The Molecular Level Modelling of Coal and Its Processing

The Molecular Level Modelling of Coal and Its Processing
===Principal Author===
Martin Grayson MartinY 14:24, 5 November 2006 (UTC), (MG has not worked in this area for many years as he
had much discouragement from people who said that coal was an old
and dirty technology and
the best thing to do was find an economically and socially acceptable
way of leaving it in the ground and forgetting about it.
However global warming has dramatically improved the prospects for clean coal processes.
Therefore the
modelling of them, is a topic whose time has now come.)
===Preface===
This timely topic is suitable for a wiki journal review because
clean coal technologies and underground gassification are some
of the more promising possibilities for dealing with global warming
as outlined in the recent comprehensive manifesto for action on global warming, Heat, How to
Stop the Planet Burning by George Monbiot
.
If modelling can contribute to a half percentage improvement in any process it amounts
to a large amount of energy over time.
The initial intention is to produce a living review which will point to
what is going on from a computer modelling point of view and see how
it develops from that. Also it is hoped to set up a project
to produce molecular level models of wood, lignite and coal using
open source modelling software as a project with Wikiversity.
The first author solicits contributions from
anyone interested and would love there to be any ideas worth stealing here
as he is not in a position to put together
a significant computer code at the current time.
===Introduction===
The development of both computer hardware and software has reached
the level where the modelling of substances of great complexity and
variable composition such as wood, lignite and coal can be contemplated.
In the small molecule reaction area quantum chemistry calculations are routine.
Molecular mechanics and dynamics calculations on large biological structures
are also routine.
The variable composition aspects of our target substances here introduce a need for new science
as well as introducing new applications of routine techniques where there is an existing record
of modelling success.
===Routine applications of proven modelling techniques===
 Quantum calculations of energy surfaces of reactions in the pyrolysis / gassification / liquefaction process.
(There is extensive experimental data, some using isotopic substitution studies
available.)
 Production of computer models for education, display, spatial and statistical
analysis
.
An initial example based on Shin
is in the appendix.
 A computerized multimedia version of the above.
 Production of new physical models for education and publicity,
(perhaps using the new technology of 3-dimensional computer output).
 Pressure simulations, thermodynamics and entropy driven processes.
 Comparision of computations with analysis and experiment.
 Thermodynamics based models with hundreds, (thousands), of reactions in them.
===New science required===
 Molecular mechanics for variable composition.
(is it possible by some kind of perturbation or particle insertion treatment?)
 Techniques to simulate ageing by removal of small hydrogen rich molecules.
 Simulating the transport of small molecules through the lattices.
 Mixed molecular mechanics / quantum mechanics for reactions
at the surface of particles
.
 Development of techniques also applicable to combinatorial chemistry
.
 Developing models which link the scales of molecular simulation,
through meso-scale simulation to fluid dynamics.
===Institutions Engaged in Research in this Area===
 World Coal Institute []
 Central Mining Research Institute (India) []
Laboratoire de Genie Chimique et de Genie Carbochimique,
Universite Liege, Belgium,
[]
 Chalmers University of Technology, Gothenburg
[]
The Instituto Nacional del Carbon (INCAR), located in Oviedo, Spain,
[]
 The Institute of Geological Sciences at the University of Wroclaw , Poland,
[]
 Max Planck Institute of Coal Research at Mulheim,
[]
 The Hatcher research group in Ohio,
[].
===Energy Surfaces===
One of the most obvious problems in the small molecule area is the potential
energy surfaces for the reactions involved with the Fischer-Tropsch synthesis,
the principal commercial method used to produce gasoline from coal.
Basically CO (carbon monoxide) and hydrogen from a producer gas / water gas cycle are
polymerised with one of several solid state catalysts
to hydrocarbons.
There is a recent account of progress in this area in a government report by
Neurock and Walthall [].
Their methodology of choice was ab initio density functional
calculations using a plane wave basis and the Vienna program (VASP)
,
,
,
,
followed by Monte Carlo simulations
using the Merck force field
,
,
These simulations have provided some potentially important suggestions about
the chemical species of the principal single carbon intermediate in the synthesis.
===Models of Coal, Wood and Lignite===
One of the intentions of this living review is to report the production
of open source models of coal, wood and lignite to be used for educational
purposes.
The Illinois No. 6 coal discussed by Stock has an elemental formula C100H87.9N1.5S1.3O8.8.
Methoxy groups are abundant in lignin but disappear with coal maturation.
Thus they are still abundant in young lignite but have completely disappeared from bituminous coals. (The schematic structural formula of Stock
has CH3 and -OH groups replacing where -OCH3 might
have been expected in lignin. It is to be noted there is still a large
amount of oxygen in coal. The nitrogen present used to be a useful source of aniline for the chemical dyestuffs industry in the past via a biproduct from the large scale distillation of coal to make town gas.
The sulfur present is mostly now a nuisance impurity causing acid rain
and boiler corrosion and is scrubbed out with calcium carbonate / oxide in clean coal fired power stations. Ammonium sulfate was also a biproduct used as a fertiliser.
The 200 atom fragment of molecule in the appendix has been used to make a preliminary property calculation of the partial charges on it using an electronegativity equalisation algorithm and some averaging:
 Atom type --- Bonded to Partial charge
 Carbon sp2 Carbon sp2 -0.0611
 Carbon sp2 Carbon sp3 -0.0320
 Carbon sp2 N (sp2) 0.0790
 Carbon sp2 Oxygen(-O) 0.1684
 Carbon sp2 Sulfur -0.0019
 Carbon sp3 Carbon sp2 -0.0010
 Carbon sp3 Carbon sp3 -0.0301
 Hydrogen Carbon sp2 0.0611
 Hydrogen Carbon sp3 0.0310
 Hydrogen Oxygen(-O) 0.2596
 Hydrogen Sulfur 0.1260
 N (sp2) Carbon sp2 -0.2801
 Oxygen(-O) Carbon sp2 -0.4617
 Oxygen(-O) Carbon sp3 -0.4044
 Sulfur Carbon sp2 -0.1813
I have not defined exactly how these numbers are computed because it is hoped to soon use a better method
to get them because though they are to some extent arbitary and difficult to define. They are however very useful for creating a visualisation of what is going on at the molecular level.
The current numbers do reflect chemical common sense in that the biggest charge separation is caused by the presence of the oxygen and nitrogen, carbon is largely near neutral except in phenolic environments and hydrogen is slightly positive, much more so in a non-alkane local environment.
(The above table should metamorphose to data containing these charges in the form of 1) the most realistic calculation for the situation in coal rather than small molecules, 2) the list of charges used by the common molecular modelling programs which might be applied to this problem. 2) might differ quite considerably from 1) but it is very important as the Coulomb terms which these generate are the largest and most long range contribution to the energy.)
===Diffusion of Small Molecules Through Coal===
This is especially revelent to the problem of simultaneous sequestration
of carbon dioxide with enhanced recovery of methane from coal
measures.
There is extensive experimental data on the porosity of coal
and some theory relating the porosity to the fractal dimension of the
absorbing surface.
It is also expected that the nuclear industry has produced much data
on the the diffusion of CO2 and He through graphite as part of
the research into the behaviour of graphite moderated reactors.
===References===
===Appendix===
====Some coordinates====
A small fragment of coal model according to Shin
in x,y,z format:
 223 a 200+ atom fragment of illinois coal (Shin)
C -4.765989 4.147264 -0.559943
C -4.195224 2.992378 -1.104201
C -4.939147 2.219473 -1.994670
N -6.177811 2.491014 -2.393377
C -6.712399 3.598250 -1.886415
C -6.064084 4.447921 -0.989815
H -3.173213 2.675433 -0.850082
H -4.415158 1.314332 -2.379595
H -7.747828 3.827808 -2.228016
H -6.588011 5.348805 -0.630357
C -4.042110 5.069734 0.410407
C -3.019483 5.924085 -0.356303
C -1.892069 5.041411 -0.829312
C -1.301055 4.202278 0.125900
C -1.868437 4.350881 1.530199
C -3.416019 4.427408 1.675797
H -4.796704 5.810347 0.767256
H -3.546353 6.445489 -1.186001
H -2.597029 6.725386 0.294992
H -1.416211 5.287117 1.933438
H -1.509143 3.544645 2.195761
H -3.616269 5.130173 2.521965
C 0.167787 3.291568 -1.570549
C -0.450015 4.133517 -2.496604
C -1.463829 5.025045 -2.158521
C -0.244233 3.334027 -0.226750
H -0.112202 4.093159 -3.545304
C -2.040004 5.899537 -3.252433
H -1.272010 6.069975 -4.043486
H -2.269754 6.919538 -2.867777
C -3.277157 5.260907 -3.895597
H -4.104283 5.134782 -3.161789
H -3.666043 5.893152 -4.727130
H -3.038765 4.256123 -4.315039
O 1.156428 2.466984 -2.012128
H 1.278766 2.534850 -2.973527
C -4.019149 3.084136 2.149754
O -4.832779 0.547338 2.677672
C -5.859501 1.475489 2.355049
C -5.512625 2.825025 2.176826
C -6.506909 3.790797 2.048563
C -7.846703 3.415566 2.005342
C -8.205718 2.071231 2.111210
C -7.210485 1.106218 2.297780
H -6.256856 4.858088 1.977147
C -3.421110 0.357382 4.679662
C -2.596005 0.994053 5.610888
C -2.252838 2.336812 5.479713
C -2.701163 3.061223 4.379076
C -3.496344 2.434635 3.420231
C -3.890340 1.097566 3.585709
H -2.224314 0.430738 6.483335
H -1.619362 2.822422 6.241359
H -2.413897 4.120667 4.288514
H -3.665683 2.405028 1.345649
C 0.450507 2.452386 0.817913
C 1.991957 2.340713 0.772984
O 2.486669 1.257563 0.002709
C 1.948610 0.009535 0.395041
C 0.432946 -0.003845 0.171752
C -0.211245 1.080406 1.038696
H 0.327931 3.008496 1.770664
H 2.443982 3.283157 0.379667
H 2.405163 2.208078 1.802849
H 2.435185 -0.775027 -0.234374
H 2.217452 -0.195444 1.459245
H 0.199382 0.171523 -0.904183
H -0.091866 0.781366 2.109252
H 0.018257 -1.004924 0.440325
O -1.595064 1.141045 0.785338
H -1.997096 0.322765 1.030037
O -3.789716 -0.945322 4.837111
H -3.401104 -1.321443 5.644925
C -9.550782 1.695204 2.058336
C -9.927803 0.357574 2.190925
C -8.935083 -0.602430 2.386789
C -7.592999 -0.230241 2.441611
H -10.320786 2.471555 1.914896
H -9.200206 -1.667602 2.500139
H -6.841446 -1.022550 2.594521
H -8.615571 4.197514 1.883639
S -11.622006 -0.158060 2.131834
H -12.157135 1.003762 1.716517
C 9.928848 1.746446 3.755404
C 10.501334 0.430845 4.234823
C 9.757550 -0.749568 4.170951
C 8.357080 -0.716870 3.617303
H 10.377649 2.589288 4.330132
C 7.312730 -1.623399 4.280218
C 6.312499 2.916671 4.264322
C 7.705591 2.954166 4.127684
C 8.433748 1.791144 3.905767
C 7.707605 0.614267 3.849894
C 6.324908 0.561329 4.021912
C 5.559205 1.728943 4.194884
C 5.968260 -0.909185 4.019304
C 11.802226 0.374713 4.735575
C 10.335114 -1.945574 4.597695
H 12.376698 1.314496 4.774064
H 9.718267 -2.851879 4.514172
C 14.231590 -2.016985 6.096337
C 13.689599 -0.803837 5.670608
C 12.377880 -0.821794 5.174955
C 11.637064 -2.010549 5.107348
C 12.198685 -3.224041 5.539491
C 13.504812 -3.201235 6.033157
H 15.260822 -2.041280 6.492631
H 14.001039 -4.117473 6.387393
C 2.111979 3.142473 4.662807
C 1.350027 1.979550 4.533235
C 1.926137 0.738754 4.284386
C 3.314555 0.705188 4.169581
H 0.253092 2.018304 4.608127
H 3.697199 -0.288429 3.929179
C 5.679240 4.136405 4.490482
C 4.301598 4.195818 4.641195
C 3.510598 3.050325 4.542604
C 4.152698 1.816877 4.308455
H 6.256657 5.074895 4.560229
H 3.883761 5.194872 4.823708
H 8.256995 3.907331 4.189013
O 14.421381 0.345760 5.740942
H 15.305432 0.173665 6.106774
C 11.416292 -4.524236 5.476967
H 10.487112 -4.398936 6.082201
H 11.123796 -4.702490 4.414987
C 12.115445 -5.797299 5.975030
H 11.439990 -6.679432 5.879004
H 13.029160 -6.026612 5.379015
H 12.392941 -5.721721 7.051978
H 7.329209 -2.673499 3.902477
H 7.501306 -1.645121 5.381636
H 5.278431 -1.196266 4.846489
H 5.564198 -1.201198 3.020882
O 1.174771 -0.390779 4.144682
H 0.233885 -0.200595 4.298714
C 1.327790 4.428033 4.921265
O 1.781734 5.098283 6.088686
C 0.959565 6.198046 6.439006
C 0.963146 7.234067 5.318648
C 0.446800 6.606591 4.017717
C 1.293453 5.367436 3.702584
H 1.379515 6.641828 7.374295
H 0.495675 7.339894 3.177401
H 0.866131 4.838284 2.820989
O 0.128998 8.314090 5.676448
H 0.559767 8.829654 6.339095
H 0.266732 4.145760 5.127284
H -0.071870 5.835667 6.669874
H 1.995769 7.637039 5.165649
H -0.622698 6.312525 4.142498
H 2.315552 5.691326 3.403887
H 10.187104 1.880285 2.679716
H 8.395153 -0.904006 2.517656
C -6.147148 -7.291948 11.529299
C -6.867446 -8.481896 11.666799
C -6.154408 -9.682121 11.696662
C -4.765097 -9.690080 11.582315
H -6.694910 -6.335460 11.515135
H -6.671452 -10.647068 11.814580
H -4.232381 -10.655985 11.609812
C -4.047461 -6.092783 11.271824
C -4.755412 -7.287732 11.412586
C -4.056527 -8.496187 11.439113
C -2.665212 -8.489746 11.327276
H -4.591987 -5.134899 11.258781
H -2.110031 -9.442502 11.346336
C -0.443591 -7.365454 11.057547
C 0.266886 -6.004552 11.138058
C -2.656868 -6.087133 11.151841
C -1.951987 -7.296250 11.189787
H -0.227002 -7.826815 10.065063
H 0.341604 -5.678197 12.202292
C -8.373837 -8.416440 11.793732
C -9.066154 -7.742004 10.596617
C -10.550518 -8.134139 10.713703
C -10.602476 -9.314460 11.700024
C -9.139415 -9.746529 11.876768
H -8.924048 -6.635536 10.574786
H -11.159146 -7.281351 11.099142
H -11.003217 -8.968815 12.683425
H -8.968288 -10.291953 12.835476
H -8.861136 -10.410494 11.023814
C -1.906219 -4.788168 11.028046
C -0.553402 -4.994736 10.337568
C -0.026848 -3.560796 10.189781
C -1.297883 -2.728877 9.904568
C -2.501976 -3.653847 10.184622
H -1.334002 -1.824652 10.557254
H -3.336260 -3.119893 10.698265
H -2.891198 -4.072073 9.225502
O 0.572861 -3.142127 11.397415
H 0.930574 -2.278739 11.271249
H -0.024170 -8.045244 11.836600
H 1.305776 -6.076227 10.736755
H -8.602594 -7.832150 12.718493
H -8.643258 -8.161930 9.652442
H -10.961244 -8.419525 9.715768
H -11.250405 -10.149250 11.340648
H -1.749178 -4.408944 12.066930
H -0.716423 -5.400627 9.308011
H 0.741136 -3.475281 9.381282
H -1.317192 -2.376099 8.845845
**
====Some Properties by Molecular Mechanics====
(For partial charges see above)
 Total charge on molecule is 0
 Atom-based properties
 ---------------------
 Number of atoms = 203
 Molecule has 774 electrons
 Molecular weight (Natural Abundances) = 1454.867200
 Molecular weight (Commonest Isotope) = 1453.667669
 Total Atomic Energy / 3-21G (aus) = -4443.417203
 Zero point vibrational energy (estimate /KJmol-1) = 2164.044867
 Molecular velocity (298K,25C) 71.478 ms-1 159.610 mph
 Bond Properties
 ---------------
 Atom1 Atom2 Bond E % ionic Bond Moment MM2-types
 kJ character x10**30Cm
 -----------------------------------------------------------
 C C 610.9 0 0.00( ) Carbon sp2 Carbon sp2
 N C 615.0 25 1.26(*) N (sp2) Carbon sp2
 H C 414.2 8 2.97( ) Hydrogen Carbon sp2
 C C 347.3 4 0.25(*) Carbon sp3 Carbon sp2
 C C 347.3 0 0.00( ) Carbon sp3 Carbon sp3
 H C 414.2 4 1.30( ) Hydrogen Carbon sp3
 O C 0.0 45 1.99(*) Oxygen(-O) Carbon sp2
 H O 464.4 61 5.04( ) Hydrogen Oxygen(-O)
 O C 359.8 53 -2.50( ) Oxygen(-O) Carbon sp3
 S C 0.0 7 0.42(*) Sulfur Carbon sp2
 H S 347.3 17 2.30( ) Hydrogen Sulfur
 (*) shows BDIP algorithm used for dipole estimation
 221 bonds
 Binding Energy 23594.03 kcal per mole
 98717.42 kJ per mole
 Average global bond energy 446.6846 kJ per mole, over 221 bonds.
Average bond length 1.298891
 total energy estimate for 3-21G basis -4481.017072 aus
 Molecular Volume is 8675.30 Ao ** 3
 Dipole Cm x 10**30 x y z Total
 3.117851 7.310127 7.869951 11.184591
 In Debyes 0.934709 2.191522 2.359353 3.353057
 In aus 0.367767 0.862267 0.928302 1.319281
 Polarizability parameters / au
 ------------------------------
 Par. Perp.
 -----------------------------------------------------------------
 C C 15.1767 3.5000 ( ) Carbon sp2 Carbon sp2
 N C 17.1641 2.8675 ( ) N (sp2) Carbon sp2
 H C 3.8550 3.8550 ( ) Hydrogen Carbon sp2
 C C 6.1869 2.8130 ( ) Carbon sp3 Carbon sp2
 C C 6.1869 2.8130 ( ) Carbon sp3 Carbon sp3
 H C 3.8550 3.8550 ( ) Hydrogen Carbon sp3
 O C 22.7000 10.0000 ( ) Oxygen(-O) Carbon sp2
 H O 4.2500 4.2500 ( ) Hydrogen Oxygen(-O)
 O C 17.0000 7.0000 ( ) Oxygen(-O) Carbon sp3
 S C 36.5961 18.0715 ( ) Sulfur Carbon sp2
 H S 12.1500 12.1500 ( ) Hydrogen Sulfur
 Polarizability Tensor / SI
 --------------------------
 Units are 10 ^ -41 C2m2J-1
 2224.382435 -0.162712 72.675891
 -0.162712 2203.780855 -5.613877
 72.675891 -5.613877 1666.805573
 Isotropic value 2031.66
 Polarizability per atom 10.008
 Polarizability per heavy atom 18.812
 Polarizability from inert gas alogorithm 1973.921
 Magnetizability parameters / SI
 -------------------------------
 Par. Perp.
 -----------------------------------------------------------------
 C C -16.76 -16.76 Carbon sp2 Carbon sp2
 N C -16.76 -16.76 N (sp2) Carbon sp2
 H C -79.30 -79.30 Hydrogen Carbon sp2
 C C -61.44 -61.44 Carbon sp3 Carbon sp2
 C C -90.01 -16.27 Carbon sp3 Carbon sp3
 H C -76.85 -76.85 Hydrogen Carbon sp3
 O C -99.81 -99.81 Oxygen(-O) Carbon sp2
 H O -120.92 -116.20 Hydrogen Oxygen(-O)
 O C -74.73 -74.73 Oxygen(-O) Carbon sp3
 S C 134.98 -251.92 Sulfur Carbon sp2
 H S -173.52 -173.52 Hydrogen Sulfur
 Magnetizability Tensor / SI
 ---------------------------
 Units are 10^-30 Joule Tesla ^-2
 Full Tensor
 ---------------------
about -12306 77.250159 -31.845249
 77.250159 about -12306 254.193168
 -31.845249 254.193168 about -12306
 Isotropic value -12306.2
 ( In 10^6 cm3 per mol ) -741.09
 ( Magnetizability from Pascal's rules (cgs / SI) ) 
 -916.99 -15227.15
 Magnetizability per atom -60.6215
 Magnetizability per heavy atom -113.9459
Category:Interpretations in the Physical and Computational Sciences submitted article