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Wang Z, Sun Z, Zhao H, Li J, Zhang X, Jia J, An K, Tang Z, He M, Qu Z. Effect of different defects on the competitive adsorption of formaldehyde and water on the surface of carbon materials: Density functional theory study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168745. [PMID: 37996039 DOI: 10.1016/j.scitotenv.2023.168745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/03/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023]
Abstract
The adsorption of formaldehyde by carbon materials is extremely limited and is also greatly influenced by the competitive adsorption of water. Therefore, it is of great significance to investigate the effect of different defects on the competitive adsorption of formaldehyde and water on the surface of carbon materials, and consequently the targeted modification of carbon materials to promote the adsorption of formaldehyde in air. In this study, multi-scale simulations were conducted to explore the problem of competitive adsorption of water and formaldehyde on the surface of carbon materials by quantum chemistry and molecular dynamics. IGMH, QTAIM, energy decomposition, electron transfer, and so on were used to conduct a comprehensive analysis of the problem of competitive adsorption of water and formaldehyde on the surface of carbon materials. The reasons for the formation of competitive adsorption between water and formaldehyde were firstly clarified, and then the adsorption interactions of different oxygen-containing functional groups on formaldehyde and water were investigated separately, which were found that the competitive adsorption of water and formaldehyde molecules by different types of oxygen-containing functional groups caused different results. And the introduction of intrinsic defects can promote the adsorption of formaldehyde in the presence of water competition for adsorption, which can well compensate the inhibitory effect of water on the adsorption of formaldehyde with strong polar functional groups. Finally, the results obtained from simulations were used to guide the modification experiments, and the experimental results were in accord with the simulation results. This study provides a new idea for the preparation of materials for efficient formaldehyde adsorption under certain humidity.
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Affiliation(s)
- Zhonghua Wang
- School of Civil and Architectural Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Zekun Sun
- School of Civil and Architectural Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Haiqian Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Jun Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xing Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jiuyang Jia
- School of Mechanical Science and Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Kaibo An
- School of Civil and Architectural Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Ziyu Tang
- School of Civil and Architectural Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Mingqi He
- School of Mechanical Science and Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Zhibin Qu
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, China
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Derr JB, Tamayo J, Clark JA, Morales M, Mayther MF, Espinoza EM, Rybicka-Jasińska K, Vullev VI. Multifaceted aspects of charge transfer. Phys Chem Chem Phys 2020; 22:21583-21629. [PMID: 32785306 PMCID: PMC7544685 DOI: 10.1039/d0cp01556c] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.
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Affiliation(s)
- James B Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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3
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Molecular electrets – Why do dipoles matter for charge transfer and excited-state dynamics? J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Zheng Q, Carty SN, Lazo ND. Helix Dipole and Membrane Electrostatics Delineate Conformational Transitions in the Self-Assembly of Amyloidogenic Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8389-8397. [PMID: 32628488 PMCID: PMC8095063 DOI: 10.1021/acs.langmuir.0c00723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The self-assembly of amyloidogenic peptides on membrane surfaces is associated with the death of neurons and β-cells in Alzheimer's disease and type 2 diabetes, respectively. The early events of self-assembly in vivo are not known, but there is increasing evidence for the importance of the α-helix. To test the hypothesis that electrostatic interactions involving the helix dipole play a key role in membrane-mediated peptide self-assembly, we studied IAPP[11-25(S20G)-NH2] (R11LANFLVHSGNNFGA25-NH2), which under certain conditions self-assembles in hydro to form β-sheet assemblies through an α-helix-containing intermediate. In the presence of small unilamellar vesicles composed solely of zwitterionic lipids, the peptide does not self-assemble presumably because of the absence of stabilizing electrostatic interactions between the membrane surface and the helix dipole. In the presence of vesicles composed solely of anionic lipids, the peptide forms a long-lived α-helix presumably stabilized by dipole-dipole interactions between adjacent helix dipoles. This helix represents a kinetic trap that inhibits β-sheet formation. Intriguingly, when the amount of anionic lipids was decreased to mimic the ratio of zwitterionic and anionic lipids in cells, the α-helix was short-lived and underwent an α-helix to β-sheet conformational transition. Our work suggests that the helix dipole and membrane electrostatics delineate the conformational transitions occurring along the self-assembly pathway to the amyloid.
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Affiliation(s)
- Qiuchen Zheng
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Senegal N Carty
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Noel D Lazo
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
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Wang J, Perez-Cruet JM, Huang HL, Reiss K, Gisriel CJ, Banerjee G, Kaur D, Ghosh I, Dziarski A, Gunner MR, Batista VS, Brudvig GW. Identification of a Na +-Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II. Biochemistry 2020; 59:2823-2831. [PMID: 32650633 DOI: 10.1021/acs.biochem.0c00303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions and one redox-inactive Ca2+ ion, with two nearby bound Cl- ions. Sodium is a common counterion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Here, we find that the oxygen-evolution activity of spinach PSII increases with Na+ concentration, particularly at high pH. A Na+-specific binding site next to the OEC, becomes available after deprotonation of the D1-H337 amino acid residue, is suggested by the analysis of two recently published PSII cryo-electron microscopy maps in combination with quantum mechanical calculations and multiconformation continuum electrostatics simulations.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Joshua M Perez-Cruet
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Christopher J Gisriel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Divya Kaur
- Department of Physics, City College of New York (CCNY), New York, New York 10031, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alisha Dziarski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - M R Gunner
- Department of Physics, City College of New York (CCNY), New York, New York 10031, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States.,Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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Wang J, Brudvig GW, Batista VS, Moore PB. On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets. Protein Sci 2017; 26:2410-2416. [DOI: 10.1002/pro.3314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 02/03/2023]
Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and BiochemistryYale UniversityNew Haven Connecticut06520‐8114
| | - Gary W. Brudvig
- Department of Molecular Biophysics and BiochemistryYale UniversityNew Haven Connecticut06520‐8114
- Department of ChemistryYale UniversityNew Haven Connecticut06520‐8107
| | - Victor S. Batista
- Department of ChemistryYale UniversityNew Haven Connecticut06520‐8107
| | - Peter B. Moore
- Department of Molecular Biophysics and BiochemistryYale UniversityNew Haven Connecticut06520‐8114
- Department of ChemistryYale UniversityNew Haven Connecticut06520‐8107
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Wang J. Determination of chemical identity and occupancy from experimental density maps. Protein Sci 2017; 27:411-420. [PMID: 29027293 DOI: 10.1002/pro.3325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 12/13/2022]
Abstract
Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73-Å resolution, and to an experimental CD map at 2.2-Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II-light harvesting complex II supercomplex at 3.2-Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α-helices.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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