Guide for Atomic Force Microscopy Image Analysis To Discriminate

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A Guide for AFM Image Analysis to Discriminate Heteroatoms in Aromatic Molecules Percy Zahl, and Yunlong Zhang Energy Fuels, Just Accepted Manuscript • DOI: 10.1021/acs.energyfuels.9b00165 • Publication Date (Web): 29 Apr 2019 Downloaded from http://pubs.acs.org on April 29, 2019

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A Guide for AFM Image Analysis to Discriminate Heteroatoms in Aromatic Molecules Percy Zahl1 and Yunlong Zhang2 1Center

2Corporate

for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973 Strategic Research, ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, NJ 08801

Heteroatoms are essential for functional groups in organic structures and are complementary to hydrocarbon structures in reactivities and properties. However, it is still a challenge to quickly identify heteroatoms with nc-AFM only to resolve chemical structures in complex unknown mixtures. This study aimed to understand the effect of elemental types on the contrast of AFM images using a few selected model heterocycles including dibenzothiophene (DBT), acridine (ACR), and carbazole (CBZ). We identified several features that can be used to find common heteroatoms (S and N) and discriminated them from carbon atoms (C) using nc-AFM images alone. The mechanism of the atom and bond contrast was studied with image simulations and was found to be mostly correlated to van der Waals radii, but other factors such as bonding geometry, electron density, and substrate interaction need to be considered. The work will allow for rapid identification of these common heteroatoms in petroleum with AFM.

Introduction

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The chemical structure of an organic molecule was first resolved by non-contact Atomic Force Microscopy in 2009 using a CO-functionalized tip.1 This versatile combined AFM (Atomic Force Microscopy) and STM (Scanning Tunneling Microscopy) method has been proven to be a powerful tool in chemistry, by enabling resolution of detailed molecular structures,2-7 measuring chemical properties (charge, bonding order),2,

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manipulating atomic bonds,9-10 and even

monitoring reactive intermediates in reaction mechanisms.9, 11-13 Significantly, this technique is uniquely powerful in studying heterogeneous molecular mixtures,14-15 such as petroleum asphaltenes,16 heavy oils,17 and fuel pyrolysis products.18 Although most of these previous studies have been focused on planar aromatic molecules, a few more recent studies have extended the capability to be able to investigate more challenging molecules including the nonplanar molecules such as aliphatic and alicyclic moieties19 and even their enantiomers.20 It remains a challenge to understand the contrast mechanism of the bond-like features in AFM images which is important in interpreting structures,21 but still under some controversial debates.2224

Recent significant progress in computational studies facilitated the understanding of the imaging

data, 25-26 including hydrogen bonds27 and halogen bonds.28Another challenge is the identification of heteroatoms only with AFM without the involvement of STM imaging on insulated NaCl layers which is not always possible for unknown molecular mixtures after surface deposition.29-30 Although a few examples with heteroatoms within the hydrocarbon framework have been reported, such as the identification of pyridine31 and phenazene32-33 moieties, and the detection of B and N in nanographenes;34-35 however, a systemic examination of heteroatoms in smaller organic molecules is lacking, and remains a significant challenge under nonideal imaging conditions, especially for those frequently encountered in petroleum such as N- and S-containing molecules. In this study, we attempt to address these questions by studying some selected heterocycles.


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Nitrogen and sulfur are the two major sources of NOx and SOx pollutants caused by combustion of fossil fuels, and they often exist as substituents in the carbon skeleton of aromatic hydrocarbons. Dibenzothiophene (DBT) is a sulfur-containing molecule abundant in petroleum with a central five-membered ring. DBT and particularly 4,6-dimethyldibenzothiophene have been known as the most challenging structures in hydrodesulfurization. Nitrogen, in nitrogen-containing aromatic heterocyclic compounds, is known as the worst poisons for hydroprocessing catalysts and it exists either in basic (pyridinic-type) or non-basic (pyrrolic-type) forms. The non-basic nitrogen is contained in five-membered rings of aromatic molecules, such as carbazole (CBZ) and indoles; and basic nitrogen is contained in six-membered rings of aromatic molecules, such as pyridine or acridine. Both types of N are ubiquitous in petroleum.36 Although the carbazole-types were found in a few cases, the pyridine type has not yet been unambiguously identified in petroleum sources in the previous studies.16-17 These sp2 N atoms are supposedly difficult to distinguish from sp2 C in aromatic molecules with nc-AFM. Therefore, it is important to distinguish the presence of both S, and either types of N atoms from the carbon skeletons of hydrocarbon back-bones. This work will allows for rapid identification of these atoms from AFM imaged petroleum. Methods Computational details. Structures were optimized with B3LYP/6-31+G(d) level theory and verified no imaginary frequencies.37-38 All calculations were performed in the gas phase using Gaussian 09 Revision D.01,39 and images were generated with GaussView 5.0. AFM simulations were performed using the mechanical probe particle (PP) model.21, 40-42 Gas-phase geometries from DFT were used directly and electrostatic potential (ESP) was included with a charge of q = -0.2e on CO tip. For DBT, an empirically adjustment of tilt angle of 3.9° to the surface was used in the PP simulations.


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Experimental details. Measurements were performed with a Createc-based LT-STM upgraded with AFM and custom GXSM control software.43-45 Q-Plus sensor with a FIB sharpened PtIr tip wire was used and functionalized with a CO molecule,1 and operated in constant height mode, with feedback off with no corrections needed within about an hour and more. XYZ drift and creep is less than 1 pm/h after at least 24 hours at 5 K and without major XYZ offset changes. Molecules were imaged with bimodal STM and nc-AFM under UHV conditions at 5 K after deposition using a home-built evaporator. A special valve controlled evaporator cell was used for molecules such as ACR with a high vapor pressure (see supporting information, Figure S1for more details). Optical and physical sample access was via aperture or cyro door for deposition. nc-AFM imaging was performed at a typically 40 mV bias for ACR and DBT, and 50 mV for CBZ. There was no particular reason for the exact bias besides finding the most stable imaging conditions and staying near the effective surface potential between Au111 and the actual tip apex to minimize the bias dependent electrostatic force. A PtIr tip wire with an oscillation amplitude of about 50 pm was used and a Q-Plus sensor was operated at 30 kHz with a typical Q factor around 10,000. For frequency tracking and amplitude regulation a novel Phase Amplitude Convergence detector and Phase Locked Loop was used.46 A Au (111) single crystal was used here as the substrate and cleaned with typically 3 cycles of Ar+ sputter/anneal before use. Tip tuning was performed via controlled crashing into the Au surface with following CO molecule functionalization via close proximity scanning and pickup at very low bias. Results and DiscussionTrace amounts of molecules were deposited under ultrahigh vacuum conditions via sublimation from a direct current-heated silicon carrier substrate pointing directly to the previously cleaned Au sample readily at 5 K (~15 K while opening the cryo door) inside the STM/AFM surrounded by the cryo shield. AFM images were obtained and compared in


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order to study the identity of heteroatoms. Compared to recognizable elemental labels (i.e., S, N, O) of chemical structures and color schemes in ball-and-stick models in DFT optimized structures (Figure 1), the identity of heteroatoms in nc-AFM images has to be carried out systemically with both experiment and simulation.

Figure 1. nc-AFM imaging heteroatom-containing organic compounds dibenzothiophene (DBT), carbazole (CBZ), and acridine (ACR). The chemical structures and ball-and-stick models optimized by DFT (gray C, blue N, yellow S) are shown on top of each panel. Simulated AFM images of DBT (a,b), CBZ (d,e), and ACR (g, h) obtained with the probe particle method21 were shown. The nc-AFM images of DBT at bias 40 mV (c), CBZ at 50 mV, and (f) and ACR at 40 mV (i) were obtained on Au(111) using CO functionalized tip in the constant height mode. Tip


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oscillation amplitude approximately 50 pm. A Laplace of Gauss algorithm was applied with a filter radius (determining the convolution matrix size) of 0.75 Å (here equivalent to r = 10 pixel) to reduce noise and highlight the structure while maintaining the feature shapes as good as possible. (a) Bonding geometry. Intuitively, the presence of heteroatoms is associated with their influence on the shape and size of rings (pentagon or hexagon), in conjunction with the polycyclic aromatic hydrocarbon (PAH) molecule building blocks. For example, a fully conjugated fivemembered carbon ring is impossible at the edge of a stable PAH, and can only be found inside of PAHs (e.g., fluoranthene), while a nonconjugated five-membered carbon ring with an sp3 carbon can be found inside of PAH (e.g., fluorene). S in aromatic molecules can only be found in five-, but not six-membered rings. However, N can be in either five- or six-membered rings. Hence the presence of heteroatoms and their sites can be judged by the noticeable pentagonal rings and the resulting overall molecular shapes. For instance, among the three molecules studied, the kinked tricyclic structures of DBT and CBZ due to the presence of a five-membered ring can thus be clearly distinguished from the linear hexagonal ACR, even at lower resolution of AFM images or from a general STM overview (Figure 1). The expected location of S at the convex of the central pentagonal rings of DBT can be unambiguously recognized from the pronounced feature of the S atom due to the considerably larger van der Waals radius as a third-row element (although it is similar to a CH2 unit in unknown structures), and the two significantly longer C-S bonds in DBT. Although N is not as pronounced as S, the expected location can be identified from the convex of pentagonal rings, and the faint line feature of the N-H bond in CBZ is recognizable in AFM imaging, which is also found for CH bond, but not found for S in DBT. Therefore, the two types of sp2 N in CBZ and ACR can be distinguished by the pentagonal rings.


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(b) Van der Waals radii (LJ-r0). The distinction of sp2 N from the sp2 C framework requires careful analysis because both are present in hexagonal rings and the small difference in van der Waals radii (1.70Å for C and 1.55 Å for N) and electronegativity (2.6 for C and 3.04 for N).47 Facilitated by known structure and an N atom expected at the central ring for ACR, the nitrogen can be identified by noticing a very slight faint (dark) feature (Figure 1i). The absence of a faint line expected for a C-H further corroborates this assignment. To facilitate the detection of the slight faint feature, the frequency profile along the two edges (CNC and CCC) of ACR clearly showed the decreased frequency at N (Figure 2). In order to confirm this and to understand the origin of this observation and to predict other heteroatoms, the mechanical probe particle simulations were conducted and the Lennard-Jones parameters obtained are summarized in Table 1. Consistent with previous work,21 the contrast of each atom was governed by the empirical L-J r which is related to the van der Waals radius (rvdw) although the latter is consistently 0.1 – 0.2 Å less. Therefore, elemental types can be mostly identified according to different degrees of faint or bright contrast relative to carbon (Figure S2), although electrostatic effects introduced by the presence of heteroatoms should also be considered, and sometime it is responsible for the distortions of bonding structures, as shown in previous work.24, 26

Figure 2. The frequency shift profile along the two edges (top over CNC and bottom CCC) of one ACR molecule to show the clear difference between N and C atoms. Profiles were aligned as indicated by the corresponding colored arrows shown on inserted image.


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Atom rvdw /Å

Eb /eV

r0 /Å

r /Å

vs. C

H

1.20

0.681

1.487

3.148

very faint

O

1.52

9.106

1.661

3.322

fainter

N

1.55

7.372

1.780

3.441

faint

C

1.70

3.729

1.908

3.569

-

S

1.80

10.84

2.000

3.661

bright

Table 1: The van der Waals radii (rvdw) is listed in the table to compare with the Lennard-Jones (L-J) parameters. Simulations with the mechanical probe particle method is performed assuming an oxygen probe particle and the effective atom “X” to probe particle “O” radius is r , where r = r + r is an approximation of the sum of the individual atom’s L-J parameter r0. (c) Substrate interaction. In addition to the bonding geometries of adsorbed molecules, the interactions with the specific substrate with heteroatoms can significantly affect the AFM imaging contrast. For instance, the bonding motifs formed between N and copper adatoms on surface has been reported.48 Built upon the adsorption geometry determination by AFM originally introduced by Schuler et al. on aromatic hydrocarbons,49 a robust determination of the adsorption geometry of heterocycles would be needed for broader applications, especially in catalysis and surface sciences. As noted above, in the AFM image of DBT, the contrast at the far end at the outer CC bonds (labeled as AB and CD) is noticeably higher than the side near the S atom, and the molecule seem to be tilted with S closer to the Au111 substrate (Figure 1c). In order to confirm this, a detailed AFM topography constructed from a force-volume map was obtained to evaluate the adsorption geometry of DBT (Figure 3). Using a series of force image slices (a1,a2,a3 are representative examples of the series) taken every 10 pm covering a range of 110 pm in total (see


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Figure S3 for a whole series of DBT images), a topographic like image (d, e) representation was created by evaluating an interpolated constant frequency shift reassembling a -8.5 Hz constant frequency shift image (repulsive side). This is similar to extraction of constant frequency shift isosurface introduced by Mohn et al,50 but the result is more precise than the frequency (or force) minimum. This is obvious for similar conditions (e.g., over equivalent C’s) giving a true z. It was found that the PAH part of DBT was tilted down by 3.9˚ at the sulfur atom towards the Au (111) substrate relative to the outer CC axes as indicated in (d) as A-B and C-D lines via evaluating those line profiles, indicating a stronger interaction of S with the Au substrate than with carbon atoms. This can be rationalized that the electron lone pairs on S of DBT is freely available to coordinate with Au atoms, rather than participating the aromatic system in DBT. This hypothesis is supported by the the reduced aromaticity in the central ring (-6.5 ppm) of DBT, compared to its side rings (10.1 ppm) or thiophene (-13.6 ppm),51 according to the GIAO-SCF calculated NICSs values. The S atom could be more pronounced if it is not adsorbed closer to the Au 111 substrate. Detailed simulation by the probe particle method21 using gas-phase geometries with mechanical adjustment tilt angle by 3.9˚ and flat DBT relative to the surface clearly indicate the difference (Figure S3). This confirmed our initial estimate on the tilt of DBT, indicating the added complexity for atom identification by an adsorption geometry. Although a relaxed geometries on the surface could be used to predict the adsorption geometry as shown in previous studies,49 herein we demonstrate that a simple combination of the probe particle method with gas-phase geometries and empirical adjustment of tilt angle adequately allow for rapid structure assignment, and without the involvement of expensive calculations.


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Figure 3. Adsorption geometry of DBT (a1-a3) AFM images of DBT on Au (111) at selected imaging heights, (b) simulated AFM images of a fat (untilted) molecule as a reference at comparable heights to the AFM data, (c) simulated AFM images with adjusted tilt angle of 3.9˚ along the A-B and C-D direction as indicated in (d) showing a reconstructed topographic representation computed from an image series taken at 10 pm Z steps reconstructing a isofrequency shift image. (e) 3D restoration of (d).


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Figure 4. STM/AFM image of dibenzothiophene (DBT), carbazole (CBZ) and acridine (ACR) on Au (111). (a) STM image of DBT and CBZ and their AFM images (b). (c) STM image of ACR and AFM images. STM bias was 100 mV and current set point was 20 pA. The substrate interactions also affect the mobility of the adsorbed molecules, and this should be taken into consideration for smaller or unstable molecules. A mixture was created by introducing some CBZ molecules while DBT was still on the surface and this allows us to observe the distinction between these two molecules (Figures 4 and S4). In addition to obvious differences in STM and AFM due to their different molecular shape and the pronounced feature of the S atom, it was found that CBZ molecules are quite mobile on Au (111) and frequently moved by the tip at 5 K during imaging, compared to DBT which is quite steady on the surface due to the strong interaction of S with the Au substrate. Even without a five-membered ring feature, ACR was also quite mobile on Au 111 during imaging at 5 K, and it is nearly impossible to get close enough to obtain high resolution AFM imaging on individual ACR molecules without pushing them around (SI, movie 1). This high surface mobility facilitates the formation of molecular clusters due to


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intermolecular interactions. Therefore, while ACR tends to move during scanning in the AFM mode, stable image of clusters can be obtained. This is consistent with the hydrogen bond between aromatic the CH and the lone pair on N as previously reported.31 AFM simulations on a dimer of ACR were performed to confirm this observation (Figure S5). Conclusions In this study, a few heterocyclic aromatic molecules containing N and S as those frequently encountered in petroleum molecules have been studied as a template to facilitate their identification in an unknown molecular mixture. We identified the features that help discriminate heteroatom types and their sites within organic structures using AFM imaging, AFM simulations and DFT calculations. The protruding feature of the S atom in DBT can be easily identified due to its larger atomic radius. Two types of nitrogen can be distinguished by the five- and six-membered rings. Distinguishing them from carbon within the carbon skeleton of organic molecules requires high resolution AFM imaging, especially within the context of non-planarity, adsorption geometries of organic molecules, or non-ideal imaging conditions (such as combination of tip, substrate and mobility). We demonstrated that the contrast of atoms in AFM images was largely correlated to the van der Waals radius of each element, but other factors such as bonding geometries, electron density, and specific substrate interactions should also be considered. All these studies will allow for rapid identification of these moieties in petroleum and other complex mixtures in the future. Supporting Information. Video of ACR dimer moving during AFM imaging (Video 1), a new device designed for volatile compounds, some additional raw data (nc-AFM images), filtered images, and simulated images in Figure S1-S4.


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ORCID Yunlong Zhang 0000-0002-3071-8625 AUTHOR INFORMATION Corresponding Author *Yunlong Zhang Tel: 908-335-2792, email: [email protected] *Percy Zahl, Tel (631) 344-2968, email: [email protected] ACKNOWLEDGMENT The authors are grateful to insightful discussions with D. Stacchiola, P. Hapala and L. Gross. This research used resources of the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Laboratory under Contract No. DESC0012704. REFERENCES 1. 2. 3.

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Guide for Atomic Force Microscopy Image Analysis To Discriminate

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