1
|
Sun S, Gu B, Hu H, Lu L, Tang D, Chernyak VY, Li X, Mukamel S. Direct Probe of Conical Intersection Photochemistry by Time-Resolved X-ray Magnetic Circular Dichroism. J Am Chem Soc 2024; 146:19863-19873. [PMID: 38989850 DOI: 10.1021/jacs.4c03033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The direct probing of photochemical dynamics by detecting the electronic coherence generated during passage through conical intersections is an intriguing challenge. The weak coherence signal and the difficulty in preparing purely excited wave packets that exclude coherence from other sources make it experimentally challenging. We propose to use time-resolved X-ray magnetic circular dichroism to probe the wave packet dynamics around the conical intersection. The magnetic field amplifies the relative strength of the electronic coherence signal compared to populations through the magnetic field response anisotropy. More importantly, since the excited state relaxation through conical intersections involves a change of parity, the magnetic coupling matches the symmetry of the response function with the electronic coherence, making the coherence signal only sensitive to the conical intersection induced coherence and excludes the pump pulse induced coherence between the ground state and excited state. In this theoretical study, we apply this technique to the photodissociation dynamics of a pyrrole molecule and demonstrate its capability of probing electronic coherence at a conical intersection as well as population transfer. We demonstrate that a magnetic field can be effectively used to extract novel information about electron and nuclear molecular dynamics.
Collapse
Affiliation(s)
- Shichao Sun
- Department of Chemistry, University of California, Irvine, California 92697, United states
- Departmnet of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Bing Gu
- Department of Chemistry and Department of Physics, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Hang Hu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lixin Lu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Diandong Tang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Vladimir Y Chernyak
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
- Department of Mathematics, Wayne State University, 656 West Kirby, Detroit, Michigan 48202, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697, United states
- Departmnet of Physics and Astronomy, University of California, Irvine, California 92697, United States
| |
Collapse
|
2
|
Roy PP, Leonardo C, Orcutt K, Oberg C, Scholes GD, Fleming GR. Infrared Signatures of Phycobilins within the Phycocyanin 645 Complex. J Phys Chem B 2023; 127:4460-4469. [PMID: 37192324 DOI: 10.1021/acs.jpcb.3c01352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Aquatic photosynthetic organisms evolved to use a variety of light frequencies to perform photosynthesis. Phycobiliprotein phycocyanin 645 (PC645) is a light-harvesting complex in cryptophyte algae able to transfer the absorbed green solar light to other antennas with over 99% efficiency. The infrared signatures of the phycobilin pigments embedded in PC645 are difficult to access and could provide useful information to understand the mechanism behind the high efficiency of energy transfer in PC645. We use visible-pump IR-probe and two-dimensional electronic vibrational spectroscopy to study the dynamical evolution and assign the fingerprint mid-infrared signatures to each pigment in PC645. Here, we report the pigment-specific vibrational markers that enable us to track the spatial flow of excitation energy between the phycobilin pigment pairs. We speculate that two high-frequency modes (1588 and 1596 cm-1) are involved in the vibronic coupling leading to fast (<ps) and direct energy transfer from the highest to lowest exciton, bypassing the intermediate excitons.
Collapse
Affiliation(s)
- Partha Pratim Roy
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cristina Leonardo
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kaydren Orcutt
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Catrina Oberg
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
3
|
Gao Y, Wang X, Yu N, Wong BM. Harnessing deep reinforcement learning to construct time-dependent optimal fields for quantum control dynamics. Phys Chem Chem Phys 2022; 24:24012-24020. [PMID: 36128792 DOI: 10.1039/d2cp02495k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an efficient deep reinforcement learning (DRL) approach to automatically construct time-dependent optimal control fields that enable desired transitions in dynamical chemical systems. Our DRL approach gives impressive performance in constructing optimal control fields, even for cases that are difficult to converge with existing gradient-based approaches. We provide a detailed description of the algorithms and hyperparameters as well as performance metrics for our DRL-based approach. Our results demonstrate that DRL can be employed as an effective artificial intelligence approach to efficiently and autonomously design control fields in quantum dynamical chemical systems.
Collapse
Affiliation(s)
- Yuanqi Gao
- Department of Electrical and Computer Engineering, University of California-Riverside, Riverside, CA, USA
| | - Xian Wang
- Department of Physics and Astronomy, University of California-Riverside, Riverside, CA, USA
| | - Nanpeng Yu
- Department of Electrical and Computer Engineering, University of California-Riverside, Riverside, CA, USA.
| | - Bryan M Wong
- Department of Chemical and Environmental Engineering, Materials Science and Engineering Program, Department of Chemistry, and Department of Physics and Astronomy, University of California-Riverside, Riverside, CA, USA.
| |
Collapse
|
4
|
Stovbun S, Skoblin A, Mikhaleva MG, Vedenkin AS, Gatin AK, Usachev SV, Nikolsky SN, Politenkova GG, Zlenko DV. Role of the Exchange Interactions in the Stability of the Cellulose. Phys Chem Chem Phys 2022; 24:22871-22876. [DOI: 10.1039/d2cp02346f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The problem of the origin of biochirality and the related problem of the initial monomers' selection are still under discussion, and the main point here is not the mechanics of...
Collapse
|
5
|
Abstract
The fundamental principle governing the robust excitation energy transfer (EET) in the light-harvesting complexes remained elusive. Recent spectroscopic observations of the EET attract attention toward the role of the quantum effects in the biological systems. In this study, along with the time evolution, the distance between the quantum states of the pigments is also considered for a detailed illustration of the effect of the quantum coherence on the speed of the excitation transfer. The comparative analysis of the coherently delocalized EET with the incoherent discrete hopping reveals that the coherent superposition speedup the excitation transfer process, for instance, with the initially localized excitation, coherence provides a ∼4-fold enhancement to the excitation transfer rate.
Collapse
Affiliation(s)
- Davinder Singh
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| |
Collapse
|
6
|
Wang X, Kumar A, Shelton CR, Wong BM. Harnessing deep neural networks to solve inverse problems in quantum dynamics: machine-learned predictions of time-dependent optimal control fields. Phys Chem Chem Phys 2020; 22:22889-22899. [PMID: 32935687 DOI: 10.1039/d0cp03694c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inverse problems continue to garner immense interest in the physical sciences, particularly in the context of controlling desired phenomena in non-equilibrium systems. In this work, we utilize a series of deep neural networks for predicting time-dependent optimal control fields, E(t), that enable desired electronic transitions in reduced-dimensional quantum dynamical systems. To solve this inverse problem, we investigated two independent machine learning approaches: (1) a feedforward neural network for predicting the frequency and amplitude content of the power spectrum in the frequency domain (i.e., the Fourier transform of E(t)), and (2) a cross-correlation neural network approach for directly predicting E(t) in the time domain. Both of these machine learning methods give complementary approaches for probing the underlying quantum dynamics and also exhibit impressive performance in accurately predicting both the frequency and strength of the optimal control field. We provide detailed architectures and hyperparameters for these deep neural networks as well as performance metrics for each of our machine-learned models. From these results, we show that machine learning, particularly deep neural networks, can be employed as cost-effective statistical approaches for designing electromagnetic fields to enable desired transitions in these quantum dynamical systems.
Collapse
Affiliation(s)
- Xian Wang
- Department of Physics & Astronomy, University of California-Riverside, Riverside, CA 92521, USA
| | | | | | | |
Collapse
|
7
|
Ring currents modulate optoelectronic properties of aromatic chromophores at 25 T. Proc Natl Acad Sci U S A 2020; 117:11289-11298. [PMID: 32385159 DOI: 10.1073/pnas.1918148117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The properties of organic molecules can be influenced by magnetic fields, and these magnetic field effects are diverse. They range from inducing nuclear Zeeman splitting for structural determination in NMR spectroscopy to polaron Zeeman splitting organic spintronics and organic magnetoresistance. A pervasive magnetic field effect on an aromatic molecule is the aromatic ring current, which can be thought of as an induction of a circular current of π-electrons upon the application of a magnetic field perpendicular to the π-system of the molecule. While in NMR spectroscopy the effects of ring currents on the chemical shifts of nearby protons are relatively well understood, and even predictable, the consequences of these modified electronic states on the spectroscopy of molecules has remained unknown. In this work, we find that photophysical properties of model phthalocyanine compounds and their aggregates display clear magnetic field dependences up to 25 T, with the aggregates showing more drastic magnetic field sensitivities depending on the intermolecular interactions with the amplification of ring currents in stacked aggregates. These observations are consistent with ring currents measured in NMR spectroscopy and simulated in time-dependent density functional theory calculations of magnetic field-dependent phthalocyanine monomer and dimer absorption spectra. We propose that ring currents in organic semiconductors, which commonly comprise aromatic moieties, may present new opportunities for the understanding and exploitation of combined optical, electronic, and magnetic properties.
Collapse
|
8
|
Oviedo-Casado S, Šanda F, Hauer J, Prior J. Magnetic pulses enable multidimensional optical spectroscopy of dark states. J Chem Phys 2020; 152:084201. [DOI: 10.1063/1.5139409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Santiago Oviedo-Casado
- Racah Institute of Physics, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
- Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202, Spain
| | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
- Fakultät für Chemie, TU München, Oettingenstraße 67, 80538 Munich, Germany
| | - Jürgen Hauer
- Fakultät für Chemie, TU München, Oettingenstraße 67, 80538 Munich, Germany
- Photonics Institute, TU Wien, Gußhausstraße 27-29, 1040 Vienna, Austria
| | - Javier Prior
- Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada 18071, Spain
| |
Collapse
|
9
|
Lee IS, Filatov M, Min SK. Formulation and Implementation of the Spin-Restricted Ensemble-Referenced Kohn–Sham Method in the Context of the Density Functional Tight Binding Approach. J Chem Theory Comput 2019; 15:3021-3032. [DOI: 10.1021/acs.jctc.9b00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- In Seong Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| |
Collapse
|
10
|
Crowder induced structural modulation of a multi-domain protein during its early stages of aggregation: A FRET-based and protein solvation study. Int J Biol Macromol 2019; 127:563-574. [DOI: 10.1016/j.ijbiomac.2019.01.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/02/2019] [Accepted: 01/11/2019] [Indexed: 12/31/2022]
|
11
|
Allec SI, Sun Y, Sun J, Chang CEA, Wong BM. Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems. J Chem Theory Comput 2019; 15:2807-2815. [PMID: 30916958 DOI: 10.1021/acs.jctc.8b01239] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce a new heterogeneous CPU+GPU-enhanced DFTB approach for the routine and efficient simulation of large chemical and biological systems. Compared to homogeneous computing with conventional CPUs, heterogeneous computing approaches exhibit substantial performance with only a modest increase in power consumption, both of which are essential to upcoming exascale computing initiatives. We show that DFTB-based molecular dynamics is a natural candidate for heterogeneous computing, since the computational bottleneck in these simulations is the diagonalization of the Hamiltonian matrix, which is performed several times during a single molecular dynamics trajectory. To thoroughly test and understand the performance of our heterogeneous CPU+GPU approach, we examine a variety of algorithmic implementations, benchmarks of different hardware configurations, and applications of this methodology on several large chemical and biological systems. Finally, to demonstrate the capability of our implementation, we conclude with a large-scale DFTB MD simulation of explicitly solvated HIV protease (3974 atoms total) as a proof-of-concept example of an extremely large/complex system which, to the best of our knowledge, is the first time that an entire explicitly solvated protein has been treated at a quantum-based MD level of detail.
Collapse
|