Adsorption Selectivities between Hydroxypyridine and Pyridone Adsorbed on the Ge(100) Surface: Conjugation and Geometric Configuration Effects on Adsorption Structures

Abstract

The most stable adsorption structures and their corresponding energies of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine have been investigated by Density Functional Theory (DFT) calculation and high-resolution photoemission spectroscopy (HRPES). We confirmed that between the two reaction centers of 4- and 2-pyridone, only O atom of carbonyl functional group can act as a Lewis base while both the two reaction centers of 4- and 2-hydroxypyridine (tautomers of 4- and 2-pyridone) can successfully function as a Lewis base. On the other hand, owing to their molecular structures, there is a remarkable difference between the adsorption structures of 4- and 2-hydroxypyridine. Through the analysis of the N 1s and O 1s core level spectra obtained using HRPES, we also could corroborate that two different adducts coexist on the surface at room temperature due to their activation energy investigating the coverage dependent variation of bonding configurations when these molecules are adsorbed on the Ge(100) surface.

Introduction

Over the past decades, many researchers have studied the interactions between functional groups being included in organic molecules and semiconductor surfaces due to possible industrial applications in a number of fields such as nanobiotechnology, chemical biology and biomedical science. It is clear that these technologies which have a direct correlation to the interactions between biomolecules and semiconductor surfaces can play a significant role in promising applications in biosensors, molecular electronics and immunoassay sensors.1-10

Among many different kinds of bio-molecules, we present the results of the adsorption energies, optimized structures and geometric configurations using DFT calculation method and high-resolution photoemission spectroscopy (HRPES) when 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine are adsorbed on Ge(100) surfaces. The Ge(100) surface, which is one of the Group IV semiconductor surfaces, possesses a strong σ bond and a weak π bond resulting in the formation of surface dimers. Since these dimers are tilted, they can produce unequal charge distribution on Ge(100) surfaces, allowing the Ge(100) surfaces to have zwitterion-like properties. Owing to this intrinsic and characteristic property that the Ge(100) surfaces can function as a Lewis acid and a base, many different kinds of biomolecules and organic molecules can be successfully adsorbed on the Ge(100) surfaces through σ bond dissociation or dative bond formation.11,12

We observed adsorption energies, optimized structures and configurations of four organic molecules in this study: 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine hydroxypyridine (see Scheme 1). Pyridone and pyridone derivatives can successfully function as an anti-bacterial agent in human body and thus, they actively have been studied.13-19 Hence, the study of the interaction between these molecules and semiconductors would make a practical contribution to the promising applications in biosensors. Interestingly, these molecules have in common with each other in that they have the same molecular formula. In detail, pyridone and hydroxypyridine are tautomers of each other, which are organic compounds that can be interconvertible by a chemical reaction called tautomerization resulting in the migration of hydrogen with a switch of a single bond and adjacent double bond.20,21

Tautomerism is a special case of structure isomerism as well as plays a crucial role in non-canonical base pairing in DNA and especially RNA molecules.22-28 In the case of pyridone and hydroxypyridine, the protomeric tautomerism of heteroaromatic compounds involving the transfer of hydrogen between cyclic nitrogen and a substituent atom adjacent to the ring has been studied by many researchers due to importance in biological processes such as mutagenesis.29

As shown in Scheme 1, all of these organic molecules have the two reactive centers, respectively: an O atom of hydroxyl functional group, a cyclic N atom in hydroxypyridine, an O atom of carbonyl functional group and a cyclic N atom in pyridone.

Scheme 1.(a) The structures of the two tautomers of 4-pyridone (left) and 4-hydroxypyridine (right) and (b) those of 2-pyridone (left) and 2-hydroxypyridine (right). The red, purple, white and gray balls indicate oxygen (O), nitrogen (N) hydrogen (H) and carbon (C), respectively.

In this paper, after observing the possible adsorption structures of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2- hydroxypyridine through DFT calculation method, we will substantiate which adduct is the most stable adsorption structure among them when they are adsorbed on the Ge(100) surface using the analysis N 1s and O 1s core level spectra acquired from HRPES. Also, we will suggest which reaction center of these molecules can act as a Lewis base and which reaction pathway can be favored.

 

Experimental and Computational Details

DFT calculations were conducted to predict the energetics of the reaction pathways and the geometrically optimized structures of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridinewhen they adsorbed on the Ge(100) surfaces. All the DFT adsorption energy calculations were carried out with the JAGUAR 9.1 software package by employing a hybrid density functional method that included the Becke’s three-parameter nonlocal exchange functional and the correlation functional of Lee–Yang–Parr (B3LYP).30 The geometries corresponding to the important local minima and transition states on the potential energy surface were determined at the B3LYP/LACVP** level of theory. The LACVP** basis set is a mixed basis set that uses the LACVP basis set to describe Ge atoms and the 6-31G basis set to describe the remaining atoms. For each cluster, optimization was performed by fixing the bottom two layers of the Ge atoms in ideal Ge crystal positions while allowing the top layer of Ge atoms (including the dimer atoms) and the atoms of the chemisorbed adsorbate to relax.

The Ge(100) surfaces (p-type, R = 0.10-0.39 W) were cleaned by several cycles of Ar+ ion sputtering at 1 keV for 20 minutes at 700 K, followed by annealing at 900 K for 10 minutes. The cleanness of the Ge(100) surfaces was checked by performing low-energy electron diffraction (LEED) measurements. 2-pyridone and 4-pyridone (C5H5NO, 98% purity) was purchased from Aldrich and further purified with several sublimation and pumping cycles to remove dissolved gases prior to exposure to the Ge(100) surface.

The HRPES measurements were conducted at the 10D beamline of the Pohang Accelerator Laboratory. The N 1s and O 1s core-level spectra were obtained with a PHOIBOS 150 electron energy analyzer equipped with a two-dimensional charge-coupled device (2D CCD) detector (Specs GmbH). Photon energies of 460 eV and 590 eV were used to enhance the surface sensitivity. The binding energies of the three core-level spectra were calibrated with respect to that of the clean Au 4f core-level spectrum (84.0 eV) for the same photon energy. The base pressure of the chamber was maintained below 1.2 × 10–10 Torr. All spectra were recorded in the normal emission mode. The photoemission spectra were carefully analyzed by using a standard nonlinear least squares fitting procedure with Voigt functions.31 We have estimated the coverage based on the N 1s multi-layer peak. The peak of multi-layer structures of nitrogen-containing molecules such as amino acids is usually obtained near at 399 eV. 2-pyridone and 4-pyridoneis deposited every 30 seconds until the multi-layer peak is observed. We defined the coverage as we obtained around the time when we observed multi-layer peak as 1.10 ML.

 

Results and Discussion

To begin with, we acquired the possible adsorption structures and their respective energies of 4-and 2-pyridone (See Figure 1). Among possible adsorption structures through only one functional group of 4- and 2-pyridone, we obtained that the N-H dissociated bonding structure is the most stable. However, the N-H dissociation pathway cannot proceed at room temperature although the N-H dissociated state is the most stable. In ultra-high vacuum (UHV) condition, the X-H dissociation (X = O or N) should proceed via the X dativebonded state because there is no solvent, which is able to interact with molecules or the surface material, allowing the products to dissociate their hydrogen and to be adsorbed on the surface material.32 In this case, the lone pair on the N atom of the hetero-ring is too stable to react and form a Ndative bond to a Ge(100) surface, because the lone pair is fully conjugated with the other π electrons in the ring. In other words, the N-H dissociation pathway cannot proceed because the conjugation effect prevents the molocule from forming the N-dative bonded state to the Ge(100) surface. For this reason, the O-dative bonded adducts of 4-and 2-pyridone with their carbonyl functional group are not only the most kinetically facile but also thermodynamically stable at room temperature considering the adsorption energy of 4-pyridone (−28.84 kcal/mol) and that of 2-pyridone (−28.94 kcal/mol). Also, in the case of 4- and 2-pyridone, only one reaction center (the O atom of carbonyl functional group) can act as a Lewis base forming dissociated or dative bonding.

Figure 1.The possible adsorption structures through one functional group of 4- and 2-pyridone (a) N-H dissociated bonding structure (left) and O dative bonding structure (right) of 4-pyridone (b) N-H dissociated bonding structure (left) and O dative bonding structure (right) of 2-pyridone.

Figure 2.The possible adsorption structures through one functional group of 4- and 2-hydroxypyridine (a) O dative bonding structure (left), O-H dissociated bonding structure (center) and N dative bonding structure (right) of 4-hydroxypyridine (b) O dative bonding structure (left), O-H dissociated bonding structure(center) and N dative bonding structure (right) of 2-hydroxypyridine.

Figure 2 presents some possible adsorption structures of 4- and 2-hydroxypyridine. Among the possible adsorption structures through only one functional group, the O-H dissociated bonding structures are the most thermodynamically stable. In this adsorption reaction, the O-H dissociation pathway can proceed via O dative-bonded state on the Ge(100) surface with the adsorption energy of −39.88 kcal/mol in 4- hydroxypyridine and −41.94 kcal/mol in 2-hydroxypyridine. This means that this pathway is highly exothermic and thus, can form considerably stable adducts on the Ge(100) surface at room temperature, according to the calculated energy values and structures that we present on Figure 2.

Given that 4- and 2-hydroxypyridine have another reaction center (See Scheme 1), it is possible for them to react through another one to form another bonding with inter- or intra-dimer of the Ge(100) surface. To consider the possibilities for another inter- or intra-dative bonding reaction, we calculated these adsorption energies starting from the O-H dissociated state. In the case of 4-hydroxypyridine, the cyclic N atom can form a N dative bond to a germanium atom because there is a reactive lone pair on the atom. As shown in Figure 3, inter-bonding adsorption energy of -55.40 kcal/ mol is significantly lower than intra-bonding adsorption energy of -35.28 kcal/mol.

Figure 3.The O-H dissociated N dative bonding structure of 4-hydroxypyridine (a) The N dative intra-bonding structure (b) The N dative inter-bonding structure.

Figure 4.Potential energy surfaces, calculated using DFT methods, for the formation of dissociated N dative intra-bonding.

Moreover, when comparing Figures 4 and 5, the transition state energy of the N dative intra-bonding is considerably higher than that of the N dative inter-bonding. Also, the N dative intra-bonding reaction is endothermic, which means that the reaction pathway is rarely favored at room temperature. For these reasons, the O-H dissociated N dative interbonding structure is the most thermodynamically stable and kinetically facile and thus, this reaction pathway is far more favored than the other one. In this reaction pathway, both the two reaction centers (the cyclic N atom and the O atom of hydroxyl functional group) can successfully function as a Lewis base forming dissociated and dative bonding.

On the other hand, the N-dative inter-bonding pathway starting from the O-H dissociated state of 4-hyroxypyridine shown in Figure 5 is kinetically facile due to the low activation energy of −38.23 kcal/mol. In contrast, the activation energy of the O-H dissociation pathway is just slightly lower than the entrance channel. In other words, it is not easy for 4-hydroxypyridine to proceed the O-H dissociation reaction but it is significantly favorable for it to form the N dative inter-bonding from the O-H dissociated state. Therefore, 4-hydroxypyridine is likely to exist between the two adducts, the O-dative bonded state and the O-H dissociated N dative bonded state, and the O-H dissociated state rarely exists at room temperature.

Figure 5.Potential energy surfaces, calculated using DFT methods, for the formation of O-H dissociated N dative inter bonding. (a) O dative bonding, (b) transition state for O-H dissociated bonding, (c) O-H dissociated bonding, (d) transition state for O-H dissociated N dative inter bonding and (e) O-H dissociated N dative inter bonding of 4-hyroxypyridine on the Ge(100) surface.

Figure 6.Potential energy surfaces, calculated using DFT methods, for the formation of O-H dissociation bonding. (a) O dative bonding, (b) transition state for O-H dissociated bonding and (c) O-H dissociated bonding of 2-hyroxypyridine on the Ge(100) surface.

Whereas 4-hydroxypyridine is able to form the O-H dissociated N-dative bonding on the Ge(100) surface, 2-hydroxypyridine cannot form any N dative bonding to a germanium atom due to its molecular structure. Figure 6 shows that since 2-hydroxypyridine cannot react anymore from the O-H dissociated state, the O-H dissociated bonding structure is the final adsorption structure which is the most stable. This is due to the fact that the cyclic N atom is directly adjacent to the hydroxyl functional group and thus, it is too long to form any N dative intra- or inter-bonding to a germanium atom, which means that only O atom of hydroxyl functional group can practically form dissociated or dative bonding on the Ge(100) surface. Therefore, there is a huge difference between 4- and 2-hydroxypyridine in the most stable adsorption structures on the Ge(100) surface: the most stable adduct of 4-hydroxypyridine is the O-H dissociated N-dative interbonding structure but that of 2-hydroxypyridine is the O-H dissociated bonding structure.

According to Figure 6, 2-hydroxypyridine is likely to exist between the two states, the O-dative bonded state and the O-H dissociated state, at room temperature. This is because it is not easy for all 2-hydroxypyridine to form only the O-H dissociation bonding on the Ge(100) surface due to the activation energy which is only slightly lower than the entrance channel, even if the O-H dissociated state is considerablely stable than the O-dative bonded state considering its adsorption energy. As a result, 2-hydroxypyridine exists between these two adducts, the O dative bonded state and the O-H dissociated state, at room temperature.

We obtained HRPES data for the core-levels in a 2-pyridone molecule with its tautomer 2-hydroxy pyridine (Figure 7) and in a 4-pyridone molecule with its tautomer 4-hydroxy pyridine (Figure 8) adsorbed onto the Ge(100) surface to substantiate our DFT calculation results.33,34

Figure 7.O 1s and N 1s core-level spectra for 2-pyridone adsorbed on the Ge(100) surface as a function of coverage: O 1s core level spectra obtained from (a) 0.15 ML, (b) 0.45 ML and (c) 0.75 ML and N 1s core level spectra acquired from (d) 0.15 ML, (e) 0.45 ML and (f) 0.75 ML. The dots indicate experimental values and the solid lines represent the results of peak fitting.

To begin with, Figure 7 shows a series of O 1s and N 1s core-level spectra as a function of the 2-pyridone with its tautomer, according to three distinct coverage levels (0.15 ML, 0.45 ML, and 0.75 ML). As shown in this figure, there are two distinct bonding features corresponding to the two oxygen of 2-pyridone and 2-hydroxypyridine (see Figure 7). Considering electronegativity and binding energy, we assigned the bonding features O1 to O-H dissociated bonding structure (530.7 eV) and O2 to O dative bonding structure (532.5 eV). As shown in the O 1s core-level spectrum in Figure 7(a) acquired after the formation of a sample of 0.15 ML 2-pyridone with its tautomer, the intensity of O1 peak is higher than that of O2 peak, which means that O-H dissociation bonding structure is easier to appear on the Ge(100) surfaces through the adsorption than O dative bonding structure at the low coverage. This also corroborates our DFT calculation results that the adsorption energy of the OH dissociation bonding structure of 2-hydroxy pyridine is lower than that of the O dative bonding structure because a molecule with a low adsorption energy is easier to be adsorbed on the Ge(100) surfaces at the low coverage than with a high adsorption energy. As we increased the coverage level from 0.15 ML to 0.75 ML, the intensity of O1 peak decreased whereas that of O2 increased, which implies that the O dative bonding structure with a high adsorption energy is more likely to be formed on the Ge(100) surfaces at the high coverage. Based on this HRPES data analysis, we can confirm our DFT calculation data that the O-H dissociation bonding structure is more stable than the O dative bonding structure but these two different states coexist on the Ge(100) surfaces at room temperature due to its activation energy. N 1s core-level spectra also supports this phenamenon in that according to the increase in the coverage level from 0.15 ML to 0.75 ML, the intensity of N1 peak decreased while that of N2 peak increased given that from electronegativity and binding energy, N1 (398.0 eV) and N2 (399.4 eV) is assigned to an imino and amino nitrogen, respectively.

Figure 8.O 1s and N 1s core-level spectra for 4-pyridone adsorbed on the Ge(100) surface: O 1s core level spectra obtained from (a) 0.15 ML, (b) 0.45 ML and (c) 0.75 ML and N 1s core level spectra obtained from (a) 0.15 ML, (b) 0.45 ML and (c) 0.75 ML. The dots indicate experimental values and the solid lines represent the results of peak fitting.

Figure 8 presents a series of O 1s and N 1s core-level spectra as a function of the 4-pyridone with its tautomer, according to three distinct coverage levels (0.15 ML, 0.45 ML, and 0.75 ML). Given that the N1, N2 and N3 peak are respectively assigned to imino nitrogen (398.0 eV), amino nitrogen (399.4 eV) and O-H dissociated N dative nitrogen (401.3 eV) according to their electronegativity and binding energy, we can assign O1, O2 and O1' peak to O-H dissociation bonding feature (530.7 eV), O dative bonding feature (532.5 eV) and O-H dissociated N dative bonding feature (531.0 eV), respectively. As shown in Figure 8(a), the adsorption energy of O-H dissociated N dative bonding feature is lower than that of O dative bonding feature because they are more populated at the low coverage with high intensity. According to the increase in the coverage level, the intensity of O2 peak increased while that of O1' significantly decreased. In addition, a new O1 (530.7 eV) and N1 (398.0 eV) peak appears with a disappearance of O1' and N3 peak in the O 1s and N 1s core-level spectra which indicates that O-H dissociation bonding structure is preponderant at the high coverage. This can also corroborate that the binding energy shifts from 531.0 eV (marked as O1') to 530.7 eV (marked as O1) with an increase in the coverage level. Based on this analysis, we substantiate our DFT calculation data that the O-H dissociated N dative bonding structure is the most thermodynamically stable among any other structures. However because of the activation energy which is slightly lower than the entrance level, there are two bonding states (the O dative and the O-H dissociated N-dative bonding structure) at room temperature.

Figure 9 shows the final adsorption structures of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine, which are the most stable respectively, considering their adsorption energies and the HRPES data. However, given that the activation energies of O-H dissociation pathway of 4-and 2-hydroxypyridine are just slightly lower than the entrance channel, they are likely to exist between two states at room temperature: O dative bonded state and O-H dissociated N dative inter-bonded state in 4-hydroxypyridine and O dative bonded state and O-H dissociated state in 2-hydroxypyridine.

Figure 9.The most stable adsorption structures of 4-, 2-hydroxy pyridine and 4-, 2-pyridone (a) the O dative bonding of 4-pyridone, (b) the O-H dissociated N dative inter-bonding of 4-hydroxypyridine, (c) the O dative bonding of 2-pyridone and (d) the O-H dissociated bonding structure of 2-hydroxypyridine.

 

Conclusion

Using DFT calculation method, we observed the possible adsorption structures and energies of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine. Through this, we could confirm the most stable adsorption structure and the most favorable reaction pathway of them. We investigated that the final adsorption structure of 4-pyridone and 2-pyridone is the O dative bonded state owing to the conjugation which prevent the lone pair of the cyclic N atom from participating in bond formation. Therefore, only O atom of carbonyl functional group is able to act as a reaction center which can form dative or dissociated bonding on the Ge(100) surface between the two reaction centers, an O atom of carbonyl functional group and a cyclic N atom of heteroring, of 4- and 2-pyridone.

In contrast, all of the two reaction centers of 4- and 2-hydroxypyridine can act as a Lewis base because the lone pair of the cyclic N atom does not participate in conjugation with the other π electrons. In the case of 4-hydroxypyridine, since both the O atom of hydroxyl functional group and the cyclic N atom of hetero-ring successfully participate in bond formation, the O-H dissociated N dative inter-bonding is the most stable. On the other hand, 2-hydroxypyridine also can proceed the O-H dissociation reaction through the O dative bonding but it cannot form any N dative bonding due to its molecular structure. As a result, the most stable adsorption structure of 2-hydroxypyridine is the O-H dissociated state and only O atom of hydroxyl functional group can practically contribute to bond formation on the Ge(100) surface.

Last but not least, considering HRPES data when 4- and 2-hydroxypyridine and their tautomers are adsorbed on the Ge(100) surface, they are likely to exist between the two states. This is because, the activation energy of the O-H dissociation pathway is nearly the same as the entrance channel although the final adsorption adduct is significantly stable.

In summary, when 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine is on the Ge(100) surface, the most stable adsorption adduct is the O-H dissociated N dative inter-bonding structure of 4-hydroxypyridine because all of the two reaction centers play a significant role in bond formation. Considering some factors affecting reaction centers, we confirm that a conjugation prevents them from acting as Lewis base with the case of 4- and 2-pyridone. Moreover, a molecular structure has an effect on dative bond formation, given that 2-hydroxypyridine cannot form any dative bond from the O-H dissociated state because it is too long for the N atom, which is directly adjacent to hydroxyl functional group, to form a dative bond to a germanium atom.