Dear Mahyar Cheraghi , thanks for sharing this interesting question. Let us assume that APTMS is (3-Aminopropyl)trimethoxysilane, if this is right, it means your molecule has a silicon atom bonded tetrahedrically to 3 methoxy groups (-OCH3) and to 1 one aminopropyl group. If your substrate is glass and its surface is rich in -OH groups (normally or enhanced by a treatment with piranha solution), then the three groups methoxy will interact with the -OH groups on the glass surface, releasing a methanol molecule by each -OCH3 group linked to an -OH group on the glass surface. In the end you get your APTMS molecule bonded to the glass by 3 sylane groups, while the aminoproyl group remains pointing towards the open space, showing the -NH2 group, which is ready to interact with a new layer, well by chemical reaction or well by electrostatic interactions.
This is the conventional orientation of APTMS, but it would be possible somewhat invert it if the substrate will have some functionalization more akin to the amino group than to the three methoxy groups.
Hope this helps. Good luck with your research and my best wishes!
Hello @dear manuel Gomez Thank you very much for your answer.
In different articles, they have divided the orientation of APTMS or APTES molecules into 4 categories according to the solvent used. As you mentioned, I activate the surface with Piranha and then cover it in a solution containing APTMS. I use water and ethanol separately as solvents. The orientation I expect to happen is what you said.
because I need the amine group for the next bonds. My specific question is, what solvent should I use to make sure this orientation happens?
You need the methoxy groups to be free to intermolecularly interact with the hydroxyl groups in the glass. When dissolving APTMS in water, alcohol, methoxy groups will intermolecularly interact with hydroxyl groups. Therefore, you are better off using more hydrophobic solvents, acetone, maybe even hexane.