Direct Trace Fitting of Experimental Data Using the Master Equation: Testing Theory and Experiments on the OH + C₂H₄ Reaction

Abstract

The supplementary information (369 pages) contains: Pages S2 -S6 Fits to all 96 traces showing the raw data and final fit. At the top of each trace are the associated experimental conditions. Pages S7 -S99 An example MESMER input file for the analysis. The majority of the information, from page S12 onwards, are the experimental input data for each trace. Pages S100 -S369 The associated MESMER log file. The data from page S104 onwards are the experimental data and associated fit. S2 Trace FitsPlots of the trace fits are shown below. Blue lines are the MESMER traces the red lines connect experimental points. For clarity only every other experimental point is plotted. S3 S4 S5 S6 S7 MESMER Input file Following is the MESMER input file for the fitting of the OH + C2H4 trace data. <?xml version="1.0" encoding="utf-8" ?> <?xml-stylesheet type='text/xsl' href='../../mesmer2.xsl' media='other'?> <?xml-stylesheet type='text/xsl' href='../../mesmer1.xsl' media='screen'?> <me:mesmer xmlns="http://www.xml-cml.org/schema" xmlns:me="http://www.chem.leeds.ac.uk/mesmer" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><me:title>Ethylene + OH</me:title> <moleculeList convention=""> <molecule id="ethylene_OH" spinMultiplicity="2"> <atomArray> <atom id="a1" elementType="C" spinMultiplicity="2" x3="1.247247" y3="-0.253391" z3="0.024084" /> <atom id="a2" elementType="H" x3="1.242208" y3="-1.290996" z3="-0.272051" /> <atom id="a3" elementType="H" x3="2.185882" y3="0.247949" z3="0.200300" /> <atom id="a4" elementType="C" x3="-0.011092" y3="0.520162" z3="-0.035598" /> <atom id="a5" elementType="H" x3="-0.064239" y3="1.089354" z3="-0.978097" /> <atom id="a6" elementType="O" x3="-1.102603" y3="-0.376517" z3="0.052221" /> <atom id="a7" elementType="H" x3="-1.919062" y3="0.107985" z3="-0.076664" /> <atom id="a8" elementType="H" x3="-0.040898" y3="1.257225" z3="0.777829" /> </atomArray> <bondArray> <bond id="b1" atomRefs2="a5 a4" order="1" /> <bond id="b2" atomRefs2="a2 a1" order="1" /> <bond id="b3" atomRefs2="a7 a6" order="1" /> <bond id="b4" atomRefs2="a4 a1" order="1" /> <bond id="b5" atomRefs2="a4 a6" order="1" /> <bond id="b6" atomRefs2="a4 a8" order="1" /> <bond id="b7" atomRefs2="a1 a3" order="1" /> </bondArray> <propertyList> <property title="program"> <scalar>Gaussian 09, Revision D.01</scalar> </property> <property title="basis"> <scalar>6-311++G(3df,2p) (5D, 7F)</scalar> </property> <property title="File Format"> <scalar>g03</scalar> </property> <property dictRef="me:ZPE"> <scalar units="kJ/mol" lower="-155" upper="-100" stepsize="0.01" fitted="20191029_234957" chiSquared="0.00059954">-112.133</scalar> </property> <property title="SpinMultiplicity" dictRef="me:spinMultiplicity"> <scalar>2.00</scalar> </property> <property dictRef="me:frequenciesScaleFactor"> <scalar>0.964</scalar> </property> <property title="Hessian" dictRef="me:hessian"> <matrix rows="24" matrixType="squareSymmetricLT" units="Hartree/Bohr2">5.

Nitrene formation is the first step of the thermal and photochemical decomposition reactions of organic azides

“…Finally, rate constants associated to transition states (adiabatic reactions) as well as intersystem crossings (nonadiabatic reactions) have been determined with the program MESMER version 5.2. [58][59][60][61][62] Microcanonical rate constants of transitions states have been computed with the Rice and Ramsperger-Kassel-Marcus (RRKM) theory [63][64][65][66] and the microcanonical rate coefficients of ISCs have been calculated with the Landau-Zener 67,68 model with inclusion of tunnelling corrections as described by Harvey and Aschi. 69…”

Kinetics of the Reactions of Hydroxyl Radicals with Furan and Its Alkylated Derivatives 2-Methyl Furan and 2,5-Dimethyl Furan

“…Simulations using the full potential energy surfaces described by Yuan et al and those with the minor modifications indicated that such modifications reduce the computational cost of the fits, without any significant loss in accuracy. Collisional energy transfer was modelled using <ΔE>down = 250 × (T/298) 0.25 cm -1 for N2, 29,[41][42][43] 180 × (T/298) 0.5 cm -1 for Ar, 41,43 and 125 cm -1 × (T/298) 1.0 for He. 41,43 The initial reaction between OH and the furan occurs on barrierless surfaces to form pre-reaction complexes (see Figures 5 and S1).…”

An experimental and computational study of the reaction between 2-methylallyl radicals and oxygen molecules: optimizing master equation parameters with trace fitting

“…As mentioned in the Introduction, in some cases it is advantageous to directly use experimental traces for parameter optimization. The particulars of the trace fitting feature in MESMER are explained in ref (3). Briefly, the error function that is minimized is…”

“…This issue has been addressed by Medeiros et al using a least squares fit of the amplitude of the calculated trace to the measured trace. The details are presented in ref (3).…”

“…Trace fitting was implemented in MESMER version 6.0. 2 The details of this implementation are presented by Medeiros et al 3 In version 6.1, this feature was extended to allow the user to specify first-order loss rates (diffusive losses) for all species present in the reaction system. The purpose of these loss rates is to account for processes other than the studied reaction which have an effect on the measured traces.…”