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Triphenylphosphine is used typically as a reducing agent for organic peroxides as it is a good nucleophile. So, if I wanted to computationally model a reaction like: $$\ce{PR3 + ROOH -> OPR3 + ROH}$$

Can something like a trimethylphosphine be used instead of triphenylphosphine, since it is an even better nucleophile, and the strength of the P=O is what's driving the reaction/reduction? Or am I missing some information?

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Yes it can. It also has the advantage that the trimethyl phosphine oxide produced is water soluble and thus easier to remove from a reaction mixture than triphenylphosphine oxide which is notoriously difficult to get rid of. I have used it for a Staudinger reduction of an alkyl azide when triphenyl phosphine was unreactive.

However, trimethyl phosphine is more expensive, pyrophoric, has an unpleasant odour and is toxic requiring full personal protective equipment. Safety data here: https://www.alfa.com/en/content/msds/english/30143.pdf

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