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Mardyukov A, Hernández FJ, Song L, Crespo-Otero R, Schreiner PR. Experimentally Delineating the Catalytic Effect of a Single Water Molecule in the Photochemical Rearrangement of the Phenylperoxy Radical to the Oxepin-2(5 H)-one-5-yl Radical. J Am Chem Soc 2024; 146:19070-19076. [PMID: 38968610 DOI: 10.1021/jacs.4c03461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Abstract
Catalysis plays a pivotal role in both chemistry and biology, primarily attributed to its ability to stabilize transition states and lower activation free energies, thereby accelerating reaction rates. While computational studies have contributed valuable mechanistic insights, there remains a scarcity of experimental investigations into transition states. In this work, we embark on an experimental exploration of the catalytic energy lowering associated with transition states in the photorearrangement of the phenylperoxy radical-water complex to the oxepin-2(5H)-one-5-yl radical. Employing matrix isolation spectroscopy, density functional theory, and post-HF computations, we scrutinize the (photo)catalytic impact of a single water molecule on the rearrangement. Our computations indicate that the barrier heights for the water-assisted unimolecular isomerization steps are approximately 2-3 kcal mol-1 lower compared to the uncatalyzed steps. This decrease directly coincides with the energy difference in the required wavelength during the transformation (Δλ = λ546 nm - λ579 nm ≡ 52.4-49.4 = 3.0 kcal mol-1), allowing us to elucidate the differential transition state energy in the photochemical rearrangement of the phenylperoxy radical catalyzed by a single water molecule. Our work highlights the important role of water catalysis and has, among others, implications for understanding the mechanism of organic reactions under atmospheric conditions.
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Affiliation(s)
- Artur Mardyukov
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | | | - Lijuan Song
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
| | - Rachel Crespo-Otero
- UCL Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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Zhang R, Yan S, Song H, Guo H, Ning C. Probing the activated complex of the F + NH 3 reaction via a dipole-bound state. Nat Commun 2024; 15:3858. [PMID: 38719855 PMCID: PMC11079065 DOI: 10.1038/s41467-024-48202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Experimental characterization of the transition state poses a significant challenge due to its fleeting nature. Negative ion photodetachment offers a unique tool for probing transition states and their vicinity. However, this approach is usually limited to Franck-Condon regions. For example, high-lying Feshbach resonances with an excited HF stretching mode (vHF = 2-4) were recently identified in the transition-state region of the F + NH3 → HF + NH2 reaction through photo-detaching FNH3- anions, but the direct photodetachment failed to observe the lower-lying vHF = 0,1 resonances and bound states due apparently to negligible Franck-Condon factors. Indeed, these weak transitions can be resonantly enhanced via a dipole-bound state (DBS) formed between an electron and the polar FNH3 species. In this study, we unveil a series of Feshbach resonances and bound states along the F + NH3 reaction path via a DBS by combining high-resolution photoelectron spectroscopy with high-level quantum dynamical computations. This study presents an approach for probing the activated complex in a reaction by negative ion photodetachment through a DBS.
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Affiliation(s)
- Rui Zhang
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, 100084, Beijing, China
| | - Shuaiting Yan
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, 100084, Beijing, China
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Hua Guo
- Department of Chemistry and Chemical Biology, Center for Computational Chemistry, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Chuangang Ning
- Department of Physics, State Key Laboratory of Low Dimensional Quantum Physics, Frontier Science Center for Quantum Information, Tsinghua University, 100084, Beijing, China.
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Sari L, Bali S, Joachimiak LA, Lin MM. Hairpin trimer transition state of amyloid fibril. Nat Commun 2024; 15:2756. [PMID: 38553453 PMCID: PMC10980705 DOI: 10.1038/s41467-024-46446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Protein fibril self-assembly is a universal transition implicated in neurodegenerative diseases. Although fibril structure/growth are well characterized, fibril nucleation is poorly understood. Here, we use a computational-experimental approach to resolve fibril nucleation. We show that monomer hairpin content quantified from molecular dynamics simulations is predictive of experimental fibril formation kinetics across a tau motif mutant library. Hairpin trimers are predicted to be fibril transition states; one hairpin spontaneously converts into the cross-beta conformation, templating subsequent fibril growth. We designed a disulfide-linked dimer mimicking the transition state that catalyzes fibril formation, measured by ThT fluorescence and TEM, of wild-type motif - which does not normally fibrillize. A dimer compatible with extended conformations but not the transition-state fails to nucleate fibril at any concentration. Tau repeat domain simulations show how long-range interactions sequester this motif in a mutation-dependent manner. This work implies that different fibril morphologies could arise from disease-dependent hairpin seeding from different loci.
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Affiliation(s)
- Levent Sari
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milo M Lin
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Yuan DF, Liu Y, Trabelsi T, Zhang YR, Li J, Francisco JS, Guo H, Wang LS. Probing the dynamics and bottleneck of the key atmospheric SO 2 oxidation reaction by the hydroxyl radical. Proc Natl Acad Sci U S A 2024; 121:e2314819121. [PMID: 38285944 PMCID: PMC10861908 DOI: 10.1073/pnas.2314819121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
SO2 (Sulfur dioxide) is the major precursor to the production of sulfuric acid (H2SO4), contributing to acid rain and atmospheric aerosols. Sulfuric acid formed from SO2 generates light-reflecting sulfate aerosol particles in the atmosphere. This property has prompted recent geoengineering proposals to inject sulfuric acid or its precursors into the Earth's atmosphere to increase the planetary albedo to counteract global warming. SO2 oxidation in the atmosphere by the hydroxyl radical HO to form HOSO2 is a key rate-limiting step in the mechanism for forming acid rain. However, the dynamics of the HO + SO2 → HOSO2 reaction and its slow rate in the atmosphere are poorly understood to date. Herein, we use photoelectron spectroscopy of cryogenically cooled HOSO2- anion to access the neutral HOSO2 radical near the transition state of the HO + SO2 reaction. Spectroscopic and dynamic calculations are conducted on the first ab initio-based full-dimensional potential energy surface to interpret the photoelectron spectra of HOSO2- and to probe the dynamics of the HO + SO2 reaction. In addition to the finding of a unique pre-reaction complex (HO⋯SO2) directly connected to the transition state, dynamic calculations reveal that the accessible phase space for the HO + SO2 → HOSO2 reaction is extremely narrow, forming a key reaction bottleneck and slowing the reaction rate in the atmosphere, despite the low reaction barrier. This study underlines the importance of understanding the full multidimensional potential energy surface to elucidate the dynamics of complex bimolecular reactions involving polyatomic reactants.
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Affiliation(s)
- Dao-Fu Yuan
- Hefei National Research Center for Physical Science at Microscale, University of Science and Technology of China, Hefei230026, China
- Department of Chemistry, Brown University, Providence, RI02912
| | - Yang Liu
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing401331, China
- Department of Chemistry and Chemical Biology, Center for Computational Chemistry, University of New Mexico, Albuquerque, NM87131
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences, University of Pennsylvania, Philadelphia, PA19104
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA19104
| | - Yue-Rou Zhang
- Department of Chemistry, Brown University, Providence, RI02912
| | - Jun Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing401331, China
| | - Joseph S. Francisco
- Department of Earth and Environmental Sciences, University of Pennsylvania, Philadelphia, PA19104
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA19104
| | - Hua Guo
- Department of Chemistry and Chemical Biology, Center for Computational Chemistry, University of New Mexico, Albuquerque, NM87131
| | - Lai-Sheng Wang
- Department of Chemistry, Brown University, Providence, RI02912
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Song H, Guo H. Theoretical Insights into the Dynamics of Gas-Phase Bimolecular Reactions with Submerged Barriers. ACS PHYSICAL CHEMISTRY AU 2023; 3:406-418. [PMID: 37780541 PMCID: PMC10540288 DOI: 10.1021/acsphyschemau.3c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 10/03/2023]
Abstract
Much attention has been paid to the dynamics of both activated gas-phase bimolecular reactions, which feature monotonically increasing integral cross sections and Arrhenius kinetics, and their barrierless capture counterparts, which manifest monotonically decreasing integral cross sections and negative temperature dependence of the rate coefficients. In this Perspective, we focus on the dynamics of gas-phase bimolecular reactions with submerged barriers, which often involve radicals or ions and are prevalent in combustion, atmospheric chemistry, astrochemistry, and plasma chemistry. The temperature dependence of the rate coefficients for such reactions is often non-Arrhenius and complex, and the corresponding dynamics may also be quite different from those with significant barriers or those completely dominated by capture. Recent experimental and theoretical studies of such reactions, particularly at relatively low temperatures or collision energies, have revealed interesting dynamical behaviors, which are discussed here. The new knowledge enriches our understanding of the dynamics of these unusual reactions.
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Affiliation(s)
- Hongwei Song
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hua Guo
- Department
of Chemistry and Chemical Biology, University
of New Mexico, Albuquerque, New Mexico 87131, United States
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Li J, Tu Z, Xiang H, Li Y, Song H. Theoretical studies on the kinetics and dynamics of the BeH + + H 2O reaction: comparison with the experiment. Phys Chem Chem Phys 2023; 25:20997-21005. [PMID: 37503894 DOI: 10.1039/d3cp02322b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The reaction of BeH+ with background gaseous H2O may play a role in qubit loss for quantum information processing with Be+ as trapped ions, and yet its reaction mechanism has not been well understood until now. In this work, a globally accurate, full-dimensional ground-state potential energy surface (PES) for the BeH+ + H2O reaction was constructed by fitting a total of 170 438 ab initio energy points at the level of RCCSD(T)-F12/aug-cc-pVTZ using the fundamental invariant-neural network method. The total root-mean-square error of the final PES was 0.178 kcal mol-1. For comparison, quasi-classical trajectory calculations were carried out on the PES at an experimental temperature of 150 K. The obtained thermal rate constant and product branching ratio of the BeD+ + H2O reaction agreed quite well with experimental results. In addition, the vibrational state distributions and energy disposals of the products were calculated and rationalized using the sudden vector projection model.
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Affiliation(s)
- Jiaqi Li
- College of Physical Science and Technology, Huazhong Normal University, Wuhan 430079, China.
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Zhao Tu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- School of Chemical and Environmental Engineering, Hubei Minzu University, Enshi 445000, China
| | - Haipan Xiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- School of Physics and Electronics, Hunan University, Changsha 410082, China
| | - Yong Li
- College of Physical Science and Technology, Huazhong Normal University, Wuhan 430079, China.
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
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Liu S, Chen J, Zhang X, Zhang DH. Feshbach resonances in the F + CHD 3 → HF + CD 3 reaction. Chem Sci 2023; 14:7973-7979. [PMID: 37502322 PMCID: PMC10370578 DOI: 10.1039/d3sc02629a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
The signature of dynamics resonances was observed in the benchmark polyatomic F + CH4/CHD3 reactions more than a decade ago; however, the dynamical origin of the resonances is still not clear due to the lack of reliable quantum dynamics studies on accurate potential energy surfaces. Here, we report a six-dimensional state-to-state quantum dynamics study on the F + CHD3 → HF + CD3 reaction on a highly accurate potential energy surface. Pronounced oscillatory structures are observed in the total and product rovibrational-state-resolved reaction probabilities. Detailed analysis reveals that these oscillating features originate from the Feshbach resonance states trapped in the peculiar well on the HF(v' = 3)-CD3 vibrationally adiabatic potential caused by HF chemical bond softening. Most of the resonance structures on the reaction probabilities are washed out in the well converged integral cross sections (ICS), leaving only one distinct peak at low collision energy. The calculated HF vibrational state-resolved ICS for CD3(v = 0) agrees quantitatively with the experimental results, especially the branching ratio, but the theoretical CD3 umbrella vibration state distribution is found to be much hotter than the experiment.
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Affiliation(s)
- Shu Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jun Chen
- State Key Laboratory of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Xiaoren Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning 116023 China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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Neumark DM. Spectroscopy of Radicals, Clusters, and Transition States Using Slow Electron Velocity-Map Imaging of Cryogenically Cooled Anions. J Phys Chem A 2023; 127:4207-4223. [PMID: 37094039 DOI: 10.1021/acs.jpca.3c01537] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Slow electron velocity-map imaging of cryogenically cooled anions (cryo-SEVI) is a high-resolution variant of anion photoelectron spectroscopy that has been applied with considerable success over the years to the study of radicals, size-selected clusters, and transition states for unimolecular and bimolecular reactions. Cryo-SEVI retains the versatility of conventional anion photoelectron spectroscopy while offering sub-meV resolution, thereby enabling the resolution of vibrational structure in the photoelectron spectra of complex anions. This Feature Article describes recent experiments in our laboratory using cryo-SEVI, including a new research direction in which anions are vibrationally pre-excited with an infrared laser pulse prior to photodetachment.
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Affiliation(s)
- Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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