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The Molecular Level Modelling of Coal and Its Processing

Principal AuthorEdit

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.)

PrefaceEdit

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 [1]. 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.

IntroductionEdit

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 techniquesEdit

  • 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 [2] [3] [4]. An initial example based on Shin [5] 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 requiredEdit

  • 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 [6].
  • Development of techniques also applicable to combinatorial chemistry [7] [8].
  • Developing models which link the scales of molecular simulation, through meso-scale simulation to fluid dynamics.

Institutions Engaged in Research in this AreaEdit

  • World Coal Institute [[1]]
  • Central Mining Research Institute (India) [[2]]
  • Laboratoire de Genie Chimique et de Genie Carbochimique, Universite Liege, Belgium, [[3]]
  • Chalmers University of Technology, Gothenburg [[4]]
  • The Instituto Nacional del Carbon (INCAR), located in Oviedo, Spain, [[5]]
  • The Institute of Geological Sciences at the University of Wroclaw , Poland, [[6]]
  • Max Planck Institute of Coal Research at Mulheim, [[7]]
  • The Hatcher research group in Ohio, [[8]].

Energy SurfacesEdit

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 [[9]]. Their methodology of choice was ab initio density functional calculations using a plane wave basis and the Vienna program (VASP) [9], [10], [11], [12], followed by Monte Carlo simulations using the Merck force field [13], [14], 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 LigniteEdit

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 CoalEdit

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 [15] 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.

ReferencesEdit

  1. G. Monbiot (2006). "{{{title}}}". Heat, How to Stop the Planet Burning, Allen Lane, Peguin Books.
  2. L. M. Stock (1989). "Coal Pyrolysis". Acc. Chem. Res. 22, 427..
  3. Faulon, J.-L., Carlson, G. A. and Hatcher, P. G. (1992). "A structural model for lignin-derived vitrinite from high-volatile bituminous coal (coalified wood)".  Energy & Fuels 6 813-820.
  4. Faulon, J.-L., Carlson, G. A. and Hatcher, P. G. (1994). "Statistical models for bituminous coal: A three-dimensional evaluation of structural, and physical properties based on computer-generated structures".  Energy & Fuels 7 1062-1072.
  5. J. H. Shinn (1984). "{{{title}}}". Fuel 63, 1187..
  6. C. J. Cramer (2004). "{{{title}}}". Essentials of Computational Chemstry,Second Edition, Chapter 13,, Wiley, Chichester.
  7. J. Eichler and R. A. Houghten (1995). "{{{title}}}". Molecular Medicine Today 1, 174.
  8. X. D. Xiang, X. D. Sun, G. Briceno, Y. L. Lou, K. A. Wang, H. Y. Chang, W. G. Wallace-Freedman, S. W. Chen, and P. G. Schultz (1995). "{{{title}}}". Science 268, 5218.
  9. Kresse, G. and J. Hafner (1993). "Abinitio Molecular-Dynamics for Liquid-Metals". Physical Review B, 47 558-561.
  10. Kresse, G. and J. Hafner (1994). "Ab-Initio Molecular-Dynamics Simulation of the Liquid-Metal Amorphous-Semiconductor Transition in Germanium". Physical Review B, 49 14251-14269.
  11. Kresse, G. and J. Furthmuller (1996). "Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set". Physical Review B, 54 11169-11186.
  12. Kresse, G. and J. Furthmuller (1996). "Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set". Computational Materials Science, 6 15-50.
  13. Halgren, T.A. (1996). "Merck molecular force field .1. Basis, form, scope, parameterization, and performance of MMFF94". Journal of Computational Chemistry, 17 490-519.
  14. Halgren, T.A. (1996). "Merck molecular force field .2. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions". Journal of Computational Chemistry, 17 520-552.
  15. P. L. Walker (1981). "Microporosity in Coal: Its Characterization and its Implications for Coal Utilization". Phil. Trans. R. Soc. A, 300 pp. 65-81.

AppendixEdit

Some coordinatesEdit

A small fragment of coal model according to Shin [1] 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 MechanicsEdit

(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


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