DATABASES OF ATMOSPHERIC KINETIC DATA - NOVEMBER 2018 I VEREECKEN LUC
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DATABASES OF ATMOSPHERIC KINETIC DATA NOVEMBER 2018 I VEREECKEN LUC
ATMOSPHERIC KINETIC DATA The need for kinetic data for atmospheric chemistry Isoprene is emitted by a tree. What happens to the isoprene? a) It is mostly removed by OH radicals. How fast? Which products are formed? Whence the OH radicals? b) Some dominant products are methacrolein and methylvinylketone How much? What happens to these... etc. c) Does the above depend on reaction conditions ? - Temperature, pressure = place, time - Alternative reactions: OH vrs. O3 / NO3 / - photochemistry (=time, light, clouds) Isoprene MACR MVK Page 2
ATMOSPHERIC KINETIC DATA Information needed for kinetic data of elementary processes a) Chemical reaction / physical processes / pseudo-process - CH4 + OH CH3 + H2O - HCOOH (gas) HCOOH (aq) - isoprene emission b) Rate of change : differential equations with rate coefficient [ 4 ] [ ] [ 2 ] [ 3 ] = k [CH4] [OH] = = = c) Value of rate coefficient k : specific to the given reaction Can depend on temperature, pressure, light intensity and spectrum, ... Pseudo processes: time- and place-dependence. E.g emission E(x,y,z,t) d) Lumped reactions : multiple steps in a single process description Page 3
ATMOSPHERIC KINETIC DATA Information needed/useful for kinetic model of atmosphere a) Chemical mechanism as a set of coupled, non-linear differential equations Usually written as a large list of reactions (mathematics implied) b) Sources, sinks, boundary conditions as differential equations, field strengths, etc... Emission fields, spectral intensities, etc. : see other modules c) Data for comparison Measurements of concentrations, column values, ... e) Earth system model (ESM) Includes e.g. Transport, links to other models Prediction of time-dependent concentrations for all species is then "merely" a matter of solving the differential equations. Page 4
WHY DATABASES WITH KINETIC INFORMATION Size of chemical mechanisms Gecko-A : Automatic mechanism Master chemical mechanism (MCM) : generator for atmospheric chemistry semi-explicit chemical kinetic mechanism 143 emitted organic species 6700 model species 17000 reactions 10 Image source right: Aumont, B., Szopa, S. and Number of functional groups Madronich, S.: Atmos. Chem. Phys., 5, 2497– 9 -pinene 2517, doi:10.5194/acp-5-2497-2005, 2005. 8 Octane 7 Image source left: Vereecken, L., Aumont, B., Barnes, I., Bozzelli, J. W., Goldman, M. J., 6 Green, W. H., Madronich, S., Mcgillen, M. R., 5 Mellouki, A., Orlando, J. J., Picquet-Varrault, B., 4 Rickard, A. R., Stockwell, W. R., Wallington, T. J. and Carter, W. P. L.: Int. J. Chem. Kinet., 3 50(6), 435–469, doi:10.1002/kin.21172, 2018. 2 1 0 0.0 5.0x103 1.0x104 1.5x104 2.0x104 2.5x104 Number of compounds Page 5
DATATYPES IN A KINETICS-ORIENTED DATABASE
THE MOLECULE AS DATA Properties of a molecule Atoms in the molecule (stoichiometry, mass) Connectivity of the atoms (molecular graph, substructures) Spatial shape of the molecule Physical properties (color/spectrum, solubility, boiling/freezing point, density,...) Chemical properties (reactivity, acidity, decomposition stability, energy/enthalpy, ...) Biological properties (metabolism, toxicity, skin/eye irritation, bioaccumulation,...) Technological properties (flash point, combustion, production, critical temperatures,...) Etc... Page 7
THE MOLECULE AS DATA Example of a database of chemical compounds : PubChem Website : https://pubchem.ncbi.nlm.nih.gov/ PubChem is an open chemistry database at the National Institute of Health (NIH) Compounds : ~100 million compounds, 250 million substances Multiple search options Web interfaces with text search, structure search Programmatic interfaces (PUG, SOAP, REST) Hands-on examples : methacrolein (https://pubchem.ncbi.nlm.nih.gov/compound/methacrolein) Try searching for a) isoprene (C5H8) c) b) the methyl radical (CH3) Page 8
THE MOLECULE AS DATA Molecular identifiers (or "how to name a molecule") Very complex problem, which is only partially solved Systematic names: allows to reconstruct the molecular graph based on the name IUPAC (human readable), SMILES (pseudo-readable), formula, InChI Systematic vrs. canonical vrs. understandable Code names Trivial names (human readable, memorizable) InChI key, CAS ID, Pubchem ID, MCM ID, SAPRC, ... Graph representation SMILES (connectivity), InChI, little schemes drawn in a figure (most popular) Page 9
THE MOLECULE AS DATA Example : methacrolein IUPAC: 2-methyl-prop-2-enal Trivial name : methacrolein, 2-methylacrolein, methacrylaldehyde InChI=1S/C4H6O/c1-4(2)3-5/h3H,1H2,2H3 InChI key : STNJBCKSHOAVAJ-UHFFFAOYSA-N "Canonical" smiles : CC(=C)C=O Other smiles : O=CC(C)=C ; C=C(C)C=O ; C(C)(=C)C=O ; CC1=C.O=C1 CAS : 78-85-3 MCM : MACR etc... Page 10
THE MOLECULE AS DATA How to search for a molecule Graph matching : most reliable, but computationally expensive (and... graph entry?) Canonization of identifiers (e.g. "canonical" smiles, InChI, "canonical" IUPAC name) Search in list of known names (can never be exhaustive) How to search for similar molecule What is similarity ? Part of structure / (reactive) substituents / properties / ... Subgraph isomorphism matching is computationally expensive Can be improved by pre-calculation (e.g. fingerprinting) How to search for spatial information 3D information is critical e.g. in catalysts, enzymes, ... Most molecules have multiple possible 3D forms (conformers, internal rotation) Page 11
THE CHEMICAL REACTION AS DATA Reaction identifiers (or "how to find a reaction") Once the reactants and products are identified, the reaction identifier problem is trivial. Except for: Elementary vrs. lumped reactions Catalysts ; third-body ; phase/lattice structure/activities Unidentified reactants/products (especially experimental data) Reaction properties (all as a function of reaction conditions and environment) Transformation mapping Rate coefficient / -specific quantum yields Equilibrium constant Energetic properties (reaction barrier, reaction energy,...) Product yields (multiple channels are not independent) Page 12
ADDITIONAL INFORMATION NEEDED FOR DATABASES Data provenance Methodology : Experimental / theoretical / evaluation / estimate / simplification... Source : literature identifier (DOI, ISBN,...) Data entry : Manual / automated ; operator ; software/form version Database transactions : timestamp addition, corrections Release : Snapshot identification Uncertainty information Often not available As provided by source, from meta analysis, or from evaluation Page 13
ADDITIONAL INFORMATION NEEDED FOR DATABASES Meta data Typically categorical data tagging the data quantity of interest Most often omitted due to cost of entry Meta data is often the key to leveraging the data to the fullest (data mining) Example : TheoKinDB entry forms TheoKinDB is database for theoretically obtained kinetic data Core data is energetic and kinetic data of reactions Theoretical methodology is added as meta data Provenance : source / data entry / versioning Page 14
ADDITIONAL INFORMATION NEEDED FOR DATABASES Example meta-data: Benchmarking of theoretical methodologies (uncertainty analysis) Analysis without meta-data gives a statistically correct, but simplistic result Analysis with meta-data reveals underlying structure, and allows better use of data 40 = f(reaction class) = -0.17 2.39 kcal/mol 35 30 25 Count 20 15 10 5 0 -6 -4 -2 0 2 4 6 Difference M06-2X vrs. CCSD(T)//M06-2X (kcal/mol) Page 15
ADDITIONAL INFORMATION NEEDED FOR DATABASES Example provenance: Active Thermochemical Tables (~1400 species) https://atct.anl.gov/ version 1.122d click on species (e.g. H2O, Cl) Old style thermodynamics : determine enthalpies relative to another compound New style thermodynamics: - make database with all relative enthalpies (experimental and theoretical) - construct "thermochemical network" linking all species - optimize entire network to minimize errors best results + uncertainty - analyze provenance : - which are the strongest determinants for a given value - identify strongest missing links for improvement. Page 16
DATABASES WITH KINETIC INFORMATION
IUPAC EVALUATED KINETIC DATA http://iupac.pole-ether.fr/ Kinetic and photochemical data Evaluated by the IUPAC Task Group on Atmospheric Chemical Kinetic Data Evaluation Datasheets for individual reactions available as PDF/Word file Main advantage : Evaluation by specialists, with recommendations and error analysis Good provenance Disadvantages : Limited selection of reactions for large mechanisms Not searchable Only uses experimental data Page 18
NIST CHEMICAL KINETICS DATABASE https://kinetics.nist.gov/kinetics/ Kinetic and photochemical data Literature overview, no additional evaluation Has mostly experimental data, some theoretical data, reviewed data Only limited meta-data Better searchability (see "Getting started") Example : search for CH4 + OH CH3 + H2O C2H5OO + NO2 Page 19
STRUCTURE-ACTIVITY RELATIONSHIPS
STRUCTURE-ACTIVITY RELATIONSHIPS What to do if no data is available for a given reaction? Structure-Activity relationships (SARs) may help: summarizes reactivity trends Example : alkoxy radical decomposition rate by estimating the barrier height Source : Vereecken, L. and Peeters, J.: Phys. Chem. Chem. Phys., 11(40), 9062– 9074, doi:10.1039/b909712k, 2009. Page 21
STRUCTURE-ACTIVITY RELATIONSHIPS Example : Carbonyl oxide reactivity (unimolecular or reaction with water) Simple interactive SAR: http://iek8810-gw.iek.kfa-juelich.de/~luc/TdW_Vereecken/SAR.html Reactivity depends on substitution on either side of the carbonyl oxide Less than 10 of these reactions have been measured, about 40 calculated explicitly Reactivity of about 150 CI reactions was summarized in the SAR Source : Vereecken, L., Novelli, A. and Taraborrelli, D.: Phys. Chem. Chem. Phys., 19, 31599–31612, doi:10.1039/C7CP05541B, 2017. Page 22
DATABASES WITH KINETIC MODELS
KINETIC MODELS Mechanistic information is essentially a "set of reactions" Applying the mechanisms to all compounds in a set gives the kinetic model Few people make a difference between "mechanism" and "kinetic model" Kinetic models in publications: - static, not easily searchable, fixed-format Example : -pinene+OH model Vereecken, L. and Peeters, J.: Phys. Chem. Chem. Phys., 14(11), 3802–3815, doi:10.1039/c2cp23711c, 2012. Page 24
KINETIC MODELS Browseable model - Exploring the chemistry Visualisation of the mechanism Kinetic model interactively browseable tool for exploring / learning the model Example : BOREAM model for -pinene chemistry, with aerosol formation http://tropo.aeronomie.be/boream/ Page 25
KINETIC MODELS Extractable model - Querying a database for a submechanism - Database of chemical reactions - Select relevant species, query list of all related chemistry (1st, 2nd,.. nth generation) Example : Master Chemical Mechanism (MCM) http://mcm.leeds.ac.uk/MCM/ - Browse/search the mechanism - Extract a subset in different formats - Kinetic model easily useable in your own research - Some provenance information with extensive mechanistic "protocols" Page 26
PUBLICLY AVAILABLE DATABASES
PUBLICLY AVAILABLE DATABASES (SELECTION) Properties / names / graphs / identifiers Chemspider : http://www.chemspider.com/ PubChem : https://pubchem.ncbi.nlm.nih.gov/ NIST webbook : https://webbook.nist.gov/chemistry/ CHEBI : Chemical entities of biological interest : https://www.ebi.ac.uk/chebi ADME/T : Water solubility database : http://modem.ucsd.edu/adme/databases/databases_logS.htm Energy / geometry: BEGDB: Benchmark energy and geometry database : www.begdb.com CCCBDB: Computational Chemistry Comparison and Benchmark DataBase : https://cccbdb.nist.gov/ ATcT : Active Thermochemical Tables : https://atct.anl.gov/ Prof. Burcat Thermodynamic Data : Ideal Gas Thermodynamic Data in Polynomial form for Combustion and Air Pollution Use http://garfield.chem.elte.hu/Burcat/burcat.html Page 28
PUBLICALLY AVAILABLE DATABASES (SELECTION) Kinetics: ERADB: Chemical Kinetics Database on oxygenated VOCs gas phase reactions : http://era-orleans.org/eradb/index.php IUPAC Task Group on Atmospheric Chemical Kinetic Data Evaluation: http://iupac.pole-ether.fr/ NIST Chemical kinetics database: https://kinetics.nist.gov/kinetics/ KIDA: Kinetic database for astrochemistry : http://kida.obs.u-bordeaux1.fr/ JPL : Chemical kinetics and photochemical data for use in atmospheric studies : https://jpldataeval.jpl.nasa.gov/ MPI-Mainz UV/VIS : Spectral atlas of gaseous molecules of atmospheric interest : http://satellite.mpic.de/spectral_atlas Gecko-A : Generator for explicit chemistry and kinetics of organics in the atmosphere : http://geckoa.lisa.u-pec.fr/ Chemical mechanisms Master Chemical Mechanism (MCM) : http://mcm.leeds.ac.uk/MCM/ BOREAM Model : atmospheric reactions of alpha-Pinene : http://tropo.aeronomie.be/boream Structure-activity relationships Gecko-A : Generator for explicit chemistry and kinetics of organics in the atmopshere : http://geckoa.lisa.u-pec.fr/ Page 29
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