Optimal control design of laser pulses for mode specific vibrational excitation in an enzyme–substrate complex

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

“…Several methods have emerged recently to address this problem by introducing elegant ways of sampling with the high efficiency of computationally expedient lower level methods while retaining the accuracy of a more expensive high level treatment of the electronic structure . More accurate treatments of the nuclear quantum motion are also being implemented in a QM/MM framework in combination with optimal control . The most severe unsolved challenge is probably linked to the issue of how to go beyond the “single macromolecule” level and embed the QM/MM information into a wider biological context.…”

“…224 More accurate treatments of the nuclear quantum motion are also being implemented in a QM/MM framework in combination with optimal control. 376 The most severe unsolved challenge is probably linked to the issue of how to go beyond the "single macromolecule" level and embed the QM/MM information into a wider biological context. Several attempts in this direction are currently ongoing, for example, as part of the Human Brain project.…”

Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase

“…Its importance as a paradigm, and the intriguing temperature dependence of its KIEs, has led to AADH being investigated by a variety of modeling and simulation techniques. ,, QM/MM techniques have been used to calculate spectroscopic properties of the TTQ cofactor and also to investigate the multiple steps in the reductive half-reaction of tryptamine with AADH, identifying several intermediates in the reaction . Ren et al used DFT QM/MM techniques to calculate the potential energy surfaces and dipole moment surfaces for the motion of the reactive proton in the AADH/tryptamine system. Optimal control theory was then used to design a pulse to excite the proton from its lowest vibrational state to selected vibrationally excited states.…”