- 标题
- 摘要
- 关键词
- 实验方案
- 产品
-
Analysis of trajectory similarity and configuration similarity in on-the-fly surface-hopping simulation on multi-channel nonadiabatic photoisomerization dynamics
摘要： 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 Fréchet 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.
关键词： trajectory similarity,multi-channel nonadiabatic photoisomerization dynamics,Fréchet distance,dimensionality reduction,phytochromobilin chromophore,on-the-fly surface-hopping simulation,configuration similarity,clustering analysis
更新于2025-09-23 15:23:52
-
Phonon-Driven Energy Relaxation in PbS/CdS and PbSe/CdSe Core/Shell Quantum Dots
摘要： We study the impact of the chemical composition on phonon-mediated exciton relaxation in the core/shell quantum dots (QDs), with 1-nm core made of PbX and the monolayer shell made of CdX, where X=S and Se. For this, time-domain non-adiabatic dynamics (NAMD) based on Density Functional Theory (DFT) and Surface Hopping techniques are applied. Simulations reveal twice faster energy relaxation in PbS/CdS than PbSe/CdSe due to dominant couplings to higher-energy optical phonons in structures with sulfur anions. For both QDs, the long-living intermediate states associated with the core-shell interface govern the dynamics. Therefore, a simple exponential model is not appropriate, and the four-state irreversible kinetic model is suggested instead, predicting 0.9 ps and 0.5 ps relaxation rates in PbSe/CdSe and PbS/CdS QDs, respectively. Thus, 2-nm PdSe/CdSe QDs with a single monolayer shell exhibit the phonon-mediated relaxation time sufficient for carrier multiplications to outpace energy dissipation and benefit the solar conversion efficiency.
关键词： Density Functional Theory,phonon-driven energy relaxation,PbSe/CdSe,PbS/CdS,core/shell quantum dots,Surface Hopping techniques,non-adiabatic dynamics
更新于2025-09-23 15:21:01
-
QM/MM photodynamics of Retinal in the Channelrhodopsin Chimera C1C2 with OM3/MRCI
摘要： The photoisomerization of all-trans retinal in channelrhodopsins triggers the opening of a cation channel in the membrane of certain green algae. The stimulus resulting from cell depolarization enables the algae to perceive and react to the present lighting conditions. This property makes channelrhodopsins especially interesting for neuroscientific applications in optogenetics. We investigate the initial photoreaction in the channelrhodopsin chimera C1C2 with a combined quantum mechanical/molecular mechanical (QM/MM) strategy. For geometry optimizations, the OM3/RHF and OM3/MRCI/Amber protocols are used. Trajectory surface hopping calculations are performed with OM3/MRCI/Amber and a statistically relevant number of molecules to obtain reaction rates and quantum yields. The utilized models include a direct hydrogen bond of the retinal Schiff base to the proposed counterions in C1C2, i.e. either toward glutamate or aspartate. Static and dynamic aspects are compared to experimental findings including time constants and spectral traces. The calculations provide a rationale for the observed short and long time components in the photokinetics of C1C2 and yield detailed insight into the photoreaction mechanisms that include bicycle pedal and hula twist motions.
关键词： C1C2,QM/MM,surface hopping,photodynamics,Channelrhodopsin
更新于2025-09-23 15:21:01
-
Nonadiabatic Dynamics in a Laser Field: Using Floquet Fewest Switches Surface Hopping To Calculate Electronic Populations for Slow Nuclear Velocities
摘要： We investigate two well-known approaches for extending the fewest switches surface hopping (FSSH) algorithm to periodic time-dependent couplings. The first formalism acts as if the instantaneous adiabatic electronic states were standard adiabatic states, which just happen to evolve in time. The second formalism replaces the role of the usual adiabatic states by the time-independent adiabatic Floquet states. For a set of modified Tully model problems, the Floquet FSSH (F-FSSH) formalism gives a better estimate for both transmission and reflection probabilities than the instantaneous adiabatic FSSH (IA-FSSH) formalism, especially for slow nuclear velocities. More importantly, only F-FSSH predicts the correct final scattering momentum. Finally, in order to use Floquet theory accurately, we find that it is crucial to account for the interference between wavepackets on different Floquet states. Our results should be of interest to all those interested in laser-induced molecular dynamics.
关键词： Electronic Populations,Nonadiabatic Dynamics,Floquet Fewest Switches Surface Hopping,Slow Nuclear Velocities,Laser Field
更新于2025-09-23 15:19:57
-
Volume-conserving photoisomerization of a nonplanar GFP chromophore derivative: Nonadiabatic dynamics simulation
摘要： Nonadiabatic dynamics of a nonplanar green fluorescent protein (GFP) chromophore derivative was examined theoretically by trajectory surface hopping approach at the CASSCF level based on Zhu-Nakamura theory. The geometry optimizations show that there are four ground-state minima and four conical intersections between the ground (S0) and first excited (S1) states. Four S1-state minima were found at a perpendicularly twisted conformation around the imidazolinone-bridged bond. Upon excitation to S1 state, the main decay pathways of four isomers involve different S0/S1 potential energy surface conical intersections. The dominant excited-state relaxation mechanism of this GFP chromophore derivative is the twists of two bridging bonds and the methyl group in the bridge combined with the pyramidalization character of the central carbon atom. Further twists of two bridging bonds and the methyl group occur sequentially in the S0 state. It is worth to mention that the special volume-conserving motion of this molecule is attributed to twists of two bridging bonds in the same direction during the whole photoisomerization processes. The theoretical investigation presented herein provides important insights into the volume-conserving photoisomerization mechanisms of a nonplanar GFP chromophore derivative. We believe that the present work can benefit the design of the photochromic molecule devices in confined media.
关键词： GFP chromophore derivative,Reaction pathways.,Surface hopping dynamics,Photoisomerization
更新于2025-09-19 17:15:36
-
Coulomb Explosion Imaging for the Visualization of a Conical Intersection
摘要： Coulomb explosion imaging is proposed as a method to directly map the presence of conical intersections encountered by a propagating wave packet in a molecular system. The case of choice is the non-adiabatic coupling between two dissociative surfaces in the methyl iodide molecule, probed by Coulomb explosion with short, intense near-infrared pulses causing multiple ionization. On-the-fly multidimensional trajectory calculations with surface hopping using perturbation theory and including spin-orbit coupling are performed to visualize the dynamics through the conical intersection and compare with experimental results. The possibilities and limitations of the technique are examined and discussed.
关键词： ultrafast dynamics,strong laser fields,methyl halides,Nonadiabatic processes,surface hopping
更新于2025-09-04 15:30:14