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Xu J, Finlayson-Pitts BJ, Gerber RB. Nanoparticles grown from methanesulfonic acid and methylamine: microscopic structures and formation mechanism. Phys Chem Chem Phys 2017; 19:31949-31957. [PMID: 29177355 DOI: 10.1039/c7cp06489f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanisms of particle formation and growth in the atmosphere are of great interest due to their impacts on climate, health and visibility. However, the microscopic structures and related properties of the smallest nanoparticles are not known. In this paper we pursue computationally a microscopic description for the formation and growth of methanesulfonic acid (MSA) and methylamine (MA) particles under dry conditions. Energetic and dynamics simulations were used to assess the stabilities of proposed model structures for these particles. Density functional theory (DFT) and semi-empirical (PM3) calculations suggest that (MSA-MA)4 is a major intermediate in the growth process, with the dissociation energies, enthalpies and free energies indicating considerable stability for this cluster. Dynamics simulations show that this species is stable for at least 100 ps at temperatures up to 500 K, well above atmospheric temperatures. In order to reach experimentally detectable sizes (>1.4 nm), continuing growth is suggested to occur via clustering of (MSA-MA)4. The dimer (MSA-MA)4(MSA-MA)4 may be one of the smaller experimentally measured particles. Step by step addition of MSA to (MSA-MA)4, is also a likely potential growth mechanism when MSA is excess. In addition, an MSA-MA crystal is predicted to exist. These studies demonstrate that computations of particle structure and dynamics in the nano-size range can be useful for molecular level understanding of processes that grow clusters into detectable particles.
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Affiliation(s)
- Jing Xu
- Department of Chemistry, University of California, Irvine, CA 92697, USA.
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Wang J, Yang F, Zhao J. Selectively Probing the Structures and Dynamics of β-Peptide Aggregates Using the Amide-A Vibrational Marker. J Phys Chem B 2015; 119:15451-9. [PMID: 26601794 DOI: 10.1021/acs.jpcb.5b10249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N-H stretching vibration in a β-peptide model compound, N-ethylpropionamide (NEPA), was characterized by one-dimensional infrared (1D IR) and two-dimensional (2D) IR experiments and ab initio anharmonic frequency computations. A narrowband pump-broadband probe 2D IR method was applied to selectively probe a subensemble of the N-H stretching vibrations from a mixture of different NEPA molecular aggregates that were formed via an intermolecular hydrogen bond. Vibrational lifetime and anharmonicity were found to be sensitive to the aggregation ensembles. In particular, diagonal anharmonicities were observed experimentally and confirmed computationally to be smaller for NEPA trimer than for dimer, which was explained by the presence of non-negligible off-diagonal anharmonicities in coupled N-H stretching modes.
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Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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Wang J, Yang F, Shi J, Zhao J. Structural dynamics of N-ethylpropionamide clusters examined by nonlinear infrared spectroscopy. J Chem Phys 2015; 143:185102. [PMID: 26567687 DOI: 10.1063/1.4935579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH3CN, CHCl3, and CCl4), were examined using the N-H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics of NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N-H stretching mode was observed.
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Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Jipei Shi
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
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Gerber RB, Shemesh D, Varner ME, Kalinowski J, Hirshberg B. Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters. Phys Chem Chem Phys 2014; 16:9760-75. [DOI: 10.1039/c3cp55239j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent progress in “on-the-fly” trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available.
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Affiliation(s)
- R. B. Gerber
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
- Department of Chemistry
- University of California
| | - D. Shemesh
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
| | - M. E. Varner
- Department of Chemistry
- University of California
- Irvine 92697, USA
| | - J. Kalinowski
- Department of Chemistry
- University of Helsinki
- , Finland
| | - B. Hirshberg
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
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Shemesh D, Lan Z, Gerber RB. Dynamics of Triplet-State Photochemistry of Pentanal: Mechanisms of Norrish I, Norrish II, and H Abstraction Reactions. J Phys Chem A 2013; 117:11711-24. [DOI: 10.1021/jp401309b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dorit Shemesh
- Department of Physical Chemistry
and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
| | - Zhenggang Lan
- Key Laboratory of Biobased Materials
and the Qingdao Key Lab of Solar Energy Utilization and Energy Storage
Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qinqdao 266101, China
| | - R. Benny Gerber
- Department of Physical Chemistry
and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
- Department of Chemistry, University of California—Irvine, Irvine, California
92597, United States
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Achar TK, Prakash V, Biswal HS, Mal P. An isoquinoline as cation assisted ON–OFF–ON fluorescence switch with methionine and fluoride ion. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2012.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Roy TK, Gerber RB. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications. Phys Chem Chem Phys 2013; 15:9468-92. [DOI: 10.1039/c3cp50739d] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pincu M, Brauer B, Gerber RB. When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:15382-91. [DOI: 10.1039/c3cp52220b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Xie HB, Jin L, Rudić S, Simons JP, Gerber RB. Computational Studies of Protonated β-d-Galactose and Its Hydrated Complex: Structures, Interactions, Proton Transfer Dynamics, and Spectroscopy. J Phys Chem B 2012; 116:4851-9. [DOI: 10.1021/jp3028325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong-bin Xie
- Key Laboratory of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Lin Jin
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Svemir Rudić
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
- Institute of Chemistry
and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Hirshberg B, Gerber RB. Decomposition mechanisms and dynamics of N6: Bond orders and partial charges along classical trajectories. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.01.088] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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