Atomic force microscopy molecular structure

We have considered briefly the important macroscopic description of a solid adsorbent, namely, its speciflc surface area, its possible fractal nature, and if porous, its pore size distribution. In addition, it is important to know as much as possible about the microscopic structure of the surface, and contemporary surface spectroscopic and diffraction techniques, discussed in Chapter VIII, provide a good deal of such information (see also Refs. 55 and 56 for short general reviews, and the monograph by Somoijai [57]). Scanning tunneling microscopy (STM) and atomic force microscopy (AFT) are now widely used to obtain the structure of surfaces and of adsorbed layers on a molecular scale (see Chapter VIII, Section XVIII-2B, and Ref. 58). On a less informative and more statistical basis are site energy distributions (Section XVII-14) there is also the somewhat laige-scale type of structure due to surface imperfections and dislocations (Section VII-4D and Fig. XVIII-14). 

Overney R, Howald L, Frommer J, Meyer E, Brodbeck D and Guntherodt H 1992 Molecular surface structure of organic crystals observed by atomic force microscopy Ultramicroscopy 42-A4 983... 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

Funami, T., Hiroe, M., Noda, S., Asai, I., Ikeda, S., and Nishinari, K. (2007). Influence of molecular structure imaged with atomic force microscopy on the rheological behavior of carrageenan aqueous system in the presence or absence of cations. Food Hydrocolloids 21, 617-629. 

Atomic force microscopy (AFM) can be used to obtain high-resolution imagery of molecular orientation and ordering for materials adsorbed onto substrates. Early AFM studies on gluconamides were hampered by the tendency of the fibers to unravel on substrates forming bilayer sheets.41 These layers showed the head-to-tail packing of a monolayer which is similar to the crystal structure reported for anhydrous gluconamides.38 A procedure to retain the fiber networks on surfaces with the addition of a small fraction of... 

The technique of atomic force microscopy (AFM) has permitted the direct observation of single polysilane molecules. Poly[//-decyl-(high molecular weight (4/w = 5,330,000 and Mn = 4,110,000), PSS, helicity, and rigid rod-like structure due to the aliphatic chiral side chains, was deposited from a very dilute (10-10 Si-unit) dm-3] toluene solution onto a (hydrophobic) atomically flat (atomic layer steps only present) sapphire (1012) surface. After drying the surface for a few minutes in a vacuum, AFM images were taken at room temperature in air in the non-contact mode.204,253 An example is shown in Figure 22, in which the polymer chain is evident as a yellow trace. 

Table 5.2 Summary of selected analytical methods for molecular environmental geochemistry. AAS Atomic absorption spectroscopy AFM Atomic force microscopy (also known as SFM) CT Computerized tomography EDS Energy dispersive spectrometry. EELS Electron energy loss spectroscopy EM Electron microscopy EPR Electron paramagnetic resonance (also known as ESR) ESR Electron spin resonance (also known as EPR) EXAFS Extended X-ray absorption fine structure FUR Fourier transform infrared FIR-TEM Fligh-resolution transmission electron microscopy ICP-AES Inductively-coupled plasma atomic emission spectrometry ICP-MS Inductively-coupled plasma mass spectrometry. Reproduced by permission of American Geophysical Union. O Day PA (1999) Molecular environmental geochemistry. Rev Geophysics 37 249-274. Copyright 1999 American Geophysical Union...

The investigation was then extended to a monolayer formed from dipalmitoyl phosphatidyl choline and the same amphiphilic photochromic polypeptide XXIII.11211 When the monolayer was kept in the dark, the polypeptide molecules arranged themselves perpendicularly to the membrane (the water/air interface) and formed a bundle of helices which could be observed by atomic force microscopy as a transmembranous particle of about 4 nm in diameter. Irradiation with UV light and the consequent trans—>tis isomerization of the azobenzene moiety caused a bending of the molecular main chain, which in turn produced a destabilization and dena-turation of the bundle of helices in the monolayer. After removal of the light, the polypeptide molecules reverted to their original bundle structure. 1211... 

Adsorption. Sulfur and phosphorus ratios change with rubbing time. Tribofilms accumulated on the surface become thicker with time. All co-additives cause reduction in ZDDP surface coverage under all conditions studied. A surface force apparatus (SFA), and atomic force microscopy were used to determine tribofilm thiclaiess, molecular structure and mechanical properties. For the neutral ZDDP, monomolecular layer thickness is 1 nm and for basic ZDDP it is 1.6 nm (Sutherland et al., 1993 Bames et al., 2001 Bee et al., 1999 Dacre and Bovington, 1983 Georges et al., 1998 Paddy et al., 1990 Wu and Dacre, 1997). 

---