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Yang Y, Zheng W, Ren L, Xu X. A theoretical study on the proton affinity of sulfur ylides. NEW J CHEM 2022. [DOI: 10.1039/d2nj00948j] [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 proton affinities of sulfoxide ylides, carbonyl ylides, allyl ylides, benzenyl ylides and heterocyclic ylides with typical substituents were investigated using the SOGGA11-X functional.
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Affiliation(s)
- Yaxin Yang
- 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
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Lufei Ren
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Xiaofei Xu
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
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2
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Yang Y, Zheng W, Xie H, Ren L, Xu X, Liang Y. Theoretical study on adiabatic electron affinity of fatty acids. NEW J CHEM 2021. [DOI: 10.1039/d1nj02456f] [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 AEA of saturated fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids with typical substituents were calculated by the ωB97X method.
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Affiliation(s)
- Yaxin Yang
- 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
| | - Hongyun Xie
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Lufei Ren
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Xiaofei Xu
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Yingning Liang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
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3
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Tian Y, Wu KH, Cao L, Saputera WH, Amal R, Wang DW. Unlocking high-potential non-persistent radical chemistry for semi-aqueous redox batteries. Chem Commun (Camb) 2019; 55:2154-2157. [DOI: 10.1039/c8cc09304k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stabilizing non-persistent radical opens the gate to low-cost high-potential cathode for all-organic aqueous redox batteries with fast reversible rate capability.
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Affiliation(s)
- Yuheng Tian
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
| | - Kuang-Hsu Wu
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
| | - Liuyue Cao
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
| | - Wibawa H. Saputera
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
- Department of Chemical Engineering
| | - Rose Amal
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
| | - Da-Wei Wang
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
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4
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Prats-Mateu B, Bock P, Schroffenegger M, Toca-Herrera JL, Gierlinger N. Following laser induced changes of plant phenylpropanoids by Raman microscopy. Sci Rep 2018; 8:11804. [PMID: 30087373 PMCID: PMC6081397 DOI: 10.1038/s41598-018-30096-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/24/2018] [Indexed: 12/26/2022] Open
Abstract
Raman microscopy is a powerful imaging technique for biological materials providing information about chemistry in context with microstructure. A 532 nm laser is often used as excitation source, because high spatial resolution and signal intensity can be achieved. The latter can be controlled by laser power and integration time, whereby high power and long times give good signal to noise ratio. However, most biological materials absorb in the VIS range and fluorescence masking the signal or even sample degradation might be hindering. Here, we show that on lignified plant cell walls even very short integration times and low laser powers induce a change in the ratio of the lignin bands at 1660 and 1600 cm-1. Time series on lignin model compounds revealed this change only in aromatic molecules with two OH-groups, such as coniferyl alcohol. Therefore, we conclude that monolignols are present in the cell wall and responsible for the observed effect. The solvent selectivity of the changes points to a laser induced polymerization process. The results emphasize how crucial careful adjustment of experimental parameters in Raman imaging of biological materials is and show the potential of time series and repeated imaging to get additional insights (e.g. monolignols).
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Affiliation(s)
- Batirtze Prats-Mateu
- Institute for Biophysics, Department of Nanobiotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 11/II, 1190, Vienna, Austria
| | - Peter Bock
- Institute for Biophysics, Department of Nanobiotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 11/II, 1190, Vienna, Austria
| | - Martina Schroffenegger
- Institute of Biologically inspired materials, Department of Nanobiotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 11/II, 1190, Vienna, Austria
| | - José Luis Toca-Herrera
- Institute for Biophysics, Department of Nanobiotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 11/II, 1190, Vienna, Austria
| | - Notburga Gierlinger
- Institute for Biophysics, Department of Nanobiotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 11/II, 1190, Vienna, Austria.
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5
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Chen C, Shrestha R, Jia K, Gao PF, Geisbrecht BV, Bossmann SH, Shi J, Li P. Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs. J Biol Chem 2015. [PMID: 26205819 DOI: 10.1074/jbc.m115.658807] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which has received much attention due to their potential applications in lignin degradation. A new DyP from Thermomonospora curvata (TcDyP) was identified and characterized. Unlike other A-type enzymes, TcDyP is highly active toward a wide range of substrates including model lignin compounds, in which the catalytic efficiency with ABTS (kcat(app)/Km(app) = (1.7 × 10(7)) m(-1) s(-1)) is close to that of fungal DyPs. Stopped-flow spectroscopy was employed to elucidate the transient intermediates as well as the catalytic cycle involving wild-type (wt) and mutant TcDyPs. Although residues Asp(220) and Arg(327) are found necessary for compound I formation, His(312) is proposed to play roles in compound II reduction. Transient kinetics of hydroquinone (HQ) oxidation by wt-TcDyP showed that conversion of the compound II to resting state is a rate-limiting step, which will explain the contradictory observation made with the aspartate mutants of A-type DyPs. Moreover, replacement of His(312) and Arg(327) has significant effects on the oligomerization and redox potential (E°') of the enzyme. Both mutants were found to promote the formation of dimeric state and to shift E°' to a more negative potential. Not only do these results reveal the unique catalytic property of the A-type DyPs, but they will also facilitate the development of these enzymes as lignin degraders.
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Affiliation(s)
| | | | | | - Philip F Gao
- the Protein Production Group, University of Kansas, Lawrence, Kansas 66045
| | | | | | - Jishu Shi
- Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506 and
| | - Ping Li
- From the Departments of Chemistry,
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Elbashir AA, Aboul-Enein HY. Capillary Electrophoresis and Molecular Modeling as a Complementary Technique for Chiral Recognition Mechanism. Crit Rev Anal Chem 2013. [DOI: 10.1080/10408347.2013.803358] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Sviatenko LK, Gorb L, Hill FC, Leszczynski J. Theoretical study of ionization and one-electron oxidation potentials ofN-heterocyclic compounds. J Comput Chem 2013; 34:1094-100. [DOI: 10.1002/jcc.23228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/12/2012] [Accepted: 12/16/2012] [Indexed: 11/08/2022]
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8
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Brown ME, Barros T, Chang MCY. Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium. ACS Chem Biol 2012; 7:2074-81. [PMID: 23054399 DOI: 10.1021/cb300383y] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plant biomass represents a renewable feedstock that has not yet been fully tapped because of the difficulty in accessing the carbon in its structural biopolymers. Lignin is an especially challenging substrate, but select microbes have evolved complex systems of enzymes for its breakdown through a radical-mediated oxidation process. Fungal systems are well-characterized for their ability to depolymerize lignin, but the ability of bacteria to react with this substrate remains elusive. We have therefore focused on elucidating strategies used by lignin-reactive soil bacteria and describing their oxidative enzyme systems. We now report the identification and characterization of an unusual C-type dye-decolorizing peroxidase from Amycolatopsis sp. 75iv2 (DyP2), which belongs to a family of heme peroxidases reported to be involved in bacterial lignin degradation. Biochemical studies indicate that DyP2 has novel function for this family, with versatile and high activity both as a peroxidase and Mn peroxidase (k(cat)/K(M) ≈ 10(5)-10(6) M(-1) s(-1)). It also has a Mn-dependent oxidase mode of action that expands its substrate scope. Crystallographic studies of DyP2 at 2.25 Å resolution show the existence of a Mn binding pocket and support its key role in catalysis.
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Affiliation(s)
- Margaret E. Brown
- Department
of Chemistry, ‡Department of Molecular and Cell Biology, and §Howard Hughes Medical Institute, University of California, Berkeley,
California 94720-1460, United States
| | - Tiago Barros
- Department
of Chemistry, ‡Department of Molecular and Cell Biology, and §Howard Hughes Medical Institute, University of California, Berkeley,
California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department
of Chemistry, ‡Department of Molecular and Cell Biology, and §Howard Hughes Medical Institute, University of California, Berkeley,
California 94720-1460, United States
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9
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Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, Smith JC. Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study. J Phys Chem B 2012; 116:4760-8. [DOI: 10.1021/jp2122449] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amandeep K. Sangha
- UT/ORNL Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United
States
| | - Jerry M. Parks
- UT/ORNL Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United
States
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee 37831, United States
| | - Robert F. Standaert
- Department of Biochemistry
and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee 37831, United States
- Biology and Soft
Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Angela Ziebell
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Mark Davis
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Jeremy C. Smith
- UT/ORNL Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United
States
- Department of Biochemistry
and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee 37831, United States
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10
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Milczarek G, Inganas O. Renewable Cathode Materials from Biopolymer/Conjugated Polymer Interpenetrating Networks. Science 2012; 335:1468-71. [DOI: 10.1126/science.1215159] [Citation(s) in RCA: 387] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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11
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Takahashi LK, Zhou J, Kostko O, Golan A, Leone SR, Ahmed M. Vacuum-Ultraviolet Photoionization and Mass Spectrometric Characterization of Lignin Monomers Coniferyl and Sinapyl Alcohols. J Phys Chem A 2011; 115:3279-90. [DOI: 10.1021/jp111437e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lynelle K. Takahashi
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Jia Zhou
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Amir Golan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen R. Leone
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Watts HD, Mohamed MNA, Kubicki JD. Comparison of Multistandard and TMS-Standard Calculated NMR Shifts for Coniferyl Alcohol and Application of the Multistandard Method to Lignin Dimers. J Phys Chem B 2011; 115:1958-70. [DOI: 10.1021/jp110330q] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Heath D. Watts
- Department of Geosciences and the Earth and Environmental Systems Institute and ‡Center for NanoCellulosics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohamed Naseer Ali Mohamed
- Department of Geosciences and the Earth and Environmental Systems Institute and ‡Center for NanoCellulosics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - James D. Kubicki
- Department of Geosciences and the Earth and Environmental Systems Institute and ‡Center for NanoCellulosics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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13
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Rodrigo CP, James WH, Zwier TS. Single-conformation ultraviolet and infrared spectra of jet-cooled monolignols: p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol. J Am Chem Soc 2011; 133:2632-41. [PMID: 21294542 DOI: 10.1021/ja109218j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-conformation spectroscopy of the three lignin monomers (hereafter "monolignols") p-coumaryl alcohol (pCoumA), coniferyl alcohol (ConA), and sinapyl alcohol (SinA) has been carried out on the isolated molecules cooled in a supersonic expansion. Laser-induced fluorescence excitation, dispersed fluorescence, resonant two-photon ionization, UV-UV hole-burning, and resonant ion-dip infrared spectroscopy were carried out as needed to obtain firm assignments for the observed conformers of the three molecules. In each case, two conformers were observed, differing in the relative orientations of the vinyl and OH substituents para to one another on the phenyl ring. In pCoumA, the two conformers have S(0)-S(1) origins nearly identical in size, split from one another by only 7 cm(-1), in close analogy with previous results of Morgan et al. on p-vinylphenol ( Chem. Phys. 2008 , 347 , 340 ). ConA, with its methoxy group ortho to the OH group, also has two low-energy conformers forming a syn/anti pair, in this case with the OH group locked into an orientation in which it forms an intramolecular H-bond with the adjacent methoxy group. The electronic frequency shift between the two conformers is dramatically increased to 805 cm(-1), with the dominant conformer of ConA (with S(0)-S(1) origin at 32 640 cm(-1)) about 5 times the intensity of its minor counterpart (with S(0)-S(1) origin at 33 444 cm(-1)). The presence of an OH···OCH(3) intramolecular H-bond is established by the shift of the OH stretch fundamental of the OH group to 3599 cm(-1), as it is in o-methoxyphenol ( Fujimaki et al. J. Chem. Phys. 1999 , 110 , 4238 ). Analogous single-conformation UV and IR spectra of o-methoxy-p-vinylphenol show a close similarity to ConA and provide a basis for a firm assignment of the red-shifted (blue-shifted) conformer of both molecules to the syn (anti) conformer. The two observed conformers of SinA, with its two methoxy group straddling the OH group, have S(0)-S(1) origins split by 239 cm(-1) (33 055 and 33 294 cm(-1)), a value between those in pCoumA and ConA. A combination of experimental data and calculations on the three monolignols and simpler derivatives is used to establish that the conformational preferences of the monolignols reflect the preferences of each of the ring substituents separately, enhanced by the presence of the intramolecular OH···OCH(3) H-bond. Taken as a whole, the presence of multiple flexible substituents locks in certain preferred orientations of the groups relative to one another, even in the apparently flexible allyl alcohol side chain (-CH═CH-CH(2)OH), where the OH group orients itself so that the hydrogen is pointed back over the vinyl π cloud in order to minimize interactions between the oxygen lone pairs and the π electrons.
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Affiliation(s)
- Chirantha P Rodrigo
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
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14
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Wang HJ, Shi J, Fang M, Li Z, Guo QX. Design of new neutral organic super-electron donors: a theoretical study. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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DFT/B3LYP study of the substituent effect on the reaction enthalpies of the individual steps of sequential proton loss electron transfer mechanism of phenols antioxidant action: Correlation with phenolic CO bond length. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Klein E, Lukeš V. DFT/B3LYP study of O–H bond dissociation enthalpies of para and meta substituted phenols: Correlation with the phenolic C–O bond length. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.04.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Gomes JR, Ribeiro da Silva MA. A computational study on the enhanced stabilization of aminophenol derivatives by internal hydrogen bonding. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Namazian M, Siahrostami S, Noorbala MR, Coote ML. Calculation of two-electron reduction potentials for some quinone derivatives in aqueous solution using Møller–Plesset perturbation theory. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.11.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Study of N–H, O–H, and S–H bond dissociation enthalpies and ionization potentials of substituted anilines, phenols, and thiophenols. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.10.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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