Surface mapping

TOF-SIMS can be applied to identify a variety of molecular fragments, originating from various molecular surface contaminations. It also can be used to determine metal trace concentrations at the surface. The use of an additional high current sputter ion source allows the fast erosion of the sample. By continuously probing the surface composition at the actual crater bottom by the analytical primary ion beam, multi element depth profiles in well defined surface areas can be determined. TOF-SIMS has become an indispensable analytical technique in modem microelectronics, in particular for elemental and molecular surface mapping and for multielement shallow depth profiling. 

Figure 9. Phase reconstruction of image reported in Figure 6 using the reference of image reported in Figure 8. The phase map is shown in (a), which includes a laterally averaged line-scan of 15 pixels, (b) A surface map of the two particles shape is displayed. The surface plot has been heavily noise filtered through Gaussian smoothing to better display the particles shape.

Fig. 4.5 Schematic projection of the energetics of a reaction. The diagram shows the Born-Oppenheimer energy surface mapped onto the reaction coordinate. The barrier height AE has its zero at the bottom of the reactant well. One of the 3n — 6 vibrational modes orthogonal to the reaction coordinate is shown in the transition state. H and D zero point vibrational levels are shown schematically in the reactant, product, and transition states. The reaction as diagrammed is slightly endothermic, AE > 0. The semiclassical reaction path follows the dash-dot arrows. Alternatively part of the reaction may proceed by tunneling through the barrier from reactants to products with a certain probability as shown with the gray arrow...

Ryu, K. S. et al. Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a. J Biol Chem 2003, 278, 36621-7. 

Mussel adhesive protein (MAP) is a 130-kDa protein produced by the blue mussel Mytilus edulis), which provides strong adhesion to submerged surfaces. MAP films were prepared by drying and stored under nitrogen atmosphere. These films showed twice the adhesion strength of polycarbophil when tested on porcine duodenum in vitro [95]. 

R.L. Protein surface mapping by chemical oxidation structural analysis by mass spectrometry. Anal. Biochem. 2003, 313, 216-225. 

Smoothed contour surface maps (contour maps where the areas between the isolines are filled with colours) were produced. 

A review of the Journal of Physical Chemistry A, volume 110, issues 6 and 7, reveals that computational chemistry plays a major or supporting role in the majority of papers. Computational tools include use of large Gaussian basis sets and density functional theory, molecular mechanics, and molecular dynamics. There were quantum chemistry studies of complex reaction schemes to create detailed reaction potential energy surfaces/maps, molecular mechanics and molecular dynamics studies of larger chemical systems, and conformational analysis studies. Spectroscopic methods included photoelectron spectroscopy, microwave spectroscopy circular dichroism, IR, UV-vis, EPR, ENDOR, and ENDOR induced EPR. The kinetics papers focused on elucidation of complex mechanisms and potential energy reaction coordinate surfaces. 

Concerning properties, SFM has become a unique technique in probing local adhesion, friction and elastic response of various materials. This is based on the ability to measure forces as small as picoNewtons and probe areas well below 100 nm. The peculiar sensitivity of the force probe to different types of static and dynamic interactions provides a great number of contrast mechanisms which can map the surface structure regarding the chemical composition and physical properties. However, in most SFM measurements the interpretation of the surface maps remain to be very intricate, mostly because of the concurrent contribution of different forces into the net force. The progress in this field relies on new developments in technique which would allow to measure the properties like stiffness, adhesion, friction and viscosity, separately. 

Barre, A., Borges, J.R, Culerrier, R., and Rouge, R 2005. Homology modelling of the major peanut allergen Ara h 2 and surface mapping of IgE-binding epitopes. Immunol Lett 100(2) 153-158. 

Figure 17. Top Surface map of HSA showing positive (light gray) and negative (dark gray) charge distributions. The crevice is shown in the center with tryptophan (black patch in white circle) sitting at its bottom. Bottom Schematic representation of conformational transitions, from the contracted configuration in basic pH, to the flexible globule structure at neutral pH, and to the extended form in acidic pH. The location of W214 is indicated by the white dot in domain IIA.

Figure 34. Surface map representations of the structure of wild-type hTrx and two mutants. The structures were generated with MD simulation. The white, light gray, and dark gray colors represent nonpolar, positively, and negatively charged residues, respectively, and W31 is shown as sticks. Note that local protein environment is very nonpolar.

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