Biological enzyme modeling molecular dynamics simulations

Excited-states simulations were mainly limited to small and medium-sized molecules before the 90s. However, many important photophysical processes, as for example, the photoisomerization of rhodopsin, take place in a biological environment, seldom not without the presence of an enzyme. To study photochemical processes in the large-size systems, alternative methods are required. One such method, the QM/MM method," was developed by Warshel and Levitt in 1976. This approach combines the accuracy of quantum chemical models with the speed of molecular mechanics. An alternative method to combine different quantum chemical approaches, the ONIOM method, was developed by Morokuma and co-workers." These methods were initially used in the context of ground-state reactions. Early applications of the QM/MM hybrid method to photochemical processes can be found as early as 1982," however, it was not until at the beginning of this century that the method started to be used extensively for photochemical and photophysical dynamics. To find representative investigations of that time consult the reference list." " ... 

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