![Page 1: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/1.jpg)
RMG Study GroupBelinda Slakman
December 1, 2016
![Page 2: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/2.jpg)
Topics
• Silicon hydrides
• Solvation kinetics
• For each, will present theory, some results & its implementation in RMG-Py
![Page 3: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/3.jpg)
Northeastern University
Enable silicon hydride chemistry in RMG
• Simulate silicon hydride chemical vapor deposi9on, silicon nanopar9cle forma9on
• Need to update and/or add reac9on families, libraries, thermodynamics
• Need reasonable experimental comparisons
3
![Page 4: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/4.jpg)
Northeastern University
Two new reac9on families and reac9on libraries added to RMG
• Silylene Inser9on (new)
• Silylene-‐to-‐Silene Isomeriza9on (new)
• Hydrogen Abstrac9on (updated)
• Radical Recombina9on (updated)
• Reac9on libraries, including ring opening reac9ons
4Giunta et al., J. Appl. Phys. 67, 1990, 1062-1075 Dollet and de Persis, J. Anal. Appl. Pyrolysis 80, 2007, 460-470 Adamczyk et al. Phys. Chem. Chem. Phys. 12, 2010, 12676-12696
Adamczyk et al. ChemPhysChem 11, 2010, 1978-1994 Adamczyk et al. J. Phys. Chem. A 113 2009, 10933-10946 Adamczyk et al. Theor Chem Acc 128, 2011, 91-113
X is H or SiX
H:Si
R1
R2
X
HSi
R1
R2⇌
Si.R1 R3
R2 .R4
SiR1 R3
R2 R4⇌
HSi
R1 R3
R2.R4 H
Si.R1 R3
R2R4⇌
H
:SiSi
HSiSi⇌R1
R1
R2R2R3 R3
![Page 5: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/5.jpg)
Northeastern University
Thermodynamics data added to RMG
• Common species available in NIST database
• High level calcula9ons for some ring species1
• Group addi9vity values for stable species2
• Newly developed hydrogen bond increment (HBI) values for radicals:* these were using G3//B3LYP
5
Slakman et al., Ind. Eng. Chem. Res., 2016 1 Katzer et al., J. Phys. Chem. A. 101, 1997, 3942-3958. 2 Wong et al., J. Phys. Chem. A. 108, 2004, 874-897.
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Northeastern University
Addi9ons to Cantherm
6
• Spin orbit coupling value for Si
• Atomic energies for G3//B3LYP, CBS-‐QB3, and M062X/MG3S
• BAC for G3//B3LYP
![Page 7: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/7.jpg)
Northeastern University
Comparison to SiH4 decomposi9on experiment
7Onischuk et al., Int. J. Chem. Kinetics 30(2), 1998, 99-110 Goodwin et al., Cantera, http://www.cantera.org
𝛕 ≈ 0.8 s
T = 913 K P = 39 kPa y0(SiH4) = 1.6 x 10-‐4 in Argon
613 K ≤ T ≤ 963 K P = 39 kPa y0(SiH4) = 1.6 x 10-‐4 in Argon
With/without pressure dependence, With/without radical reac9ons
Cantera
y (Si
H4)
y 0
(SiH
4)
![Page 8: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/8.jpg)
Northeastern University
Model matches experiment within uncertainty
8Onischuk et al., Int. J. Chem. Kinetics 30(2), 1998, 99-110 Slakman et al., Ind. Eng. Chem. Res., 2016.
Experiment = 913 K
Model matches experiment within a 20 K temperature difference
Corresponds to 1-2 kcal/mol difference in activation energy
![Page 9: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/9.jpg)
Northeastern University
Model cannot capture effect of changing ini9al ySiH4
9
Experiment
Model
Onischuk et al., Int. J. Chem. Kinetics 30(2), 1998, 99-110 Slakman et al., Ind. Eng. Chem. Res., 2016.
![Page 10: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/10.jpg)
Northeastern University
RMG-‐Py implementa9on
10
• On branch ‘bslakman/RMG-‐Py/silicon-‐hydrides’ and ‘bslakman/RMG-‐database/silicon-‐hydrides’
• Will get up to date with current master, and submit a pull request
• See hgp://pubs.acs.org/doi/abs/10.1021/acs.iecr.6b02402
![Page 11: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/11.jpg)
Northeastern University
Framework needed for liquid phase mechanism genera9on
11
Solvation thermo
Linear solvation energy relationships (LSERs) and a molecular structure
group additivity approach
Diffusion-limited kinetics
Stokes-Einstein theory for bimolecular reaction rates
Solvation kinetics
How can we generalize solvent effects in a quick, high-
throughput way?
✔
✔
𝙭
A Jalan et al., J. Phys. Chem. B, 117(10), 2013
![Page 12: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/12.jpg)
Northeastern University
Reac9on barrier is affected by solva9on
Barrier height changes depending on differing effect of solvent on reactant and transi9on state
12
Adapted from Crim, F.F., Farad. Discuss., 2012
�EA = EliquidA � Egas
A
![Page 13: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/13.jpg)
Northeastern University
SMD energy calcula9on provides tradeoff between accuracy and speed
13
• SMD is a con9nuum solva9on model with some correc9ons for the first solvent shell1
• Full electron density used • A single point energy calcula9on based on SMD is performed on gas-‐phase geometries and transi9on states to calculate ∆EA
• 8 solvents chosen to span a range of dielectric constant and 6 solvent categories2
�EA = EliquidA � Egas
A
1. A.V. Marenich et al., J. Phys. Chem. B., 113(18), 2009. 2. Schmid, Handbook of Solvents. George Wypych, ed., Ch. 13, 2001.
![Page 14: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/14.jpg)
Northeastern University
Results suggest ∆EA can be predicted
• Method should modify gas phase EA based on – molecular structure of reactants – solvent
• Molecular structure tree for each solvent category, based on trends observed
14
X-H 1.37
R-O-H 1.28 R-C-H -0.31
-1.26 0.61 1.17C H
C/H
C/H
C/H C HO HCCO
![Page 15: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/15.jpg)
Northeastern University
Results: Trained group values from 47 ∆EA values
15
Example: CH3OH + •OOH ⇔ CH3O• + H2O2
∆EA = 2.78 kJ/mol
General
X-H
1.37 + 0.51 = 1.88
Y•-0.01 + 0.91 = 0.90
Specific
• O—O—
C O
H
H
H
![Page 16: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/16.jpg)
Northeastern University
Will kine9c solva9on correc9ons make a difference in exis9ng models?• Ben Amara et al. (2013) used RMG to build a detailed kine9c model for nC12/methyl oleate oxida9on, and compared to experiments1 – Liquid-‐phase thermodynamic correc9ons were used
• 2924 of 3275 reac9ons (89%) were hydrogen abstrac9on
• We modified the H-‐abstrac9on rates using the group contribu9on method for ∆EA and simulated it with Cantera2
161. Ben Amara et al., Energy & Fuels, 27, 2013. 2. D.G. Goodwin et al. http://www.cantera.org, 2015. Version 2.2.0.
Figure 3a from Ben Amara et al.; Comparison of induction times from detailed kinetic model with experiments.
![Page 17: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/17.jpg)
Northeastern University
0.01$
0.1$
1$
10$
100$
2.1$ 2.2$ 2.3$ 2.4$ 2.5$
IP#(h
)#
1000/T#(1/K)##
5%$MO,$original$
5%$MO,$modified$
0%$MO,$original$
0%$MO,$modified$
Model simula9on with
17
0.01$
0.1$
1$
10$
100$
2.1$ 2.2$ 2.3$ 2.4$ 2.5$
IP#(h
)#
1000/T#(1/K)##
5%$MO,$original$
0%$MO,$original$
0.01$
0.1$
1$
10$
100$
2.1$ 2.2$ 2.3$ 2.4$ 2.5$
IP#(h
)#
1000/T#(1/K)##
5%$MO,$original$
5%$MO,$modified$
0%$MO,$original$
0%$MO,$modified$
Updated model shows larger induc4on periods for 0% and 5% v/v methyl oleate contentOur Cantera simula4on with Ben Amara et al. model is similar to their simula4on
![Page 18: RMG Study Group...Dec 01, 2016 · Adamczyk et al. Theor Chem Acc 128, 2011, 91-113 X is H or Si X H:Si R1 R2 X H Si R1 R2 ⇌ Si. R1 R3 R2.R4 Si R1 R3 R2 R4 ⇌ H Si R1 R3 R2.R4](https://reader033.vdocuments.us/reader033/viewer/2022060303/5f08d5177e708231d423f03b/html5/thumbnails/18.jpg)
Northeastern University
Octane and methyl heptane mechanisms
18
• Recently, we modified updated mechanisms from IFP group, now with many more training reac9ons (> 1000), and for both hydrogen abstrac9on and intra-‐H migra9on reac9ons.
0.1
1
10
100
2.2 2.3 2.4 2.5 2.6 2.7 2.8
180 160 140 120 100
Indu
ctio
n Pe
riod
(hou
rs)
1000/T (K-1)
Temperature (°C)
Chatelain(2016)Unpublished
Skolniak(2015)Van Sickle(1973)
Fit ExpModel C8
model C8 corrected 0.1
1
10
100
2.2 2.3 2.4 2.5 2.6 2.7 2.8
180 160 140 120 100
Indu
ctio
n Pe
riod
(hou
rs)
1000/T (K-1)
Temperature (°C)
UnpublishedFit Exp
Model MH01Model MH02
Model MH01 correctedModel MH02 corrected
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Northeastern University
RMG-‐Py implementa9on
19
• Currently, a post processing script – ‘bslakman/my_scripts/modifyReac9onBarriers.py’ – Can add to script repository
– Need to use with my updated solva9on branches of RMG-‐Py and RMG-‐database
– In process of making automated during mechanism genera9on
– Benchmarking (Jason Cain)