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Nonalternant Aromaticity and Partial Double Bond in Petroleum Molecules Revealed: Theoretical Understanding of Polycyclic Aromatic Hydrocarbons Obtained by Non-contact Atomic Force Microscopy Yunlong Zhang Energy Fuels, Just Accepted Manuscript • DOI: 10.1021/acs.energyfuels.8b03284 • Publication Date (Web): 16 Nov 2018 Downloaded from http://pubs.acs.org on November 16, 2018

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Nonalternant Aromaticity and Partial Double Bond in Petroleum Molecules Revealed: Theoretical Understanding of Polycyclic Aromatic Hydrocarbons Obtained by Non-contact Atomic Force Microscopy Yunlong Zhang*

Corporate Strategic Research, ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, NJ 08801, USA

ABSTRACT. Systemic studies are lacking to derive an understanding from the limited number of individually imaged diverse structures from nc-AFM and relate them to the chemistry of a macroscopic ensemble of heterogeneous petroleum mixture. This initial study intents to fill this gap by studying polycyclic aromatic hydrocarbons (PAHs) and

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understanding their aromaticity and bonding orders. Both alternant and nonalternant PAH are present in petroleum molecules, and the significance of nonalternant hydrocarbons in disrupting electron distribution of aromatic hydrocarbons was revealed by quantifying local aromaticity using Nucleus-Independent Chemical shift (NICS), complemented by the qualitative prediction with the Clar’s sextet theory. We found local aromaticity is maximized, resulting in a new understanding of large aromatic structures in petroleum. In addition, bond order analysis on PAHs from AFM imaging revealed that partial double bond character is common in petroleum molecules and could reach a significant degree in certain sites in a structure, with important implications in a wide range of reactivities and properties. Overall, this preliminary study provides means and methodology to connect finite structures from single molecule imaging with infinite diverse molecules in petroleum.

Introduction Fundamental questions concerning the composition and chemical structure of petroleum, especially heavy oils and asphaltenes, remain significant scientific challenges


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with tremendous economic impact.1-2 A breakthrough in understanding this complexity is the recent use of non-contact Atomic Force Microscopy (NC-AFM) by imaging molecules at the atomic level.3 A number of heavy oil and asphaltene samples from different sources and with varying processes and sources were studied with NC-AFM, with a total of 497 molecular images obtained, and 137 attempted (or partial) chemical structures assigned (28%).4-6 Many chemical structures were reported, but with little theoretical understanding reported on their electronic structures and intrinsic connections. Herein, we report a detailed computational study on these PAH structures. This allows us to identify common pattern within these diverse structures and to deduce the general chemical reactivities of bulk samples, overcoming the intrinsic sampling limit of this single molecule imaging technique.

Computational Details: All the theoretical computations were performed with density functional theory (DFT) as implemented in Gaussian 09 Revision D.01.7 DFT employed the B3LYP keyword which invokes Becke’s three-parameter hybrid exchange functional with the Lee−Yang−Parr


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correlation functional (B3LYP)

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Geometries were optimized with B3LYP and 6-

31+G(d,p) basis sets, and vibrational frequency calculations on the optimized geometries were performed at the same level of theory to characterize all stationary points as minima. All calculations were in the gas phases. NICS(1) calculation was done at the level of B3LYP/6-31+G(d,p) by placing a dummy atoms one angstrom above the center of each ring.10 Electrostatic potential surfaces (ESP) was computed using cubegen function in Gaussian and results were visualized with GaussView5.0.8. Population analysis was performed with natural bond orbital (NBO) program version 3.1

11-13

under

Gaussian09 program package, and the bond order by Wiberg bond index is employed.

Results and Discussion All molecular structures in this study are based on heptane (C7) asphaltenes which are obtained from tars produced from steam cracking of crude oils (shown in Figure 1) and other petroleum molecules imaged in earlier AFM studies.4-6


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1

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Figure 1. Molecular structures of steam cracked tar C7 asphaltenes revealed by previous NC-AFM studies and three types of PAH compounds observed.4

(a) Classification of alternant and nonalternant PAH in petroleum These hydrocarbon structures (Figure 1) can be characterized as either alternant or nonalternant PAHs. Alternant PAHs have even-membered rings only and are known as benzenoids if composed of only hexagonal rings (e.g., pyrene).While benzenoidal structures are the most common structure motifs in petroleum,14 nonalternant PAHs are less frequently observed and they contain at least one odd-membered ring, such as a


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five-membered carbocycle (e.g., fluoranthene), or a PAH with a non-conjugated CH2 bridge (e.g., fluorene). Despite their geometric five-membered ring, heterocycles such as thiophene or pyrrole are better considered as a special alternant case because of six  electrons. While the majority of PAHs observed were the expected benzenoids, about one third of the molecules were nonalternant. Even though nonalternant hydrocarbons have been reported in pyrolytic products6 or interstellar molecules,15 few reports of their presence in native petroleum crude oils were studied, with little information on their abundance and implications for chemical and physical properties.5,

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Nonalternant

structural motifs suggest that certain diagenetic pathways generate these molecules, because nonalternant structures are rarely found in biological molecules and it is not obvious how biological molecules with five-membered rings, such as steranes and steroids, can be transformed into aromatic nonalternant hydrocarbon molecules. Nonalternant hydrocarbons are known to have unique electronic structure and reactivities, such as asymmetric molecular orbital arrangement, uneven charge distribution, and unique electronic absorptions, compared to their more common alternant counterparts. The large dipole moments of nonalternant hydrocarbons could impart


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significant polarity to petroleum hydrocarbon molecules, in addition to heteroatoms which are often associated with polar groups. It is anticipated that these nonalternant hydrocarbons play important roles in many petroleum properties which may not be adequately predicted if only benzenoids are considered. For example, Lapinas et al. have shown that the kinetics and cleavage pathways in hydrocracking of fluoranthene are significantly different from those observed for the six-carbon-membered-ring-containing (alternant) polynuclear aromatic compounds and should be regarded as a separate class in modeling the conversion of heavy oil feedstocks.17 (b) Accessing the stability of PAH structures with Clar’s sextet theory Benzenoids were found to have a wide range of ring counts, from 2 to up to ~13 rings in a steam cracked tar asphaltene, and up to 17 rings in hydroprocessed asphaltene samples.4 Most of them are pericondensed, although catacondensed PAHs are observed (4, 6). Many structures have adjacent bay regions, frequently with a heteroatomcontaining ring and five-membered carbocycles inside the coves (two adjacent bays, e.g., 20, 23) or fjords (three adjacent bays, e.g. 1, 3), and hence are slightly strained; even helical structures were observed in rare cases (1, 10, supporting information, SI). This


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steric hindrance suggests that these PAH heteroatoms will potentially be very hard to remove during hydroprocessing.

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Figure 2. Clar’s structure according to the sextet rule to understand the stability of AFM imaged PAH structures.

It is generally believed that petroleum is composed of only the most stable molecules, considering the geological timescale over which it is formed. For example, aromatic and aliphatic moieties are abundant, but olefins are scarce in virgin crudes because of their reactivity.20 The relative stability of different PAH topologies can be conveniently assessed using the Clar’s sextet theory.21 For example, the fully benzenoid as defined by Clar,22 with only a single Clar structure of only aromatic sextets (indicated by inscribed circles) and empty rings, is the most stable form (e.g., 4 in Figure 2). It was


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a premise that fully benzenoids were observed preferentially in pyrolysis products, but less so in native crude oils. For example, recent X-ray Raman Scattering spectroscopy study and molecular orbital analysis of oil shale kerogen showed that PAHs are predominantly fully benzenoids.23 However, the topology of benzenoids in petroleum structures revealed by AFM imaging is found to be more diverse. For example, the most stable fully benzenoidal structures were found in only one molecule (triphenylene, 4). Nonetheless, most of the benzenoids observed fall into the second most stable PAH class: benzenoids with several Clar’s structures of the same number of sextets (e.g. 2 in Figure 2). Furthermore, the next stable type of benzenoids are those with only one Clar’s structure with fixed double bonds (e.g. 12) which are also frequently found. Finally, the least stable benzenoids are those linear polyacenes with only one sextet possible and their stability decreases as the number of rings increases. For example, the highly unstable heptacene can only stable at low temperatures.11, 24 This least stable type of compounds are also devoid except those with less than three co-linear rings. We refer to this limit as the “rule of three” (e.g, 10, 13 and 16). Recently imaged fuel pyrolysis products are also consistent with this observation.6 Overall, petroleum benzenoids observed so far


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contain a wide diversity of structures, but are nonetheless devoid of the most and least stable species. This implies a subtle interplay of kinetic reactivity and thermodynamic stability in the formation of these compounds. (c) Quantification of local PAH aromaticity and a new way of understanding the  system in petroleum molecules Although Clar’s sextet theory is also useful in understanding local aromaticity of benzenoidal PAHs, it is not applicable to nonalternant (nonbenzenoids) and does not allow quantitative comparison of aromaticity between different molecules. Aromaticity, especially for nonalternant PAHs, can be conveniently assessed with the aromaticity index NICS (nucleus-independent chemical shifts) proposed by Schleyer

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widely used as a measure of local aromaticity of each ring of a PAH (Figure 3).16, 19, 25


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Figure 3. (a) The local aromaticity provided by NICS(1) (one angstrom above the center of each ring) computed with B3LYP/6-311G(d,p). Color schemes are aromatic (-10 - -5 ppm) in red, nonaromatic (- 5 ppm to +5 ppm) in blue, and antiaromatic (> +5ppm) in pink. (b) Electrostatic potential surfaces (ESP isoval 0.004) mapped onto total electron density (isoval 0.02) for fluorene, fluoranthene, and molecule 21.

For example, the predicted NICS at the centers of the two benzene rings in nonconjugated fluorene are -9.5 ppm (-10.2 ppm for benzene as a reference) and -2.4 ppm. Notably, nonalternant fluoranthene is predicted to be +0.5 ppm at the central ring, even less aromatic than the nonconjugated fluorene, signifying the presence of a fivemembered ring in a nonalternant PAH. Therefore, the fluoranthene can also be seen as benzene and naphthalene connected by CC single bonds, just as fluorene can be viewed as two individual phenyl group connected by CC single bonds. Calculations on a several benzenoids are shown in Figure 3. Based on these insights from local aromaticity, a coherent view develops for all the PAH structures (both alternant and nonalternant): the central five-membered ring acts as a divider within PAH molecules rather than as part of


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a fully conjugated system. This view is also supported by the electrostatic potential surfaces which clearly shows the depletion of electron density in the middle of fivemembered ring (Figure 3). We refer to this finding as selfish aromatics since the local aromaticity of PAH systems are maximized and sharing of their electron density is minimized, which otherwise are expected as preferred. This perspective of local aromaticity in petroleum molecules provides a new insight into the traditional continental model of asphaltene structure since the apparently uniform monolithic PAH core can be viewed as having different regions of isolated aromaticity. Such a model of aromaticity can potentially explain charge distribution and dipole moments for these heavy hydrocarbons, and even the intermolecular interactions that drive their aggregation behavior. (d) Quantitative analysis of bond order to understand the local reaction sites of PAHs The localized double bond predicted by Clar’s sextet rule for PAH structures are not quantitative, thus computational studies of natural bond order prediction overcome this limit (Fig. 4).19, 26


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Figure 4. Computation of bond order with natural molecular orbitals. Left: the scale of bond order benchmarked by some aromatic molecules with calculated bond order shown for the specific bond location indicated in red. Right: the bond with highest bond orderr in each molecule are highlighted in red.

The Wiberg bond order calculated from natural bond orbitals is shown in Figure 4.11 As a reference, the bond order is predicted to be 2.04 for ethylene and 1.04 for ethane. Benzene has bond order of 1.44 as the reference bond order for the most aromatic molecule, and the bond order in naphthalene is slightly increased (1.56). The CC bond order of the 9,10-position of phenanthrene is higher (1.65), closer to that of a formal double bond. Based on benchmark of these reference compounds, it is now


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possible to calibrate the bond orders present in the AFM structures. It can be seen that significant partial double bonds are present in these molecules. The bond order of PAH bonds can vary from nearly single bond to double bond order. While olefins are scarce in virgin petroleum, the wide range of bond order in PAHs might allow certain sites to take part in olefinic reactions. A proper accounting of this partial double bond content provides a new perspective on these structures, and allows quantitative assessment of the reactive sites in PAHs. Conclusion In summary, this theoretical analysis of aromaticity for structures obtained from AFM molecular images illustrates the potential for harnessing this new analytical tool to understand and predict reactivity in complex mixtures. It is generally understood that aromaticity is the extra stability of a molecule associated with the loss of olefinic character. However, we have shown that many petroleum PAHs maintain some degree of double bond character, and that the local aromaticity and bonding order analysis presented here provides a coherent and effective way to rationalize and understand the PAH structures.


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Non-contact AFM images of molecular structure, when coupled with a theoretical analysis, will enable a better understanding—and design—of their reaction chemistry. Supporting Information

Computational methods and details are available in supporting information. Corresponding Author Yunlong Zhang*

* To whom correspondence should be addressed. Telephone: +1-908-335-2792. Email: [email protected]

ACKNOWLEDGMENT The author is grateful to Michael Siskin and Steven P. Rucker for helpful discussions and comments on the manuscript.

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