The Experts below are selected from a list of 23913 Experts worldwide ranked by ideXlab platform
Todd J. Martínez - One of the best experts on this subject based on the ideXlab platform.
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nonadiabatic photodynamics of retinal protonated schiff base in channelrhodopsin 2
Journal of Physical Chemistry Letters, 2019Co-Authors: Todd J. Martínez, Ruibin Liang, Fang LiuAbstract:Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for Photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the Photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn–Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the “aborted bicycle-pedal” mechanism. In addition, RPSB Photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which...
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dynamical correlation effects on Photoisomerization ab initio multiple spawning dynamics with ms caspt2 for a model trans protonated schiff base
Journal of Physical Chemistry B, 2016Co-Authors: Todd J. MartínezAbstract:We investigate the Photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multistate second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this Photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well-described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the Photoisomerization are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.
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Ultrafast excited state dynamics in the green fluorescent protein chromophore
Femtochemistry and Femtobiology, 2004Co-Authors: A. Toniolo, Seth Olsen, L. Manohar, Todd J. MartínezAbstract:The textbook picture of photo-induced cis-trans isomerization in unsaturated hydrocarbons is one-dimensional, focusing on simple torsion about a C=C bond. The resulting large amplitude motion seems inconsistent with the steric constraints imposed by protein environments. This observation led to many proposals for minimal-volume Photoisomerization pathways in protein environments. Recent work has shown that the mechanism for Photoisomerization is considerably more complicated than simple torsion, implying that the inconsistency mentioned above may be only apparent. In fact, Photoisomerization often involves both torsion and pyramidalization, leading to excited state dynamics much more akin to a “slicing” motion as opposed to the “sweeping” motion most naturally envisioned for a simple torsion. Thus, the question is to what extent the protein environment modifies the photochemical reaction pathway associated with Photoisomerization. This chapter discusses theoretical studies of Photoisomerization in the chromophore of green fluorescent protein (GFP).
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Ab Initio Study of Cis-Trans Photoisomerization in Stilbene and Ethylene
The Journal of Physical Chemistry A, 2003Co-Authors: Jason Quenneville, Todd J. MartínezAbstract:The photochemistry of stilbene is investigated using ab initio quantum chemistry with complete active space self-consistent field (CASSCF) and multireference perturbation theory (CASPT2) methods. We characterize Photoisomerization pathways from both the cis and trans isomers, including a minimal energy conical intersection. Similarities to Photoisomerization in ethylene are found and emphasized. In contrast to traditional one-dimensional models of stilbene Photoisomerization, torsion and pyramidalization are required to reach the minimal energy conical intersection which is expected to dominate in quenching to the ground electronic state. This intersection is characterized as an interaction between charge transfer and covalent states. The present results suggest that the qualitative features of the Photoisomerization dynamics elucidated for ethylene can also be expected to apply to stilbene, and call for reconsideration and refinement of the Photoisomerization mechanism in stilbene.
Zhenggang Lan - One of the best experts on this subject based on the ideXlab platform.
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analysis of trajectory similarity and configuration similarity in on the fly surface hopping simulation on multi channel nonadiabatic Photoisomerization dynamics
Journal of Chemical Physics, 2018Co-Authors: Yu Xie, Zhenggang LanAbstract:We propose an “automatic” approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic Photoisomerization dynamics by considering the trajectory similarity and the configuration similarity. We choose a representative system phytochromobilin (PΦB) chromophore model to illustrate the analysis protocol. After a large number of trajectories are obtained, it is possible to define the similarity of different trajectories by the Frechet distance and to employ the trajectory clustering analysis to divide all trajectories into several clusters. Each cluster in principle represents a photoinduced isomerization reaction channel. This idea provides an effective approach to understand the branching ratio of the multi-channel Photoisomerization dynamics. For each cluster, the dimensionality reduction is employed to understand the configuration similarity in the trajectory propagation, which provides the understanding of the major geometry evolution features in each reaction channel. The results show that this analysis protocol not only assigns all trajectories into different Photoisomerization reaction channels but also extracts the major molecular motion without the requirement of the pre-known knowledge of the active Photoisomerization site. As a side product of this analysis tool, it is also easy to find the so-called “typical” or “representative” trajectory for each reaction channel.We propose an “automatic” approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic Photoisomerization dynamics by considering the trajectory similarity and the configuration similarity. We choose a representative system phytochromobilin (PΦB) chromophore model to illustrate the analysis protocol. After a large number of trajectories are obtained, it is possible to define the similarity of different trajectories by the Frechet distance and to employ the trajectory clustering analysis to divide all trajectories into several clusters. Each cluster in principle represents a photoinduced isomerization reaction channel. This idea provides an effective approach to understand the branching ratio of the multi-channel Photoisomerization dynamics. For each cluster, the dimensionality reduction is employed to understand the configuration similarity in the trajectory propagation, which provides the understanding of the major geometry evolution features i...
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analysis of trajectory similarity and configuration similarity in on the fly surface hopping simulation on multi channel nonadiabatic Photoisomerization dynamics
arXiv: Chemical Physics, 2018Co-Authors: Yu Xie, Zhenggang LanAbstract:We propose an 'automatic' approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic Photoisomerization dynamics by considering the trajectory similarity and the configuration similarity. We choose a representative system phytochromobilin chromophore model to illustrate the analysis protocol. After a large number of trajectories are obtained, it is possible to define the similarity of different trajectories by the Frechet distance and to employ the trajectory clustering analysis to divide all trajectories into several clusters. Each cluster in principle represents a photoinduced isomerization reaction channel. This idea provides an effective approach to understand the branching ratio of the multi-channel Photoisomerization dynamics. For each cluster the dimensionality reduction is employed to understand the configuration similarity in the trajectory propagation, which provides the understanding of the major geometry evolution features in each reaction channel. The results show that this analysis protocol not only assigns all trajectories into different Photoisomerization reaction channels, but also extracts the major molecular motion without the requirement of the pre-known knowledge of the active Photoisomerization site. As a side product of this analysis tool, we can also easily to find the so-called 'typical' or 'representative' trajectory for each reaction channel.
Ruibin Liang - One of the best experts on this subject based on the ideXlab platform.
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nonadiabatic photodynamics of retinal protonated schiff base in channelrhodopsin 2
Journal of Physical Chemistry Letters, 2019Co-Authors: Todd J. Martínez, Ruibin Liang, Fang LiuAbstract:Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for Photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the Photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn–Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the “aborted bicycle-pedal” mechanism. In addition, RPSB Photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which...
Keiji Morokuma - One of the best experts on this subject based on the ideXlab platform.
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photodynamics of all trans retinal protonated schiff base in bacteriorhodopsin and methanol solution
Journal of Chemical Theory and Computation, 2011Co-Authors: Lung Wa Chung, Keiji MorokumaAbstract:Nonadiabatic ONIOM(CASSCF:AMBER) and CASSCF simulations elucidated different photodynamics of an all-trans retinal protonated Schiff base (RPSB) in bacteriorhodopsin and methanol as well as without an environment. The bR protein matrix holds RPSB tight via specific interactions and promotes bond-specific (along the C13═C14 bond), unidirectional, and ultrafast Photoisomerization with a high quantum yield. In contrast, in methanol and for the twisted bare RPSB, Photoisomerization is not bond-specific (mainly along the C11═C12 bond), is nonunidirectional, and is ineffective. Therefore, bR efficiently “catalyzes” Photoisomerization and stores enough energy to promote the subsequent proton pumping and protein conformational changes.
Fang Liu - One of the best experts on this subject based on the ideXlab platform.
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nonadiabatic photodynamics of retinal protonated schiff base in channelrhodopsin 2
Journal of Physical Chemistry Letters, 2019Co-Authors: Todd J. Martínez, Ruibin Liang, Fang LiuAbstract:Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for Photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the Photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn–Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the “aborted bicycle-pedal” mechanism. In addition, RPSB Photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which...
