To further deactivate the surface of the particle, a smaller reagent is used in the end-capping reaction. For example, Cl(CH3)2SiCH3 is one common end-capping reagent. You can see that substituting a methyl group for the large C18 group used above makes this reagent much smaller, allowing it to have access to some of the residual silanol groups on the surface. After this second reaction is completed, we say that the column is end-capped (right side of Figure 1).
It is interesting to note that even when end-capping is done as thoroughly as possible, such as repeating the reaction (“double end-capping”), approximately half of the silanols are still unbonded. You might think that this is a problem, but on the contrary, I suspect that if we were to eliminate the silanols completely, we might be disappointed at the performance of the column. For example, if silica is replaced by a polymer, such as in the polymer reversed-phase materials, we often find that these columns lack adequate selectivity to get satisfactory separations. More important is to have the silanols well shielded so that their interactions with the sample and mobile phase are controlled.
If only the end-capping reagent is used (no C18), the surface is not very stable, with rapid loss of end-capping at low pH (e.g., pH