surface potential distribution at zero current, can be a promising alternative. SECPM shares most of the hardware setup with EC-STM except for the current amplifier being substituted by a potentiometer. It is easy to switch between SECPM and EC-STM to compare the topographical profile of the same area by mapping electron density and surface potential2. In our study, SPM techniques are used to study various biological objects, from nanometer-sized DNA and redox proteins to micrometer-sized bacteria spores. Since high-resolution images of DNA origami nanostructures can be achieved by using AFM3, we use both EC-AFM and SECPM techniques to investigate the morphology and potential-dependent adsorption behaviour of DNA scaffold and origamis4 on the modified HOPG surface. We found DNA scaffold can adsorb on HOPG in a certain potential range, and the adsorption structure changes with the applied electrochemical potential. Horseradish peroxidase (HRP), a redox enzyme, was studied using both, EC-STM and SECPM under in situ conditions5. HRP molecules were adsorbed on highly oriented pyrolytic graphite (HOPG) surfaces and imaged in phosphate buffered saline. We found that SECPM shows a better resolution than EC-STM in imaging this biomolecule. SECPM is also capable of measuring the surface charge distribution of the adsorbed biomolecules at the electrochemical interfaces. AFM in liquid was used to investigate the morphology and cellular process of Streptomycetes venezuelae both the wild type and the mutant6. To immobilize the bacteria on the surface for imaging, we use SiC patterned by photolithography with hole arrays (1.5×1.5×0.6 µm) to trap the bacteria and then measure under the physiological condition. The designed hole arrays trap the bacteria without causing any denaturation and due to the high electronic conductivity, they can serve as the working electrode under electrochemical conditions for EC-AFM and SECPM studies. EC-AFM was applied to image the morphology of the bacterial spore under different potential, and we found the morphology of the spore didn’t change in the wide potential window. (1) Choi, E.; Kim, A.; Son, H.; Pyo, S. G. J. Nanosci. Nanotechnol. 2014, 14 (1), 924. (2) Herpich, M.; Friedl, J.; Stimming, U. In Surface Science Tools for Nanomaterials Characterization; Springer Berlin Heidelberg: Berlin, Heidelberg, 2015; pp 1–67. (3) Bald, I.; Keller, A. Molecules 2014, 19 (9), 13803. (4) Kozyra, J.; Ceccarelli, A.; Torelli, E.; Lopiccolo, A.; Gu, J.-Y.; Fellermann, H.; Stimming, U.; Krasnogor, N. ACS Synth. Biol. 2017, 6 (7), 1140. (5) Baier, C.; Stimming, U. Angew. Chem. Int. Ed. Engl. 2009, 48 (30), 5542. (6) Santos-Beneit, F.; Gu, J.-Y.; Stimming, U.; Errington, J. Heliyon. Accepted

Scanning Probe Microscopy (SPM) techniques, including Conductive-Atomic Force Microscopy (C-AFM), Kelvin Probe Force Microscopy (KPFM), and Piezoresponse Force Microscopy (PFM) or Electrochemical Strain Microscopy (ESM), are critical for the in situ, non-destructive analysis of material interfaces with high spatial resolution. Despite substantial advancements in SPM technologies, challenges related to their reliability and accuracy remain, primarily due to measurement artifacts and electrochemical reactions on the sample surface. These artifacts can significantly skew results, leading to misconceptions unless critically analyzed.This study explores the influence of the dielectric gap on electric characterization, particularly focusing on how variations in permittivity affect the results obtained from C-AFM and PFM techniques. By adjusting the permittivity of the dielectric medium (air, water with εr = 79, and silicone oil with εr = 2.1-2.8), we demonstrate that high permittivity media can significantly correct the discrepancies commonly observed in coercive field measurements, aligning them closer to values obtained from conventional capacitor-based polarization methods.Our findings illuminate the critical role of the dielectric gap in SPM, suggesting methodological adjustments for improved accuracy in the nanoscale electrical characterization of electrochemical materials. These insights offer significant implications for advancing the precision and reliability of SPM techniques in studying electronic materials.

We report the designof a time-shared switching scheme, aiming to realize the manipulation and working modes (imaging mode and transport measurement mode) switching between multiple scanning tunneling microscope (STM) probes one by one with a shared STM control system (STM CS) and an electrical transport characterization system. This scheme comprises three types of switch units, switchable preamplifiers (SWPAs), high voltage amplifiers, and a main control unit. Together with the home-made software kit providing the graphical user interface, this scheme achieves a seamless switching process between different STM probes. Compared with the conventional scheme using multiple independent STM CSs, this scheme possesses more compatibility, flexibility, and expansibility for lower cost. The overall architecture and technique issues are discussed in detail. The performances of the system are demonstrated, including the millimeter scale moving range and atomic scale resolution of a single STM probe, safely approached multiple STM probes beyond the resolution of the optical microscope (1.1 µm), qualified STM imaging, and accurate electrical transport characterization. The combinational technique of imaging and transport characterization is also shown, which is supported by SWPA switches with ultra-high open circuit resistance (909TΩ). These successful experiments prove the effectiveness and the usefulness of the scheme. In addition, the scheme can be easily upgraded with more different functions and numbers of probe arrays, thus opening a new way to build an extremely integrated and high throughput characterization platform.

Scanning probe microscopy (SPM) has continued to advance into new applications and disciplines every year. The development of new techniques and instrumentation for SPM's have enabled researchers to study sample surfaces in a variety of ambient conditions and using a number of contrast mechanisms. A review of new SPM techniques and instrumentation will be presented.Phase imaging is a new technique that provides nanometer-scale information about variations in surface properties, such as adhesion, friction, viscoelasticity, composition and perhaps others, not revealed by any other single SPM technique. An example using phase imaging to differentiate component phases of composite materials is shown in Fig. 1 of wood pulp fiber. The left image is a normal topographic image acquired using the TappingMode™ technique. The right image is the simultaneous phase image. The phase image highlights cellulose microfibrils and a lignin component atop the cellulose component not seen in the topographic image. The details of phase imaging will be discussed.

Piezoelectric and ferroelectric materials have garnered significant interest owing to their excellent physical properties and multiple potential applications. Accordingly, the need for evaluating piezoelectric and ferroelectric properties has also increased. The piezoelectric and ferroelectric properties are evaluated macroscopically using laser interferometers and polarization–electric field loop measurements. However, as the research focus is shifted from bulk to nanosized materials, scanning probe microscopy (SPM) techniques have been suggested as an alternative approach for evaluating piezoelectric and ferroelectric properties. In this Progress Report, the recent progress on the nanoscale evaluation of piezoelectric and ferroelectric properties of diverse materials using SPM‐based methods is summarized. Among the SPM techniques, the focus is on recent studies that are related to piezoresponse force microscopy and conductive atomic force microscopy; further, the utilization of these two modes to understand piezoelectric and ferroelectric properties at the nanoscale level is discussed. This work can provide guidelines for evaluating the piezoelectric and ferroelectric properties of materials based on SPM techniques.

Summary form only given. Higher areal storage densities increase the relevance of smaller media defects which might play a major role in HDD performance. In particular, the decrease in distance of the write and read elements to the spinning media (a decrease from 20 nm to 5 nm is expected in the next 5 years) requires a very careful control of defect heights. Furthermore, anti-ferromagnetic coupled media may cause new types of defects, which cannot be detected by any topographic sensitive measurement technique. We have developed a non-destructive, clean-room compatible measurement tool which allows us to test the entire surface with respect to magnetic and topographic properties of the magnetic storage media as well as to characterize specific areas on a nm/sup 2/ scale by means of scanning probe microscopy (SPM). SPM techniques are already used for defect characterization but they suffer from a small throughput, are often destructive and defect areas cannot be re-tested with exactly the same recording parameters. We have combined a spin stand tester (SST) and a SPM to a single unit. A positioning procedure allows us to automatically position specific areas which have been detected by the SST for SPM characterization.

The characterization of the local multifield coupling phenomenon (MCP) in various functional/structural materials by using scanning probe microscopy (SPM)-based techniques is comprehensively reviewed. Understanding MCP has great scientific and engineering significance in materials science and engineering, as in many practical applications, materials and devices are operated under a combination of multiple physical fields, such as electric, magnetic, optical, chemical and force fields, and working environments, such as different atmospheres, large temperature fluctuations, humidity, or acidic space. The materials' responses to the synergetic effects of the multifield (physical and environmental) determine the functionalities, performance, lifetime of the materials, and even the devices' manufacturing. SPM techniques are effective and powerful tools to characterize the local effects of MCP. Here, an introduction of the local MCP, the descriptions of several important SPM techniques, especially the electrical, mechanical, chemical, and optical related techniques, and the applications of SPM techniques to investigate the local phenomena and mechanisms in oxide materials, energy materials, biomaterials, and supramolecular materials are covered. Finally, an outlook of the MCP and SPM techniques in materials research is discussed.

High-resolution scanning probe microscopy (SPM) is a fundamental and efficient technology for surface characterization of modern materials at the subnanometre scale. The bottleneck of SPM is the probe and scanning tip. Materials with stable electrical, thermal, and mechanical properties for high-aspect-ratio (AR) tips are continuously being developed to improve their accuracy. Among these, GaN is emerging as a significant contender that serves as a replacement for standard Si probes. In this paper, for the first time, we present an approach that demonstrates the application of GaN microrods (MRs) as high-AR SPM probes. GaN MRs were grown using molecular beam epitaxy, transferred and mounted on a cantilever using focused electron beam-induced deposition and milled in a whisker tip using a focused ion beam in a scanning electron/ion microscope. The presence of a native oxide layer covering the GaN MR surface was confirmed by X-ray photoelectron spectroscopy. Current-voltage map measurements are also presented to indicate the elimination of the native oxide layer from the tip surface. The utility of the designed probes was tested using conductive atomic force microscopy and a 24-hour durability test in contact mode atomic force microscopy. Subsequently, the graphene stacks were imaged.

In this chapter, we discuss recent developments in the characterization of polarization doped wide bandgap semiconductor (WBS) heterojunctions with an emphasis on characterization by scanning probe microscopy (SPM). Wide bandgap semiconductors, such as SiC and GaN, have a wide variety of applications in electronic and optoelectronic devices [1–6]. The operation of devices made from these materials is dominated by the polarization properties of III-N and SiC semiconductor crystals. For example, polarization doped 2 dimensional electron gas (2DEG) channels in undoped GaN/AlGaN and SiC polytypic heterojunctions have been fabricated with current densites in excess of 1A/mm. Other effects, such as surface charge instability stemming from polarization, offer interesting potentials and challenges.While some of these effects may be studied using more conventional techniques such as currentvoltage (IV) and capacitance-voltage (CV) techniques (described in sections 2 and 3), others require probes capable of investigation on the nanometer scale. Transmission electron microscopy (TEM) can be used to investigate such polarizationinduced phenomena with atomic resolution, but involves destructive and laborious sample preparation. SPM techniques offer powerful, non-destructive tools to effectively and conveniently probe electronic materials and devices. Since the discovery of scanning tunneling microscopy (STM) in 1981 by Binnig and Rohrer [7], the field of SPM has advanced to encompass a large number of variations including, (i) STM, (ii) Atomic force microscopy (AFM), (iii) Electrostatic force microscopy (EFM), (iv) Scanning capacitance microscopy (SCM), (v) Scanning conduction microscopy (SCM), (vi) Magnetic force microscopy (MFM), (vii) Piezoelectric force microscopy (PFM), and (vii) Near field scanning optical microscopy (NSOM). Of the above modes, the first five modes have been extensively used for semiconductor characterization [8–15]. For WBS characterization, especially III-N, AFM, EFM and SCM modes are the most important due to the strong polarization of III-N and SiC. In the latter half of this chapter, we focus on the characterization of III-N by EFM operated in

Imaging micro-cracks in gold films: a comparative study of scanning tunneling and atomic force microscopies

Organic semiconductors are promising materials for future electronic and electroluminescence applications. A detailed understanding of organic layers and nano-sized crystals down to single molecules can address fundamental questions of contacting organic semiconductors at the nanometer limit and obtaining luminescence from them. In this thesis, electroluminescence spectra from pentacene, a policyclic hydrocarbon (acene), are discussed. The luminescence is induced by the current from the tip of a scanning tunneling microscope (STM). Pentacene is an organic semiconductor which gained a lot of attention in technology because of its electronic properties suitable for applications in thin film devices. Moreover, recent fundamental studies employed pentacene as a standard to demonstrate sub-molecular resolution by scanning probe techniques. This work reports the first observation of light emission from nanometer-sized pentacene crystals grown on an ultrathin insulating layer on noble metal surfaces. Different STM-techniques are combined to characterize the individual systems studied with respect to topography, crystal structure, electronic properties and work function changes. The initial step of the project was the implementation of an optical system for light collection from the tunnel-junction of a low-temperature STM. In the set-up, a novel approach based on the use of in situ adjustable lenses has been realized. Three lenses placed in the vicinity of the tip-apex allow light collection into three independent channels which can be used for versatile optical analysis. An important part in the characterization of the organic system was to clarify the interaction between adsorbed molecules and substrates. We investigated individual pentacene molecules on different ultrathin insulator-metal systems. With the STM tip in tunnel contact, the molecules are situated in a double barrier junction formed by the insulating layer on one side and the vacuum gap on the other side. The metal surface and the STM-tip form the electrodes. The electronic properties of pentacene in this configuration have been characterized. Insulator-metal-systems, which provide a good electronic decoupling for pentacene from the metal, have been chosen as substrates for the growth of pentacene nanocrystals. Using the sub-molecular resolution of the STM we resolved the structure of the top-layer of the pentacene nanocrystals and found that the crystal phase agrees with the pentacene bulk structure. Moreover, the comparison of charge injection barriers between individual molecules and nanocrystals of pentacene indicates a significant change of electronic properties after the formation of ordered structure from the individual building blocks. Optical spectroscopy of the emitted light reveals an excitonic emission from the nanocrystals, which is in very good agreement with photoemission spectra of macroscopic crystals. Although a highly localized current-injection by the STM tip is used for excitation, it can be concluded that the source of light emission is delocalized. In contrast to luminescence measurements reported for other organic materials in STM, the excitation is not localized on the individual molecule, into which a charge is injected by the STM-tip. Our study indicates the importance of inter-molecular coupling leading to a high mobility of the excited state which has to be considered in the framework of STM-induced luminescence. A further result is the observation of the Stark shift of pentacene luminescence, that has so far not been measured at large electric fields of the order of 1V/nm. The evaluation of the Stark shift provides information on dipole and polarizability change during the decay of an exciton. The measured large dipole change of the lowest singlet exciton in pentacene indicates a mixing of the Frenkel exciton (FE) with a small contribution of charge-transfer (CT). Finally, we developed a set-up for photon correlation measurements in the STM. The properties of photon statistics is a means which can unambiguously prove that the luminescence is due to a single-photon source, i.e. a light source which emits no more than one photon at a time. A typical example of such a source is the emission from a single molecule. We performed photon correlations measurements of the luminescence from pentacene and C60 nanocrystals. While the excitonic bulk emission of pentacene is not expected to represent a single photon emitter, we also did not observe anticorrelations in the case of C60 indicating the importance of the local environment in the STM-junction, e.g. the short distance to the metal electrodes.

Crystallographic image processing (CIP) techniques may be utilized in scanning probe microscopy (SPM) to glean information that has been obscured by signals from multiple probe tips. This may be of particular importance for scanning tunneling microscopy (STM) and requires images from samples that are periodic in two dimensions (2D). The image-forming current for double-tips in STM is derived with a slight modification of the independent-orbital approximation (IOA) to allow for two or more tips. Our analysis clarifies why crystallographic averaging works well in removing the effects of a blunt STM tip (that consists of multiple mini-tips) from recorded 2D periodic images and also outlines the limitations of this image-processing technique for certain spatial separations of STM double-tips. Simulations of multiple mini-tip effects in STM images (that ignore electron interference effects) may be understood as modeling multiple mini-tip (or tip shape) effects in images that were recorded with other types of SPMs as long as the lateral sample feature sizes to be imaged are much larger than the effective scanning probe tip sizes.

Mesoporous materials possess highly ordered periodic arrays of uniformly sized channels. Therefore, these compounds have attracted considerable attention for many researchers (Luo et al., 2000; Xu & Xue, 2006; Liu et al., 2009 a, Salehirad & Anderson, 1996; 1998a; 1998b; 1998c). Since the shape and texture of the materials strongly affect their properties, these materials due to their large surface areas, controllable pore size and easy functionalization have been used in separation science, drug delivery and various processes such as adsorption and catalysis (Liu et al., 2009a; Duan et al., 2008; Liu et al., 2009 b; Liu & Xue, 2008; Mohanty & Landskron, 2008; Salehirad, 2004; Alibouri, 2009a; 2009b). Zeolites as crystalline aluminosilicates are microporous materials with well-defined channels and cavities have been used as ion-exchangers, adsorbents, heterogeneous catalysts and catalyst supports (Zhang et al., 2000; Zhang et al., 2000). Many parameters are found to be highly important in the physical appearance of final zeolite products (Aghabozorg et al., 2001). Morphology and crystal size of these compounds have an important role for their specific applications in industries (Zabala Ruiz et al., 2005). The ability to accommodate various organic and inorganic species in zeolites makes them ideal host materials for supramolecular organization (Bruhwiler & Calzaferri, 2004; Schulz-Ekloff et al., 2002; Sadegh Hassani et al., 2010a). In many cases, surface adsorption sites in zeolites lead to interesting photochemical properties for these compounds. (Zabala Ruiz et al., 2005; Hashimoto, 2003). Studying the surface structure of zeolites and dynamic phenomena occurring on the surface of these compounds under various conditions will accelerate the development of these compounds as catalyst or materials with versatile functions (Sugiyama Ono et al., 2001; Anderson, 2001; Sadegh Hassani et al., 2010a). Nucleation mechanisms and growth of zeolites are not well understood for many of the systems involved. In most cases, the problem is compounded with the presence of a gel phase. This gel also undergoes a continuous polymerization type reaction during nucleation and growth. Improved understanding of zeolite growth should enable a more targeted approach to zeolite synthesis in the future and may ultimately lead to the possibility of zeolite design to order. Numerous techniques have been used for study the structure of the zeolites. Among them, scanning probe microscopy (SPM) is an appropriate technique that can be applied in atmospheric condition. However, many SPM techniques can be used in essentially any environment, including ambient, UHV, organic solvent vapour and