MOLECULAR MECHANICS TO MODEL COAL CHAR
STRUCTURES AND DFT TO MODEL THEIR
REACTIVITY WITH CO2 GAS FOR SYNTHETIC GAS
PRODUCTION
Mokone J. Robertsa, Raymond C. Eversona, Hein W. J. P. Neomagusa, Jonathan P. Mathewsc, George Domazetise,
Cornelia G.C.E. van Sittertd
a Coal
Research Group, School of Chemical and Minerals Engineering, North-West University,
Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa.
c John and Willie Leone Family Department of Energy and Mineral Engineering, The EMS Energy
Institute, The Pennsylvania State University, University Park, PA 16802, USA
d Laboratory of Applied Molecular Modelling, Chemical Resource Beneficiation Focus Area, North-West
University, Potchefstroom 2520, South Africa
e Chemistry Department, La Trobe University, Melbourne, VIC 3086, Australia
CONTENTS
• Background and motivation
• Char characterisation
• Construction and properties of large-scale molecular
structures of chars using molecular mechanics
• Reactivity modelling of chars using quantum mechanics
• Modelling of the fundamental char-CO2 reaction mechanism
• Conclusions
• Acknowledgements
2
BACKGROUND AND MOTIVATION
• The generation of char is generally an important
intermediate step in coal conversion processes, e.g.,
gasification1
• Coal chars can be described on mineral matter free basis
– as polyaromatic hydrocarbons (PAHs) with a network structure
– in which hetero atoms (O, N and S) are dispersed2
• Exploring the structure of chars at an atomic scale is vital to
facilitate understanding of the relationship between char
structure and reactivity (with CO2 in this investigation).
1. Sadhukhan 2009.Fuel Processing Technology 90, 692–700
2. Chen et al. 2011. Ind. Eng. Chem. Res, 50, 2562–2568
3
CHARACTERISATION
TECHNIQUE
STRUCTURAL
INFORMATION
SPECIFIC
INFORMATION
Petrographic analysis on
parent coal (PSD =0.31.0 mm)
None
v% Inertinite and
vitrinite
Standard analysis
Bulk properties
wt% C H O N S
Density measurements
Physical properties
Helium density
XRD
Structural ordering of
carbons
% Aromaticity
NMR
Structural parameters
%Aromaticity
HRTEM
Surface structure
Size distribution of
aromatic fraction
Basic construction
requirements
4
REACTIVITY MEASUREMENTS5,6,7
• Thermax 500 TGA* supplied by Thermo Fisher Scientific,
RSA
• Char-CO2 gasification experiment using 100% CO2 and -75
μm PSD.
• TGA data were evaluated using 𝑋 =
𝑚𝑜 −𝑚𝑡
𝑚0 −𝑚𝑎𝑠ℎ
• Reactivity was determined by random pore model (RPM)
5. Everson et al. 2008. Fuel 87(15-16): 3403-3408.
6. Everson et al. 2013. Fuel, 2013. 109:148-156.
7. Hattingh et al. 2011. Fuel Processing Technology. 92(10): 2048-2054.
* TGA = Thermogravimetric analyser
5
CHARACTERATION RESULTS
CHARACTERISATION RESULTS WERE USED IN
STRUCTURAL AND REACTIVITY MODELLING
PROCESSES USING MOLECULAR AND
QUANTUM MECHANICS TECHNIQUES,
RESPECTIVELY.
6
MOLECULAR MODELLING
MOLECULAR MECHANICS FACILITIES MADE AVAILABLE
TO THE USER FOR THE STRUCTURAL MODELLING
• University's HPC cluster and National CHPC
• Accelrys Material Studio 6.0
• Amorphous Cell for 3D constructions
• Forcite for structural geometries and density calculations
• DREIDING forcefield
• PCFF force field for aromaticity
• Perl scripting for model characterisation
7
MOLECULAR MODELLING
STRUCTURAL CONSTRUCTION COMMENCED
WITH AROMATIC STRUCTURES FROM THE
HIGH RESOLUTION TRANSMISSION
ELECTRON MICROSCOPE (HRTEM)
8
IMAGE PROCESSING8 OF HRTEM
MICROGRAPHS
IMAGE AFTER SKELETONISATION
RAW IMAGE FROM COAL CHAR
8. Sharma et al. 1999. Fuel, 1999. 78(10): p. 1203-1212.
Lattice fringe length = 51 Å
9
ANALYSED AND INTEPRETED AS
AROMATIC CARBON RAFTS9
PARALLELOGRAM CATENATIONS9
Lattice Fringe length = 54 Å
Average length = 54 Å
Max.length
Min.length
Min. length = 39.959 Å
Max. length = 67.713 Å
9. Mathews et al. 2010. Fuel 89 1461–1469
10
HRTEM: AVERAGE AROMATIC
RAFT SIZE DISTRIBUTION
11
INITIAL H/C RATIOS FROM PAHs
DISTRIBUTION
Example: A few samples (3x3 – 25x25) from aromatic carbon
rafts size distribution from the HRTEM
12
MOLECULAR MODELLING
TRIMMING TECHNIQUES10,11,12
• To produce geometric representations according to the shapes
of the lattice fringes of chars from the HRTEM.
• To commence the adjustment of atomic H/C, O/C, N/C & S/C
ratios.
• e.g. trimming of 11x11 aromatic raft as shown:
10. Niekerk et al. 2010. Fuel 89(1): p. 73-82.
11. Weimershaus et al. 2013 Current Opinion in Immunology 25(1): p. 90-96.
12. Heifetz et al. 2003. Protein Engineering 16(3): p. 179-185.
13
HETERO ATOMS IN COAL
CHARS13,14,15,16
carbonyl-O
ether-O
Pyridinic-N
(a)
Thiophenic-S Quaternary-N
(b)
A suitable number of molecules with individual geometries was
used to form large-scale 3D molecular structures.
13. Fletcher et al. 1992. Energy & Fuels, 6, 643-650
14. Pels et al. 1995. Carbon 33 (11), 1641-1653
15. Kelemen et al. 1998. Energy & Fuels, 12, 159-173
16. Liu et al. 2007. Fuel, 86 , 360–366
14
LARGE-SCALE 3D MOLECULAR
STRUCTURES: MODELLING PROCESS
3D construction at 0.1 g.cm-3 from a combination of molecules
Energy minimisation of the 3D structure
Annealing calculations at 25-1000 ℃, 3.0 GPa over 20 cycles
Molecular Dynamics at 25 ℃ and 3.0 GPa on a frame of 1.798 g.cm-3
Automatic/manual Atomic Force field calculations
15
LARGE SCALE MODELS IN 3D:
CPK* DISPLAYED STYLE
INERTINITE CHAR MODEL
Ave. values
(Å)
d002 = 3.4
Lc
= 15.0
La
= 35.0
Nave(-) = 4
Selected for d002,
Lc and Nave (-)
(subjective
measurements)
C = green
H = white
O = red
N = blue
S = yellow
16
LARGE SCALE MODELS IN 3D:
CPK* DISPLAYED STYLE
VITRINITE CHAR MODEL
d002, Lc , La and Nave (-)
(subjective measurements)
Ave. values (Å)
d002
= 4.4
Lc
= 16.9
La
= 31.6
Nave (-) = 4
C = green
H = white
O = red
N = blue
S = yellow
Default view
* CPK = space-filling model
17
EXPERIMENTAL & MODELLING
DATA COMPARED (XRD)
Property
Inertinite char
Vitrinite char
Experimental
Modelling
Experimental
Modelling
Inter-layer spacing, d002 (Å)
3.493
3.4
3.508
4.4
Crystallite height, Lc (Å)
12.19
15.0
11.76
16.9
Crystallite diameter, La (11) (Å)
39.39
35.0
32.47
31.9
Average number of aromatic
layers Nave (-)
4.489
4
4.352
4
18
EXPERIMENTAL & MODELLING
DATA COMPARED
Property
Total molecules
Total atoms
Total C
Total H
Total O
Total N
Total S
H/C atomic ratio
O/C atomic ratio
N/C atomic ratio
S/C atomic ratio
Inertinite char
Experimental
Model
21
1130
1142
1000
1000
104
105
7
14
18
22
1
1
0.10
0.10
0.01
0.01
0.02
0.02
0.001
0.001
Vitrinite char
Experimental
Model
37
1162
1171
1000
1000
123
125
21
21
15
22
3
3
0.12
0.12
0.02
0.02
0.02
0.02
0.003
0.003
Helium density (g.cm-3)
1.87
1.87
1.82
1.82
f a (%) (from XRD)
96.0
96.0
95.0
95.0
Formula
C1000H104O7N18S1 C1000H105O14N22S1 C1000H123O21N15S3 C1000H125O21N22S3
Note that NMR results could not be obtained because of the extensive line broadening
phenomena which prevented accurate calculation of structural and lattice parameters17,18
17. Solum et al. 2001. Energy & Fuels. 15(4): p. 961-971.
18. Perry et al. 2000. Proceedings of the Combustion Institute. 28(2): p. 2313-2319.
19
DFT* REACTIVITY MODELLING
QUANTUM MECHANICS FACILITIES MADE AVAILABLE
TO THE USER FOR THE REACTIVITY MODELLING
•
•
•
•
•
•
Accelrys Material Studio
Spin unrestricted DFT calculations (DMol3 module)
Generalised gradient approximation of PW91
Basis set: Double numerical by polarisation (DNP)
Thermal smearing used to improve SCF convergence
Calculations included:
– Geometry Optimisation (GeomOpt)
– Single-point energy (1-scf)
– Transition state (TS) theory
* DFT = density functional theory. Offers highly accurate results with theoretical
soundness. Has very high but justifiable computational costs
20
DFT* REACTIVITY MODELLING:
RATIONAL OF MODELS USED
3x3
4x4
Simplified char models
sampled from the large scale
models without the trimming
and hetero atoms effects
were selected for reactivity
modelling because of DFT
size limitations.
5x5
21
DFT* REACTIVITY MODELLING:
ACTIVE SITES
FUKUI FUNCTION19,20,21
The Fukui Function (𝑓(𝑟)) is among the most basic and
commonly used reactivity indicators.
𝑓(𝑟) is defined according to reactivity governing the
• nucleophilic attack
• electrophillic attack
• radical attack
(𝑓 + (𝑟))
(𝑓 − (𝑟))
(𝑓 0 (𝑟))
• It is a property used during the 1-scf calculations
• The larger the 𝑓 + (𝑟) = the higher the reactivity 𝑅𝑓+
19. Sablon et al. 2009. Journal of Chemical Theory and Computation 5 (5): p. 1245-1253.
20. Bultinck et al. 2007. The Journal of Chemical Physics 127 (3): p. 034102.
21. Fukui et al. 1970. Springer Berlin Heidelberg. p. 1-85.
22
𝑟
DFT* REACTIVITY MODELLING:
ACTIVE SITES
3x3 edge C
+
f (r) Hirshfield
C1
C2
C6
C7
C13
C14
C17
C18
C19
C23
C27
C28
C29
C30
0.034 0.031 0.031 0.026 0.028 0.028 0.026 0.028 0.028 0.026 0.026 0.031 0.034 0.031
4x4 edge C
C1
f + (r) Hirshfield
4x4 edge C
0.023 0.019 0.019 0.015 0.015 0.018 0.019 0.015 0.015 0.019 0.018 0.016 0.016 0.016
C45
C46
C47
C48
f + (r) Hirshfield
0.016 0.021 0.024 0.021
5x5 edge C
C1
+
C2
C2
C6
C6
C7
C7
C14
C14
C15
C15
f (r) Hirshfield
5x5 edge C
0.02
C54
f + (r) Hirshfield
0.012 0.012 0.013 0.012 0.013 0.017
C16
C21
C21
C22
C22
C25
C28
C26
C29
C33
C31
C34
C40
C35
C43
C49
0.017 0.017 0.013 0.012 0.012 0.015 0.015 0.013 0.012 0.012 0.015 0.015 0.012
C55
C62
C65
C66
C68
C69
C70
0.02
0.017
The results showed that:
1. Each edge C had a 𝑅𝑓+ 𝑟 value.
2. Their 𝑅𝑓+ 𝑟 occupied different levels, e.g.,
edge C at the tip (Ct) > zigzag edge next to Ct (Cz) > armchair
edge Cs (Cr) > zigzag edge intermediate between Cz and Cr (Czi).
23
DFT* REACTIVITY MODELLING:
ACTIVE SITES
Czi
Cz
Cr2
Cz
Ct
𝑅𝑓+
Cr1
3x3
𝑟
4x4
Ct
: Ct > Cz > Cr1 and Cr2 > Czi
This mixture of 𝑅𝑓+ 𝑟 values Cz
at the edge carbon sites of char C
t
models possibly represented
preferred (or less stable) and
less preferred sites (or more
stable) active sites
24
Czi
Czi Cr1 Cr2
Czi
Czi
Czi Cr1
Cr2
5x5
DFT* REACTIVITY MODELLING:
ACTIVE SITES
Since all edge were active sites, the 𝑅𝑓+
𝑅𝑒𝑎𝑐𝑡𝑖𝑣𝑖𝑡𝑦 𝑅𝑓+
𝑟
𝑟𝑎𝑡𝑖𝑜 =
𝑟
was expressed as:
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑎𝑐𝑡𝑖𝑣𝑒 𝑠𝑖𝑡𝑒𝑠
… (1)
𝑇𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑐𝑎𝑟𝑏𝑜𝑛𝑠 𝑖𝑛 𝑡ℎ𝑒 𝑏𝑎𝑠𝑎𝑙 𝑝𝑙𝑎𝑛𝑒
𝑹 𝒇+
𝒓
ratio vs size of char molecules
1.0
Reactivity ratio (f+)
0.9
0.8
0.7
0.6
0.5
0.4
0.3
3x3
4x4
Size of char model
In summary, the:
25
5x5
REACTIVITY-ATOMIC STRUCTURE
RELATIONSHIP
Inertinite chars
Vitrinite chars
Inertinite chars
Vitrinite chars
Fig.2 Size distribution of char molecules
Fig.3 TGA reactivity of chars (RPM)
1. The 𝑅𝑓+ 𝑟 ratio decreases with increasing size of char molecules.
2. Structural results showed that the two chars were similar except that
inertinite char had high distribution of large molecules than vitrinite chars
(Fig. 2).
3. Reactivity experiments showed that inertinite chars recorded lower
reactivity than vitrinite chars (Fig. 3).
4. Hence an important contribution to understand the structural-reactivity
relationship of coal chars derived from inertinite- and vitrinite-rich coals
26
DFT REACTIVITY WITH CO2
• DFT: Fundamental CO2-char reaction mechanism22,23
• Active sites (C*) exposed by C-H breakdown.
1. Adsorption of CO2.
2. Dissociation of CO2 gas molecule.
3. Desorption of CO as a dissociation product, leaving Ocomplex.
4. Disintegration reaction where 6C……5C
6. Desorption of CO as a gasification product.
7. End of simplified gasification reaction, where,
8.
………………………….(2)
.
22. Frederick et al. 1993. Ind. & Eng. Chemistry Research, 32, 1747-1753.
23. Moulijn, et al. 2010. Carbon, 33, 1155-1165.
27
CALCULATED ENRGIES NEEDED
FOR THE C-H BOND BREAKDOWN
Energy required
Active site
Average
(kcal/mol)
Ct
Cz
Cr1
Cr2
C-H bond breakdown 124.97 125.02 124.88 124.91 124.94
Cz
Czi
Cr1 Cr2
Ct
The active sites with highest and 2nd highest 𝑅𝑓+ 𝑟 were chosen to
form a Ct-Cz (C-C) edge to model the fundamental reaction mechanism
28
DFT GEOM_OPT REACTION
CONFIGURATIONS ON Ct - Cz EDGE
O1 C1 O2
C2
CO2 approaching
CO2 adsorption
CO2 dissociation
to form CO and O
Disintegration of
C-ring to form
29
REACTION MECHANISM ON Ct - Cz
EDGE
RESULTS OF GEOM.OPT* CONFIGURATIONS
Ct - Cz edge active site
Reaction
configurations (target Ct)
1
2
3
4
5
CO2 adsorption on Ct
CO2 dissociation
CO formation 1
Decomposition
CO formation 2
Barrier
(kcal/mol)
1.85
Bond length (nm) (stability)
C1-O1 C1-O2 Ct-O2 Ct-C2 Ct-Cz Ct-Cnew
0.385 0.390 0.386
0.393 0.394 0.391
lost broken 0.407
lost broken 0.400
lost broken lost
1.62
2.30
0.419 0.411
0.420 0.414
0.438 0.440
decomposed 0.434
decomposed broken
These bond lengths results showed that reaction mechanism of
CO2 with char model proceeded favorably, from adsorption to
the 2nd formation of CO
30
SIMPLIFIED ENTHALPY CHANGES
FOR THE REACTION MECANISM
160.0
Config.4
140.0
Config.3
Enthalpy change (kJ/mol
120.0
Ct
100.0
80.0
Cz
60.0
Cr1
40.0
20.0
Config.1
Config.2
0.0
-20.0
-40.0
CO2 at a distance
(Start)
CO2…..adsorbs
CO…..formation 1
CO…..formation 2
N.B. Configuration 4 can represent gasification process since
the char lattice carbon is allocated to the O-complex to
form gaseous CO molecule.
31
CONCLUSIONS
• Molecular structures of coal chars derived from inertiniteand vitrinite-rich South African coals were constructed on the
basis of experimental data.
• These structures provided possibilities to explore atomic
structure-reactivity relationships.
• DFT calculations contributed to the rational behind variations
in reactivity of coal chars on mineral matter free basis, using
the Fukui function property.
• The carbon ring disintegration from 6 to 5 carbons and the
allocation of lattice carbon to form the 2nd CO gas molecule
can essentially be called a gasification process.
32
ACKNOWLEDGEMENTS
• Colleagues
• SANERI
• DST
• Universities (Wits, UCT, SU, PSU, RU, UKZN, LaTrobe,
Nottingham)
• National CHPC and NWU HPC
• Coal mining industry
33
THANK YOU
34
CALCULATIONS ON UNCAPPED
CHAR MODEL
Here it was found that both
the dissociative CO2
adsorption and re-adsorption
of CO just formed were
possible, e.g.,
C28-O32 = 0.3634 more stable than
C31-O32 = 0.3654, and
C27-O33 = 0.3659 more stable than
C31-O27 = 0.3999
Therefore O-complex on C28 and
CO could form, but the CO could
adsorb onto C27
35
LARGE SCALE MODELS IN 3D:
CPK* DISPLAYED STYLE
INERTINITE CHAR MODEL
Ave. values (Å)
d002
= 3.4
Lc
= 15.0
La
= 35.0
Nave (-) = 4
C = green, H = white, O = red, N = blue
S = yellow
* CPK = space-filling model
36
LARGE SCALE MODELS IN 3D*: d002,
Nave (-) and Lc MEASUREMENTS
INERTINITE CHAR MODEL
Default view
* Ball and stick
37
LARGE SCALE MODELS IN 3D*: d002,
Nave (-) and Lc MEASUREMENTS
VITRINITE CHAR MODEL
* Ball and stick
38
Enthaly change (kJ/mol)
SIMPLIFIED ENTHALPY CHANGES
FOR THE REACTION MECANISM
140
120
100
80
60
40
20
0
-20
-40
Config. 1: CO2 is introduced to 3x3 char model (start)
Config. 2: CO2 chemi-adsorbs on Ct active site
Config. 3:
1st
Config.6
Config.4
Hidden intermediate
Config. 4: 1st CO formation (dissociation)
Config.5
Config. 5: 2nd Hidden intermediate
Config. 6: : 2nd CO formation
Config.1
Config.2
Config.3
N.B. Configuration 4 can represent gasification process since
the char lattice carbon is allocated to the O-complex to
form gaseous CO molecule.
39
RESEARCH OBJECTIVES &
QUESTIONS
Objective
• To present the atomic structures of chars derived from
different types of coals and their impact on reactivity with CO2
gas.
Research questions
• What is the effect of the nature and origin of chars on
reactivity?
• How well do predictions from structural chemistry and
molecular representations of chars compare with direct
reactivity measurements?
40
COAL SOURCES IDENTIFIED
Map 2
Map 1
Waterberg coalfield
Witbank coalfield
Map 1. from http://www.mml.co.za/docs/FET_CAPS/Platinum-grade-12-activity.pdf on 28/09/2013 at 16:25
Map 2. from Pinetown et al. 2007. International Journal of Coal Geology. 70(1-3) p. 166-183.
41