Computer-Aided Construction of Coal Molecular Structure Using

VOLUME 11, NUMBER 5

SEPTEMBER/OCTOBER 1997

© Copyright 1997 American Chemical Society

Articles Computer-Aided Construction of Coal Molecular Structure Using Construction Knowledge and Partial Structure Evaluation Takenao Ohkawa,* Takashi Sasai, and Norihisa Komoda Department of Information Systems Engineering, Faculty of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565, Japan

Satoru Murata and Masakatsu Nomura Department of Applied Chemistry, Faculty of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565, Japan Received August 1, 1996. Revised Manuscript Received July 15, 1997X

A computer-aided construction of molecular structure model for coal organic materials is proposed in this paper. In this method, the chemical fragments of coal organic materials are obtained by using the structural data of typical Japanese bituminous Akabira coal. First, some partial structures are selected from candidates of the structure, which are constructed by connecting input fragments based on construction knowledge from basic chemical experiments and practical experiments. Next, the partial structures are narrowed down to an appropriate one in terms of three-dimensional conformation by using partial structure evaluation. We found that this method can derive molecular structures more scientifically and in more time-saving way than the handmade structures.

1. Introduction Construction of a model of the molecular structure of coal is one of the most important tasks in understanding the relationships between coal structure and reactivity. However, obtaining geometrical information about coal from crystallographic data with X-ray analysis is difficult because coal is believed to be heterogeneous. Therefore, new methodologies for molecular construction are relevant to computer-aided molecular design because they can determine the connectivity among molecular species in the target molecule and they can fulfill the need for a reasonable three-dimensional conforma* Corresponding author. Tel: +81-6-879-7826. Fax: +81-6-8797827. E-mail: [email protected]. X Abstract published in Advance ACS Abstracts, September 1, 1997.

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tion. The molecular structure of coal is constructed by connecting fragments that come from chemical analytical results so as to adjust the H/C ratio and the other structural parameters of the resulting model to those of the original coal. Coal chemists usually connect the fragments by hand with a three-dimensional molecular model by using basic knowledge about the chemical bondings between fragments. This is because there are many uncertainties about these chemical bondings. Since this work is a kind of art (not science) and is extremely time consuming, computational approaches would be very useful. Recently, Faulon developed an efficient program called SIGNATURE in order to enumerate all the constitutional isomers of large molecules, which can © 1997 American Chemical Society

938 Energy & Fuels, Vol. 11, No. 5, 1997

retain nonredundancy and exhaustivity, based on graph theory.1 The method can generate a lot of structures by combining input atoms or fragments, and it randomly gives a sample of the molecular structures that statistically represents all the possible structures by using a stochastic approach.2 Faulon et al. applied this method in order to elucidate coal structure.3 However, this method may generate impractical structures because it has no mechanism to choose preferred structures. In addition, an add-in program for calculating the potential energy of all of the sampled structures should be attached in order to narrow the generated structures down to plausible ones from the perspective of threedimensional conformation. The method has been improved by introducing stochastic searches of constitutional spaces with a simulated annealing technique.4 As a result, this method can find optimal structures, i.e., the most stable structure from a conformational perspective, by using the potential energy as a cost function during simulated annealing. However, since cost estimation for entire structures is required in each step of the annealing process, it takes too much time to construct a macromolecule such as coal. This paper proposes a new method for the construction of a coal molecular model by using construction knowledge and partial structure evaluation. Here, a molecular structure is constructed in an analogous way that experts use construction knowledge from the empirical knowledge of experts.5 In addition, we will introduce a process for the evaluation of tentative structures by using molecular mechanics to remove inappropriate structures in terms of their geometric aspects. This process will be applied to a small part of a structure in a limited scope, the size of which was defined in advance, to reduce computational time. 2. Computer-Aided Construction of a Coal Molecular Structure Model The steps involved in the molecular structure construction of a coal model are as follows: 1. Chemical Analysis of a Sample. A coal sample is analyzed by various chemical methods such as the elemental analysis, information about the distribution of aromatic compounds that make up coal organic matter,6-8 quantitative analysis of OH groups,9 and quantitative analysis of alkyl groups with an organic synthetic method10 among others. 2. Estimation of Fragments in a Sample. Using the results of the above chemical analyses, a set of the aromatic fragments that make up a coal molecule is (1) Faulon, J. L. J. Chem. Inf. Comput. Sci. 1992, 32, 338-348. (2) Faulon, J. L. J. Chem. Inf. Comput. Sci. 1994, 34, 5, 1204-1218. (3) Faulon, J. L.; Hatcher, P. G.; Carlson, G. A.; Wenzel, K. A. Fuel Process. Technol. 1993, 34, 277-293. (4) Faulon, J. L. J. Chem. Inf. Comput. Sci. 1996, 36, 731-740. (5) Sasai, T.; Nagatomo, K.; Ohkawa, T.; Komoda, N. Proc. High Performance Comput. ASIA’95 1995, CD-ROM. (6) Nomura, M.; Ida, T.; Miyake, M.; Kikukawa, T.; Shimono, T. Chem. Lett. 1989, 645-648. (7) Matsubayashi, K.; Nomura, M.; Miyake, M. Chem. Lett. 1990, 291. (8) Nomura, M.; Matsubayashi, K.; Miyake, M. Chem. Lett. 1990, 1563. (9) Blom, L.; Edelhausen, K.; van Krevelen, D. W. Fuel 1957, 36, 135. (10) Murata, S.; Uesaka, K.; Inoue, H.; Nomura, M. Energy Fuels 1994, 8, 1379-1383.

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Figure 1. An example of aromatic compounds in a set of fragments.

Figure 2. Constructing process using heuristics.

estimated. An example of part of the aromatic fragments is shown in Figure 1.11 3. Constructing Molecular Structures. As for the analyses about the molecular structure of coal, a combination of the pyrolysis method and solid 13C NMR measurement is considered to be best. However, these methods still cannot give the exact information about chemical bondings among aromatic fragments. Recently, the RuO4 oxidation of coal organic materials has given coal chemists information about the connecting bonds of aromatic fragments: according to this information, biphenyl type bonding and methylene bridge should be taken into consideration along with the contributions of ether bonds like -O- and -OCH2-. Once a set of aromatic fragments has been obtained, connecting the aromatic fragments with above bridge bonds can lead to a plausible structure. This is done by referring to the exact information about bridge bonds based on repetitive trial-and-error tasks. As for an aliphatic structure, we have to select and estimate appropriate portions by referring to the pyrolytic analyses and solid 13C NMR data in order to get correct H/C ratio that is near the value of the original coal. 4. Simulation of Constructed Molecular Structures. The obtained molecular structure is examined by molecular simulation software where the values for physical properties, such as density of the molecule and its potential energy can be estimated. 5. Evaluating Inferred Molecular Structures. The results of the structural simulation are compared with the chemically analyzed data for sample coal. The (11) Nomura, M.; Matsubayashi, K.; Ida, T.; Murata, S. Fuel Process. Technol. 1992, 31, 169-179.

Coal Molecular Structure Construction

molecular structure that satisfies various chemical parameters is determined to be the molecular structure of the sample coal. The most difficult part in this process is the construction of a molecular structure by connecting fragments. Coal chemists have to achieve this time-consuming task by hand and by referring to experienced knowledge: obtaining exact information about how fragments are connected is still difficult or impossible. Our method is designed to solve this problem by modeling heuristics as construction knowledge and by evaluating structure candidates from a physical perspective. 3. Molecular Structure Construction Using Construction Knowledge The input data in our method consists of a set of molecular fragments of aromatic compounds such as benzene, naphthalene, and fluorene, and a set of interfragments such as -O-, -OH, and -CH2-. A molecular structure of coal organic matter can be constructed by connecting all of the fragments with interfragments. In our method, a graph structure, which has been used in many previous methods, was introduced in order to express molecular structures. A node is defined as an aromatic compound and an edge is defined as interfragments. A graph that consists of some nodes and edges expresses a molecular structure and is called a molecular graph. 1. Basic Construction Process. A molecular structure is constructed by combining inferred fragments one by one, thereby imitating the coal chemists’ empirical approach. This operation, the “basic construction process”, is as follows: 1. Select an edge that should be added to the molecular graph from an input edge list. 2. Select a node that should be connected with the selected edge from a molecular graph that is being constructed. 3. Select a node that should be added to the molecular graph from an input node list. If the input node list is empty, select a node that should be connected with the selected edge and a node from the molecular graph that is under construction. 4. Select connection points in the two selected nodes. 5. Connect the two selected nodes at the selected connection points with the selected edge. In this procedure, an input node list is defined as a list of aromatic compounds that have not been used in molecular construction. An input edge list is defined as a list of interfragments that have not been used in molecular construction. This process is repeated until both the input node and the input edge lists are empty. As a result, a final molecular graph, which shows a constructed molecular structure, can be obtained. This procedure can only construct one structure at a time. There is no guarantee that the same structure as was previously found will not occur, because this procedure has no mechanism that can check for redundancies. 2. Construction Knowledge. Repeating the basic construction process leads to a molecular structure. However, this process lacks in information about how the node and the edge are selected. Obtaining this information from chemical analytical results is very difficult or impossible.

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Figure 3. Connection probability for benzene.

Coal chemists have experiential knowledge that was obtained through constructing molecular structures by hand. Certain coal chemists have proposed molecular structure models of coal based on their researches.11-19 Therefore, using coal chemists’ knowledge is valuable in regard to applying the basic construction process. Here, a knowledge base, wherein the three types of construction knowledge that correspond to phases 2, 3, and 4 in the basic construction process are formalized, is introduced in order to imitate the coal chemists’ construction method. Use of this knowledge is shown in Figure 2. The method can emulate the empirical methods of various coal chemists by modifying or changing the contents of the knowledge base. Examples of each type of knowledge are given in the following: 1. Knowledge about Selecting a Node from a Molecular Graph. We obtained empirical knowledge that was used to select a fragment from the coal structure that was being constructed. This is summarized as follows: ‚ A large fragment is difficult to connect to other fragments. ‚ A newly added fragment should be connected with a fragment in less crowded areas of the molecular graph that is being constructed. The above cannot be obtained only through experimental analyses of coal even if very sophisticated analytical techniques are used. However, by using the empirical experience of coal chemists in regard to the calculation of the density of coal organic materials, the guidelines above were used to obtain more realistic coal density values: packing coal molecules as closely as possible is very important in order to accomplish reliable coal density values at least as far as bituminous coal is concerned. Therefore, the above two guidelines can be employed as empirical knowledge. The size of a fragment can be estimated by using its molecular weight. Similarly, the crowdedness of an area in a structure can be evaluated by using the sum of the weight of a node (a center node) and its neighboring nodes in the area. Therefore, we have formalized the following: 1. Calculate the value of the sum as defined as the following formula for each node (a selectable node) in a molecular graph: (12) Given, P. H. Fuel 1960, 39, 147. (13) Wiser, W. H. NATO ASI Ser. C 1984, 124, 325. (14) Solomon, P. R. New Approaches in Coal Chemistry. ACS Symp. Ser. 1981, 169, 61. (15) Shinn, J. H. Fuel 1984, 63, 1187. (16) Huttinger, K. J.; Michenfelder, A. W. Fuel 1987, 66, 1164. (17) Hatcher, P. G.; Faulon, J. L.; Wenzel, K. A.; Cody, G. D. Energy Fuels 1992, 6, 813. (18) Stock, L. M.; Muntean, J. V. Energy Fuels 1993, 7, 704. (19) Nakamura, K.; Takanohasi, T.; Iino, M.; Kumagai, H.; Sato, M.; Yokoyama, S.; Sanada, Y. Energy Fuels 1995, 9, 1003-1010.


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sum ) (weight of a selectable node) × 2 + (sum of the weight of its neighboring nodes) 2. Rank the selectable nodes in ascendant order of the sum value. In the definition of sum, the weight of a selectable node is overestimated in comparison with its neighboring nodes because a large fragment is difficult to connect to other fragments. 2. Knowledge about Selecting a Node from an Input Node List. Empirical knowledge about selecting a node that is added to a molecular graph can be summarized as follows. ‚ The density of a coal molecular structure is uniform. This can also be obtained through the construction of a coal molecule as based on density calculation experiments where the mixing of coal structures such as densely arranged and roughly arranged parts leads to a lower density value. At present, any calculation of the density of a bituminous coal model failed to give a realistic density value, as the calculated values were always low.20-22 The above guideline, therefore, is a reasonable one. The above guideline suggests that a node whose weight is small should be selected if the weight of the selected node in the molecular graph is large. In other words, a node that is selected from an input node list depends on the weight of the selected node in the molecular graph. After adding the node in the input node list to the molecular graph, its neighboring area should be uniform. Therefore, the desirable weight of a selected node can be calculated by the following formula: 1. Calculate the desirable weight value:

desirable weight ) (average weight of all fragments) × {(the number of the selected node’s neighboring nodes) + 2} (total weight of the selected and neighboring nodes) 2. Rank the nodes in the input node list in ascending order according to the differences between the weight of the node and the desirable weight. 3. Knowledge about Selecting Connection Points. Empirical knowledge about selecting the connection points in selected nodes, which is obtained from chemists, is shown as follows: ‚ There are some useful points in the connectable points in the fragments. Aromatic compounds such as benzene have some points that are easy to connect in bonded conditions. The suitability of the connection in the points in the fragments can be defined as connection probability. Connection probability is according to bonded conditions. For example, the connection probability for benzene is shown in Figure 3. This idea has been formalized as follows: 1. Provide the connection probability at connectable points in the various bonded conditions. (20) Nakamura, K.; Murata, S.; Nomura, M. Energy Fuels 1993, 7, 347-350. (21) Murata, S.; Nomura, M.; Nakamura, K.; Kumagai, H.; Sanada, Y. Energy Fuels 1993, 7, 469-472. (22) Dong, T.; Murata, S.; Miura, M.; Nomura, M.; Nakamura, K. Energy Fuels 1993, 7, 1123-1127.

Figure 4. Structure construction using construction knowledge and structure evaluation.

2. Rank the connectable points in fragments randomly according to the connection probability. Connection probability was calculated according to the principles about directing effect of substituents based on experimental results. Of course, at the present time, it is still uncertain through what sort of mechanism coalification proceeded. However, as for the substitution on aromatic rings following two mechanisms, electrophilic substitution and radical-induced substitution are believed to proceed in a similar way:23 in coal organic materials, the substituents such as alkyl groups and oxygen-containing groups (OH and OR) which are prevailing show electron-donating behavior. The connection probability shown in Figure 3 can be explained as follows if we assume the coalification follows the above-mentioned mechanism: as for compound 2, ortho and para are activated. If we express connection probability to one place of decimals, ortho, para should be 0.4, 0.4 and meta being 0.2. In compound 3, four positions are equivalent in the above sense, and therefore, each position has 0.25 as connection probability. In compound 4, similarly, since ortho and para should have higher probability than meta, 0.3 is given at each of three positions corresponding to ortho and para. In compound 5, all the positions are equivalent as in compound 3, so that each has 0.5. As for the ortho position, there is ortho effect; however, Hatcher et al. used the relatively crowded structures in the arrangement of OH or OMe groups side by side on benzene rings as an analogy to lignin structures.17 Therefore, in this study and in this consideration we neglected the ortho effect. 4. Partial Structure Evaluation 1. Overview. In the knowledge-based approach to the structure construction as mentioned above, the number of final constructed structures depends on how many candidates of the ranked selectable nodes in the molecular graph we use, how many candidates of the ranked nodes in the input node list we select, and how (23) Stock, L. M. Aromatic Substitution Reactions; Prentice Hall, Inc.: Englewood Cliffs, NJ, 1968; pp 40-58.



Figure 5. An example of scope.

many candidates of the ranked connectable points we use in each cycle of the basic construction process. If we select one candidate at every stage in all of the cycles, only one molecular structure can be constructed. However, a structure that is constructed using construction knowledge is not always appropriate because this knowledge is neither absolute nor perfect enough to discuss the superiority between the structures that have no fatal defects. In addition, it allows physically unstable structures. To alleviate this problem, we introduce the process of evaluating tentative structures by using molecular simulation. Several structures that were constructed and selected according to the above knowledge are evaluated in terms of their three-dimensional conformations in each cycle of the basic construction process. Figure 4 shows one cycle of the basic construction process with construction knowledge and structure evaluation. In this example, the knowledge constructs four candidates and one of them was selected by structure evaluation. Similar operation is applied to the selected structure in the next cycle and the process is iterated until a final structure is derived. In the structure evaluation process, steric energy is calculated by using molecular mechanics simulation which is based on a MM2 force field.24 The structure with the lowest energy is regarded as the most appropriate structure. 2. Scope. Although molecular mechanics is one of the most efficient techniques for searching for conformational space, the calculation for a large molecule is time-consuming. Therefore, determining the superiority between the tentative structures that were constructed during the basic construction process by using molecular mechanics for the entire structure is impractical. Here we will introduce a scope as a way to improve efficiency. The scope intuitively means areas that include fragments connected with newly added fragments and its neighboring fragments within a certain distance. It is formally defined as follows: If V and E are a set of nodes and a set of edges, (V,E) denotes a molecular graph that consists of V and E. Let vn be a new node that has been added to (V,E), en be a new edge that has been added to (V,E), and v be a node in (V,E) connected with vn through en, respectively. We can define a size k scope of v as (V′,E′), a subgraph of (V ∪ {vn},E ∪ {en}), where V′ consists of nodes within a given distance (the minimum number of edges between (24) Allinger, N. L. J. Am. Chem. Soc. 1993, 99, 8127-8134.

Figure 6. Overview of structure construction. Table 1. Evaluation of Scope Size 1st 2nd 3rd 4th 5th

Ss ) ∞

Ss ) 2

Ss ) 1

20 (100%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)

16 (80%) 4 (20%) 0 (0%) 0 (0%) 0 (0%)

15 (75%) 3 (15%) 2 (10%) 0 (0%) 0 (0%)

nodes) of k from node v and E′ consists of edges that are connected between nodes in V′. For example, Figure 5 illustrates a size one scope of node v6 when adding node v7. The scope is helpful in order to exclude physical inconsistencies that occur around a connection between a partial molecular structure and a newly added fragment. Figure 6 shows a rough structure construction procedure that introduces partial structure evaluation using the scope. 3. Discussion on the Size of the Scope. The size of scope Ss should be determined carefully. If Ss is too small, the evaluation itself may be of less significance. Needless to say, the most useful scope in regard to conformation is a whole molecular graph. If Ss is too large, however, the computational value may decrease.


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Figure 7. Average values of steric energy.

Figure 9. An example of constructed structure of coal (steric energy -247.3398 kcal/mol).

Figure 8. Input fragments and interfragments.

The preferable scope is the smallest one in which the evaluation results are almost equivalent to those in a whole molecular graph. We discovered an appropriate Ss through the following experiment. Molecular graphs with about 10 aromatic compound fragments were prepared. By applying one step of the basic construction process to each of them, candidates for the molecular graphs in the next step were constructed and ranked according to the knowledge. We selected the best five structures for each and evaluated them in three ways: (1) for a scope of Ss ) 1, (2) for a scope of Ss ) 2, and (3) for a whole structure (Ss ) ∞). The results for a whole structure are an absolutely correct evaluation. We did research about how well the structure that we evaluated as the best one in our evaluation that used a scope by referring to the results in a whole structure. Table 1 summarizes the results for 20 molecular graphs. We can see that structure evaluation with a scope is quite similar to structure evaluation without scope by

Figure 10. Distribution of steric energy of constructed structures. Table 2. Steric Energy of Constructed Structures steric energy (kcal/mol) method with construction knowledge only with construction knowledge and partial structure evaluation chemists’ empirical method

av value

min value

-127.3 -181.0

-163.8 -247.3 -130.7

looking at the results. In addition, the scope of Ss ) 1 and the scope of Ss ) 2 are not particularly different. As a result, a scope of Ss ) 1 is sufficient to evaluate structures, taking into account the trade-off in computational cost. 4. Discussion on the Breadth of a Search. First, in the above-mentioned structure construction, a few structures are selectively constructed by using construction knowledge and then one structure is extracted by using the structure evaluation. The number of struc-



Figure 11. Snapshot of the molecular construction system.

tures that are left in the first step, in other words, the breadth of a search, influences the second step and the quality of the final structure as well. For example, if only one structure is constructed in the first step, the structure evaluation has no influence. Therefore, an appropriate breadth of search must be found in order to obtain high-quality structures. We performed an experiment in order to discover an appropriate breadth of a search. The smallest value of the steric energy in the partial structure evaluation step was calculated by varying the breadth of a search (Bs). The target molecule structures consisted of nine fragments and eight interfragments which corresponded to about one-third scale of a complete coal structure. We prepared 10 targets. Figure 7 illustrates the average value of the steric energy in a size one scope for various breadth of searches in all of the cycles of the basic construction process. Very large values of energy were calculated at Bs ) 3 or less, which suggests that construction knowledge does not evaluate molecular conformation at all. Since the value of energy is saturated at Bs ) 5 in this experiment, a value of Bs g 5 at least is required. 5. Experimental Results In order to examine the effectiveness of the proposed method, we constructed some structures of an actual coal sample. Figure 8 shows a set of fragments and interfragments that were derived for an Akabira coal sample.11 The set consisted of 26 aromatic compounds (21 types), 27 cross-links (two types), and 16 substituents (two types). The total molecular weight of the set is 4412, and by appending a long-chain aliphatic hydrocarbon to it, the final molecular weight was estimated to be about 5000, this being a relatively small coal model. In the experiment, the parameters were set as Ss ) 1 and Bs ) 5, respectively. In our method, a part of the tentative structures was randomly constructed because of the nondeterministic property of the construction

knowledge. As a result, the final structure changed each time. We did 20 structure construction trials and obtained a structure for each. It takes about 3 h to construct a structure. Figure 9 is the best result in regard to steric energy (-247.3 kcal). Table 2 and Figure 10 show an evaluation of structures from the perspective of steric energy. The structures that were constructed by our method are compared with (1) results using the same method as we propose in this paper, except that there was no partial structure evaluation, and (2) a handmade structure reported previously.11 We can see that partial structure evaluation can effectively construct significant structures by selecting potentially useful fragment connections. In addition, it is noteworthy that the structure that we constructed is just the beginning phase of the construction of a practical whole coal molecular structure; however, compared with a structure that was proposed by experts, which took 2 or 3 weeks to construct, this method is more scientific and is quicker. According to the comment of one reviewer of this paper who advised us compare our result with similar work, we constructed tentatively a plausible structure by appending aliphatic long chains and -OMe groups to one of typical (incomplete) structures presented by our method so that each elememt content (C 81.10%, H 6.43%, O 10.92%, N 1.55%) can approximately follow experimental value (C 81.1%, H 5.7%, O 10.4%, N 2.0%) that was obtained by elemental analysis. A constructed tentative structure was compared with Shinn’s structure15 in terms of total steric energy per atom25 of minimized structure using the same MM2 software. The calculated energies of our structure and of Shinn’s structure were 0.183 and 0.319 kcal/mol, respectively, which suggests that our structure is energetically more stable. At present, information about the aromatic portion of coal is available based on the combined data from the pyrolytic technique and solid 13C NMR. However, as for the aliphatic portion, exact information that (25) Carlson, G. A. Energy Fuels 1992, 6, 771-778.


is comparable to that from the aromatic portion is very difficult to obtain: for example, the pyrolytic technique accompanies a secondary reaction, which makes the results vague, and the results for an RuO4 oxidation reaction are not quantitative. Therefore, the coal structures that have been proposed to date all have some kinds of ambiguities. Coal chemists now have more exact information about the aliphatic portion, so that they can apply this information in order to get more reliable coal model structures by using our computeraided construction method in the near future. 6. Conclusions This paper proposed a molecular structure construction system that is based on construction knowledge that coal chemists use to experimentally construct molecules and on partial structure evaluation. Through application to a coal sample, we found that our system

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could generate suitable molecular structures in comparison with an empirical approach that is used by coal chemists. We developed a molecular construction system for coal that is based on above. The system was implemented on a Sun SPARCstation 5 workstation using C++ language and Tcl/Tk. Figure 11 displays a snapshot of the system. It can load and save input data, execute construction, etc. through a user-friendly graphical user interface. As mentioned above, it takes the system about 3 h to construct a structure for a sample whose molecular weight is about 5000, and therefore, greater efficiency is required. We plan to use a database that stores three-dimensional structures that consist of some fragments that have been optimized in advance. An effective method that can retrieve data that is structurally similar to a partial structure in scope is one of the remaining questions that we are going to explore in the very near future. EF960121D

Computer-Aided Construction of Coal Molecular Structure Using

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