Autocatalytic Dissociative Adsorption of Imidazole on the Ge(100)-2

Satta, M.; Flammini, R.; Goldoni, A.; Baraldi, A.; Lizzit, S.; Larciprete, R. Fundamental Role of the H-Bond Interaction in the Dissociation of NH3 on...
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Autocatalytic Dissociative Adsorption of Imidazole on the Ge(100)‑2 × 1 Surface Bonggeun Shong,†,‡ Jessica Kachian,†,§ and Stacey F. Bent*,† †

Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, California 94305, United States Department of Chemical Engineering, Hongik University, 94 Wausan-ro, Mapo-gu, Seoul 04066, South Korea

S Supporting Information *

ABSTRACT: The adsorption of imidazole on the Ge(100)-2 × 1 surface is studied with ultrahigh vacuum infrared spectroscopy experiments and density functional theory calculations. Imidazole datively bonds to the surface through its pyridinic nitrogen at low coverage, while dissociation of the pyrrolic N−H is observed upon larger exposure. The coverage-dependent change in the product distribution is explained by autocatalytic activation of the dissociative adsorption via interaction between adjacent imidazole adsorbates. These results suggest an alternative explanation for the previously studied adsorption chemistry of bifunctional ethylenediamine on Ge(100)-2 × 1.

INTRODUCTION Direct functionalization of semiconductor surfaces with organic molecules has drawn much interest since many physical and chemical properties of the surface can be manipulated at the molecular level toward various applications, including catalysis, electronics, and optoelectronics.1−5 Upon proper preparation under vacuum, the technologically important (100) surfaces of Ge and Si undergo (2 × 1) reconstruction to form repeating arrays of ordered dimers. Each dimer on these (2 × 1) reconstructed Group 14 (100) surfaces comprises an electrophilic “down” atom and nucleophilic “up” atom that undergo specific reactions with organic molecules, including acid−base reactions and cycloadditions.6 Among organic molecules, aromatic heterocyclic compounds containing nitrogen are essential in many fields, especially in biochemistry and medicinal chemistry,7,8 as well as in emerging applications such as ionic liquids and metal−organic frameworks.9−11 Pyrrolic (N(sp3)-H) and pyridinic (N(sp2):) nitrogen centers of aromatic heterocycles show distinctly different reactivity resulting from differences in the level of participation of the lone pair electrons in the aromatic conjugation;12 while pyrrolic nitrogen is less basic/nucleophilic and more acidic than aliphatic amines, pyridinic nitrogen exhibits significant basicity and nucleophilicity. Aromaticity can be an important factor in determining product structure upon adsorption of organic molecules on solid surfaces, in that reaction pathways which break the aromaticity of the reactant are generally disfavored.13 Adsorption of several N-containing aromatic heterocycles on the Ge(100)-2 × 1 surface, including pyrrole,14,15 pyridine,16−18 pyrimidine,19 pyridazine,20 thiazole,21 hydroxypyridine and pyridone,22 3-methyl-5-pyrazolone,23 guanine,24 and purine,25 have been studied to date. As discussed above, the nitrogen © XXXX American Chemical Society

moieties of these heterocycles show different reactivity upon adsorption; pyrrole undergoes N−H dissociation,14,15 while molecules with pyridinic nitrogen form N−Ge dative bonds.16−21 Imidazole is a rigid five-membered aromatic heterocycle that possesses both pyrrolic (N1) and pyridinic (N3) nitrogens. The adsorption chemistry of a few molecules that include imidazole as part of their structure, but not that of imidazole itself, has been investigated on Group 14 semiconductor surfaces. For example, N3-dative bonding and interadsorbate hydrogen bonding on Ge(100)-2 × 126,27 and a single-dimer N−H dissociative adsorption on Si(100)-2 × 128 have been considered for the imidazole moiety of histidine; the imidazole moiety of purine undergoes interdimer N−H dissociation once the molecule is anchored on Ge(100)-2 × 1 by double-dative bonding of two pyridinic nitrogens.25 These reactions provide insight into the adsorption chemistry of imidazole on Ge(100)-2 × 1, although the reactivity of an organic functional group may change when anchored to the surface through another part of the molecule.29,30 Interadsorbate interactions can also affect the chemistry of the molecules on solid surfaces. Examples of such cooperative surface reactions can be found among both adsorption and desorption/decomposition.31−35 An exemplary autocatalytic adsorption on semiconductor surfaces is the reaction of NH3 with Si(100)-2 × 1, for which clustering of N−H dissociated products was observed due to enhanced adsorption in the vicinity of other adsorbates. Several mechanisms for interReceived: August 3, 2017 Revised: August 29, 2017


DOI: 10.1021/acs.jpcc.7b07691 J. Phys. Chem. C XXXX, XXX, XXX−XXX


The Journal of Physical Chemistry C

Figure 1. Possible products and transition states of the reaction of (a) one isolated imidazole molecule with Ge(100)-2 × 1 and (b) two adjacent imidazole molecules with Ge(100)-2 × 1. Reaction steps that are likely to proceed are marked with black solid lines, while the steps unlikely to proceed according to the DFT calculation results are marked with gray dotted lines. For the DFT-optimized geometries, yellow = dimer Ge, green = subsurface Ge, blue = N, gray = C, and white = H. Terminating H atoms of Ge15H16 cluster are not shown for simplicity.

EXPERIMENTAL AND THEORETICAL METHODS FTIR spectroscopy experiments were conducted under ultrahigh vacuum (UHV) conditions in a previously described chamber41 with a base pressure of 99%, Sigma-Aldrich) was further purified by degassing under high vacuum for several hours. The clean Ge(100)-2 × 1 surface at room temperature was exposed to imidazole vapor in equilibrium with its solid at room temperature through a variable leak valve using a directed doser. The dose of the vapor is reported in L (langmuir, 1 L = 10−6 Torr·s), which should be used as a relative measure because the pressure gauge was not in the line of sight with the doser. FTIR spectra were collected by a Nicolet 6700 FTIR spectrometer in multiple internal reflection (MIR) geometry using an external HgCdTe detector. Absorption of the IR light by CaF2 viewports resulted in a low-frequency cutoff of ∼1000 cm−1. Baseline sloping of FTIR spectra was corrected by subtracting spline functions fit to points devoid of spectral features. DFT calculations were performed with the Gaussian 03 software.42 A Ge15H16 cluster with two dimers within the same dimer “row” was used to model the Ge(100)-2 × 1 surface. The bottom two Ge layers of the cluster were fixed at the ideal crystal positions. The B3LYP hybrid functional was used with a split basis set utilizing 6-311++G(d,p) for adsorbate molecules

adsorbate interactions have been proposed for NH3/Si(100)-2 × 1, including adsorbate-induced change in local electronic36 or geometrical37 structure of the substrate, as well as formation of hydrogen bonds between the molecules.38 Self-assembly of pyrazine on Si(100)-2 × 1 provides another example of enhancement of the adsorption probability at sites nearby other adsorbates for which additional stabilization can be achieved by occupation of dangling bonds on the surface.39,40 All of these effects can likewise be present during adsorption of imidazole at the Ge(100)-2 × 1 surface, which also can donate electronic density to the surface and has an acidic N−H moiety. In this study, we investigate the coverage-dependent adsorption behavior of imidazole on the Ge(100)-2 × 1 surface using Fourier-transform infrared (FTIR) spectroscopy and density functional theory (DFT) calculation. It is found that imidazole, at low coverage, adsorbs by dative bonding of pyridinic nitrogen, which is the only energetically allowed product for imidazole adsorbates isolated from each other. Upon higher exposure, intermolecular interactions between two adjacent imidazole adsorbates enable N−H dissociation of these molecules, converting the dative bonded product to a surface imidazolate and a hydrogen adatom. The proposed reaction mechanism of imidazole on the Ge(100)-2 × 1 surface is summarized in Figure 1. Our study provides a new example of an autocatalytic reaction of an organic molecule on a semiconductor surface and yields insight into the adsorption behavior of bifunctional molecules. B

DOI: 10.1021/acs.jpcc.7b07691 J. Phys. Chem. C XXXX, XXX, XXX−XXX


The Journal of Physical Chemistry C

aromaticity can be excluded. The low-coverage product can be assigned to molecular adsorption via dative bonding. The observed spectra are similar to those of molecular or anionic imidazole adsorbates on metallic surfaces in the literature.45−47 However, although IR spectra of molecularly and dissociatively adsorbed imidazole were calculated by DFT (Figure S1, Supporting Information), all vibrational features of both molecular imidazole and N−H dissociated imidazolate in the 1100−1600 cm−1 region are combinations of multiple vibrational modes (CC and CN stretching, C−H bending),48 and thus, assignment of the currently observed spectral features in this range is obscured. DFT calculations show that the energetics of the reaction of imidazole with the Ge(100)-2 × 1 surface changes from molecular adsorption to dissociative adsorption according to the absence or presence of a neighbor (Figure 3). For an isolated imidazole molecule on Ge(100), the adsorption energy (Eads) of dative bonding through the pyridinic N3 (N3-dat) is as large as −28.3 kcal/mol, while the analogous structure with an N1−Ge bond (N1-dat) could not be located. Since formation of dative bonding on Si or Ge surfaces is barrierless,49,50 N3-dat is a relevant product, both kinetically and thermodynamically. Moreover, it is reasonable to assume that dative bonded imidazole species are separated from one another at low coverages since strongly electron-donating adsorbates face surface-mediated repulsive interactions.36,51 At the same time, other reaction products of a single, isolated imidazole on Ge(100), including dissociative adsorption or cycloaddition, are unlikely to form for the following reasons. The N1−H bond is considered for dissociation since it is the most acidic moiety of imidazole.52 However, according to DFT calculations, the transition states for intradimer N1−H dissociation (intra-diss) are prohibitively endothermic through either direct (N1−Ge formation/N1−H dissociation, N1-intra-TS) or cooperative (N3−Ge formation/N1−H dissociation, N3-intra-TS) transition states, kinetically hindering such reactions. Interdimer N1−H dissociation accompanied by N3−Ge bond formation, analogous to the reaction of purine with Ge(100),25 is also considered. However, while the energy of interdimer transition state (N3-inter-TS) lies lower than those of intradimer pathways, Eads of the product (inter-diss) is smaller than that of N3-dat, making the reaction thermodynamically unfavorable. In addition, three possible cycloaddition products are considered, of which all products are significantly less stable than N3-dat: (i) [2 + 2] addition of C2−N3 (could not be located), (ii) [2 + 2] addition of C4−C5 (Eads = −1.1 kcal/mol), and (iii) [4 + 2] addition of C2−C5 (Eads = −4.6 kcal/mol). Therefore, the DFT results suggest that isolated imidazole adsorbates at low coverage will be trapped in the dative bonding state, confirming the assignment made from the experimentally measured, low-coverage IR data. The adsorption energetics can change notably when coverage increases. DFT calculations suggest that N−H dissociative adsorption will occur when two N3-dative bonded imidazole molecules are placed adjacent to each other, due to favorable interactions between the two adsorbates (Figure 3). Dative bonding of a second adsorbate on the two-dimer Ge cluster (2N3-dat) is exothermic by 23.0 kcal/mol from N3-dat, 5 kcal/ mol smaller than Eads of N3-dat. The dependence of Eads on the density of dative bonding adsorbates manifests the repulsive interactions between this species. Successive N−H dissociations of 2-N3-dat through an interdimer pathway are kinetically and thermodynamically allowed with lowered activation barriers

and Ge dimers, LANL2DZ for subsurface Ge, and 6-31G(d) for the terminating H. The transition state geometries were initially guessed and then confirmed after optimization to have an imaginary vibrational frequency along the reaction coordinate. Zero-point energy correction was not applied to the reported energies. Harmonic vibrational frequencies were analytically determined with assignment of a mass of 74.0 u to the terminating H atoms and were scaled by a factor of 0.97.43 Lorentzian lineshapes with a full width at half-maximum (fwhm) of 10 cm−1 and relative calculated intensities were used to represent the calculated IR peaks.

RESULTS AND DISCUSSION In the coverage-dependent IR spectra of imidazole adsorbed on Ge(100)-2 × 1 at room temperature, a transition from one product structure to another was observed (Figure 2). Intensity

Figure 2. Coverage-dependent IR spectra of imidazole adsorbed on Ge(100)-2 × 1 at room temperature with exposures between 0.7 and 8.7 L. The dotted spectrum at the bottom represents the difference spectrum between 8.7 and 0.7 L.

of the initially appearing set of peaks at