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Duché G, Sanderson JM. The Chemical Reactivity of Membrane Lipids. Chem Rev 2024; 124:3284-3330. [PMID: 38498932 PMCID: PMC10979411 DOI: 10.1021/acs.chemrev.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024]
Abstract
It is well-known that aqueous dispersions of phospholipids spontaneously assemble into bilayer structures. These structures have numerous applications across chemistry and materials science and form the fundamental structural unit of the biological membrane. The particular environment of the lipid bilayer, with a water-poor low dielectric core surrounded by a more polar and better hydrated interfacial region, gives the membrane particular biophysical and physicochemical properties and presents a unique environment for chemical reactions to occur. Many different types of molecule spanning a range of sizes, from dissolved gases through small organics to proteins, are able to interact with membranes and promote chemical changes to lipids that subsequently affect the physicochemical properties of the bilayer. This Review describes the chemical reactivity exhibited by lipids in their membrane form, with an emphasis on conditions where the lipids are well hydrated in the form of bilayers. Key topics include the following: lytic reactions of glyceryl esters, including hydrolysis, aminolysis, and transesterification; oxidation reactions of alkenes in unsaturated fatty acids and sterols, including autoxidation and oxidation by singlet oxygen; reactivity of headgroups, particularly with reactive carbonyl species; and E/Z isomerization of alkenes. The consequences of reactivity for biological activity and biophysical properties are also discussed.
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Affiliation(s)
- Genevieve Duché
- Génie
Enzimatique et Cellulaire, Université
Technologique de Compiègne, Compiègne 60200, France
| | - John M Sanderson
- Chemistry
Department, Durham University, Durham DH1 3LE, United Kingdom
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Huang M, Jia Z, Luo S, Cheng JP. Quantitative Thermodynamic and Kinetic Parameters of Radical. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202106018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sarver PJ, Bacauanu V, Schultz DM, DiRocco DA, Lam YH, Sherer EC, MacMillan DWC. The merger of decatungstate and copper catalysis to enable aliphatic C(sp3)–H trifluoromethylation. Nat Chem 2020; 12:459-467. [DOI: 10.1038/s41557-020-0436-1] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/03/2020] [Indexed: 12/24/2022]
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Ding L, Zheng W, Wang Y. Homolytic C–O Cleavage in Phosphates and Sulfonates. J Phys Chem A 2015; 119:3488-99. [DOI: 10.1021/acs.jpca.5b00569] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lanlan Ding
- College of Chemistry and
Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Wenrui Zheng
- College of Chemistry and
Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Yingxing Wang
- College of Chemistry and
Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
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Wang YX, Zheng WR. A comparison of the C‒H bond dissociation enthalpies of sulfur-containing fused heterocyclic compounds to the C‒H bond dissociation enthalpies in other heterocycles. J Sulphur Chem 2015. [DOI: 10.1080/17415993.2014.996222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yu HZ, Fu F, Zhang L, Fu Y, Dang ZM, Shi J. Accurate predictions of C–SO2R bond dissociation enthalpies using density functional theory methods. Phys Chem Chem Phys 2014; 16:20964-70. [DOI: 10.1039/c4cp02005g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
M06-2X/6-31G(d) was found to be accurate in calculating C–S BDEs, and preliminary mechanistic studies were performed using it.
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Affiliation(s)
- Hai-Zhu Yu
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
| | - Fang Fu
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
| | - Liang Zhang
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
| | - Yao Fu
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
| | - Zhi-Min Dang
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
| | - Jing Shi
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
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Fortier S, Walensky JR, Wu G, Hayton TW. Synthesis of a Phosphorano-Stabilized U(IV)-Carbene via One-Electron Oxidation of a U(III)-Ylide Adduct. J Am Chem Soc 2011; 133:6894-7. [DOI: 10.1021/ja2001133] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Skye Fortier
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Justin R. Walensky
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Guang Wu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Trevor W. Hayton
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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Yan F, Fujimori DG. RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc Natl Acad Sci U S A 2011; 108:3930-4. [PMID: 21368151 PMCID: PMC3054002 DOI: 10.1073/pnas.1017781108] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RlmN and Cfr are Radical SAM enzymes that modify a single adenosine nucleotide--A2503--in 23S ribosomal RNA. This nucleotide is positioned within the peptidyl transferase center of the ribosome, which is a target of numerous antibiotics. An unusual feature of these enzymes is their ability to carry out methylation of amidine carbons of the adenosine substrate. To gain insight into the mechanism of methylation catalyzed by RlmN and Cfr, deuterium labeling experiments were carried out. These experiments demonstrate that the newly introduced methyl group is assembled from an S-adenosyl-L-methionine (SAM)-derived methylene fragment and a hydrogen atom that had migrated from the substrate amidine carbon. Rather than activating the adenosine nucleotide of the substrate by hydrogen atom abstraction from an amidine carbon, the 5'-deoxyadenosyl radical abstracts hydrogen from the second equivalent of SAM to form the SAM-derived radical cation. This species, or its corresponding sulfur ylide, subsequently adds into the substrate, initiating hydride shift and S-adenosylhomocysteine elimination to complete the formation of the methyl group. These findings indicate that rather than acting as methyltransferases, RlmN and Cfr are methyl synthases. Together with the previously described 5'-deoxyadenosyl and 3-amino-3-carboxypropyl radicals, these findings demonstrate that all three carbon atoms attached to the sulfonium center in SAM can serve as precursors to carbon-derived radicals in enzymatic reactions.
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Affiliation(s)
- Feng Yan
- Department of Cellular and Molecular Pharmacology and Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94158
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology and Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94158
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Taylor MS, Ivanic SA, Wood GPF, Easton CJ, Bacskay GB, Radom L. Hydrogen Abstraction by Chlorine Atom from Small Organic Molecules Containing Amino Acid Functionalities: An Assessment of Theoretical Procedures. J Phys Chem A 2009; 113:11817-32. [DOI: 10.1021/jp9029437] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Mark S. Taylor
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Sandra A. Ivanic
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Geoffrey P. F. Wood
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Christopher J. Easton
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - George B. Bacskay
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Leo Radom
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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ZHU C, RUI L, FU Y. Homolytic Bond Dissociation Enthalpies of C-C and C-H Bonds in Highly Crowded Alkanes. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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FANG, Ming M, LI Z, FU Y. Substituent Effect on the C-NO2and N-NO2Bond Dissociation Energies of Nitroaromatic Molecules. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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MENG XM, ZOU LF, XIE M, FU Y. Strength of C–H Bonds at Nitrogenα-Position:Implication for Metabolic Stability of Nitrogen-containing Drug Molecules. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Fu Y, Yu TQ, Wang YM, Liu L, Guo QX. α-Substituent Effects on Si–H, P–H and S–H Bond Dissociation Energies. CHINESE J CHEM 2006. [DOI: 10.1002/cjoc.200690057] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Williams RV, Edwards WD, Mitchell RH, Robinson SG. A DFT Study of the Thermal, Orbital Symmetry Forbidden, Cyclophanediene to Dihydropyrene Electrocyclic Reaction. Predictions to Improve the Dimethyldihydropyrene Photoswitches. J Am Chem Soc 2005; 127:16207-14. [PMID: 16287311 DOI: 10.1021/ja054553r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The orbital symmetry forbidden thermal electrocyclic equilibria between a series of cyclophanedienes and dimethyldihydropyrenes (CPD<==>DDPs) were studied using density functional theory (DFT). These reactions are important not only because of their fundamental interest but also in how they restrict the potential utility of the DDP photoswitches by limiting the thermal lifetime of the CPDs. The transition states (TSs) for these reactions could not be modeled using restricted DFT (RB3LYP) but were located using unrestricted DFT (UB3LYP). Each TS possesses significant biradical character as indicated by their spin contaminated wave functions, S2 not = 0. Specific substitution by nitrile or trifluoromethyl group(s) is predicted to strongly affect the magnitude of the activation barriers for these reactions. In particular, replacing the internal methyl groups of the CPDs/DDPs with nitrile groups is predicted to have the maximum effect and to raise the activation barriers and lifetimes of the CPDs considerably.
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Zhao SW, Liu L, Fu Y, Guo QX. Assessment of the metabolic stability of the methyl groups in heterocyclic compounds using C?H bond dissociation energies: Effects of diverse aromatic groups on the stability of methyl radicals. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.856] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Feng Y, Liu L, Wang JT, Huang H, Guo QX. Assessment of Experimental Bond Dissociation Energies Using Composite ab Initio Methods and Evaluation of the Performances of Density Functional Methods in the Calculation of Bond Dissociation Energies. ACTA ACUST UNITED AC 2003; 43:2005-13. [PMID: 14632451 DOI: 10.1021/ci034033k] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Composite ab initio CBS-Q and G3 methods were used to calculate the bond dissociation energies (BDEs) of over 200 compounds listed in CRC Handbook of Chemistry and Physics (2002 ed.). It was found that these two methods agree with each other excellently in the calculation of BDEs, and they can predict BDEs within 10 kJ/mol of the experimental values. Using these two methods, it was found that among the examined compounds 161 experimental BDEs are valid because the standard deviation between the experimental and theoretical values for them is only 8.6 kJ/mol. Nevertheless, 40 BDEs listed in the Handbook may be highly inaccurate as the experimental and theoretical values for them differ by over 20 kJ/mol. Furthermore, 11 BDEs listed in the Handbook may be seriously flawed as the experimental and theoretical values for them differ by over 40 kJ/mol. Using the 161 cautiously validated experimental BDEs, we then assessed the performances of the standard density functional (DFT) methods including B3LYP, B3P86, B3PW91, and BH&HLYP in the calculation of BDEs. It was found that the BH&HLYP method performed poorly for the BDE calculations. B3LYP, B3P86, and B3PW91, however, performed reasonably well for the calculation of BDEs with standard deviations of about 12.1-18.0 kJ/mol. Nonetheless, all the DFT methods underestimated the BDEs by 4-17 kJ/mol in average. Sometimes, the underestimation by the DFT methods could be as high as 40-60 kJ/mol. Therefore, the DFT methods were more reliable for relative BDE calculations than for absolute BDE calculations. Finally, it was observed that the basis set effects on the BDEs calculated by the DFT methods were usually small except for the heteroatom-hydrogen BDEs.
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Affiliation(s)
- Yong Feng
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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