1
|
Roet S, Daub CD, Riccardi E. Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning. J Chem Theory Comput 2021; 17:6193-6202. [PMID: 34555907 PMCID: PMC8515787 DOI: 10.1021/acs.jctc.1c00458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
We propose to analyze
molecular dynamics (MD) output via a supervised machine
learning (ML) algorithm, the decision tree.
The approach aims to identify the predominant geometric features which
correlate with trajectories that transition between two arbitrarily
defined states. The data-driven algorithm aims to identify these features
without the bias of human “chemical intuition”. We demonstrate
the method by analyzing the proton exchange reactions in formic acid
solvated in small water clusters. The simulations were performed with ab initio MD combined with a method to efficiently sample
the rare event, path sampling. Our ML analysis identified relevant
geometric variables involved in the proton transfer reaction and how
they may change as the number of solvating water molecules changes.
Collapse
Affiliation(s)
- Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Christopher D Daub
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Enrico Riccardi
- Department of Informatics, UiO, Gaustadalléen 23B, 0373 Oslo, Norway
| |
Collapse
|
2
|
Zhong J, Kumar M, Anglada JM, Martins-Costa MTC, Ruiz-Lopez MF, Zeng XC, Francisco JS. Atmospheric Spectroscopy and Photochemistry at Environmental Water Interfaces. Annu Rev Phys Chem 2019; 70:45-69. [PMID: 31174459 DOI: 10.1146/annurev-physchem-042018-052311] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The air-water interface is ubiquitous in nature, as manifested in the form of the surfaces of oceans, lakes, and atmospheric aerosols. The aerosol interface, in particular, can play a crucial role in atmospheric chemistry. The adsorption of atmospheric species onto and into aerosols modifies their concentrations and chemistries. Moreover, the aerosol phase allows otherwise unlikely solution-phase chemistry to occur in the atmosphere. The effect of the air-water interface on these processes is not entirely known. This review summarizes recent theoretical investigations of the interactions of atmosphere species with the air-water interface, including reactant adsorption, photochemistry, and the spectroscopy of reactants at the water surface, with an emphasis on understanding differences between interfacial chemistries and the chemistries in both bulk solution and the gas phase. The results discussed here enable an understanding of fundamental concepts that lead to potential air-water interface effects, providing a framework to understand the effects of water surfaces on our atmosphere.
Collapse
Affiliation(s)
- J Zhong
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68566, USA
| | - M Kumar
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68566, USA
| | - J M Anglada
- Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya-Consejo Superior de Investigaciones Cientificas (IQAC-CSIC), E-08034 Barcelona, Spain
| | - M T C Martins-Costa
- Le Laboratoire Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), CNRS UMR 7019, Université de Lorraine, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - M F Ruiz-Lopez
- Le Laboratoire Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), CNRS UMR 7019, Université de Lorraine, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - X C Zeng
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68566, USA
| | - Joseph S Francisco
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68566, USA.,Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6316, USA;
| |
Collapse
|
3
|
Hänninen V, Murdachaew G, Nathanson GM, Gerber RB, Halonen L. Ab initio molecular dynamics studies of formic acid dimer colliding with liquid water. Phys Chem Chem Phys 2018; 20:23717-23725. [PMID: 30191926 DOI: 10.1039/c8cp03857k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory. The two energetically lowest FA dimer isomers were collided with a water slab at thermal and high kinetic energies up to 68kBT. Our simulations agree with recent experimental observations of nearly a complete uptake of gas-phase FA dimer: the calculated average kinetic energy of the dimers immediately after collision is 5 ± 4% of the incoming kinetic energy, which compares well with the experimental value of 10%. Simulations support the experimental observation of no delayed desorption of FA dimers following initial adsorption. Our analysis shows that the FA dimer forms hydrogen bonds with surface water molecules, where the hydrogen bond order depends on the dimer structure, such that the most stable isomer possesses fewer FA-water hydrogen bonds than the higher energy isomer. Nevertheless, even the most stable isomer can attach to the surface through one hydrogen bond despite its reduced hydrophilicity. Our simulations further show that the probability of FA dimer dissociation is increased by high collision energies, the dimer undergoes isomerization from the higher energy to the lowest energy isomer, and concerted double-proton transfer occurs between the FA monomers. Interestingly, proton transfer appears to be driven by the release of energy arising from such isomerization, which stimulates those internal vibrational degrees of freedom that overcome the barrier of a proton transfer.
Collapse
Affiliation(s)
- Vesa Hänninen
- Department of Chemistry, University of Helsinki, P. O. Box 55 (A.I. Virtasen aukio 1), FI-00014, Finland.
| | | | | | | | | |
Collapse
|
4
|
Zheng W, Huang C, Sun W, Zhao L. Microstructures of the Sulfonic Acid-Functionalized Ionic Liquid/Sulfuric Acid and Their Interactions: A Perspective from the Isobutane Alkylation. J Phys Chem B 2018; 122:1460-1470. [PMID: 29309149 DOI: 10.1021/acs.jpcb.7b09755] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The all-atom force field for concentrated sulfuric acid (98.30 wt %) was developed in this work based on ab initio calculations. The structural and dynamical properties of sulfuric acid and the mixing behaviors of sulfuric acid with ionic liquids (ILs), i.e., SFIL (1-methyl-3-(propyl-3-sulfonate) imidazolium bisulfate ([PSMim][HSO4])) and non-SFIL (1-methyl-3-propyl imidazolium bisulfate ([PMim][HSO4])), were investigated using a molecular dynamics simulation. For sulfuric acid, most H3O+ ions were found beside HSO4- ions, forming a contact ion pair with the HSO4- ions, and three-dimensional hydrogen-bonding networks existed in the sulfuric acid. Analyses indicate that both ILs could be miscible with sulfuric acid with a strong exothermic character. The new strong interaction site between the sulfonic acid group of SFIL and an H2SO4 molecule through a strong hydrogen-bonding interaction was observed, which was beneficial to the catalytic activity and stability of the sulfuric acid. This observation is in good agreement with the experimental results that indicate SFILs could enhance the reusability of sulfuric acid for the isobutane alkylation about 4-fold compared to that of non-SFILs. Hopefully this work will provide insights into the screening and designing of new isobutane alkylation catalysts based on sulfuric acid and SFILs.
Collapse
Affiliation(s)
- Weizhong Zheng
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Chizhou Huang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Weizhen Sun
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Ling Zhao
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology , Shanghai 200237, China
| |
Collapse
|
5
|
Niskanen J, Sahle CJ, Ruotsalainen KO, Müller H, Kavčič M, Žitnik M, Bučar K, Petric M, Hakala M, Huotari S. Sulphur Kβ emission spectra reveal protonation states of aqueous sulfuric acid. Sci Rep 2016; 6:21012. [PMID: 26888159 PMCID: PMC4757876 DOI: 10.1038/srep21012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/14/2016] [Indexed: 11/08/2022] Open
Abstract
In this paper we report an X-ray emission study of bulk aqueous sulfuric acid. Throughout the range of molarities from 1 M to 18 M the sulfur Kβ emission spectra from H2SO4 (aq) depend on the molar fractions and related deprotonation of H2SO4. We compare the experimental results with results from emission spectrum calculations based on atomic structures of single molecules and structures from ab initio molecular dynamics simulations. We show that the S Kβ emission spectrum is a sensitive probe of the protonation state of the acid molecules. Using non-negative matrix factorization we are able to extract the fractions of different protonation states in the spectra, and the results are in good agreement with the simulation for the higher part of the concentration range.
Collapse
Affiliation(s)
- Johannes Niskanen
- University of Helsinki, Department of Physics, Helsinki, FI-00014, Finland
| | - Christoph J. Sahle
- University of Helsinki, Department of Physics, Helsinki, FI-00014, Finland
- European Synchrotron Radiation Facility, ESRF, Grenoble, France
| | | | - Harald Müller
- European Synchrotron Radiation Facility, ESRF, Grenoble, France
| | - Matjaž Kavčič
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
| | - Matjaž Žitnik
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, Ljubljana, Slovenia
| | - Klemen Bučar
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
| | - Marko Petric
- Jožef Stefan Institute, Jamova cesta 39, SI-1001 Ljubljana, Slovenia
| | - Mikko Hakala
- University of Helsinki, Department of Physics, Helsinki, FI-00014, Finland
| | - Simo Huotari
- University of Helsinki, Department of Physics, Helsinki, FI-00014, Finland
| |
Collapse
|
6
|
Murdachaew G, Nathanson GM, Benny Gerber R, Halonen L. Deprotonation of formic acid in collisions with a liquid water surface studied by molecular dynamics and metadynamics simulations. Phys Chem Chem Phys 2016; 18:29756-29770. [DOI: 10.1039/c6cp06071d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formic acid has a lower barrier to deprotonation at the air–water interface than in bulk liquid water.
Collapse
Affiliation(s)
- Garold Murdachaew
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
| | | | - R. Benny Gerber
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
- Institute of Chemistry and the Fritz Haber Research Center
| | - Lauri Halonen
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
| |
Collapse
|
7
|
Partanen L, Murdachaew G, Gerber RB, Halonen L. Temperature and collision energy effects on dissociation of hydrochloric acid on water surfaces. Phys Chem Chem Phys 2016; 18:13432-42. [DOI: 10.1039/c6cp00597g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Niskanen J, Sahle CJ, Juurinen I, Koskelo J, Lehtola S, Verbeni R, Müller H, Hakala M, Huotari S. Protonation Dynamics and Hydrogen Bonding in Aqueous Sulfuric Acid. J Phys Chem B 2015; 119:11732-9. [DOI: 10.1021/acs.jpcb.5b04371] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johannes Niskanen
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Christoph J. Sahle
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- ESRF—The European Synchrotron, CS40220, 38043, Grenoble Cedex 9, France
| | - Iina Juurinen
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Jaakko Koskelo
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Susi Lehtola
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Roberto Verbeni
- ESRF—The European Synchrotron, CS40220, 38043, Grenoble Cedex 9, France
| | - Harald Müller
- ESRF—The European Synchrotron, CS40220, 38043, Grenoble Cedex 9, France
| | - Mikko Hakala
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Simo Huotari
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| |
Collapse
|
9
|
Gerber RB, Varner ME, Hammerich AD, Riikonen S, Murdachaew G, Shemesh D, Finlayson-Pitts BJ. Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces. Acc Chem Res 2015; 48:399-406. [PMID: 25647299 DOI: 10.1021/ar500431g] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO(+))(NO3(-)) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl(-) on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on isolated defects where it involves formation of H3O(+)-acid anion contact ion pairs. This behavior is found in simulations of a model of the ice quasi-liquid layer corresponding to large defect concentrations in crystalline ice. The results are in accord with experiments. (iv) Ionization of acids on wet quartz. A monolayer of water on hydroxylated silica is ordered even at room temperature, but the surface lattice constant differs significantly from that of crystalline ice. The ionization processes of HCl and H2SO4 are of high yield and occur in a few picoseconds. The results are in accord with experimental spectroscopy. (v) Photochemical reactions on water and ice. These simulations require excited state quantum chemical methods. The electronic absorption spectrum of methyl hydroperoxide adsorbed on a large ice cluster is strongly blue-shifted relative to the isolated molecule. The measured and calculated adsorption band low-frequency tails are in agreement. A simple model of photodynamics assumes prompt electronic relaxation of the excited peroxide due to the ice surface. SEMD simulations support this, with the important finding that the photochemistry takes place mainly on the ground state. In conclusion, dynamics simulations using quantum chemical potentials are a useful tool in atmospheric chemistry of water media, capable of comparison with experiment.
Collapse
Affiliation(s)
- R. Benny Gerber
- Institute
of Chemistry and Fritz Haber Center, Hebrew University, Jerusalem 91904, Israel
- Department
of Chemistry, University of California, Irvine, California 92697, United States
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mychel E. Varner
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Audrey D. Hammerich
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sampsa Riikonen
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Garold Murdachaew
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Dorit Shemesh
- Institute
of Chemistry and Fritz Haber Center, Hebrew University, Jerusalem 91904, Israel
| | | |
Collapse
|
10
|
|
11
|
Murdachaew G, Gaigeot MP, Halonen L, Gerber RB. First and second deprotonation of H2SO4on wet hydroxylated (0001) α-quartz. Phys Chem Chem Phys 2014; 16:22287-98. [DOI: 10.1039/c4cp02752c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present anab initiomolecular dynamics study of deprotonation of sulfuric acid on wet quartz, a topic of atmospheric interest.
Collapse
Affiliation(s)
- Garold Murdachaew
- Laboratory of Physical Chemistry
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki, Finland
| | - Marie-Pierre Gaigeot
- LAMBE
- CNRS UMR 8587
- Université d'Evry val d'Essonne
- Boulevard François Mitterrand
- 91025 Evry, France
| | - Lauri Halonen
- Laboratory of Physical Chemistry
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki, Finland
| | - R. Benny Gerber
- Laboratory of Physical Chemistry
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki, Finland
- Institute of Chemistry and the Fritz Haber Research Center
| |
Collapse
|
12
|
Tobias DJ, Stern AC, Baer MD, Levin Y, Mundy CJ. Simulation and Theory of Ions at Atmospherically Relevant Aqueous Liquid-Air Interfaces. Annu Rev Phys Chem 2013; 64:339-59. [DOI: 10.1146/annurev-physchem-040412-110049] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, California 92697-2025; ,
| | - Abraham C. Stern
- Department of Chemistry, University of California, Irvine, California 92697-2025; ,
| | - Marcel D. Baer
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352; ,
| | - Yan Levin
- Insituto de Física, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil;
| | - Christopher J. Mundy
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352; ,
| |
Collapse
|
13
|
Hammerich AD, Finlayson-Pitts BJ, Gerber RB. NOx Reactions on Aqueous Surfaces with Gaseous HCl: Formation of a Potential Precursor to Atmospheric Cl Atoms. J Phys Chem Lett 2012; 3:3405-3410. [PMID: 26290963 DOI: 10.1021/jz3014985] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chlorine atoms are highly reactive free radicals known to catalyze ozone depletion in the stratosphere and organic oxidation in the troposphere. They are readily produced photolytically upon irradiation of some stable Cl containing species, for instance, nitrosyl chloride, ClNO. We predict the formation of ClNO using ab initio molecular dynamics (AIMD) simulations of an NO2 dimer on the surface of a thin film of water upon which gaseous HCl impinges. The reactant is chloride ion formed when HCl ionizes on the water film. The same mechanism for ClNO production may occur in humid environments when ONONO2 (the asymmetric NO2 dimer examined here) comes in contact with either HCl or sea salt. The film of water serves to (1) stabilize ONONO2 on the film surface so that it is localized and physically accessible for reaction, (2) provide the medium to ionize HCl, and (3) activate ONONO2 making it more susceptible to nucleophilic attack by chloride. This substitution/elimination mechanism is new for NOx chemistry on thin water films and could not be derived from studies on small clusters.
Collapse
Affiliation(s)
- Audrey Dell Hammerich
- †Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | | | - R Benny Gerber
- ‡Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
- §Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904 Israel
- ∥Laboratory of Physical Chemistry, University of Helsinki, P.O. Box 55, FIN-00014, Helsinki, Finland
| |
Collapse
|