Abstract
Chemical reactions play important roles in biological functions. In order to elucidate molecular mechanism of the chemical reactions in biosystems, so-called hybrid quantum mechanical/molecular mechanical (QM/MM) methods have been developed and applied to many biochemical reactions recently. The methods permit one to calculate electronic states of reaction substrate molecules in protein binding pockets by taking into account molecular interactions with the surrounding protein environment. In this review, we survey our QM/MM studies for chemical reactions in rhodopsin photoreceptor proteins and F1-ATP synthase along with a brief introduction of the methodology.
