Carbon & Hydrocarbon (HC) Contamination of EM Specimens
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In general, hydrocarbon contaminations on EM specimen surfaces are always unavoidable even though TEM analysts care more about specimen contaminations and SEM analysts care less. For instance, after a few hours in air or a night in a microscope with ‘poor’-vacuum, a new layer of organic molecules can be formed on biological TEM specimen surfaces. Old designs of TEMs had given rise to the characteristic appearance of contamination deposits; however, contamination has been significantly reduced by improving the column design and vacuum systems in modern microscopes.
During TEM observation, the contaminated area is normally a crown, annular spot, or needle
with a diameter nearly equal to that of the illumination size. The thickness of the surface contamination varies with time. However, the actual shape of contamination structure and contamination rate depend mainly on a couple of factors:
Figure 4392a. Schematic illustration of the shape of formed contamination structures: (a) Contamination needle with small beam sizes (< 20 nm), e.g. in CBED and STEM modes, when the electron probe is stationary, (b) Medium beam sizes, (c) Contamination film with large beam sizes, e.g. with parallel beam in TEM, or scanned area in STEM or SEM.
For SEM, at low beam current densities, the thickness (tc) of the contamination film is given by,
Equation 4392a indicates that the contamination rate is higher under low-voltage SEM condition than under "high"-voltage SEM systems. Table 4392 lists some experimentally measured specimen contamination rates (dzc/dt) depending on accelerating voltage (E0) current density (j) and vacuum pressure (P).
Table 4392. Experimentally measured specimen contamination rates (dzc/dt).
At high beam current densities in TEM and SEM observations, the growth rate of contamination film (for scanning beam) or needle (for stationary beam) saturates because all the molecules that reach the irradiated area by diffusion are polymerized immediately. Therefore, the growth rate of hydrocarbon only depends on the irradiation time t rather than the beam current density j. On the other hand, the stronger contamination appears on the side region of the scanned area because most molecules cannot reach the central area before depositing.
Contamination rate can practically be evaluated by EELS technique in TEM, backscattered electron signal in SEM and elastic scattering method in STEM. In modern TEMs, the contamination rates is generally well below 1 nm3min-1. The contamination sources in TEM are mainly:
The partial pressure of hydrocarbon (HC), back-streaming of oil from the rotary pump and of silicon oils from the diffusion pump, the grease of vacuum seals, and fingerprints on TEM sample holder and specimen induce HC contamination in the EMs (electron microscopes) specimen chamber. This HC diffuses along the specimen surface into the beam-irradiating area, where they become polymerized. The polymerization dose has been measured as 1.6 mC/cm2 and the surface diffusion coefficient as 55,000 nm2/s at 18 °C . Carbon-metal bonds can be strong while C–C bonds are even stronger. Non uniform HC contaminants can distort the final image of the specimen. Note that the contamination induced by thermal diffusion is normally larger than direct deposition of organic molecules from the vacuum. All these contaminants are pinned by electron radiation when arriving at the irradiated area.
These contaminants on the TEM specimen surfaces limit a number of applications, e.g. HRTEM, low energy EDS analysis and EELS analysis. Various methods can be used to reduce or remove contaminations:
Figure 4392b. Formed diffusion barrier (in black) and interesting area (in yellow): (a) Top view, and (b) Cross-section.
vi) Optimized vacuum. However, note that a "correct" vacuum alone does not solve the contamination problem if the specimen itself is neither clean nor prepared inside an ultra-high vacuum specimen chamber.
Figure 4392c. Vacuum in TEMs: (a) Modern TEMs, and (b) Some TEMs.
vi.b) Check and fix air leaks in the vacuum.
Again, some of the methods above cannot directly address the sources of specimen-born contamination, while cleaning process can directly reduce or eliminate the contamination source. However, the cleaning procedure is different from case to case because the sticking coefficients for hydrocarbons depend on the materials in the TEM specimen, resulting in different contamination rates and different amount of hydrocarbon on the specimen.
 J. S. Wall. Scanning Electron Microscopy (1980) I in: O. Johari (Ed.), SEM Inc.