Imaging of Molecules

One of the first triumphs of STM imaging in UHV was the resolution of the (3x3) adlayer structure of benzene coadsorbed with CO as a stabilizing agent on the Rh(l 11) surface. Itaya and coworkers resolved similar structures under in situ conditions in the absence of adsorbed CO (cf. Fig. 24). The authors proposed that stabilizing benzene molecules adsorption effect of CO in UHV 

Another STM-UHV imaging success was the resolution of the internal structure of copper-phthalocyanine molecules. It was attained by Ogaki et al. under in situ conditions in 1996. They demonstrated an image of a specific modified porphyrin adsorbed on Ag(lll)-I surface, revealing the internal structure and molecular orientation in the ordered layer, as shown in Fig. 25. 

Itaya s group presented images of benzene, naphthalene and anthracene on Cudll), and naphthalene and anthracene on Rh(l 11)/ Wandlowski and coworkers monitored adsorption of uracil on gold surfaces They reported imaging chemisorbed molecules as well as physisorbed molecules and determined their adlattice structures. They also made a correlation between the structure and lateral interaction forces of adsorbed molecules. They showed that application of sufficiently positive electrode potentials results in uracil deprotonation, leading to different surface structure and geometric orientation. 

A few groups examined larger systems by in situ STM. Examples include the deposition of polymers, polypyrrole, polyaniline,and polymethylthiophene. Hagenstrom et al. reported studies on imaging of self-assembled monolayers (SAM). They showed the possibihty of imaging detailed stmetures, and order-disorder transitions in dependence on electrochemical parameters. 

The use of in situ STM for the identification of structurally similar molecules on the basis of tlreir redox properties was reported by Tao. By adjusting the substrate potential, he aligned its Fermi level to different energy levels of molecules, which resulted in a nearly ten-fold increase in the tunneling current flowing through molecules due to resonant tuimehng. This phenomenon can be used to follow the reaction of individual molecules under in situ conditions in the future. 

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STM can operate in air or in a liquid, making images of molecules in their natural environment possible... 

STM images of molecules are often a sensitive function of the tunnel conductance. For example, when examining TMPyP on Au( 111 )-I, the iodine underlayer was imaged at a tunnel resistance of 5 X 10 ohms while the electron density of TMPyP was observed at 8 X 10 ohms [484], Similar effects have been noted for protoporphyrins [488] and purines [489,490] adsorbed on graphite. 

The Fourier transform describes precisely the mathematical relationship between an object and its diffraction pattern. In Figs. 2.7-2.10, the diffraction patterns are the Fourier transforms of the corresponding objects or arrays of objects. To put it another way, the Fourier transform is the lens-simulating operation that a computer performs to produce an image of molecules (or more precisely, of electron clouds) in the crystal. This view of p(x,y,z) as the Fourier transform of the structure factors implies that if we can measure three parameters— amplitude, frequency, and phase — of each reflection, then we can obtain the function p(x,y,z), graph the function, and "see" a fuzzy image of the molecules in the unit cell. 

In producing an image of molecules from crystallographic data, the computer simulates the action of a lens, computing the electron density within the unit cell from the list of indexed intensities obtained by the methods described in Chapter 4. In this chapter, I will discuss the mathematical relationships between the crystallographic data and the electron density. 

Bonino brought forward a further contribution to the theory of infrared spectra of organic liquids by incorporating the Bohr-Sommerfeld quantum conditions, including the correspondence principle of Bohr as well. This paved the way toward establishing a correlation between the physical and chemical image of molecules in the study of infrared spectra. From this series of papers on infrared spectroscopy, one can already observe the interdisciplinary character of Bonino s thought. In a lecture delivered some years later, Bonino offered these reflections on his chosen field of research ... 

When one inserts an image of molecule from the Molecule Editor into a ChemText document, one actually inserts a computable representation of the structure. As this is a new concept, let me illustrate with an example. Suppose you have a ChemBase data base of your compounds. (See Fig. 1.8) You pull out the structure of your new compound and insert it into your manuscript which you... 

Figure 2. The exchange repulsion contours for several molecules, obtained for interactions with rare-gas atoms, and defined by two polar coordinates measured from the center of mass (Energy, 0) [31,32], The contours are the images of molecules shapes, probed by structureless atoms. In contrast to plots that show isoeneigetic regions, these contours reveal an enhanced anisotropy. Convex and concave regions indicate, respectively, the areas of increased and reduced exchange repulsion.

Figure 2.16 Three-dimensional structures with corresponding in situ STM images of molecules immobilized on Au(l 11) electrode surfaces modified by a mercaptodecanoic acid...

The AFM, invented in 1985, uses repulsive forces between atoms on the probe s tip and those on the sample s surface to form images on the computer screen. An advantage of the AFM is that it does not have to work in a vacuum, so its samples require no special preparation. AFMs can provide images of molecules in living tissue and peel off membranes of living cells one layer at a time. 

Elastic resonant tunneling and/or through bond tunneling has also become a central theme in the interpretation and theoretical development of STM imaging of molecules adsorbed on metal surfaces [2, 3, 39, 44, 45], Numerous images of molecules adsorbed on metallic surfaces display a likeness to the shape of the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals of... 

Spin-Polarization Indices and Antiferromagnetic Image of Molecule... 

This defines chirality, an equivalence relation on the set of all molecules. This separates molecules into sets containing a single molecule or a pair of mirror images of molecules. 

The Pherobase database is an extensive compilation of behavior-modifying compounds listed in the various pheromone categories aggregation, alarm, releaser, primer, territorial, trail, sex pheromones, and others. The database contains over 30,000 entries. Jmol images of molecules are shown. The molecules can be projected as either space-filling or wire-frame models. They can be rotated in 3-dimensional space. In addition, the database includes mass spectral, NMR, and synthesis data for more than 2,500 compounds. This is a fun site ... 

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