1
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Cheng Y, Ding C, Zhang T, Wang R, Mu R, Li Z, Li R, Shi J, Zhu C. Barrierless reactions of C2 Criegee intermediates with H 2SO 4 and their implication to oligomers and new particle formation. J Environ Sci (China) 2025; 149:574-584. [PMID: 39181669 DOI: 10.1016/j.jes.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 08/27/2024]
Abstract
The formation of oligomeric hydrogen peroxide triggered by Criegee intermediate maybe contributes significantly to the formation and growth of secondary organic aerosol (SOA). However, to date, the reactivity of C2 Criegee intermediates (CH3CHOO) in areas contaminated with acidic gas remains poorly understood. Herein, high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations are used to explore the reaction of CH3CHOO and H2SO4 both in the gas phase and at the air-water interface. In the gas phase, the addition reaction of CH3CHOO with H2SO4 to generate CH3HC(OOH)OSO3H (HPES) is near-barrierless, regardless of the presence of water molecules. BOMD simulations show that the reaction at the air-water interface is even faster than that in the gas phase. Further calculations reveal that the HPES has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters, meanwhile the oligomerization reaction of CH3CHOO with HPES in the gas phase is both thermochemically and kinetically favored. Also, it is noted that the interfacial HPES- ion can attract H2SO4, NH3, (COOH)2 and HNO3 for particle formation from the gas phase to the water surface. Thus, the results of this work not only elucidate the high atmospheric reactivity of C2 Criegee intermediates in polluted regions, but also deepen our understanding of the formation process of atmospheric SOA induced by Criegee intermediates.
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Affiliation(s)
- Yang Cheng
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Chao Ding
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Tianlei Zhang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China.
| | - Rui Wang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ruxue Mu
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Zeyao Li
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Rongrong Li
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Juan Shi
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100190, China.
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2
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Orr-Ewing AJ, Osborn DL. Collection on the Spectroscopy, Structure, and Reactivity of Stabilized Criegee Intermediates. J Phys Chem A 2024; 128:2909-2911. [PMID: 38632956 DOI: 10.1021/acs.jpca.4c01459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Affiliation(s)
- Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - David L Osborn
- Combustion Research Facility, Mail Stop 9055, Sandia National Laboratories, Livermore, California 94551-0969, United States
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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3
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Ritacco I, Gatta G, Caporaso L, Farnesi Camellone M. Ab initio molecular dynamics of solvation effects and reactivity at the interface between water and ascorbic acid covered anatase TiO 2 (101). Chemphyschem 2024; 25:e202300768. [PMID: 38153248 DOI: 10.1002/cphc.202300768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 12/29/2023]
Abstract
In this work, we present a detailed study of the interaction between ascorbic acid (L-asc) and anatase TiO2 (101) surface both in gas phase and in contact with water by using density functional theory and ab initio molecular dynamics simulations. In gas phase, L-asc strongly binds the TiO2 (101) surface as a dianion (L-asc2- ), adopting a bridging bidentate coordination mode (BB), with the two acid protons transferred to two surface 2-fold bridging oxygens (O2c). AIMD simulations show that the interaction between the organic ligand and the anatase surface is stable and comparable to the vacuum one despite the possible solvent effects and/or possible structural distortions of the ligand. In addition, during the AIMD simulations hydroxylation phenomena occur forming transient H3 O+ ions at the solid-liquid interface. For the first time, our results provide insight into the role of the ascorbic acid on the electronic properties of the TiO2 (101), the influence of the water environment on the ligand-surface interaction and the nature of the solid-liquid interface.
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Affiliation(s)
- Ida Ritacco
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gianluca Gatta
- Dipartimento di Medicina di Precisione Divisione di Radiologia, Università della Campania Luigi Vanvitelli, Napoli, Italia, 80131
| | - Lucia Caporaso
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Matteo Farnesi Camellone
- CNR-IOM, Consiglio Nazionale delle Ricerche -, Istituto Officina dei Materiali, c/o SISSA, 34136, Trieste, Italy
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4
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Ma Y, Li Z, Chen X, Ding B, Li N, Lu T, Zhang B, Suo B, Jin Z. Machine-learning assisted scheduling optimization and its application in quantum chemical calculations. J Comput Chem 2023; 44:1174-1188. [PMID: 36648254 DOI: 10.1002/jcc.27075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023]
Abstract
Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi-level optimization framework to optimize the computational sequences. Machine-learning (ML) assisted static load-balancing, and different dynamic load-balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high-throughput drug suit, solvent model, P38 protein, and SARS-CoV-2 systems. The results show that the usage rate of given computational resources for high throughput and large-scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high-performance computing (HPC) clusters.
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Affiliation(s)
- Yingjin Ma
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - ZhiYing Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Xin Chen
- ShenZhen Bay Laboratory, Shenzhen, China
| | - Bowen Ding
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- College of Chemistry and Materials Engineering, Wenzhou University, Wen Zhou, China
| | - Teng Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - BingBing Suo
- Department of Physics, Northwest University, Xi'an, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
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5
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Zhang T, Wen M, Ding C, Zhang Y, Ma X, Wang Z, Lily M, Liu J, Wang R. Multiple evaluations of atmospheric behavior between Criegee intermediates and HCHO: Gas-phase and air-water interface reaction. J Environ Sci (China) 2023; 127:308-319. [PMID: 36522063 DOI: 10.1016/j.jes.2022.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 06/17/2023]
Abstract
Given the high abundance of water in the atmosphere, the reaction of Criegee intermediates (CIs) with (H2O)2 is considered to be the predominant removal pathway for CIs. However, recent experimental findings reported that the reactions of CIs with organic acids and carbonyls are faster than expected. At the same time, the interface behavior between CIs and carbonyls has not been reported so far. Here, the gas-phase and air-water interface behavior between Criegee intermediates and HCHO were explored by adopting high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations. Quantum chemical calculations evidence that the gas-phase reactions of CIs + HCHO are submerged energy or low energy barriers processes. The rate ratios speculate that the HCHO could be not only a significant tropospheric scavenger of CIs, but also an inhibitor in the oxidizing ability of CIs on SOx in dry and highly polluted areas with abundant HCHO concentration. The reactions of CH2OO with HCHO at the droplet's surface follow a loop structure mechanism to produce i) SOZ (), ii) BHMP (HOCH2OOCH2OH), and iii) HMHP (HOCH2OOH). Considering the harsh reaction conditions between CIs and HCHO at the interface (i.e., the two molecules must be sufficiently close to each other), the hydration of CIs is still their main atmospheric loss pathway. These results could help us get a better interpretation of the underlying CIs-aldehydes chemical processes in the global polluted urban atmospheres.
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Affiliation(s)
- Tianlei Zhang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Mingjie Wen
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Chao Ding
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Yongqi Zhang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Xiaohui Ma
- School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Zhuqing Wang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Makroni Lily
- Environmental Research Institute, Shandong University, Qingdao 266237, China
| | - Junhai Liu
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China; Qinba Mountains of Bio-Resource Collaborative Innovation Center of Southern Shaanxi Province, Shaanxi University of Technology, Hanzhong 723001, China
| | - Rui Wang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
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6
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Liang Q, Zhu C, Yang J. Water Charge Transfer Accelerates Criegee Intermediate Reaction with H 2O - Radical Anion at the Aqueous Interface. J Am Chem Soc 2023; 145:10159-10166. [PMID: 37011411 DOI: 10.1021/jacs.3c00734] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Criegee intermediates (CIs) are important carbonyl oxides that may react with atmospheric trace chemicals and impact the global climate. The CI reaction with water has been widely studied and is a main channel for trapping CIs in the troposphere. Previous experimental and computational reports have largely focused on reaction kinetic processes in various CI-water reactions. The molecular-level origin of CI's interfacial reactivity at the water microdroplet surface (e.g., as found in aerosols and clouds) is unclear. In this study, by employing the quantum mechanical/molecular mechanical (QM/MM) Born-Oppenheimer molecular dynamics with the local second-order Møller-Plesset perturbation theory, our computational results reveal a substantial water charge transfer up to ∼20% per water, which creates the surface H2O+/H2O- radical pairs to enhance the CH2OO and anti-CH3CHOO reactivity with water: the resulting strong CI-H2O- electrostatic attraction at the microdroplet surface facilitates the nucleophilic attack to the CI carbonyl by water, which may counteract the apolar hindrance of the substituent to accelerate the CI-water reaction. Our statistical analysis of the molecular dynamics trajectories further resolves a relatively long-lived bound CI(H2O-) intermediate state at the air/water interface, which has not been observed in gaseous CI reactions. This work provides insights into what may alter the oxidizing power of the troposphere by the next larger CIs than simple CH2OO and implicates a new perspective on the role of interfacial water charge transfer in accelerating molecular reactions at aqueous interfaces.
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Affiliation(s)
- Qiujiang Liang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100190, People's Republic of China
| | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, People's Republic of China
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7
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Theoretical Study on the Gas Phase and Gas-Liquid Interface Reaction Mechanism of Criegee Intermediates with Glycolic Acid Sulfate. Int J Mol Sci 2023; 24:ijms24043355. [PMID: 36834768 PMCID: PMC9965808 DOI: 10.3390/ijms24043355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Criegee intermediates (CIs) are important zwitterionic oxidants in the atmosphere, which affect the budget of OH radicals, amines, alcohols, organic/inorganic acids, etc. In this study, quantum chemical calculation and Born-Oppenheimer molecular dynamic (BOMD) simulation were performed to show the reaction mechanisms of C2 CIs with glycolic acid sulfate (GAS) at the gas-phase and gas-liquid interface, respectively. The results indicate that CIs can react with COOH and OSO3H groups of GAS and generate hydroperoxide products. Intramolecular proton transfer reactions occurred in the simulations. Moreover, GAS acts as a proton donor and participates in the hydration of CIs, during which the intramolecular proton transfer also occurs. As GAS widely exists in atmospheric particulate matter, the reaction with GAS is one of the sink pathways of CIs in areas polluted by particulate matter.
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8
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Wang S, Zhao Y, Chan AWH, Yao M, Chen Z, Abbatt JPD. Organic Peroxides in Aerosol: Key Reactive Intermediates for Multiphase Processes in the Atmosphere. Chem Rev 2023; 123:1635-1679. [PMID: 36630720 DOI: 10.1021/acs.chemrev.2c00430] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Organic peroxides (POs) are organic molecules with one or more peroxide (-O-O-) functional groups. POs are commonly regarded as chemically labile termination products from gas-phase radical chemistry and therefore serve as temporary reservoirs for oxidative radicals (HOx and ROx) in the atmosphere. Owing to their ubiquity, active gas-particle partitioning behavior, and reactivity, POs are key reactive intermediates in atmospheric multiphase processes determining the life cycle (formation, growth, and aging), climate, and health impacts of aerosol. However, there remain substantial gaps in the origin, molecular diversity, and fate of POs due to their complex nature and dynamic behavior. Here, we summarize the current understanding on atmospheric POs, with a focus on their identification and quantification, state-of-the-art analytical developments, molecular-level formation mechanisms, multiphase chemical transformation pathways, as well as environmental and health impacts. We find that interactions with SO2 and transition metal ions are generally the fast PO transformation pathways in atmospheric liquid water, with lifetimes estimated to be minutes to hours, while hydrolysis is particularly important for α-substituted hydroperoxides. Meanwhile, photolysis and thermolysis are likely minor sinks for POs. These multiphase PO transformation pathways are distinctly different from their gas-phase fates, such as photolysis and reaction with OH radicals, which highlights the need to understand the multiphase partitioning of POs. By summarizing the current advances and remaining challenges for the investigation of POs, we propose future research priorities regarding their origin, fate, and impacts in the atmosphere.
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Affiliation(s)
- Shunyao Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai200444, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, OntarioM5S 3E5, Canada
| | - Yue Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Arthur W H Chan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, OntarioM5S 3E5, Canada
- School of the Environment, University of Toronto, Toronto, OntarioM5S 3E8, Canada
| | - Min Yao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zhongming Chen
- State Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing100871, China
| | - Jonathan P D Abbatt
- Department of Chemistry, University of Toronto, Toronto, OntarioM5S 3H6, Canada
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9
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Liu J, He X. Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
- New York University‐East China Normal University Center for Computational Chemistry New York University Shanghai Shanghai China
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10
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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11
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Liu J, He X. Ab initio molecular dynamics simulation of liquid water with fragment-based quantum mechanical approach under periodic boundary conditions. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai 200062, China
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12
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Hisama K, Orimoto Y, Pomogaeva A, Nakatani K, Aoki Y. Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules. J Chem Phys 2021; 155:044110. [PMID: 34340364 DOI: 10.1063/5.0050096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.
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Affiliation(s)
- Keisuke Hisama
- Department of Interdisciplinary Engineering Sciences, Chemistry and Materials Science, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Anna Pomogaeva
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
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13
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Wen B, Selloni A. Hydrogen Bonds and H 3O + Formation at the Water Interface with Formic Acid Covered Anatase TiO 2. J Phys Chem Lett 2021; 12:6840-6846. [PMID: 34279942 DOI: 10.1021/acs.jpclett.1c01886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Carboxylic acid-modified TiO2 surfaces in aqueous environment are of widespread interest, yet atomic-scale understanding of their structure is limited. We here investigate formic acid (FA) on anatase TiO2 (101) (A-101) in contact with water using density functional theory (DFT) and ab initio molecular dynamics (AIMD). Isolated FA molecules adsorbed in a deprotonated bridging bidentate (BD) form on A-101 are found to remain stable at the interface with water, with the acid proton transferred to a surface oxygen to form a surface bridging hydroxyl (ObrH). With increasing FA coverage, adsorbed monolayers of only BD and successively of alternating monodentate (MD) and BD species give rise to a higher concentration of surface ObrH's. Simulations of these adsorbed monolayers in water environment show that some protons are released from the surface ObrH's to water resulting in a negatively charged surface with nearby solvated H3O+ ions. These results provide insight into the complex acid-base equilibrium between an oxide surface, adsorbates and water and can also help obtain a better understanding of the wetting properties of chemically modified TiO2 surfaces.
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Affiliation(s)
- Bo Wen
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- School of Physics and Electronics, Henan University, Kaifeng 475001, P. R. China
| | - Annabella Selloni
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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