1
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Tian Y, Zhou Y, Li L, Huang C, Lin L, Li C, Ye Y. Effect of substrate composition on physicochemical properties of the medium-long-medium structured triacylglycerol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:942-955. [PMID: 37708388 DOI: 10.1002/jsfa.12982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Nutritional and functional qualities and applications of structured lipids (SL) depend on the composition and molecular structure of fatty acids in the glycerol backbone of triacylglycerol (TAG). However, the relationship between the substrate composition and physicochemical qualities of SL has not been revealed. The investigation aims to disclose the effect of substrate composition on the physicochemical properties of medium-long-medium structured lipids (MLM-SLs) by enzymatic interesterification of Lipozyme TLIM/RMIM. RESULTS The medium-long-chain triacylglycerol (MLCT) yield could reach 70.32%, including 28.98% CaLCa (1,3-dioctonyl-2-linoleoyl glyceride) and 24.34% CaOCa (1,3-didecanoyl-2-oleoyl glyceride). The sn-2 unsaturated fatty acid composition mainly depended on long-chain triacylglycerol (LCT) in the substrate. The increased carbon chain length and double bond in triacylglycerol decreased its melting and crystallization temperature. The balanced substrate composition of MCT/LCT increased the size and finer crystals. Molecular docking simulation revealed that the MLCT molecule mainly interacted with the catalytic triplets of Lipozyme TLIM (Arg81-Ser83-Arg84) and the Lipozyme RMIM (Tyr183-Thr226-Arg262) by OH bond. The oxygen atom of the ester on the MLCT molecule was primarily bound to the hydrogen of hydroxyl and amino groups on the binding sites of Lipozyme TLIM/RMIM. The intermolecular interplay between MLCT and Lipozyme RMIM is more stable than Lipozyme TLIM due to the formation of lower binding affinity energy. CONCLUSION This research clarifies the interaction mechanism between MLCT molecules and lipases, and provides an in-depth understanding of the relationship between substrate composition, molecular structure and physicochemical property of MLM-SLs. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yunong Tian
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Yanhui Zhou
- Hunan Singular Biological Technology Co. Ltd, Changsha, China
| | - Lu Li
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Chuanqing Huang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Yong Ye
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
- SCUT - Zhuhai Institute of Modern Industrial Innovation, Zhuhai, China
- Jiangxi Environmental Engineering Vocational College, Ganzhou, China
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2
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Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural insights into functional properties of the oxidized form of cytochrome c oxidase. Nat Commun 2023; 14:5752. [PMID: 37717031 PMCID: PMC10505203 DOI: 10.1038/s41467-023-41533-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frank R Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Altos Labs, Redwood City, CA, 94065, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Robert E Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural basis for functional properties of cytochrome c oxidase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.530986. [PMID: 36993562 PMCID: PMC10055264 DOI: 10.1101/2023.03.20.530986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes, thereby establishing the proton gradient required for ATP synthesis1. The full turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized by molecular oxygen to the metastable oxidized OH state, and a reductive phase, in which OH is reduced back to the R state. During each of the two phases, two protons are translocated across the membranes2. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation2,3. How the O state structurally differs from OH remains an enigma in modern bioenergetics. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX)4, we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state5,6, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, a residue covalently linked to one of the three CuB ligands and critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide new insights into the proton translocation mechanism of CcO.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305 USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Robert E. Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Denis L. Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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4
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Yang J, Li Y, Qiu Q, Wang R, Yan W, Yu Y, Niu L, Pei H, Wei H, Ouyang L, Ye H, Xu D, Wei Y, Chen Q, Chen L. Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. J Med Chem 2022; 65:9159-9173. [PMID: 35762925 DOI: 10.1021/acs.jmedchem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here, we report a novel mechanism to selectively degrade target proteins. 3-(3-Phenoxybenzyl)amino-β-carboline (PAC), a tubulin inhibitor, promotes selective degradation of αβ-tubulin heterodimers. Biochemical studies have revealed that PAC specifically denatures tubulin, making it prone to aggregation that predisposes it to ubiquitinylation and then degradation. The degradation is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a low-barrier hydrogen bond (LBHB). In contrast, another two tubulin inhibitors that only form normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. We then screened for compounds capable of forming an LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimer degradation through the LBHB. Our study provided a unique example of LBHB function and identified a novel approach to obtain tubulin degraders.
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Affiliation(s)
- Jianhong Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Qiu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Yan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yamei Yu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lu Niu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heying Pei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoche Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoyu Ye
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuquan Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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5
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Morency M, Néron S, Iftimie R, Wuest JD. Predicting p Ka Values of Quinols and Related Aromatic Compounds with Multiple OH Groups. J Org Chem 2021; 86:14444-14460. [PMID: 34613729 DOI: 10.1021/acs.joc.1c01279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quinonoid compounds play central roles as redox-active agents in photosynthesis and respiration and are also promising replacements for inorganic materials currently used in batteries. To design new quinonoid compounds and predict their state of protonation and redox behavior under various conditions, their pKa values must be known. Methods that can predict the pKa values of simple phenols cannot reliably handle complex analogues in which multiple OH groups are present and may form intramolecular hydrogen bonds. We have therefore developed a straightforward method based on a linear relationship between experimental pKa values and calculated differences in energy between quinols and their deprotonated forms. Simple adjustments allow reliable predictions of pKa values when intramolecular hydrogen bonds are present. Our approach has been validated by showing that predicted and experimental values for over 100 quinols and related compounds differ by an average of only 0.3 units. This accuracy makes it possible to select proper pKa values when experimental data vary, predict the acidity of quinols and related compounds before they are made, and determine the sites and orders of deprotonation in complex structures with multiple OH groups.
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Affiliation(s)
- Mathieu Morency
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Sébastien Néron
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Radu Iftimie
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - James D Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
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6
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Vealey ZN, Foguel L, Vaccaro PH. Hydrogen-Bonding Motifs and Proton-Transfer Dynamics in Electronically Excited 6-Hydroxy-2-formylfulvene. J Phys Chem A 2019; 123:6506-6526. [DOI: 10.1021/acs.jpca.9b05025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zachary N. Vealey
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Lidor Foguel
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Patrick H. Vaccaro
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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7
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Karim A, Schulz N, Andersson H, Nekoueishahraki B, Carlsson ACC, Sarabi D, Valkonen A, Rissanen K, Gräfenstein J, Keller S, Erdélyi M. Carbon’s Three-Center, Four-Electron Tetrel Bond, Treated Experimentally. J Am Chem Soc 2018; 140:17571-17579. [DOI: 10.1021/jacs.8b09367] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alavi Karim
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Nils Schulz
- Faculty of Chemistry and Biochemistry, Organic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hanna Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Department of Chemistry−BMC, Uppsala University, SE 751 20 Uppsala, Sweden
| | - Bijan Nekoueishahraki
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Anna-Carin C. Carlsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Arto Valkonen
- Department of Chemistry, University of Jyvaskyla, P.O. Box. 35, FI-40014 Jyväskylän yliopisto, Finland
| | - Kari Rissanen
- Department of Chemistry, University of Jyvaskyla, P.O. Box. 35, FI-40014 Jyväskylän yliopisto, Finland
| | - Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), 67663 Kaiserslautern, Germany
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Department of Chemistry−BMC, Uppsala University, SE 751 20 Uppsala, Sweden
- The Swedish NMR Centre, Medicinaregatan 5, SE-413 90 Gothenburg, Sweden
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8
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Vealey ZN, Foguel L, Vaccaro PH. Spectral Signatures of Proton-Transfer Dynamics at the Cusp of Low-Barrier Hydrogen Bonding. J Phys Chem Lett 2018; 9:4949-4954. [PMID: 30101590 DOI: 10.1021/acs.jpclett.8b02199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite their importance in diverse chemical and biochemical processes, low-barrier hydrogen bonds remain elusive targets to classify and interpret spectroscopically. Here the correlated nature of hydrogen bonding and proton transfer in the low-barrier regime has been probed for the ground and excited electronic states of 6-hydroxy-2-formylfulvene by acquiring jet-cooled fluorescence spectra of the parent and monodeuterated isotopologs. While excited-state profiles reveal regular vibronic patterns devoid of obvious dynamical signatures, their ground-state counterparts display a radically altered energy landscape characterized by spectral bifurcations comparable in magnitude to typical vibrational spacings (>100 cm-1). Quantitative analyses yield unusual deuterium kinetic isotope effects that straddle limiting values attributed to above-barrier vibration and below-barrier tunneling of the proton adjoining donor/acceptor sites. Our findings provide compelling experimental evidence for ultrafast hydron-migration events commensurate with the onset of low-barrier hydrogen bonding and afford a trenchant glimpse of molecular phenomena taking place at the "tipping point" between disparate dynamical regimes.
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Affiliation(s)
- Zachary N Vealey
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 United States
| | - Lidor Foguel
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 United States
| | - Patrick H Vaccaro
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 United States
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9
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Liu Z, Liu Y, Zeng G, Shao B, Chen M, Li Z, Jiang Y, Liu Y, Zhang Y, Zhong H. Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review. CHEMOSPHERE 2018; 203:139-150. [PMID: 29614407 DOI: 10.1016/j.chemosphere.2018.03.179] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 03/24/2018] [Accepted: 03/26/2018] [Indexed: 05/02/2023]
Affiliation(s)
- Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Yujie Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Ming Chen
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhigang Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yilin Jiang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yu Zhang
- Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi 712046, PR China
| | - Hua Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China; State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei 430072, PR China
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10
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Yang J, Zheng J, Xu M, Zhuo Z, Yang W, Wang LW, Dai L, Lu J, Amine K, Pan F. Short Hydrogen Bonds on Reconstructed Nanocrystal Surface Enhance Oxygen Evolution Activity. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02814] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jinlong Yang
- School
of Advanced Materials, Peking University, Shenzhen Graduate School, Shenzhen 518055, People’s Republic of China
| | - Jiaxin Zheng
- School
of Advanced Materials, Peking University, Shenzhen Graduate School, Shenzhen 518055, People’s Republic of China
| | - Ming Xu
- School
of Advanced Materials, Peking University, Shenzhen Graduate School, Shenzhen 518055, People’s Republic of China
| | - Zengqing Zhuo
- School
of Advanced Materials, Peking University, Shenzhen Graduate School, Shenzhen 518055, People’s Republic of China
- Advanced
Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wanli Yang
- Advanced
Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lin-Wang Wang
- Materials
Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Liming Dai
- Department
of Macromolecular Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jun Lu
- Electrochemical
Technology Program, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Khalil Amine
- Electrochemical
Technology Program, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Feng Pan
- School
of Advanced Materials, Peking University, Shenzhen Graduate School, Shenzhen 518055, People’s Republic of China
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11
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Madurga S, Nedyalkova M, Mas F, Garcés JL. Ionization and Conformational Equilibria of Citric Acid: Delocalized Proton Binding in Solution. J Phys Chem A 2017; 121:5894-5906. [PMID: 28703587 DOI: 10.1021/acs.jpca.7b05089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microspeciation of citric acid is studied by analyzing NMR titration data. When the site binding (SB) model, which assumes fully localized proton binding to the carboxylic groups, is used to obtain microscopic energy parameters (dissociation constants, pair and triplet interaction energies between charged carboxylate groups), contradictory results are obtained. The resulting macroscopic constants are in very good agreement with the values reported in the literature using potentiometry. However, the found pair interaction energy between the terminal carboxylates and the triplet interaction energy are physically meaningless. To solve this apparent contradiction, we consider the possibility of delocalized proton binding, so that the proton can be exchanged at high velocity in the NMR time scale through short, strong, low-barrier (SSLB) hydrogen bonds. With this aim, ab initio MP2 calculations using the SMD polarizable continuum model for the solvent were performed and the fully roto-microspeciation elucidated. First, fully localized proton binding was assumed, and the resulting microstate probabilities are in reasonable agreement with those reported in previous works that use selective blocking of the carboxylic groups. They are, however, in clear disagreement with the microstate probabilities derived from the NMR titration data, which predict, within a very narrow confidence interval, a unique microspecies for the symmetric di-ionized form. Moreover, counterintuitively, the interaction between terminal charged groups is much larger than that between central and terminal groups. As a consequence, we have explored the possibility of delocalized proton binding by calculating the energy of intermediate proton positions between two carbolxylic groups. The results reveal that the exchange of the proton through the hydrogen bonds is in some cases produced without energetic barrier. This effect is specially relevant in the di-ionized form, with all the most stable conformations forming a SSLB, which together would constitute the only microstate detected by NMR. An alternative reaction scheme for the ionization process, based on proton delocalization, is proposed.
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Affiliation(s)
- Sergio Madurga
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB) , C/Martı́ i Franquès, 1, 08028 Barcelona, Catalonia, Spain
| | - Miroslava Nedyalkova
- Inorganic Chemistry Department, Faculty of Chemistry and Pharmacy "St Kliment Ohridski", University of Sofia , 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Francesc Mas
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB) , C/Martı́ i Franquès, 1, 08028 Barcelona, Catalonia, Spain
| | - Josep Lluís Garcés
- Chemistry Department and AGROTECNIO, University of Lleida (UdL) , Rovira Roure, 191, 25198 Lleida Catalonia, Spain
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Lu J, Hung I, Brinkmann A, Gan Z, Kong X, Wu G. Solid-State 17 O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong. Angew Chem Int Ed Engl 2017; 56:6166-6170. [PMID: 28225158 DOI: 10.1002/anie.201700488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Indexed: 11/07/2022]
Abstract
While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state 17 O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state 17 O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol-1 , suggesting that not all LBHBs are particularly strong.
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Affiliation(s)
- Jiasheng Lu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Andreas Brinkmann
- Measurement Science and Standards, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario, K1A 0R6, Canada
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Xianqi Kong
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
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Lu J, Hung I, Brinkmann A, Gan Z, Kong X, Wu G. Solid‐State
17
O NMR Reveals Hydrogen‐Bonding Energetics: Not All Low‐Barrier Hydrogen Bonds Are Strong. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700488] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiasheng Lu
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance National High Magnetic Field Laboratory 1800 East Paul Dirac Drive Tallahassee FL 32310 USA
| | - Andreas Brinkmann
- Measurement Science and Standards National Research Council Canada 1200 Montreal Road Ottawa Ontario K1A 0R6 Canada
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance National High Magnetic Field Laboratory 1800 East Paul Dirac Drive Tallahassee FL 32310 USA
| | - Xianqi Kong
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Gang Wu
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario K7L 3N6 Canada
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Affiliation(s)
- Charles L. Perrin
- Department of Chemistry & Biochemistry University of California, San Diego, La Jolla, California 92093-0358, United States
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McKenzie RH, Athokpam B, Ramesh SG. Isotopic fractionation in proteins as a measure of hydrogen bond length. J Chem Phys 2015; 143:044309. [DOI: 10.1063/1.4927391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Ross H. McKenzie
- School of Mathematics and Physics, University of Queensland, Brisbane 4072, Australia
| | - Bijyalaxmi Athokpam
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sai G. Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
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Smedarchina Z, Siebrand W, Fernández-Ramos A. Tunneling splitting in double-proton transfer: Direct diagonalization results for porphycene. J Chem Phys 2014; 141:174312. [DOI: 10.1063/1.4900717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Carlsson ACC, Uhrbom M, Karim A, Brath U, Gräfenstein J, Erdélyi M. Solvent effects on halogen bond symmetry. CrystEngComm 2013. [DOI: 10.1039/c2ce26745d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kontogianni VG, Charisiadis P, Primikyri A, Pappas CG, Exarchou V, Tzakos AG, Gerothanassis IP. Hydrogen bonding probes of phenol –OH groups. Org Biomol Chem 2013; 11:1013-25. [DOI: 10.1039/c2ob27117f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Double Molecular Recognition with Aminoorganoboron Complexes: Selective Alcoholysis of β-Dicarbonyl Derivatives. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Oishi S, Saito S. Double Molecular Recognition with Aminoorganoboron Complexes: Selective Alcoholysis of β-Dicarbonyl Derivatives. Angew Chem Int Ed Engl 2012; 51:5395-9. [DOI: 10.1002/anie.201200304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 02/23/2012] [Indexed: 11/06/2022]
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Moreno DV, González SA, Reyes A. Turning symmetric an asymmetric hydrogen bond with the inclusion of nuclear quantum effects: The case of the [CN···H···NC]−complex. J Chem Phys 2011; 134:024115. [DOI: 10.1063/1.3521272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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