Review
Chemistry, Multidisciplinary
Yaming Yan, Yanying Liu, Tao Xing, Qiang Shi
Summary: This article reviews theoretical studies of photosynthetic light-harvesting complexes using the nonperturbative hierarchical equations of motion (HEOM) approach to simulate EET dynamics and spectroscopic signals. The results demonstrate the effectiveness of the HEOM method in understanding EET pathways and quantum effects in these complexes through simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Marcos Rubin-Osanz, Francois Lambert, Feng Shao, Eric Riviere, Regis Guillot, Nicolas Suaud, Nathalie Guihery, David Zueco, Anne-Laure Barra, Talal Mallah, Fernando Luis
Summary: This research reports a significant quantum tunnelling splitting between the two lowest electronic spin levels of mononuclear Ni complexes, with the magnetic clock transition being directly monitored through heat capacity experiments. The study also shows that the clock transition effectively suppresses intermolecular spin-spin interactions and that the quantum tunnelling splitting can be chemically tuned by modifying the ligand shell. These properties are important for realizing model spin qubits with resistance against decoherence, proper interfacing with other qubits and control circuits, and the ability to initialize them through cooling.
Article
Multidisciplinary Sciences
Quanwei Li, Kaydren Orcutt, Robert L. Cook, Javier Sabines-Chesterking, Ashley L. L. Tong, Gabriela S. Schlau-Cohen, Xiang Zhang, Graham R. Fleming, K. Birgitta Whaley
Summary: Experimental evidence shows that photosynthesis is initiated by single photons rather than intense light. It is discovered that the absorption of single photons can drive the energy transfer and fluorescence emission in photosynthesis, leading to the primary charge separation.
Article
Chemistry, Multidisciplinary
Si-Guo Wu, Ze-Yu Ruan, Guo-Zhang Huang, Jie-Yu Zheng, Veacheslav Vieru, Gheorghe Taran, Jin Wang, Yan-Cong Chen, Jun-Liang Liu, Le Tuan Anh Ho, Liviu F. Chibotaru, Wolfgang Wernsdorfer, Xiao-Ming Chen, Ming-Liang Tong
Summary: Single-molecule magnets exhibit magnetization blocking with strong magnetic anisotropy, which can be modified through molecular engineering and highlighted by hyperfine coupling. Poor understanding of relaxation mechanisms limits the exploitation of nuclear-spin molecular qubits. This study demonstrates the field-dependent oscillation of magnetization blocking barrier in a holmium metallacrown magnet, driven by the switch of relaxation mechanism involving hyperfine interaction.
Review
Biochemistry & Molecular Biology
Heiko Lokstein, Gernot Renger, Jan P. Goetze
Summary: Chlorophylls, bacteriochlorophylls, and carotenoids are important pigments in photosynthetic organisms, playing a crucial role in light-harvesting and energy transformation. Recent research has made significant progress in understanding the structures and functions of light-harvesting complexes, reaction centers, and photosystems, highlighting the importance of these complexes in adapting to environmental conditions and regulating energy processes. The structural diversity in photosynthetic antenna designs is becoming increasingly apparent, with light-harvesting complexes commonly forming trimeric structures.
Review
Plant Sciences
Naama Maroudas-Sklare, Yuval Kolodny, Shira Yochelis, Nir Keren, Yossi Paltiel
Summary: This paper explores the control phenomena in biology, focusing on how photosynthetic organisms can regulate energy transfer through small conformational changes in light-harvesting complexes. The authors investigate this mechanism through theoretical work and in vitro experiments, and examine its biological relevance in desert crust and marine cyanobacteria through in vivo experiments. They demonstrate the flexibility and low energy cost of this mechanism, making it a competitive survival strategy.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Physics, Applied
Khalil Ur Rehman, Subir Das, Fu-Jen Kao
Summary: The work demonstrates contrast enhancement through polarization-resolved pump-probe microscopy by measuring spontaneous fluorescence loss induced by stimulated emission. The pump-probe measurement is compared with conventional fluorescence polarization microscopy, resulting in different anisotropy values attributed to the multiphoton mechanism. The pump-probe technique promises higher temporal resolution in lifetime measurements and enables more precise determination of the fluorescent molecules' rotational diffusion time constant.
APPLIED PHYSICS EXPRESS
(2021)
Article
Multidisciplinary Sciences
Jacob S. Higgins, Marco A. Allodi, Lawson T. Lloyd, John P. Otto, Sara H. Sohail, Rafael G. Saer, Ryan E. Wood, Sara C. Massey, Po-Chieh Ting, Robert E. Blankenship, Gregory S. Engel
Summary: Quantum coherences in the FMO pigment-protein complex in green sulfur bacteria are found to be more prevalent under reducing conditions, indicating a closer mimic of the natural environment and faster energy transfer through vibronic coupling. The presence of excited-state coherences with a mainly vibrational character suggests a coherent mechanism for excitonic energy transfer in the complex, providing a potential tool to distinguish coherent relaxation from energy transfer driven by environmental fluctuations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Liwen Ko, Robert L. Cook, K. Birgitta Whaley
Summary: We develop a method to simulate the dynamics of light harvesting systems, considering non-Markovian coupling and multi-photon excitation. We find that under weak field excitation, coherent state input and Fock state input lead to equal density matrices in the excited manifold, but only coherent state input creates off-diagonal coherence. We also analyze the absorption probability and derive expressions for short and long pulses, as well as study the difference between collective vs independent emission.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Vladimir I. Novoderezhkin
Summary: We compared the excitation dynamics in bacterial B850 antenna using different models and found that the modified Redfield method can reproduce the relaxation dynamics from higher exciton levels, but fails to explain the migration of quasi-equilibrated excitation over the B850 ring. Neglecting population-to-coherence transfers leads to unrealistic fast delocalization, while the standard Redfield method provides a better understanding of this migration, although it may be affected by artifacts from its one-phonon character.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Optics
Ji-Cai Liu, Viktoriia Savchenko, Victor Kimberg, Michael Odelius, Faris Gel'mukhanov
Summary: Theoretical studies on X-ray absorption and core-ionization spectra of molecules pumped by two coherent infrared pulses with different polarizations have shown a sensitivity to the vibrational profile of X-ray probe spectra. The polarization dependence observed is qualitatively different for X-ray absorption and X-ray photoelectron spectra. This technique can be used to select differences in Franck-Condon distributions and study molecular rotation dynamics.
Article
Chemistry, Multidisciplinary
Ignacio Gimeno, Ainhoa Urtizberea, Juan Roman-Roche, David Zueco, Agustin Camon, Pablo J. Alonso, Olivier Roubeau, Fernando Luis
Summary: Through a series of experiments, vanadyl porphyrin molecules show the potential to encode multiple qubits and exhibit electronuclear entanglement under certain conditions. These findings expand the range of chemically designed systems capable of implementing non-trivial quantum functionalities.
Article
Plant Sciences
Pushan Bag
Summary: Photosynthesis is a major natural process that converts solar energy into chemical energy, carried out by a wide range of organisms from single cellular bacteria to higher plants. Different organisms possess different types of pigment protein complexes known as photosynthetic light-harvesting antennae, with simpler organisms typically having simple antennae and higher plants having complex systems for more efficient photosynthesis. The complexity of the antenna system is related to the ability of complex organisms to acclimate and adapt to fluctuating environmental conditions.
Article
Chemistry, Physical
Edoardo Cignoni, Lorenzo Cupellini, Benedetta Mennucci
Summary: We propose a machine learning strategy to calculate the excitonic properties of light harvesting complexes. By combining molecular dynamics simulations with ML prediction of the excitonic Hamiltonian, the proposed model can account for geometric fluctuations and electrostatic interactions. The model is trained on chlorophylls but can extrapolate beyond the training set, and its accuracy is demonstrated through simulations of absorption spectra in different environments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
JunWoo Kim, Tu C. Nguyen-Phan, Alastair T. Gardiner, Richard J. Cogdell, Gregory D. Scholes, Minhaeng Cho
Summary: The study utilizes a dual-laser 2DES technique to investigate the electronic energy transfer process in bacterial light-harvesting complexes. Through principal component analysis, it is found that the energy transfer is modulated by a low-frequency vibrational mode of the exciton donor.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Tianchu Li, Yaming Yan, Qiang Shi
Summary: This study investigates the numerical stability of the hierarchical equations of motion (HEOM) method applied to systems with the Brownian oscillator (BO) and multimode BO (MBO) spectral densities. It is found that the standard HEOM may become unstable with the increase in the system-bath coupling strength, and increasing the truncation depth of the HEOM does not remove the instability at long times. To solve this problem, a new multidimensional phase space differential equation that generalizes the quantum Fokker-Planck equation (QFPE) to arbitrary temperature is derived from the HEOM. It is further shown that the numerical instability can be removed by expanding the new low-temperature QFPE in a different basis set than the one used for the conventional HEOM. The matrix product state method is used to resolve the numerical instability problem for an electron transfer model with the MBO spectral density presented in the recent literature.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Atomic, Molecular & Chemical
Jiaying Chen, Tongmei Ma, Shuming Bai, Qiang Shi
Summary: This study focused on the electronic coupling for singlet oxygen photosensitization, utilizing non-adiabatic coupling from quantum chemical calculation to approximate molecular orbital overlaps. The results demonstrate a distribution of coupling strength as a function of intermolecular distance, providing a simple yet effective way to predict the coupling of triplet fusion reactions.
CHINESE JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Tao Xing, Tianchu Li, Yaming Yan, Shuming Bai, Qiang Shi
Summary: This study investigates the application of the imaginary time hierarchical equations of motion method for calculating real time quantum correlation functions. By deriving a new set of equations that decouple the imaginary time propagation and the calculation of auxiliary density operators, the calculation process is greatly simplified and different decomposition schemes can be explored. The applicability of the method is demonstrated through numerical examples.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Xiaohan Dan, Meng Xu, Yaming Yan, Qiang Shi
Summary: In this study, a set of generalized master equations (GMEs) is derived to investigate charge transport dynamics in molecular junctions using the Nakajima-Zwanzig-Mori projection operator approach. The new GME calculates the time derivatives of population on each quantum state of the molecule and the tunneling current as the convolution of time non-local memory kernels with populations on all system states. Non-Markovian memory kernels are obtained by combining the hierarchical equations of motion (HEOM) method and a previously derived Dyson relation for the exact kernel. The perturbative expansion of these memory kernels is calculated using the extended HEOM developed in previous work. The study also analyzes properties of the exact memory kernels and the convergence properties of their perturbative expansions using resonant level and Anderson impurity models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Yuanxin Liang, Tengfei Li, Yuhsuan Lee, Zhenzhen Zhang, Yawen Li, Wenqin Si, Zesheng Liu, Chuang Zhang, Yan Qiao, Shuming Bai, Yuze Lin
Summary: Researchers developed a new organic photovoltaic catalyst (OPC) called Y6CO, which has a carbonyl core that can coordinate with transition metals. This allows for efficient deposition of platinum (Pt) cocatalyst, resulting in higher catalytic activities.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Xuan Leng, Yaming Yan, Ruidan Zhu, Jiading Zou, Wenzhao Zhang, Qiang Shi
Summary: Two-dimensional electronic spectroscopy (2DES) is commonly used to study intermolecular electronic and vibronic coherence in light-harvesting complexes. However, intramolecular vibrational coherence can also contribute to the spectra, making it difficult to distinguish the different coherences. This study explores the possibility of selectively screening vibrational coherence using polarization-dependent 2DES, and demonstrates that population and vibrational coherence signals can be largely suppressed, allowing for clearer observation of intermolecular coherence.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Physics, Multidisciplinary
Meng Xu, Yaming Yan, Qiang Shi, J. Ankerhold, J. T. Stockburger
Summary: This article introduces an effective method for handling quantum noise and extends HEOM to arbitrary temperatures and very general reservoirs. Additionally, it quantitatively verifies the accuracy of the Shiba relation in the subohmic spin-boson model at zero temperature.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Qiang Wei, Yuhsuan Lee, Weiqiu Liang, Xiaolei Chen, Bo-Shuai Mu, Xi-Yang Cui, Wangsuo Wu, Shuming Bai, Zhibo Liu
Summary: In this study, boronic acids were synthesized via photocatalytic decarboxylation of benzoic acids followed by borylation, with the assistance of guanidine-type additives. This simple process showed high step economy and good functional group compatibility, and a guanidine-based biomimetic active decarboxylative mechanism was proposed.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Chemistry, Physical
Michele Ceriotti, Lasse Jensen, David E. Manolopoulos, Todd Martinez, David R. Reichman, Francesco Sciortino, C. David Sherrill, Qiang Shi, Carlos Vega, Lai-Sheng Wang, Emily A. Weiss, Xiaoyang Zhu, Jenny Stein, Tianquan Lian
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Xiaohan Dan, Qiang Shi
Summary: In this study, hydrogen atom scattering on metal surfaces is investigated using a simplified Newns-Anderson model, which treats both the nuclear and electronic degrees of freedom quantum mechanically. The hierarchical equations of motion method is employed to simulate the scattering dynamics of the fermionic bath. It is found that the main features of recent experimental studies can be reproduced with a reasonable set of parameters. The vibrational states on the chemisorption state near the incident energy play an important role, and the scattering process is dominated by a single-pass electronic transition between the diabatic physisorption and chemisorption states. Further study reveals a transition from typical nonadiabatic transitions to dynamics in the electronic friction regime with increasing atom-surface coupling strength.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Siqin Liu, Lei Wu, Daojian Tang, Jing Xue, Kun Dang, Hanbin He, Shuming Bai, Hongwei Ji, Chuncheng Chen, Yuchao Zhang, Jincai Zhao
Summary: This study investigates the proton-coupled electron transfer (PCET) of water oxidation on five typical photoanodes through the analysis of rate laws, H/D kinetic isotope effects, and operando spectroscopic studies. The research reveals that the sequential proton-electron transfer pathway is the rate-limiting factor for water oxidation. Surface modification is found to break this limitation and improve the turnover frequency of water oxidation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Nanoscience & Nanotechnology
Dongchun Yang, Ran Jia, Xin Wang, Shuming Bai
Summary: This study constructed two types of 3D graphyne by inserting acetylenic linkages and confirmed their stability using theoretical calculations. The 3D graphyne demonstrated high Fermi velocities and excellent characteristics, making it a promising anode nanomaterial for lithium-ion batteries.
ACS APPLIED NANO MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
Xiaohan Dan, Meng Xu, J. T. Stockburger, J. Ankerhold, Qiang Shi
Summary: The hierarchical equations of motion (HEOM) approach is an accurate method for simulating open system quantum dynamics. A challenge is accurately decomposing the reservoir correlation functions in order to efficiently simulate non-Markovian effects. This work employs the barycentric representation to approximate the Fermi function and hybridization functions, reducing the number of basis functions and allowing for simulation at ultralow temperature and general band structures.
Article
Chemistry, Physical
Lingsong Wang, Jingheng Deng, Mengjia Jiang, Chun Zhen, Fei Li, Shuyu Li, Shuming Bai, Xiaotao Zhang, Weigang Zhu
Summary: Molecular co-crystallization is used to enhance photocatalytic activity by introducing arene-perfluoroarene (AP) interactions. Octafluoronaphthalene-9,10-dimethylanthracene (OFN-DMA) and octafluoronaphthalene-perylene (OFN-Pe) cocrystals are designed and grown using a liquid-assisted grinding method. The cocrystals exhibit improved photocatalytic activity due to AP interactions and molecular cocrystal engineering, which enhance charge separation and transport.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
