Molecular asphaltene models based on Clar sextet theory
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1 Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2014 Molecular asphaltene models based on Clar sextet theory Francisco J. Martín-Martínez 1, Elham H. Fini 2 and Markus J. Buehler 1 1 Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, USA. 2 Department of Civil, Architectural and Environmental Engineering, North Carolina A&T State University, 434 McNair Hall, 1601 E. Market St., Greensboro, NC Corresponding author, mbuehler@mit.edu SUPPLEMENTARY INFORMATION Clar s theory of the aromatic sextet Initially developed in 1972, Clar s theory of the aromatic sextet 1,2,3 represents the delocalization of six π-electrons in a single benzene-like ring with a circle inscribed in the hexagon, which denotes a Clar sextet (See Figure s1a). Consequently, two adjacent rings cannot host a circle at the same time, since it would mean 12 π-electrons for just 10 carbon atoms. Furthermore, according to this theory the structure with largest number of π-sextets is the most stable among all possible configurations. Based on these simple statements, Clar s theory of the aromatic sextet predicts the aromaticity distribution of PAHs and explains the stability and many of their chemical properties. 4,5,6,7,8 For instance, in the case of phenanthrene (Figure s1b) the resonance structure with two Clar sextets is more representative than the one with a single inscribed circle, and therefore outer rings have larger local aromaticity than the central one. 9,10,11 On the other hand, anthracene shows three equivalent Clar configurations and therefore the resulting structure is a superposition of the three, with similar aromaticity for the three rings. 9,10,11 As a general idea, a PAH with a given number of aromatic π-sextets is kinetically more stable than its isomers with less aromatic π- sextets. 1,2,3,12 Therefore, the higher the numbers of circles we draw in the structure, the more stable the molecule would be (see isomers in Figure s1d). 13 Further information can be found in a recent review by Solà. 3 This theory has been even proved useful in the study of many novel nanostructures such as carbon nanotubes, 14,15,16,17 graphene nanoribbons, 18,19,20,21 carbon nanocones, 22 and carbon nanotori. 19
2 Figure s1. (a) Clar sextet representation of the delocalization of six π-electrons resulting from the resonance of two Kekulé bond configurations with alternating single and double bonds. (b) Phenanthrene Clar structures with two and one Clar sextets respectively. (c) Anthracene equivalent Clar configurations that result in a final structure superposition of the three. (d) Clar structure of benzo [qr] naphto [2,1,8,7-fghi] pentacene (left) and tribenzo [fg, ij, rst] pentaphene (right).
3 PAH representative of the FAR region of asphaltenes Aiming to reduce the size of the model systems for DFT calculations, we consider smaller PAHs that contain the same FAR region. These PAHs retain the same electronic distribution and geometrical effects in the aromatic system, but with considerably smaller number of atoms. Three different molecular structures for representing A1 are investigated. The planarity of the aromatic structure is studied using the Cremer-Pople pucker amplitude. 23 This method provides a general quantification of the ring deformation by introducing ring-puckering coordinates that can be applied without approximation to any cyclic molecule, given only the coordinates of the nuclear positions of the atoms in the ring. It is also independent on the number and type of atoms and the size of the ring. The coloring is done with the color scale provided by the PaperChain representation in VMD, 24 where Cremer-Pople pucker amplitude is calculated and color-coded, 25,26 using Hill-Reilly method. 27 In this coordinate system the radius Q means the magnitude of puckering, measuring the deviation from the perfectly flat six-membered ring (Q = 0). In this scale, red rings are planar, green rings are highly deformed and the orange-colored ones are partially deformed. This representation allows us to study the deformation in the polyaromatic core of the molecules under study. Figure s2 depicts the fully optimized geometries of these molecules, where the rings are colorcoded following the Cremer-Pople pucker amplitude, as implemented in VMD molecular visualization. The values of Q are shown inside the hexagons. These color-coding allow us to quickly visualize qualitatively the deformation of the rings with respect to planarity. Red rings are those completely planar while green ones are the most deformed and the values closer to zero. The first model is the most simplified one, where hydrogen atoms saturate all terminal carbons in the structure (Figure s2a). In the second model, methane groups saturate those positions where aliphatic chains should be in the complete molecule (Figure s2b). The third model shows the complete structure where all aliphatic chains are included (Figure s2c). Remarkably, pentane effect does not depend on the aliphatic chains, but the strain that undergoes the polycyclic aromatic core remains in the three molecules independently on the edge configuration, as it is clearly noticed by the same colors for the Cremer-Pople pucker amplitude. Obviously, the higher deformation takes place in the cyclohexane ring, which is not aromatic at all, while the polycyclic aromatic system goes from orange (partially deformed) to red (planar).
4 Figure s2. Different models for A1 molecule color-coded with pucker Cremer and Pople amplitude. The values of Q are shown inside the hexagons. (a) Simplified model with hydrogen atoms saturating all carbon atoms. (b) Model with methane groups saturating positions of aliphatic chains. (c) Complete molecular structure.
5 Supplemental references (1) Clar, E. The Aromatic Sextet; Wiley: New York, (2) Randić, M. Chemical Reviews 2003, 103, (3) Solà, M. Frontiers in Chemistry 2013, 1. (4) Biermann, D.; Schmidt, W. Journal of the American Chemical Society 1980, 102, (5) Schleyer, P. v. R.; Manoharan, M.; Jiao, H.; Stahl, F. Organic Letters 2001, 3, (6) Cheng, M.-F.; Li, W.-K. Chemical Physics Letters 2003, 368, 630. (7) Ciesielski, A.; Krygowski, T. M.; Cyrański, M. K. Journal of Chemical Information and Modeling 2008, 48, (8) Poater, J.; Visser, R.; Solà, M.; Bickelhaupt, F. M. The Journal of Organic Chemistry 2007, 72, (9) Schulman, J. M.; Disch, R. L. The Journal of Physical Chemistry A 1999, 103, (10) Cyrański, M. K.; Stępień, B. T.; Krygowski, T. M. Tetrahedron 2000, 56, (11) Portella, G.; Poater, J.; Bofill, J. M.; Alemany, P.; Solà, M. The Journal of Organic Chemistry 2005, 70, (12) Ruiz-Morales, Y. The Journal of Physical Chemistry A 2004, 108, (13) Clar, E.; Zander, M. Journal of the Chemical Society (Resumed) 1958, (14) Martín-Martínez, F. J.; Melchor, S.; Dobado, J. A. Organic Letters 2008, 10, (15) Martín-Martínez, F. J.; Fias, S.; Van Lier, G.; De Proft, F.; Geerlings, P. Chemistry A European Journal 2012, 18, (16) Baldoni, M.; Selli, D.; Sgamellotti, A.; Mercuri, F. The Journal of Physical Chemistry C 2008, 113, 862. (17) Baldoni, M.; Sgamellotti, A.; Mercuri, F. Organic Letters 2007, 9, (18) Martin-Martinez, F. J.; Fias, S.; Van Lier, G.; De Proft, F.; Geerlings, P. Physical Chemistry Chemical Physics 2013, 15, (19) Baldoni, M.; Sgamellotti, A.; Mercuri, F. Chemical Physics Letters 2008, 464, 202. (20) Wassmann, T.; Seitsonen, A. P.; Saitta, A. M.; Lazzeri, M.; Mauri, F. Physical Review Letters 2008, 101, (21) Wassmann, T.; Seitsonen, A. P.; Saitta, A. M.; Lazzeri, M.; Mauri, F. Journal of the American Chemical Society 2010, 132, (22) Balaban, A. T.; Klein, D. J. The Journal of Physical Chemistry C 2009, 113, (23) Cremer, D.; Pople, J. A. Journal of the American Chemical Society 1975, 97, (24) Humphrey;, W.; Dalke;, A.; Schulten, K. Journal of Molecular Graphics 1996, 14, 33. (25) Cross, S.; Kuttel, M. M.; Stone, J. E.; Gain, J. E. Journal of Molecular Graphics and Modelling 2009, 28, 131. (26) Kuttel, M.; Gain, J.; Burger, A.; Eborn, I. Journal of Molecular Graphics and Modelling 2006, 25, 380. (27) Hill, A. D.; Reilly, P. J. Journal of Chemical Information and Modeling 2007, 47, 1031.
6 XYZ Coordinates A1-M1 C C C C C C C C C C C C C C C C C C C C C C C C C C S C C C C H H H H H H H H H H H H H H C H H
7 C H H C H H C H H A1-M2 C C C C C C C C C C C H H C C C H C H S C H C H C C H C H C C C H H H C C H C C
8 C C C H H C H H C H H C H H C H H A1-M3 C C C C C C C C C C C H H C C C H C H C H C H C H H C C H C C C C
9 C H C H H C H H C H H C H H S C C H C H C H C H A2-M1 C C C C C C C C C C C C H H H C C C C C C C C C C
10 C C C C H H H C H H C H H C H H C H H N H C H C H C C C H C H H H A2-M2 C C C C C C C C C C C C H H H C
11 C C C C C C C C H C C C C C H H H H C H H C H H C C C C H C H C H H C H H C H H N H A2-M3 C C C C C C C
12 C C C C C H H H C C C C C C C C C H C C C C C H H H H C H H C H H C C H H C H H C C C H C H C H H N H
13 A3-M1 C C C C C C C C C C C C C C H C C C H H C C H C H C H H C H H C H H C H H H H H H O H A3-M2 C C C C
14 C C C C C C C C C C H C C C H C H C H H C H H C H H C H H H H O H C C H H H H Frequencies (cm -1 ) A1-M
15 A1-M
16
17 A1-M
18 A2-M
19 A2-M
20 A2-M
21 A3-M
22 A3-M
23
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