Article
Chemistry, Multidisciplinary
Braden M. Weight, Andrew E. Sifain, Brendan J. Gifford, Han Htoon, Sergei Tretiak
Summary: This study investigates the nonradiative relaxation process in single-walled carbon nanotubes (SWCNTs) with covalent surface defects through computational modeling. The results show that the chirality and defect composition of SWCNTs have a significant impact on the population relaxation, and provide insights into the relaxation process between band-edge states and localized excitonic states.
Article
Chemistry, Multidisciplinary
Braden M. Weight, Andrew E. Sifain, Brendan J. Gifford, Han Htoon, Sergei Tretiak
Summary: Recently, there has been exploration of SWCNTs with covalent surface defects for their potential use in single-photon telecommunication emission and spintronic applications. In this study, computational modeling of nonradiative relaxation in different SWCNT chiralities with single-defect functionalizations is presented. The simulations provide insights into the relaxation process between the band-edge states and the localized excitonic state, which compete with dynamic trapping/detrapping processes observed in experiments.
Article
Chemistry, Physical
Deping Hu, Yu Xie, Jiawei Peng, Zhenggang Lan
Summary: The study implements the symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian to investigate nonadiabatic dynamics at conical intersections of polyatomic systems, utilizing different approaches for zero-point energy correction of electronic mapping variables. Results show that the gamma-adjusted version of SQC/MM dynamics performs better in certain situations, demonstrating its effectiveness in simulating photoinduced dynamics of polyatomic systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Yinan Shu, Donald G. Truhlar
Summary: This paper discusses the tendency of a time-evolved reduced density matrix for a subsystem to assume a statistical ensemble of states rather than a coherent combination of pure-state wave functions. It also explores the decoherence phenomenon in molecular processes involving changes in the electronic state and the coordinates of the nuclei. The paper presents the necessary background for understanding decoherence, including the description of pure states and mixed states using the density matrix, as well as the concepts of pointer states and decoherence time. It further discusses the treatment of decoherence in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yinan Shu, Donald G. Truhlar
Summary: Decoherence refers to the phenomenon where the density matrix of a subsystem evolves into a statistical ensemble of states instead of a coherent combination of pure-state wave functions. In molecular processes involving changes in electronic states and nuclear coordinates, the interaction between the electronic and nuclear subsystems leads to decoherence of the electronic subsystem. This paper provides background information on decoherence and discusses its treatment in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Ying Hu, Chao Xu, Linfeng Ye, Feng Long Gu, Chaoyuan Zhu
Summary: Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed to investigate the photoisomerization mechanisms of E-to-Z and Z-to-E transitions using accurate potential energy surfaces. The study found different types of conical intersections to determine the photoisomerization mechanisms, shedding light on the photoinduced isomerization in large NAIP systems.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Pratip Chakraborty, Yusong Liu, Samuel McClung, Thomas Weinacht, Spiridoula Matsika
Summary: Nonadiabatic excited state dynamics play a crucial role in various processes. The combination of theoretical and experimental developments has led to significant progress in this field, providing insights into the photophysical behavior of molecules. This Feature Article utilizes recent work combining time-resolved photoelectron spectroscopy with theoretical non-adiabatic dynamics to highlight important lessons learned. By comparing the nonadiabatic excited state dynamics of three different organic molecules, namely uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene, the study aims to elucidate the relationship between structure and dynamics. The comparison emphasizes the influence of rigidity on dynamics and the challenges in accurately capturing dynamics through calculations.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Maxim F. Gelin, Xiang Huang, Weiwei Xie, Lipeng Chen, Nada Doslic, Wolfgang Domcke
Summary: An ab initio theoretical framework is presented for simulating femtosecond time-resolved transient absorption pump-probe spectra using quasi-classical trajectories, based on a classical approximation to the representation of third-order four-wave-mixing signals. The method involves stochastic sampling of classical trajectories from a positive definite doorway distribution and evaluation of signals by averaging over a positive definite window distribution, to describe nonadiabatic excited-state dynamics. The approach has been demonstrated through simulations of different contributions to the TA PP spectrum of gas-phase pyrazine using the second-order algebraic-diagrammatic construction method.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Xin He, Baihua Wu, Tom Rivlin, Jian Liu, Eli Pollak
Summary: This study focuses on the transition path flight times for scattering on two electronic surfaces with a single crossing. The results reveal nontrivial quantum effects such as resonance lifetimes and nonclassical passage times, and show that nonadiabatic effects tend to increase flight times. A comparison between numerically exact time propagation and the Fewest Switches Surface Hopping (FSSH) method indicates that the FSSH method is reliable only when the scattering is classically allowed on the relevant adiabatic surfaces. However, for quantum-dominant effects like tunneling and resonances, the FSSH method fails to accurately predict the correct times and transition probabilities. These findings highlight the limitations of methods that do not consider quantum interference effects and emphasize the importance of measuring flight times to understand quantum effects in nonadiabatic scattering.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Victor M. Freixas, Alexander J. White, Tammie Nelson, Huajing Song, Dmitry Makhov, Dmitrii Shalashilin, Sebastian Fernandez-Alberti, Sergei Tretiale
Summary: This study compares three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). The comparisons reveal method performance for population relaxation and coherent vibronic dynamics. The numerical convergence of MCE-AIMC algorithms is also studied to provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
D. Vale Cofer-Shabica, Maximilian F. S. J. Menger, Qi Ou, Yihan Shao, Joseph E. Subotnik, Shirin Faraji
Summary: Accurately describing large molecular systems in complex environments is a challenging task in computational chemistry. This problem becomes even more challenging for photoinduced processes that involve multiple excited electronic states and their corresponding nonadiabatic couplings. Multiscale approaches such as hybrid quantum mechanics/molecular mechanics (QM/MM) offer a balanced compromise between accuracy and computational burden. In this study, we introduce an open-source software package (INAQS) for nonadiabatic QM/MM simulations that integrates the sampling capabilities of GROMACS MD package and the excited-state infrastructure of Q-CHEM electronic structure software.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Zhong-Fei Xu, Chuan-Jia Tong, Ru-tong Si, Gilberto Teobaldi, Li-Min Liu
Summary: By simulating the interplay between different electron polaron hopping regimes, this study investigates the influence of these regimes on the recombination of photogenerated charge carriers in TiO2(101) surface and reveals that fast hopping promotes ultrafast recombination while slower hopping and polaron pinning delay the recombination process. These findings provide insights into the development of photocatalytic strategies based on TiO2.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Carlotta Pieroni, Federica Agostini
Summary: This article discusses coupled-trajectory schemes for molecular dynamics simulations of excited-state processes. New strategies are proposed to capture decoherence effects, revival of coherence, and nonadiabatic interferences in long-time dynamics, compared to independent-trajectory schemes. The algorithms are tested on a one-dimensional two-state system with different model parameters inducing different dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Victor Manuel Freixas, Sergei Tretiak, Sebastian Fernandez-Alberti
Summary: Progress in organic synthesis allows the exploration of diverse molecules with new structural topologies. The recently synthesized infinitene is a helically twisted figure-eight molecule with unique optoelectronic properties suitable for applications in nanoelectronics and photonics. However, the photophysical properties of infinitene have not been investigated.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Evaristo Villaseco Arribas, Lea M. Ibele, David Lauvergnat, Neepa T. Maitra, Federica Agostini
Summary: Trajectory-based methods, derived from approximating electron-nuclear correlation terms in the exact factorization approach, successfully capture quantum effects in light-induced molecular processes. The coupling among trajectories in these methods recovers the nonlocal nature of quantum nuclear dynamics, which is overlooked in traditional algorithms. However, some of the approximations introduced in these methods do not conserve the total energy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jiawei Peng, Yu Xie, Deping Hu, Zhenggang Lan
Summary: The study applied principal component analysis to investigate the bath motion in nonadiabatic dynamics, revealing the importance of bath modes with strong vibronic coupling or frequencies close to electronic transitions. The results indicate that PCA is a powerful tool for analyzing complex nonadiabatic dynamics in systems with many degrees of freedom.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Xiang Jiang, Qijing Zheng, Zhenggang Lan, Wissam A. Saidi, Xinguo Ren, Jin Zhao
Summary: The study developed an ab initio nonadiabatic molecular dynamics method based on GW plus real-time Bethe-Salpeter equation for spin-resolved exciton dynamics. Investigations on MoS2 provided a comprehensive picture of spin-valley exciton dynamics and showed that e-h exchange interaction plays a dominant role in fast valley depolarization. The study demonstrates that e-h many-body effects are essential in understanding spin-valley exciton dynamics in transition metal dichalcogenides.
Article
Chemistry, Physical
Qinghai Cui, Jiawei Peng, Chao Xu, Zhenggang Lan
Summary: The study introduces a computational method for automatic exploration of bimolecular multireaction mechanism, which significantly reduces trajectory numbers and computational costs in BOMD simulations through pre-screening steps and simulation tricks. Experimental results demonstrate that the method shows great potential in searching for reaction mechanisms of medium-sized bimolecular compounds.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Chao Xu, Kunni Lin, Deping Hu, Feng Long Gu, Maxim F. Gelin, Zhenggang Lan
Summary: By studying nonadiabatic dynamics and spectral simulations, we can gain a better understanding and interpretation of time-resolved spectroscopic signals and microscopic mechanisms in nonadiabatic polyatomic systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Jianzheng Ma, Di Zhao, Chenwei Jiang, Zhenggang Lan, Fuli Li
Summary: A two-stroke light-driven molecular rotary motor capable of performing unidirectional and repetitive rotation by only two photoisomerization steps has been proposed. The effect of temperature on the nonadiabatic dynamics of the motor and its impact on the unidirectionality of rotation have been systematically studied.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Kunni Lin, Jiawei Peng, Chao Xu, Feng Long Gu, Zhenggang Lan
Summary: In this work, machine learning approaches were utilized to simulate the dynamical evolution of open quantum systems. The LSTM-RNN models were built and optimized using various hyperparameter optimization methods. The uncertainties of the machine learning models were analyzed, providing an efficient protocol to estimate their trustiness.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Kunni Lin, Jiawei Peng, Chao Xu, Feng Long Gu, Zhenggang Lan
Summary: The long short-term memory recurrent neural network (LSTM-RNN) approach is used to simulate the trajectory-based nonadiabatic dynamics within the framework of the symmetrical quasi classical dynamics method based on the Meyer-Miller mapping Hamiltonian (MM-SQC). The proposed method is proven to be reliable and accurate in various simulations. This work introduces a novel machine learning approach for simulating the dynamics of complex systems with a large number of degrees of freedom.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Juanjuan Zhang, Jiawei Peng, Yifei Zhu, Deping Hu, Zhenggang Lan
Summary: The impact of mode-specific vibrational excitations on initial-preparation conditions in nonadiabatic dynamics of methyl nitrate was investigated. Exciting specific modes with a single quantum of energy resulted in slower population decay rates. This study provides insights into the key mechanisms of nonadiabatic dynamics control and demonstrates the potential for controlling nonadiabatic dynamics through mode-specific vibrational excitations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Jianzheng Ma, Di Zhao, Le Yu, Chenwei Jiang, Zhenggang Lan, Fuli Li
Summary: We theoretically designed a highly efficient light-driven molecular rotary motor using electronic structure calculations and nonadiabatic dynamics simulations, which showed excellent performance in both photo- and thermal isomerization processes. By modifying the structure of a synthesized compound, we proposed an oxindole-based light-driven molecular rotary motor with significant electronic push-pull character and weak steric hindrance. The newly designed motor displayed improved quantum yield and different motion behavior compared to the original motor, suggesting the feasibility of enhancing the efficiencies of photo- and thermal isomerization in molecular motors.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yutai Zhang, Chao Xu, Zhenggang Lan
Summary: We developed an automated approach to construct complex reaction networks and explore reaction mechanisms by integrating various theoretical methods. This method combines nanoreactor-type molecular dynamics, metadynamics, semiempirical GFN2-xTB method, and hidden Markov model. It provides an efficient and accurate tool for the automated exploration of reaction networks.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Kunni Lin, Jiawei Peng, Chao Xu, Feng Long Gu, Zhenggang Lan
Summary: The LSTM-RNN model is used to simulate trajectory-based nonadiabatic dynamics in the MM-SQC framework, and has been proven to be reliable and accurate. It captures the dynamic information of the trajectory evolution and simulates the behavior of complex systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Yuan Fang, Haiyi Huang, Kunni Lin, Chao Xu, Feng Long Gu, Zhenggang Lan
Summary: This study explores the photoisomerization mechanism of the bacterial biliverdin phytochrome chromophore through nonadiabatic dynamics simulation, focusing on the influence of geometrical constrains on the dynamics. Different constrains have distinctive effects on the photoisomerization mechanism of the chromophore, contributing to understanding the role of spatial restriction in the photoinduced dynamics and providing ideas for regulating the reaction channels.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Bowen Li, Xiangyu Zou, Miao Xiong, Qiyi Li, Xu Kang, Youbing Mu, Jieyu Wang, Jian Pei, Chunming Yang, Zhenggang Lan, Xiaobo Wan
Summary: By designing and synthesizing four polymers with similar conjugated backbones, it was found that these polymers exhibit ideal linear coplanar backbones and suitable energy levels, favoring balanced ambipolar charge transport in organic transistors with high and well-balanced electron/hole mobility.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Chemistry, Physical
Yifei Zhu, Jiawei Peng, Xu Kang, Chao Xu, Zhenggang Lan
Summary: The analysis protocol proposed in this paper provides a powerful way to clarify both the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics, using dimensionality reduction and clustering approaches. The representative system keto isocytosine is used to illustrate the protocol.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Jianzheng Ma, Sujie Yang, Di Zhao, Chenwei Jiang, Zhenggang Lan, Fuli Li
Summary: The working cycle of conventional light-driven molecular rotary motors usually involves four steps, including two photoisomerization steps and two thermal helix inversion steps. This study proposes a three-stroke molecular motor that can achieve unidirectional rotation at room temperature. The photoisomerization processes of this motor exhibit high quantum yields and ultrafast reaction rates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)