研究目的
Investigating the initial photoreaction in the channelrhodopsin chimera C1C2 with a combined quantum mechanical/molecular mechanical (QM/MM) strategy to understand the photoreaction mechanisms and compare static and dynamic aspects to experimental findings.
研究成果
The study provides detailed insight into the photoreaction mechanisms of retinal in C1C2, including bicycle pedal and hula twist motions. It confirms the interaction between the close-lying S1 and S2 states and the importance of dynamic effects in understanding the photoreactivity. The OMx/MRCI method performed well for the investigation of this biologically relevant system.
研究不足
The study is limited by the computational methods used, such as the OM3/RHF Hamiltonian and the more flexible environment used in the optimization, which may lead to artificially large twists in the retinal structure. The complexity of the photoreaction requires methods that deliver qualitatively accurate results within reasonable time.
1:Experimental Design and Method Selection:
Combined QM/MM strategy for geometry optimizations using OM3/RHF and OM3/MRCI/Amber protocols. Trajectory surface hopping calculations with OM3/MRCI/Amber.
2:Sample Selection and Data Sources:
Based on the crystal structure 3UG9 of C1C2. Hydrogen atoms were added and protonation states of the amino acids were evaluated using PROPKA
3:Hydrogen atoms were added and protonation states of the amino acids were evaluated using PROPKAList of Experimental Equipment and Materials:
3.
3. List of Experimental Equipment and Materials: Program package COBRAMM for QM/MM calculations, Gaussian09 for vibrational frequency calculations.
4:Experimental Procedures and Operational Workflow:
Geometry optimizations, geometry sampling via zero-point energy sampling, excited-state dynamics calculations with velocity-Verlet integrator scheme, Tully’s fewest-switches surface-hopping algorithm.
5:Data Analysis Methods:
Exponential fitting for excited-state lifetime, analysis of photoproducts and reaction channels.
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