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Protecting groups reference template
Premium template. Preview and edit it free in MolDraw; downloading and exporting it is part of MolDraw Pro.
Boc, Cbz, Fmoc, Bn, PMB, TBS, Ac, THP and acetonide drawn on a generic O or N, with a reference table of what each protects and the condition (acid, base, H₂/Pd, fluoride, oxidation) that removes it.
What the template shows
- The common protecting groups: what they protect and the orthogonal condition that removes each
- Structures (on a generic R)
- Boc (amine)
- Cbz (amine)
- Fmoc (amine)
- PMB (alcohol)
- TBS (alcohol)
- THP (alcohol)
- Acetonide (1,2-diol)
- What each protects and how it comes off
- Group Protects Removed by Boc amine acid (TFA) Cbz amine H₂ / Pd (hydrogenolysis) Fmoc amine base (piperidine) Bn alcohol / acid H₂ / Pd (hydrogenolysis) PMB alcohol oxidation (DDQ) or acid TBS alcohol fluoride (TBAF) or acid Ac alcohol / amine base (hydrolysis) THP alcohol acid Acetonide 1,2- / 1,3-diol acid
- A protecting group masks a reactive handle (amine, alcohol, diol) so chemistry can be done elsewhere, then is removed to give the group back.
- Orthogonality is the point: Boc comes off with acid, Fmoc with base, Cbz/Bn by hydrogenolysis, TBS with fluoride — so two groups can be removed independently.
- Fmoc/Boc orthogonality underpins solid-phase peptide synthesis; silyl groups (TBS, TBDPS) differ in how easily fluoride or acid removes them.
- Choose a group stable to the planned steps and removable without harming the rest of the molecule.
- Wuts, Greene’s Protective Groups in Organic Synthesis, 5th ed., Wiley 2014 · every part of this sheet is editable
Drawn with 91 atoms, 3 shapes – every one editable in MolDraw.
Sources
How to use this template
- Press Edit in MolDraw. The template opens on the canvas of the free MolDraw editor.
- Change anything: move structures, edit atoms and labels, recolour highlights or delete what you do not need.
- Add your own structures, arrows and text next to it, or combine several templates on one page.
- Export the drawing as PNG, SVG or PDF for slides, worksheets, theses and papers.
Frequently asked questions
Is the Protecting groups reference template free?
You can preview the Protecting groups reference template here and open and edit it in MolDraw for free. Downloading or exporting it is part of MolDraw Pro, together with the other premium templates.
Can I edit the Protecting groups reference template?
Yes. It opens as an ordinary MolDraw drawing, so every structure, arrow, label and colour can be changed, and you can add your own content around it.
Is the chemistry checked?
Every structure is checked with RDKit and every curly arrow passes MolDraw’s electron-flow audit. The sources used are listed on this page.
Are the IC₅₀ values in the SAR table real?
No. They are illustrative example values so the table can be filled in with your own data; the structures and R-group positions are checked with RDKit.