除Cbz保護基外，叔丁氧羰基（Boc）是目前多肽合成中廣泛使用的氨基保護基，特別是在固相合成中，一般用Boc而不用Cbz。Boc 對于催化氫解不敏感, 對堿和親核試劑有一定的穩定性。Boc-氨基酸除個別外都能得到結晶；易于酸解除去，但有具有一定的穩定性，Boc-氨基酸能較長期的保存而不分解；酸解時產生的是叔丁基陽離子再分解為異丁烯，它一般不會帶來副反應；對堿水解、肼解,催化氫解和大多數親核試劑穩定，但比Cbz對酸敏感。當Boc和Cbz同時存在時，可以用催化氫解脫去Cbz，而Boc保持不變; 或用酸解脫去Boc, 而Cbz不受影響，因而兩者能很好地搭配。

叔丁氧羰基(Boc)導入

游離氨基酸在用NaOH 或NaHCO3 控制的堿性條件下用二氧六環和水的混合溶劑中很容易與同Boc2O反應得到N-叔丁氧羰基氨基酸化合物。這是氨基酸引入Boc常用方法之一，它的優點是其副產物很容易除去。有時對一些親核性較大的胺，一般可在甲醇中和Boc酸酐直接反應即可，無須其他的堿，其處理也方便。對水較為敏感的氨基衍生物，采用Boc2O/Et3N/MeOHor DMF 在40~50oC下進行，因為這些無水條件下用于保護O17標記的氨基酸而不會由于與水交換使O17丟失。有空間位阻的氨基酸而言，用Boc2O/Me4NOH.5H2O/CH3CN是十分有利的。

和Boc2O一樣， 2-(叔丁氧甲酰氧亞氨基)-2-苯基乙腈 (Boc-ON)是相對穩定的結晶混合物,也可以用于氨基酸的保護. 另外, 在Boc2O存在下使用催化量的羥胺得到的Boc-ONH2與胺的反應比Boc2O快1.5~2.5倍。

而Curtius Reaction通過叔丁醇也可以引入Boc。 同時在催化氫化和Boc2O存在的條件下, 也容易將芐基或Cbz等保護基可氫解除去而轉化為Boc保護; 同樣, 在KF/Et3N/Boc2O/DMF條件下, 室溫也可以將Fmoc保護基除去而轉化為Boc保護。

氨基酸Boc2O引入Boc保護示例：

A 4-L, four-necked, round-bottomed flask, equipped with an efficient stirrer, a dropping funnel, reflux condenser, and thermometer is charged with a solution of 44 g (1.1 mol) of sodium hydroxide in 1.1 L of water. Stirring is initiated and 165.2 g (1 mol) of L-phenylalanine?1?is added at ambient temperature, and then diluted with 750 mL of?tert-butyl alcohol. To the well-stirred, clear solution is added dropwise within 1 hr, 223 g (1 mol) of di-tert-butyl dicarbonate. A white precipitate appears during addition of the di-tert-butyldicarbonate. After a short induction period, the temperature rises to about 30~35°C. The reaction is brought to completion by further stirring overnight at room temperature. At this time, the clear solution will have reached a pH of 7.5~8.5. The reaction mixture is extracted two times with 250 mL of pentane, and the organic phase is extracted three times with 100 mLof saturated aqueous sodium bicarbonate solution. The combined aqueous layers are acidified to pH 1~1.5 by careful addition of a solution of 224 g (1.65 mol) of potassium hydrogen sulfate in 1.5 L of water. The acidification is accompanied by copious evolution of carbondioxide. The turbid reaction mixture is then extracted with four 400-mL portions of ethyl ether.The combined organic layers are washed two times with 200 mL of water, driedover anhydrous sodium sulfate or magnesium sulfate, and filtered. The solvent is removed under reduced pressure using a rotary evaporator at a bath temperature not exceeding 30°C. The yellowish oil that remains is treated with 150 mL of hexane and allowed to stand overnight. Within 1 day the following portions of hexane are added with stirring to the partially crystallized product: 2 × 50 mL, 4 × 100 mL, and 1 × 200 mL.The solution is placed in a refrigerator overnight; the white precipitate is collected on a Büchner funnel and washed with cold pentane. The solid is dried under reduced pressure at ambient temperature to constant weight to give a first crop. The mother liquor is evaporated to dryness leaving yellowish oil, which is treated in the same manner as described above, giving a second crop. The total yield of pure white?N-tert-butoxycarbonyl-L-phenylalanine?2?is 207~230 g?(78~87%?yield), mp 86~88°C。