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Distinguishing strain, charge and molecular orbital induced effects on the electronic structure: graphene/ammonia system

Molecular adsorption at the surface of a 2D material poses numerous questions regarding the modification to the band structure and interfacial states, which of course deserve full attention. In line with this, first-principle density functional theory is employed on the graphene/ammonia system. We identify the effects on the band structure due to strain, charge transfer and presence of molecular orbitals (MOs) of NH3 for six adsorption configurations. The induced strain upon ammonia-adsorption opens the bandgap (Eg) of graphene due to the breaking of translational symmetry and shifts the equilibrium Fermi energy (EF). The Eg and EF values and charge density distribution are dependent on the adsorption configuration, where the MO structure of NH3 plays a crucial role. The presence of MOs of N or H -originated pushes the unoccupied states of graphene towards EF. NH3 forms an interfacial occupied state originating from N2p below the EF within 1.6 - 2.2 eV for all configurations. These findings enhance the fundamental understanding of the graphene/NH3 system.


Introduction
Recently two-dimensional (2D) materials have emerged as excellent candidates for the detection of individual gas molecules. 1, 2 Among various materials, there are a number of reasons that make graphene a promising material towards detection of single molecules. 3 For instance, the lower density of scattering centers and ballistic transport, functional dependence of conductivity on the carrier concentration etc are notable features apart from high surface area to volume ratio originating from the 2D structure. In general, the origin of the gas-sensitivity is attributed to a possible electronic interaction of graphene with the test molecule, that causes a detectable change in the conductivity. 4 Various molecules in gaseous state like H2O, NH3, CO, NO2, NO have been subjected to investigation with first principle study 5,6 as well as in experiment. 6 Indeed, as an additional advantage, some of these molecules were found to be useful as a molecular dopant which open the band gap 7,8 of graphene with some degree of tunability. 9,10 In any case, deeper understanding of the cause of band gap renormalization and effect on the conductivity is of utmost importance. Experimentally, the adsorption and desorption of single ammonia molecule on graphene has shown the quantization of changes in graphene conductivity by signaling the adsorption or desorption of each individual molecule, which supported the donor nature of NH3. 3 However, the first principle studies 5,6 have indicated relatively weak adsorption energy and small 11 or almost no charge transfer from NH3 to graphene. Interestingly, the magnitude of the charge transfer is expected to be dependent on the orientation of the molecular orbitals (MOs) of NH3. If the hydrogen atoms are positioned towards (down, D) or away (up, U) from graphene a charge transfer of zero or ~0.048 × 10 -19 C/molecule is observed, respectively. When the test molecule arrives at the surface the interaction (Coulombic and/or Van der Waal's) reorganizes the potential energy landscape inducing some strain on graphene apart from a possible charge transfer. Therefore, the change in the conductivity may be due to renormalized band structure which may have contribution from either (i) strain, (ii) charge transfer and/or (iii) spatial arrangement of MOs of the host that may act as scattering centers. Theoretical studies indicated modifications to the band structure due to external strain. 12 It is also found that depending on the strength and the direction of strain, band gap can be tuned in the order of 0.1 eV. Similarly, band structure may be modified due to the transfer of charge. 13,14 The net strain is a result of interaction between substrate/graphene and graphene/molecule, while the charge transfer can be dependent on the orientation and the symmetry of the molecule. Indeed, the previous studies 5,6 assumed no significant changes to the band structure upon adsorption of NH3 and did not distinguishing the strain and charge transferinduced changes. Such an understanding is rather beneficial to unfold the mechanism of molecular doping and applicability of graphene in electronic devices and sensors, where the selectivity towards a particular molecule is challenging. 15,16 In this letter, we have investigated the effects of adsorption of ammonia on the band structure of graphene from two different perspectives viz strain and MOs/charge -induced. Importantly, we found that the adsorption of NH3 opened a direct small energy gap of about ~200 meV at high symmetry point K. In our calculations we have observed explicit differences to the occupied and unoccupied states which depends on the adsorption configuration with respect to the symmetry of NH3 molecule. In addition to this, depending on the MO orientation, NH3 forms an occupied state originated from N2p below the EF at 1.6 -2.2 eV.

Computation
Adsorption of ammonia molecule on pristine graphene was examined by first-principle methods based on Density Functional Theory, implemented in the Quantum Espresso package. 17 The exchange-correlation functional of Perdew-Burke-Ernzerhof (PBE) approximated by Generalized Gradient Approximation was used for the calculation. 18 Norm-conserving ultrasoft pseudopotentials (Rappe Rabe Kaxiras Joannopoulos) were used to describe the interaction between ionic cores and valence electrons. of the geometry of graphene/NH3 system, calculation was performed for two cases. In case 1, the very same optimized graphene/NH3 system was considered and in case 2, NH3 was removed (named as Gr-strain) however the coordinates of the C-atoms were frozen. The results are compared with relaxed counterparts. Graphene/NH3 system is denoted as Gr/NH3 which accounts for charge transfer and strain induced effects. Gr-strain considers the deformation of graphene (i.e. accounts for strain induced effects only) due to NH3 adsorption. Note that the induced strain is a function of adsorption configuration and adsorption site.

Results and discussion
In order to distinguish the effects from strain and that of charge transfer on the electronic structure of a hybrid system, it is inevitable to study their isolated counterparts. To start with, isolated ammonia is a closed shell molecule with an intrinsic dipole moment of 3.3 × 10 -30 Cm that arises due to the asymmetric charge distribution on the nitrogen atom. 20 NH3 is known to interact with graphene weakly through van der Waals forces where frontier molecular orbitals identified highly occupied molecular orbital (HOMO) and least unoccupied molecular orbital (LUMO). 5 Our calculation indicates that the HOMO of NH3 is located at ~13.6 eV, which is comparable with the experimental ionization potential of 10.2 eV. 21 For the case of pristine graphene, we have observed (results not shown here) a uniform accumulation of charge around the carbon atoms, along the bonds, however, at the center of the honeycomb the charge distribution is found to be zero. This minimum charge accumulation site is understandable, in the light of the electronegativity values of C(2.55) and H(2.1). Due to the strong covalent bonding between C-C atoms maximum charge is accumulated uniformly around C atoms and along the bonds.
For graphene/NH3 system, the charge accumulation is significantly different from their pristine counterparts, although they are characterized as weakly interacting. In this context, with reference to the phase of the electron wavefunction on graphene, FIG 2b shows the localization of LUMO* and HOMO* under equilibrium condition. 22 Hence the spatial distribution of charge density is a result of net charge transfer, which depends on the adsorption configuration. 5 On the other hand, after structural optimization of graphene/NH3 system carbon atoms are displaced in the order of 0.2 Å which is relatively more in case of U orientation than that of D. The distance between C and N atom after structural relaxation is shown in FIG 2d (right) for CD and CU configurations. The relative atomic positions of nitrogen and hydrogen in NH3 vary slightly after adsorption on graphene, however, this slight displacement, did not cause any significant changes to the DOS of NH3. This is in contrast to that of graphene and will be discussed later.  The electronic interaction between substrate and adsorbate can be characterized based on the coupling between molecular orbitals and the substrate electronic states. i.e. alignment of energy levels and localization of electrons. 25 The combined effect of these main factors results in either integral or fractional transfer of charge, apart from any Coulombic and screening effects. 26 For instance, as found in the case of organic/metal interface, the alignment of the energy levels at the interface related to the charge transfer between the donor or acceptor species and the metallic surface. 27 It is also found that the charge transfer alters the alignment of energy levels and causes structural transformations in both donating and accepting species. 28 Essentially, the potential energy landscape would be re-normalized to accommodate the extra or deficit electronic charge which leads to the (local) structural deformation. This deformation causes stress on both substrate and adsorbate while the magnitude of which depends on the microscopic mechanical properties. Indeed, our approach distinguishes the effects on EF and Eg due to the presence of (i) MOs and/or charge of NH3 from that of (ii) deformation of the graphene basal plane.
For graphene/NH3 case, the first principle studies 5, 6 have indicated relatively weak adsorption energy and small 11 or almost no charge transfer from NH3 to graphene. On the other hand, the donor nature of NH3 is experimentally supported. 3   In the context of relaxed graphene, carbon atoms are arranged in a regular honeycomb structure due to their sp 2 hybridization of 2s, 2px and 2py orbitals accommodating three out of four valence electrons. The planer sp 2 hybridization in graphene is due to the mixing of the 2s and two 2p orbitals. The electrons involved in sp 2 hybridization are localized and form σ-bonds, which do not contribute to the transport phenomenon. Again, the π-bond with 2pz electrons of neighboring carbon atoms are formed by the fourth electron, perpendicular to the plane of graphene sheet, which occupies the 2pz orbital. 29 The electrons forming π-bond are delocalized over the entire lattice and have higher energy than the electrons that form the σ-bonds. These delocalized π-electrons are responsible for most of the extraordinary properties of graphene. 30 π* and π bands correspond to the bands above and below the Fermi level respectively. If we consider pure graphene, these π bands meets at the Fermi level with zero band gap (FIG 4c), which is the so called Dirac Point, and the region around them is known as Dirac cone.
Moving onto the strain-related effects, the changes are not just limited to the Dirac cone with an induced band gap, rather they extend into CB and VB of graphene. Figure 4b

Conclusions
Our approach on the graphene/NH3 system unfolded effects of strain and charge related effects including spatial localization of MOs of NH3. Isolated graphene depicted a uniform charge distribution around carbon atom and almost none at the center of the hexagon. For isolated NH3, being in tetragonal structure, the electron density is localized on N atom. Also, we find that charge density distribution of isolated ammonia is quite distinct from that when adsorbed at the surface of graphene. We also find that charge density distribution of graphene/ NH3 is quite distinct from that of isolated counterparts. Due to the re-organization of potential energy landscape at the surface of the graphene, the presence of NH3 induced some strain on the graphene. Adsorption induced strain break the translational symmetry of graphene thus opening the band gap of graphene about 200 meV, which however, depends whether the hydrogen atoms of NH3 point toward or away from graphene. The presence of MOs of NH3 pushes the unoccupied states of graphene towards the EF. For U and D configurations, the unoccupied states close to Fermi energy depict relatively larger shifts. HOMO* localization occurred within the interface between graphene and NH3. We conclude that the effects on band structure of graphene are dependent on the symmetry and spatial distribution of MOs of NH3 and type of adsorption.
Distinguishing strain, charge and molecular orbital induced effects on the electronic structure: graphene/ammonia system Discussion: We observe that all bands overlap for both Gr-strain and ammonia adsorbed graphene (in all the configurations), except * bands. The shift is more in the case of D configuration than that of U-type adsorption. Band gap opening is found to be nearly the same for both graphene under strain and graphene/NH3 system. Essentially, the band gap is mainly contributed by the strain developed on graphene due to adsorption of ammonia, not due to the charge transfer.