Role of Electronic Structures and Dispersion Interactions in Adsorption

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

Role of Electronic Structures and Dispersion Interactions in Adsorption Selectivity of Pyrimidine Molecules with a Si(5 5 12) Surface Gyu-Hyeong Kim, Sukmin Jeong, Insup Lee, Md. Abu Hanif, Md. Akherul Islam, Kamal P. Sapkota, and Jae R. Hahn J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b03520 • Publication Date (Web): 19 Jul 2019 Downloaded from pubs.acs.org on July 22, 2019

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The Journal of Physical Chemistry

Role of Electronic Structures and Dispersion Interactions in Adsorption Selectivity of Pyrimidine Molecules with a Si(5 5 12) Surface

G-H. Kim,1 S Jeong,1,* 1Department

of Physics, Chonbuk National University, Jeonju 54896, Korea

I. Lee,2 Md. A. Hanif,2 Md. A. Islam,2 K. P. Sapkota,2 J. R. Hahn2,3,* 2Department

3Textile

of Chemistry, Chonbuk National University, Jeonju 54896, Korea

Engineering, Chemistry and Science, North Carolina State University 2401 Research Dr. Raleigh, NC 27695-8301, USA

*Corresponding authors: [email protected] (SJ) and [email protected] or [email protected] (JRH)

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Abstract We show that the resonance energy and dispersion interactions (DIs) are critical factors in determining the selectivity and configuration in the reaction of pyrimidine molecules with a silicon surface. The atomic structures of the pyrimidine molecules after they reacted with a Si(5 5 12)–2×1 surface were studied. Binding configurations of the pyrimidines were distinct from those of other molecules having with N lone-pair electrons and aromaticity. The pyrimidine molecules were adsorbed to produce two σ bonds to silicon with N2 and C5 on the adatom row (Adr) and the honeycomb chain (Hnc) sites and with C1 and C4 on the dimer row (Dmr) and the tetramer row (Ttr) sites. The reactions occurred via a [4+2]-type cycloaddition to produce planar-type configurations with a loss of aromaticity. That is, the atoms of the aromatic ring of pyrimidine form chemical bonds with silicon atoms, which is in contrast to the adsorption behaviors reported for other N-containing aromatic molecules. When pyrimidine is adsorbed, its molecular orbitals are distorted because the NSi bond axis does not coincide with the molecular orbital symmetric axis. Therefore, the vertical geometry is relatively unstable. DIs contribute a range of 0.4–0.6 eV for all stable adsorption structures and are essential for producing planar-type configurations on the Dmr and Ttr sites. In the absence of DIs, the vertical structure is stable; however, but when DIs are included, the planar-type configuration becomes more stable. Moreover, even though the aromaticity is stabilized in the vertical structure, the greater adsorption energy for the flat structure of pyrimidine is mainly attributed to the lower energy cost involved in breaking the aromaticity.


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1. Introduction Si is practically important and has various reactivities with organic molecules to form covalent bonds.1-8 Such covalent interactions result in substantial modification of the geometrical and electronic characteristics of the reactants. Various surface reactions are involved during organic reactions such as nucleophilic or electrophilic reactions, which may involve ring opening and bond breaking. Because the diversity of these reactions depends on thermodynamics and kinetics, the Si surface functionality should ideally be tunable over a wide range. However, such tuning requires precise control of the competition among and the selectivity and dynamics of the surface reactions. Covalent bonds are generally very strong; however, the energy differences among adsorbed molecular structures can be small. Their relative stabilities and the effect of the adsorbed structure is an important issue in tuning the surface functionality. In particular, van der Waals (vdW) forces or resonance stabilization, which are weaker than covalent interactions, can strongly affect the product structure. Given that even slight structural differences determine the functionality of molecules on Si surfaces, a method to account for such small forces is needed. vdW forces are weaker than typical chemical interactions, but their long-range influence and collective effects play critical roles in determining the structure of adsorbates and their interactions with substrates.9-15 Dispersion interactions (DIs) are the weakest intermolecular force among the vdW interactions. However, the DIs of the organic molecules are relatively large and an adsorption energy of 1 eV or greater is possible on an inert surface.9 The energy barrier for diffusion or hopping on the surface can be as large as ~100 meV.9 Moreover, the adsorption energies and diffusion barriers may depend on the size of the



molecular species such that that they span a far wider range. Therefore, the kinetic energy reduction of valence electrons and DIs may dominate the interactions between inert surfaces and organic molecules. Furthermore, an additional factor of resonance stabilization is encountered when aromatic molecules react with a surface. That is, organic compounds with multiple functional groups that include an aromatic ring may have an adsorption configuration that, because of the stabilization, does not break the molecule’s aromaticity. The energy associated with this stabilization effect is less than one-third of the energy of a covalent bond between an aromatic molecule and Si in the gas phase but becomes smaller after adsorption. Therefore, the resonance effect and the DIs, as well as the transformation of the covalent bond, must be considered when an aromatic organic molecule reacts with a Si surface. When organic molecules are adsorbed onto Si surfaces, the functional groups of the adsorbing molecules, the electronic structure of the surface layer, and the arrangement of the surface atoms are all critical factors.1,2,5 For a given molecule, its adsorption structure and modification depend on the arrangement and electronic structure of the Si surface atoms. Changes in the molecular structures can be substantial when the molecules are attached to the surface. That is, controlling molecular bonding to the substrate requires understanding of the interaction between a molecular functional group and the Si atom it bonds to as a whole. Thus, subtle effects related to changes in molecular structure upon attachment to a barrier comparable to vdW forces or resonance energy can ultimately dominate the bindings between organic molecules and Si substrates. In this respect, the Si(5 5 12)–2×1 is a particular target for examining binding structures of organic molecules.16,17 Unlike surfaces such as Si(001)


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and Si(111), the Si(5 5 12) contains various arrangements; the redistribution of electrons leads to reconstruction of surface atoms to produce an adatom row (Adr), dimer row (Dmr), tetramer row (Ttr), or honeycomb chain (Hnc). Because of these characteristics, the Si(5 5 12) surface is a candidate for specialized applications. This substrate can be used as a base plate for the growth of heteroepitaxial films because of its step-by-step arrangement, which is several atoms in height, and its one-dimensional structural properties.18 In this work, we use scanning tunneling microscope (STM) and density functional theory (DFT) techniques to characterize the atomic configurations of pyrimidine molecules reacted with a Si(5 5 12)–21 surface (see the Supplementary Materials for the experimental and theoretical details). Pyrimidine has both a bonding functional group (paired valence electrons in a bond) and a nonbonding group (lone-pair electrons). Both groups can react with Si atoms. Moreover, pyrimidine is aromatic and its aromaticity can be disrupted during the reaction, which is an interesting phenomenon. We found that a pyrimidine molecule is selectively adsorbed onto Adr, Ttr, Dmr, and Hnc sites through two  bonds to form a structure such as a [4+2] cycloadduct that yields a planar-type configuration. Our calculations revealed that, when pyrimidine is adsorbed, its molecular orbitals are distorted because the NSi bond axis does not coincide with the molecular orbital symmetric axis. Thus, the vertical geometry is relatively unstable. DIs contribute approximately 0.4–0.6 eV for all of the adsorption structures. In the absence of DIs, the vertical structure is stable; however, when the DISs are included, the planar configuration becomes more stable on Ttr and Dmr sites. The aromaticity of pyrimidine is disrupted because the resonance stabilization effect is slightly weaker than the bonding of a pyridine molecule.



2. Results and Discussion Figures 1a and 1b show large scan areas of the Si(5 5 12)–2×1 surface, usually with a stepped configuration in the form of a toothed wheel. The terrace area is highly planar and symmetrical in one dimension along the [110] direction. The Si atoms in the step structure can be resolved in the images. Interestingly, the surface includes single domains that do not cross one another on a scale of a few hundred micrometers. The Si(5 5 12)–2×1 is therefore a useful basis for self-organized nanostructures. Previously combined STM and DFT calculations revealed the detailed configurations of the Si(5 5 12)–2×1 surface.17,19 Si(5 5 12) is formed by a 30.5° miscut from the [001] to the [111] orientations. Reconstructing the 2 × 1 surface to minimize its free energy doubles the lattice periodicity along the [ 110] axis, creating a unit cell with dimensions of 7.7 × 53.5 Å2 (see the rectangle in Figure 1c). The unit cell is composed of three subunits (labeled D1, D2, and D3) separated by Hnc chains. The D2 and D3 subunits include a Dmr and an Adr. A Ttr is also included in the D1 and D2 subunits (Figures 1d and 1e). The three subunits are cyclically converted under local surface forces.17 Line defects (e.g., missing units) can be generated by the heterogeneous forces induced during reconstruction. After pyrimidines reacted with the Si(5 5 12), the surface was imaged by STM. Figure 2 displays a typical constant-current image (topographical) taken after a pyrimidine reaction at a coverage less than 0.02 monolayers (ML). Comparing this image with that of a clean surface reveals a difference in the protrusion structure. Typical protrusions are indicated by circles in the image and are attributed to the pyrimidines. Increasing the amount of reactant


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(dosing pressure) and the time of the reaction increases the number of these protrusions. That is, these protruding structures are due to the reaction of the pyrimidine molecules. Locations of the protrusions were assigned by closely examining the protrusions and the adjacent surface structures. The protrusions were classified into four groups according to their location: a (Adr), t (Ttr), d (Dmr), or h (Hnc). The statistical distribution of the adsorption locations of the protrusions was calculated from a total of 481 protrusions. The proportions of the a, t, d, and h protrusions were 43.4%, 29.2%, 22.4%, and 5.0%, respectively. The ratios were weighted according to the distribution of possible reactive locations for each configuration. No substantial difference was observed among the fraction production of different base units with the same characteristics. The elevation of the protrusions in the STM images provides useful information for elucidating the adsorption structure. We obtained the heights of the protrusions by analyzing a cross-section profile along the protrusions in either the [665] or [110] direction. To deduce the effect of pyrimidine on the STM protrusions, we subtracted the background surface topography from the total topographic height. This analysis shows that the topographic height of the pyrimidine protrusions is within the range 0.1–0.5 Å. This height is similar to that calculated for an adsorption structure in a flat configuration, such as was recorded for benzene (

Role of Electronic Structures and Dispersion Interactions in Adsorption

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