Effects of Protonation, Hydrogen Bonding, and Photodamaging on X

Article pubs.acs.org/JPCC

Effects of Protonation, Hydrogen Bonding, and Photodamaging on X-ray Spectroscopy of the Amine Terminal Group in Aminothiolate Monolayers Xiuneng Song,† Yong Ma,†,‡ Chuankui Wang,‡ Paul M. Dietrich,§ Wolfgang E. S. Unger,§ and Yi Luo*,†,∥ †

Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden ‡ College of Physics and Electronics, Shandong Normal University, Jinan, Shandong 250014, People’s Republic of China § BAM Federal Institute for Materials Research and Testing, 12200, Berlin, Germany ∥ National Synchrotron Radiation Laboratory and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China ABSTRACT: The amine headgroup, NH2, in aminothiolate monolayers can often generate unexpectedly rich structures in its N K-edge X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra that are difficult to assign. We have carried out density functional theory (DFT) calculations to study the XPS and NEXAFS of amine headgroup in four different aminothiolate monolayers, namely, aliphatic 11aminoundecane-1-thiol (AUDT), aromatic 4-aminobenzenethiol (ABT), araliphatic 4-aminophenylbutane-1-thiol (APBT), and 3(4″-amino-1,1′:4′,1″-terphenyl-4-yl)propane-1-thiol (ATPT), with the focus on structure changes caused by protonation, hydrogen bonding, and X-ray damaging. Spectra of all possible saturated and unsaturated species, as well as X-ray damage products, such as imine, nitrile, azo species, and cumulative double bonds, have been thoroughly examined. It is found that extra spectral structures observed in the experimental XPS spectra do not result from protonation but from the formation of a primary ammonium. The X-ray excitation can induce cross-linking between two neighboring molecules to form different complexes that contribute to the π* features in NEXAFS spectra.

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INTRODUCTION The well-defined chemical bonding and highly ordered structure have made thiol-based self-assembled monolayers (SAMs) on gold one of the most studied systems for a large number of applications.1,2 They have been used as the base to attach more functional molecules or terminal groups to utilize, for instance, the immobilization of biomolecules, such as proteins, carbohydrates, and DNA.1,3,4 The large selection of functional headgroups in these systems has also drastically extended their applicabilities in biosensors and molecular electronics.1 It has been shown that, among all functional groups, the amine is the most versatile headgroup for tethering a variety of biomolecules onto an underlying surface.5 It is well-known that a preferential orientation of SAMs can be determined by X-ray absorption spectroscopy by exploitation of the linear dichroism effect.6 The structural properties of the functional headgroups have also recently been examined by X-ray photoelectron spectroscopy (XPS) and the near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, focusing on the amine group in the ω-amino-terminated SAMs based on aliphatic, aromatic, and araliphatic backbones.7 The amine group has its distinct spectral fingerprints for the sole N atom, which © 2012 American Chemical Society

should be easily identified. However, both experimental XPS and NEXAFS spectra give extra peaks, and the origin is under discussion. Baio et al.8 investigated the 11-aminoundecane-1-thiol (AUDT) sample by N 1s XPS and observed a peak at binding energy (BE) of 399.5 eV corresponding to the N−C species of the amine headgroup and another at BE of 401.4 eV assigned to a protonated amine group. N K-edge NEXAFS revealed a broad σ* resonance near 406 eV related to the N−C bond. This peak is accompanied by an intense resonance at 400.6 eV which is assigned to primary amine (-NH2) moieties. A low-intensity preedge feature was measured at about 398 eV and had been hypothesized to result from a hybridized or dissociated state of ammonia by other authors earlier.9 The same feature had been assigned to a positively charged form of amine.10 Baio et al.8 also discussed radiation damage from the X-rays but ruled out this possibility by a careful beam damage study. Graf et al.11 and Dietrich et al.7 studied an AUDT SAM, too. Again two chemical Received: March 21, 2012 Revised: May 7, 2012 Published: May 16, 2012 12649

dx.doi.org/10.1021/jp302716w | J. Phys. Chem. C 2012, 116, 12649−12654

The Journal of Physical Chemistry C

Article

again the importance of theoretical modeling for X-ray spectroscopy of molecular complexes.

states of nitrogen were observed by N 1s XPS. The high BE signal observed between 401 and 402 eV was attributed to hydrogen bonded or protonated nitrogen and the low BE signal at BE of 399.5 eV to free amines. N K-edge NEXAFS spectra display a σ*N−C resonance at 407 eV and a free amine σ*N−H resonance at 401 eV. Another feature was observed at 397.9 eV assigned to be a σ* resonance due to the protonated amine group. Other features are found between 397.9 and 401 eV which are discussed to probably be π* resonances originating from unsaturated species as NC, NC, and N−CC formed in the course of beam damage. This interpretation was loosely underpinned by NEXAFS experiments and simulations with acetonitrile and 3butenenitrile adsorbed on Si published by Rangan et al.12 Graf et al.11 concluded that the discussion of the resonance energy for a NH+3 species in the N K-edge spectrum is not yet finished. They referred also to the opinion of Shard et al.13 who reported this resonance to be at a very different energy, at 406 eV, in a study of poly(allylamine) hydrochloride. A conclusion was that quantum chemical simulations of N K-edge NEXAFS spectra are required to find a consistent solution. Amide π* resonances occurring at energies very similar to the σ*N−H resonance have been proven by dedicated experiments to not contribute to the AUDT NEXAFS N K-edge spectra in refs 7, 8, and 11. N K-edge NEXAFS spectra of amines as terminal head groups of aromatic SAMs have also been measured by Graf et al. and Dietrich et al.7,11,14 A specific feature was here a strong resonance at 398 eV which had been tentatively assigned to represent a π*N−Ph resonance. The authors assume that both mesomeric structures, i.e., the σ-bonded free amine (represented by a shoulder at 401 eV) and the π-bonded iminium species, contribute to the spectrum. Related mesomerism phenomena were discussed in an early NEXAFS study by Pavlychev et al.,15 where spectrum simulations had been used to underpin interpretations of experimental data. In this study N K-edge data of benzalaniline (Ph−NCH−Ph) were considered and π* features due to mesomeric conjugation phenomena, a π*N−CH resonance at 398.1 eV and a π*Ph−N resonance at 401.7 eV accompanied by σ* features at 408 eV, were reported. A similar π* splitting was observed with polyaniline (399.5 and 400.5 eV) and has been discussed in terms of a mixture of imine and amine bonding.16 One could speculate about the possible sources of these spectral features relying on chemical intuition. One of them might be related to the sample preparation procedure, in which the SAMs underwent an immersion into ethanolic solution and then were rinsed in an ethanolic solution with 10% (v/v) acetic acid. This could allow the nitrogen atom of the amino group to form hydrogen bonds or get a proton from the surroundings. Moreover, the X-ray absorption measurements could also result in sample damage that could lead to the formation of new species.17,18 Therefore, it is highly desirable to obtain definite assignments for these spectra. Over the years, it has been frequently demonstrated that first principles calculations can often accurately reproduce experimental spectra and provide many details that are not directly accessible from the measurements.19−22 In this work, we have carried out a systematic study on XPS and NEXAFS spectra of ω-amino-terminated SAMs with aliphatic, aromatic, and araliphatic backbones. The effects of protonation, hydrogen bonding, and X-ray damage on the spectra of the amine headgroup have been carefully examined. By comparison with the experimental spectra, the new chemical species or structures in SAMs are discussed. This study highlights

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COMPUTATIONAL DETAILS All four different aminothiols, shown in Figure 1, aliphatic AUDT, aromatic 4-aminobenzenethiol (ABT), araliphatic 4-

Figure 1. Structures of four aminothiolate molecules, AUDT, ABT, APBT, and ATPT.

aminophenylbutane-1-thiol (APBT), and 3-(4″-amino-1,1′:4′,1″terphenyl-4-yl)propane-1-thiol (ATPT), as measured in the experimental work of Dietrich et al.,7 have been chosen in this study. With the consideration of the environments and the possible damage caused by irradiation with X-ray in the measurements, spectra from several anticipated saturated species, including amine, protonated amine (PAmi), hydrogen bonded amine (HBA), primary ammonium (PAmm), protonated amine complex (PAC), and unsaturated species, such as imine, nitrile, cumulative double bonds (CDB), azo, and crosslinking (CL) species have been calculated. Their structures are given in Figure 2. For the hydrogen bonded species and the primary ammonium species, four different negative ions, OH−, Cl−, SH−, and acetate anion (AC−) are considered. For the protonated amine complex, only the water and acetic acid (AC) molecules are considered. For the aromatic and the mixed molecule, two possible species caused by X-ray damage are also considered. One is azo which is formed by two connected nitrogen atoms with a double bond. The other one is CL in which the nitrogen atom in one molecule is connected with the carbon atom in the neighboring molecule. For the aliphatic molecule, the irradiation can cause the formation of more species, such as imine, nitrile, CDB, azo, and CL species. All the structures of the species mentioned above were optimized by density functional theory (DFT) using the B3LYP23 functional and 6-31G(d,p) basis set in GAUSSIAN 09 program.24 Optimized geometries have then been used to simulate their corresponding XPS and NEXAFS spectra by using the StoBe program.25 The N 1s ionization potentials (IPs) are obtained from ΔKohn−Sham (ΔKS) scheme26,27 through specifically computing the energy difference between the core ionized state, i.e., the full core hole (FCH) and the ground state (GS):

IP =

M−1

E FCH − MEGS

(1)

where M is the number of the electrons of the states. The absorption spectra are calculated with the full core hole approach as implemented in the StoBe program.25 The magic angle of 55° is adopted in the calculations. It should be noted that the angle 12650



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Figure 2. Possible species for the aliphatic molecule (top) and the aromatic molecules (bottom) under investigation.

energy shift has not been observed in any experiments and cannot be the origin of extra spectral features observed experimentally. One of the important interactions between an amine group and neighboring ones could be the hydrogen bond since the experimental samples were often immersed in solvent during the preparation. To examine the effect of the hydrogen bond on the N 1s IP, we have used four different molecules, water, hydrochloric acid, acetic acid, and sulfureted hydrogen to form the hydrogen bond with the amine, respectively. As it can be seen from Table 1, the presence of the hydrogen bond generally increases the core binding energy by the maximum of 1.5 eV, but reduces the relative difference among them. Most interestingly, the order of the N 1s IP for four compounds that are hydrogen bonded to hydrochloric acid and sulfureted hydrogen changes. In this case, the N 1s IP of AUDT becomes the same or even larger than that of ABT. The protonated species can also be hydrogen bonded with external agents to form the PAC and to alter the N 1s IP of the molecules. The calculated results for complexes with H2O and AC, respectively, are given in Table 1. In comparison with the PAmi, the hydrogen bond has reduced the N 1s IP by as much as 2.0 eV, for instance for the ABT. However, PAC species have still too large N 1s IP in comparison with the amine itself. There is another situation that is between the hydrogen bonding and the protonation, namely, the PAmm configure, as shown in Figure 2. For the PAmm species, only the hydroxyl ion was studied as a representative. In this case, the water molecule has almost given away its proton to the amine group. Obviously, the N 1s IP of the molecule depends on the position of the hydrogen in the middle. At this stage, we have not found a proper tool to determine the actual structure of the PAmm. We could only suggest it by fitting the experimental results with reasonable structural parameters. The best comparison with the experimental data is given in Figure 3. It shows that if we assume the bond length of O···H in PAmm species to be around 1.37 Å, and the O···H···N distance of 2.8 Å, the experimental XPS spectra for all four species can be well-reproduced.7 X-ray damage could also be the source of the extra spectral peaks. We have calculated N 1s IP of possible products, but their values, as displayed in Table 1, are not very different from those for the amine group and can certainly not explain the

dependence can be easily provided upon request. The calculated absorption spectra have been calibrated by the accurate energy value for the excitation between the 1s orbital and the lowest unoccupied molecular orbital (LUMO) obtained from ΔKS scheme. The gradient corrected BE8828 and PD8629 functionals were used to describe the exchange and correlation. The triple-ζ quality individual gauge for localized orbital (IGLO-III) basis set of Kutzelnigg et al.30 was used for the excited atom and the tripleζ plus valence polarization (TZVP) basis set for the rest of the atoms. Finally, the XPS was convoluted by Gaussian function with a full width at half-maximum (fwhm) of 1.0 eV. For the NEXAFS spectra, the different fwhm, 0.4 and 1.0 eV, were applied below and above the IP value, respectively.

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RESULTS AND DISCUSSION We will discuss the simulated XPS and NEXAFS spectra separately. Moreover, simulations are directly compared with experimental results7 to provide reasonable assignments for the features observed. X-ray Photoelectron Spectroscopy. In the experimental study, two distinct peaks have been observed in the XPS of different ω-amino-terminated SAMs with aliphatic, aromatic, and araliphatic backbones,7 which are separated on the binding energy scale by 1.5−2.0 eV, respectively. In the literature, such an energy shift for the N 1s is often attributed to the protonation of the amino group,7,31,32 but such an assignment has never been supported by theoretical calculations.31 The calculated IPs for N 1s of all considered species are listed in Table 1. It can be seen that for amine itself, the N 1s IP of AUDT has the smallest value, which might reflect the fact that in the aliphatic amine the interaction between the amine headgroup and the backbone is small. This view is supported by the observation that the calculated N−C bond length in the AUDT molecule, 1.47 Å, is the longest in all of the four amine species. On the other hand, the aromatic backbone can strongly affect the charge distribution of the amine headgroup, resulting in a blue shift in IP as large as 0.5 eV. The amine group can be easily protonated in solution and its appearance in XPS is somewhat anticipated.7 However, our calculations have shown that, for all PAmi species, the N 1s IP is significantly increased by as much as 8 eV on average. Such a large 12651


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399.7 397.3 397.1 397.4

experimental observations. It is noted that both the protonation and the hydrogen bond were considered to attribute to the extra spectral feature in XPS of these monolayers.7 With our calculations, one can at least conclude that none of them could reproduce experimental spectra and an intermediate structure, the primary ammonium, could be the cause for the changes. Near-Edge X-ray Absorption Fine Structure. The N atom bonding in the amine group is of sp3 type in AUDT but possesses certain sp2 in ATPT because of its resonant structure. For the former, its K-edge NEXAFS spectrum often exhibits a broad σ peak, while for the latter, a high-energy π*N−Ph resonance could occur close to the broad σ peak. However, preedge structures lower in energy have been observed experimentally in the NEXAFS of AUDT and ATPT,7 as recaptured in Figure 4. With the same routine as that used for the XPS calculations, we have calculated NEXAFS for all possible configurations given in Figure 2 and directly compared with the experimental results. The first transition (i.e., 1s→LUMO) of the pure amine group for AUDT is at about 400.7 eV which could be assigned to the resonance at 401 eV in the experiment. The contributions of the pure amine group are apparent above 400.7 eV, especially in the region between 401 and 404 eV. The PAmm−OH species has a contribution similar to that of the pure amine group. The PAmi and PAC−H2O both contribute to the features at about 405 eV, which have no resonance below 403 eV. These four saturated species of ATPT compound have similar contribution as in the situation of AUDT. For both compounds, the simulated spectra of the pure amine group can certainly not explain the preedge structure around 400 eV. The protonation and hydrogen bonding, and the PAmm configures also fail to generate spectral features in that energy region. It is reasonable since none of these situations can alter the intrinsic bonding character of the nitrogen and thus cannot possibly provide the low-energy π*-like spectral feature. In other words, the molecules must be severely distorted or damaged under X-ray radiation in order to change the nitrogen bonding character to produce the dominant sp2 or even the sp hybridization state. The calculated spectra for the possible damage products, such as unsaturated imine, nitrile, CDB, azo, and CL2 species, do give such π* features at the right energy position, as nicely demonstrated in Figure 4. For the AUDT compound, the experimentally observed π* structure is noticeably broader, which could be associated with the fact that there are more possible products for this species. We have only considered three X-ray damage products, azo, CL1, and CL2 species, for ATPT. The nitrogen atoms in CL1 species are in a saturated group which is similar to the free amine group without the low-energy π* peak. The low-energy π* peaks of azo and CL2 are located around 398.1 and 396.8 eV, respectively. It seems that the former gives better agreement with the experimental spectrum. The low-energy π* peaks of CL2 could give the contribution to the shoulder of the feature at 396.8 eV in the experiment.

N1 N2 N1 azo

399.0 399.2 398.7 399.2 399.3

CDB nitrile

399.1 398.5

imine HAC

405.9 406.5 405.9 406.8 406.4 406.9 406.3 407.3

H2O PAmm X OH

401.2 401.2 401.1 401.4 399.8 399.9 399.9 400.2

AC SH Cl

400.3 399.8 399.7 399.9

OH

407.3 407.9 407.1 408.7

CONCLUSION We have systematically studied different structural effects on the XPS and NEXAFS spectra of N 1s in four ω-amino-terminated SAMs with aliphatic, aromatic, and araliphatic backbones. The extra spectral features observed in the experiments have been discussed. It shows that these extra spectral features are due to the primary ammonium configuration which is between the commonly assumed protonation and hydrogen bonding, while the X-ray damage could be a problem in NEXAFS measurements

399.2 399.6 399.7 399.9

amine

■

AUDT APBT ATPT ABT

PAmi

399.8 400.1 400.0 400.3

400.7 400.5 400.4 400.7

PAC Y HBA X

Table 1. Calculated IP of N 1s (eV) for All Species under Investigations

398.6 399.5 399.3 399.7

CL1

399.2 399.6 399.5 399.7

397.6 398.0 397.4 398.0

CL2

N2


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Figure 3. Calculated N1s XPS of AUDT, ABT, APBT, and ATPT (right) compared with the corresponding experimental results7 (left). The bond lengths marked on the molecules are given in angstroms.

Figure 4. Calculated N1s NEXAFS spectra of ATPT (right) and AUDT (left) and their derivatives compared with experiment.7.

Notes

for molecular monolayers and should be carefully considered in the future.

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The authors declare no competing financial interest.

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AUTHOR INFORMATION

Corresponding Author

ACKNOWLEDGMENTS

This work is supported by the National Natural Science Foundation of China (Grant 20925311) and the Gö ran Gustafsson Foundation for Research in Natural Sciences and

*E-mail: [email protected]. Phone: +46 (8)55378414. Fax: +46 (8) 55378590. 12653



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Medicine. The Swedish National Infrastructure for Computing (SNIC) is acknowledged for computer time.

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Effects of Protonation, Hydrogen Bonding, and Photodamaging on X

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