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Zhang Y, Xu Z, Zhao Y, Zhang X. Ab initio Molecular Dynamics Simulation Study of Dissociation Electron Attachment to Lactic Acid and Isomer. Sci Rep 2019; 9:19532. [PMID: 31862917 PMCID: PMC6925224 DOI: 10.1038/s41598-019-56019-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 12/04/2019] [Indexed: 11/12/2022] Open
Abstract
Dissociation processes of lactic acid and its isomer formed by low-energy dissociation electron attachment (DEA) in the gas phase are investigated by using ab initio molecular dynamics (MD) simulations. The ab initio MD simulations using an atom-centered density matrix propagation (ADMP) method are carried out to investigate the DEA dissociation process of lactic acid and its isomer. The analysis of the simulated dissociation trajectories of lactic acid and its isomer indicates that the C-C, C-H, and C-O bonds are cleaved within femtoseconds of the simulation time scale in the DEA dissociation process, and the difference in dissociation trajectory depends on the size of the three basis sets. The simulation results enable us to gain insights into the DEA dissociation process of lactic acid and its isomer. In this work, we present a comparative study of the 6-31 + G(d,p), 6-311++G(2d,2p), and Aug-cc-pVDZ basis sets of the DEA dissociation simulation of lactic acid and its isomer. The comparative study results indicate that the 6-311++G(2d,2p) is an excellent basis set for the ADMP trajectory simulation of lactic acid and its isomer in the DEA dissociation process. The natural bond orbital (NBO) analysis is carried out to characterize variation in the charge population and charge transfer accompanied by the C-C, C-H, and C-O bond dissociation processes for lactic acid and its isomer in the ADMP trajectory simulation. ADMP simulation and NBO analysis of the dissociation trajectory is considered an important initial and decisive step in DEA dissociation dynamics for lactic acid and its isomer.
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Affiliation(s)
- Ying Zhang
- School of science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Zhongfeng Xu
- School of science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Yongtao Zhao
- School of science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Xiaoan Zhang
- Xianyang Normal University, Xianyang, Shaanxi, 712000, China
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2
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Dai X, Xu Y, Dong B. Effect of the micron-sized silica particles (MSSP) on biogas conversion of sewage sludge. WATER RESEARCH 2017; 115:220-228. [PMID: 28284088 DOI: 10.1016/j.watres.2017.02.064] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/20/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
Micron-sized silica particles (MSSP), ranging from 3 μm to 50 μm, have been widely found in the sewage sludge. The inhibition of MSSP to biogas conversion of both excess sludge (ES) and model sludge (MS) are explored in this study. It is observed that with the effect of MSSP, the net cumulative methane production (NCMP) of ES and MS were decreased by 23.5% and 22.3%, respectively, and the apparent activation energy (AAE) of organic solubilisation of ES and MS were increased by 38.7% and 215%, respectively, which implies a crucial role for MSSP in anaerobic sludge digestion. Analysis of physicochemical properties of sludges before and after interaction with MSSP reveals that MSSP can bond with organic matter from sludge on the surface sites to form a larger bioinorganic-floc. Further analysis indicates that MSSP can increase the AAE of sludge organic solubilisation by reducing the surface site density, thus resulting in poor NCMP. Through characterizing the bioinorganic-floc, it is found that the protein in sludge is the main component that bonds with MSSP. Further research show that the interactions between protein and MSSP are mainly enthalpy-driven with exothermic (the enthalpy was about -10.93 ± 0.10 kJ/mol, at 25 °C), indicating that protein is more stable after non-covalent bonding. These findings can provide a new understanding of the characteristics of sludge and important references for the improvement of anaerobic sludge digestion.
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Affiliation(s)
- Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Ying Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Bin Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
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3
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Herbert JM. The Quantum Chemistry of Loosely-Bound Electrons. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Feng WL, Tian SX. Ab Initio Molecular Dynamics Simulation Study of Dissociative Electron Attachment to Dialanine Conformers. J Phys Chem A 2015; 119:1838-45. [DOI: 10.1021/jp512173z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wen-Ling Feng
- Hefei
National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shan Xi Tian
- Hefei
National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- Department
of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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Riffet V, Jacquemin D, Cauët E, Frison G. Benchmarking DFT and TD-DFT Functionals for the Ground and Excited States of Hydrogen-Rich Peptide Radicals. J Chem Theory Comput 2014; 10:3308-18. [DOI: 10.1021/ct5004912] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vanessa Riffet
- Laboratoire
de Chimie Moléculaire, Département de Chimie, Ecole
polytechnique and CNRS, 91128 Palaiseau cedex, France
| | - Denis Jacquemin
- Laboratoire
CEISAM, UMR CNRS 6230, Université de Nantes, 2 rue de la
Houssinière - BP 92208, 44322 Nantes cedex 3, France
- Institut Universitaire
de France, 103 bd Saint-Michel, F-75005 Paris Cedex 05, France
| | - Emilie Cauët
- Service
de Chimie quantique et Photophysique, Université Libre de Bruxelles, CP160/09, 50 av. F.D. Roosevelt, 1050 Bruxelles, Belgium
| | - Gilles Frison
- Laboratoire
de Chimie Moléculaire, Département de Chimie, Ecole
polytechnique and CNRS, 91128 Palaiseau cedex, France
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Anusiewicz I, Skurski P, Simons J. Refinements to the Utah–Washington Mechanism of Electron Capture Dissociation. J Phys Chem B 2014; 118:7892-901. [DOI: 10.1021/jp5004819] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iwona Anusiewicz
- Department
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Piotr Skurski
- Department
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Jack Simons
- Chemistry
Department and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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Mentinova M, Crizer DM, Baba T, McGee WM, Glish GL, McLuckey SA. Cation recombination energy/coulomb repulsion effects in ETD/ECD as revealed by variation of charge per residue at fixed total charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1676-89. [PMID: 23568028 PMCID: PMC3795911 DOI: 10.1007/s13361-013-0606-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation (ECD) and electron transfer dissociation (ETD) experiments in electrodynamic ion traps operated in the presence of a bath gas in the 1-10 mTorr range have been conducted on a common set of doubly protonated model peptides of the form X(AG)nX (X = lysine, arginine, or histidine, n = 1, 2, or 4). The partitioning of reaction products was measured using thermal electrons, anions of azobenzene, and anions of 1,3-dinitrobenzene as reagents. Variation of n alters the charge per residue of the peptide cation, which affects recombination energy. The ECD experiments showed that H-atom loss is greatest for the n = 1 peptides and decreases as n increases. Proton transfer in ETD, on the other hand, is expected to increase as charge per residue decreases (i.e., as n increases). These opposing tendencies were apparent in the data for the K(AG)nK peptides. H-atom loss appeared to be more prevalent in ECD than in ETD and is rationalized on the basis of either internal energy differences, differences in angular momentum transfer associated with the electron capture versus electron transfer processes, or a combination of the two. The histidine peptides showed the greatest extent of charge reduction without dissociation, the arginine peptides showed the greatest extent of side-chain cleavages, and the lysine peptides generally showed the greatest extent of partitioning into the c/z•-product ion channels. The fragmentation patterns for the complementary c- and z•-ions for ETD and ECD were found to be remarkably similar, particularly for the peptides with X = lysine.
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Affiliation(s)
- Marija Mentinova
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - David M. Crizer
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Takashi Baba
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - William M. McGee
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - Gary L. Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
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Smith BH, Buonaugurio A, Chen J, Collins E, Bowen KH, Compton RN, Sommerfeld T. Negative ions of p-nitroaniline: Photodetachment, collisions, and ab initio calculations. J Chem Phys 2013; 138:234304. [PMID: 23802957 DOI: 10.1063/1.4810869] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Byron H Smith
- Department of Physics, University of Tennessee, Knoxville, Tennessee 37996, USA
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Zhang M, Zhao J, Yang H, Liu P, Bu Y. 310-Helical Peptide Acting as a Dual Relay for Charge-Hopping Transfer in Proteins. J Phys Chem B 2013; 117:6385-93. [DOI: 10.1021/jp4012526] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Meng Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Jing Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Hongfang Yang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Ping Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
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Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
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Świerszcz I, Skurski P, Simons J. Dipole and Coulomb Forces in Electron Capture Dissociation and Electron Transfer Dissociation Mass Spectroscopy. J Phys Chem A 2012; 116:1828-37. [DOI: 10.1021/jp210915c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Piotr Skurski
- Department
of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952
Gdańsk, Poland
- Chemistry
Department and Henry
Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jack Simons
- Chemistry
Department and Henry
Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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12
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Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry. Top Curr Chem (Cham) 2012; 331:79-116. [DOI: 10.1007/128_2012_384] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Simons J. Analytical Model for Rates of Electron Attachment and Intramolecular Electron Transfer in Electron Transfer Dissociation Mass Spectrometry. J Am Chem Soc 2010; 132:7074-85. [DOI: 10.1021/ja100240f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jack Simons
- Chemistry Department and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112
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Chapter 8 Electron Transfer in Gaseous Positively Charged Peptides — Relation to Mass Spectrometry. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1574-1400(09)00508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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