In this study, the interaction between the gas molecules, including H2O, N2, CO, NO, NO2 and N2O, with the WSe2 monolayer containing a Se vacancy (denoted as VSe) is theoretically studied. It is found that H2O and N2 molecules are highly prone to be physisorbed on the VSe surface. The presence of the Se vacancy should significantly enhance the sensing ability of the WSe2 monolayer toward the H2O and N2 molecules. In contrast, CO and NO molecules highly prefer to be molecularly chemisorbed on the VSe surface with the non-oxygen atom occupying the Se site. Further, the exposed O atoms of the molecularly chemisorbed CO or NO can be reacted with the additional CO or NO molecule, to produce the C-doped or N-doped WSe2 monolayer. Our electronic structure calculations show that the WSe2 monolayers are p-doped by the CO and NO molecules, as well as the C and N atoms. The calculated energies suggest that the filling of the CO or NO molecule and the removal of the exposed O atom by the additional CO or NO molecule are both energetically and dynamically favorable. However, only the NO molecule and N atom doped WSe2 monolayers exhibit significantly improved electronic structures compared with the defective WSe2 monolayer. The NO2 and N2O molecules will dissociate directly to form a O-doped WSe2 with a physisorbed NO or N2. After desorbing the physisorbed NO or N2, the O-doped WSe2 monolayer can be obtained, for which the defect levels due to the Se vacancy can be completely removed. The calculated energies suggest that although the dissociation processes for NO2 and N2O molecules are highly endothermic, the N2O dissociation may need to operate at an elevated temperature compared with the room temperature, due to its large energy barrier of ~ 1 eV.
By using first-principles calculation, the interaction of O2 and H2O molecules with the pristine and the defective InSe monolayers is studied. It is predicted that the single Se and In vacancies exhibit significantly enhanced chemical activity toward the adsorbates compared with the perfect InSe lattice site, and the Se vacancies have a much higher chemical activity than the In vacancies. H2O molecule should be only physisorbed on the various InSe monolayers at ambient conditions, according to the calculated energies. The doping of the various InSe monolayers is discussed by the physisorbed H2…
Atom controlled sub-nanometer MoS$_2$ pores have been recently fabricated. Oxidative environments are of particular interest for MoS$_2$ applications in electronics, sensing and energy storage. In this work we carried out first-principles calculations of oxygen adsorption in plain and sub-nanometer MoS$_2$ nanopores. The chemical stability of the layers and pores towards oxygen was verified using density-functional theory. Dissociation and diffusion barriers have been calculated in order to understand surface and pore oxidation and its electronic properties at the atomic scale, which opens the…
Using density functional tight-binding theory, we investigated the elastic properties and deformation and failure behaviors of pristine and defective carbon-phosphide (CP) monolayers subjected to uniform uniaxial tensile strain along armchair (AC) and zigzag (ZZ) directions. Two variants of carbon phosphide were studied and two types of carbon and phosphorous vacancies (single and double) were considered. It was found that carbon monovacancies have the lowest formation energy, while phosphorous divacancies have the highest one in both CP allotropes. A strong mechanical anisotropy for carbon ph…
The effect of vacancy and water adsorption on the electronic structure of semiconducting 2D trichalcogenide material CrPX$_3$ (X: S, Se) is studied using state-of-the-art density functional theory (DFT) approach. It is found that chalcogen vacancies play a minor role on the electronic structure of CrPX$_3$ in the vicinity of the Fermi level leading to the slightly reduced band gap for these materials, however, inducing strongly localised defect states which are placed in the energy gap formed by the valence band states. Our DFT calculations show that the interaction of water molecules with CrP…
Potential applications of monolayer of transition metal dichalcogenides (TMDs) in optoelectronic and flexible devices are under heavy investigation. Although TMDs monolayers are highly robust to external mechanical fields, their electronic structure is sensitive to compressive and tensile strain. Besides, intrinsic point defects are present in synthesized samples of these two dimensional (2D) materials which leads to the modification of their electronic and optical properties. Presence of vacancy complexes leads to absorption with larger dipole matrix elements in comparison to the case of simp…
Germanium Selenide (GeSe) is a van der Waals-bonded layered material with promising optoelectronic properties, which has been experimentally synthesized for 2D semiconductor applications. In the monolayer, due to reduced dimensionality and, thus, screening environment, perturbations such as the presence of defects have a significant impact on its properties. We apply density functional theory and many-body perturbation theory to understand the electronic and optical properties of GeSe containing a single selenium vacancy in the $-2$ charge state. We predict that the vacancy results in mid-gap …
Layered transition metal trichalcogenides MPX$_3$ (M: transition metal; X: S, Se) demonstrate a wide spectrum of properties and are widely proposed as effective materials for the water splitting reactions. Among these materials, NiPX$_3$ are the most promising ones due to the match their electronic structures for the oxygen and hydrogen evolution reactions. Here, we present first steps of a detailed theoretical description on the adsorption of water molecules on pristine and defected (chalcogen vacancies) surfaces of NiPX$_3$ and show that in all cases a physisorption takes the place with adso…
Monolayers (ML) of Group-6 transition-metal dichalcogenides (TMDs) are semiconducting two-dimensional materials with direct bandgap, showing promising applications in various fields of science and technology, such as nanoelectronics and optoelectronics. These monolayers can undergo strong elastic deformations, up to about 10\%, without any bond breaking. Moreover, the electronic structure and transport properties, which define the performance of these TMDs monolayers in nanoelectronic devices, can be strongly affected by the presence of point defects, which are often present in the synthetic s…
The mechanical behaviors of monolayer black phosphorene (MBP) are explored by molecular dynamics (MD) simulations using reactive force field. It is revealed that the temperature and strain rate have significant influence on mechanical behaviors of MBP, and they are further weakened by SW (Stone-Wales) defects. In general, the tensile strength for both of the pristine and SW defective MBP decreases with the increase of temperature or decreasing of strain rate. Surprisingly, for relatively high temperature and low strain rate, phase transition from the black phosphorene to a mixture of β-phase (…
The hydrogen dynamics on a graphene sheet is studied in the presence of carbon vacancies. We analyze the motion of atomic H by means of molecular dynamics (MD) simulations, using a tight-binding Hamiltonian fitted to density-functional calculations. Hydrogen passivates the dangling bonds of C atoms close to a vacancy, forming C--H bonds with H located at one or the other side of the layer plane. The hydrogen dynamics has been studied from statistical analysis of MD trajectories, along with the autocorrelation function of the atomic coordinates. For a single H atom, we find an effective barrier…
Transition metal dichalcogenide (TMDC) monolayers present a remarkable multifunctional material with potential to enable the development of a wide range of novel devices. However, the functionalities observed often fall short of the expectation, which hinders the device development. Here we demonstrate that the optical, catalytic, and thermal functionalities of TMDC monolayers can all be substantially enhanced by up to orders of magnitude with the intercalation of water molecules or small cations (H+ and Li+) between the monolayers and underlying substrates. In contrast, the same molecules or …
Because of its promising contribution to the bottom-up approach for nanofabrication of complex molecular architectures, self-organization is widely studied nowadays. Numerous studies have tackled supramolecular chirality or low-dimensional molecular nanostructures using in most cases small and rigid molecules adsorbed on metallic substrates. In this situation, self-assembled structures can be understood in relative simple terms considering molecule-molecule versus molecule-substrate interactions. In contrast, the case of large and three-dimensional molecules which can adopt different adsorptio…
Two dimensional transition metal dichalcogenides appear as good candidates for gas sensing and catalysis. Here, by means of density functional theory, we characterize the adsorption and dissociation of selected diatomic molecules (CO, H$_2$, O$_2$, and NO) on the MoSe$_2$ monolayer. We consider that these processes occur on the pristine $1H$-MoSe$_2$ monolayer and in the vicinity of an isolated Se vacancy. The presence of Se vacancies both enhances the molecular adsorption and reduces the energy needed for dissociation, making it energetically favorable for the case of O$_2$ and NO molecules. …
Gas sensing mechanism of H2S, NH3, NO2 and NO toxic gases on transition metal dichalcogenides based Janus MoSSe monolayers are investigated using the density functional theory. The pristine and defect included MoSSe layers are considered as a host material for adsorption study. Three types of defects (i) molybdenum vacancy, (ii) selenium vacancy, and (iii) sulfur/selenium vacancy are studied to understand their impact on electronic properties and sensing of these gas molecules. The formation energy is computed to predict the stability of these defects and noticed that selenium vacancy is the m…
Hybridization effects play a crucial role in determining the electronic properties of hybrid inorganic/organic interfaces. To gain insight into these important interactions, we perform a first-principles study based on hybrid density-functional theory including spin-orbit coupling, focusing on eight representative systems formed by two carbon-conjugated molecules-pyrene and perylene-physisorbed on the transition-metal dichalcogenide monolayers (TMDCs) MoS$_2$, MoSe$_2$, WS$_2$, and WSe$_2$. By means of band unfolding techniques, we analyze the band structures of the considered materials, ident…
Defect is no longer deemed an adverse aspect of graphene. Contrarily, it can pave ways of extending applicability of graphene. Here, we discuss the effects of three types of defects on graphene: carbon deficiency, adatom (single Fe) dopant and introduction of functional groups (carboxyl, pyran group) on NO2 gas adsorption via density functional theory method. We have observed that the unsaturated carbon in defected graphene is highly active to attract NO2 molecules. Our study suggests that introducing Fe on graphene can enhance the NO2 adsorption process. Adsorption energy calculations suggest…
The effects of fluorine functionalization on the hydrogen storage capability of alkaline decorated III\textsubscript{4}-V\textsubscript{4} monolayers is studied. This structure can store up to two hydrogen molecules per alkaline atom. Here, we demonstrate that functionalizing alkaline decorated monolayer with a high electronegative element of fluorine can significantly enhance both binding energy and the maximum number of the stored hydrogen molecules. In this regard, the hydrogen molecule storage capability is notably improved from two to four and when absolute binding is considered. In addit…
Two-dimensional ferroelectrics are important quantum materials which have found novel application in nonvolatile memories, however, the effects of reversible polarization on chemical reactions and interaction with environments are rarely studied despite of its importance. Here, based on the first-principles calculations, we found distinct gas adsorption behaviors on the surfaces of ferroelectric In2Se3 layer and the reversible gas caption and release controlled by ferroelectric switch. We rationalize the novel phenomena to the synergistic effect of the different electrostatic potential and ele…
Monolayer transition metal dichalcogenides (TMDCs) are two-dimensional (2D) materials with many potential applications. Chemical vapour deposition (CVD) is a promising method to synthesize these materials. However, CVD-grown materials generally have poorer quality than mechanically exfoliated ones and contain more defects due to the difficulties in controlling precursors' distribution and concentration during growth where solid precursors are used. Here, we propose to use thiol as a liquid precursor for CVD growth of high quality and uniform 2D MoS2. Atomic-resolved structure characterizations…
First-principles calculations are performed to investigate the effects of the adsorption of gas molecules (CO, NO, NO2, H2S, N2, H2O, O2, NH3 and H2) on the electronic properties of atomically thin indium selenium (InSe). Our study shows that the lone-pair states of Se are located at the top of the valence band of InSe and close to the Fermi energy level, implying its high sensitivity to external adsorbates. Among these gas molecules, H2 and H2S are strong donors, NO, NO2, H2O and NH3 are effective acceptors, while CO and N2 exhibit negligible charge transfer. The O2 molecule has very limited …
Two-dimensional (2D) materials have been studied extensively as monolayers 1-5, vertical or lateral heterostructures 6-8. To achieve functionalization, monolayers are often patterned using soft lithography and selectively decorated with molecules 9,10. Here we demonstrate the growth of a family of 2D materials that are intrinsically patterned. We demonstrate that a monolayer of PtSe2 can be grown on a Pt substrate in the form of a triangular pattern of alternating 1T and 1H phases. Moreover, we show that, in a monolayer of CuSe grown on a Cu substrate, strain relaxation leads to periodic patte…
In this paper we propose a mechanism for the induction of energy gaps in the spectrum of graphene and its bilayer, when both these materials are covered with water and ammonia molecules. The energy gaps obtained are within the range 20-30 meV, values compatible to those found in experimental studies of graphene bilayer. We further show that the binding energies are large enough for the adsorption of the molecules to be maintained even at room temperature.
A free-electron like band has recently been observed in a monolayer of PTCDA (3,4,9,10-perylene tetracarboxylic dianhydride) molecules on Ag(111) by two-photon photoemission [Schwalb et al., Phys. Rev. Lett. 101, 146801 (2008)] and scanning tunneling spectroscopy [Temirov et al., Nature 444, 350 (2006)]. Using density functional theory calculations, we find that the observed free-electron like band originates from the Shockley surface state band being dramatically shifted up in energy by the interaction with the adsorbed molecules while it acquires also a substantial admixture with a molecular…
The electronic structure of a monolayer of single-molecule magnets Mn$_{12}$ on a Au(111) surface is studied using spin-polarized density-functional theory. The Mn$_{12}$ molecules are oriented such that the magnetic easy axis is normal to the surface, and the terminating ligands in the Mn$_{12}$ are replaced by thiol groups (-SH) where the H atoms are lost upon adsorption onto the surface. This sulfur-terminated Mn$_{12}$ molecule has a total magnetic moment of 18 $μ_B$ in the ground state, in contrast to 20$μ_B$ for the standard Mn$_{12}$. The Mn$_{12}$ molecular orbitals broaden due to the …
The evolution of titanyl-phthalocyanine (TiOPc) thin films on Ag(111) has been investigated using IRAS, SPA-LEED and STM. In the (sub)monolayer regime various phases are observed that can be assigned to a 2D gas, a commensurate and a point-on-line phase. In all three phases the non-planar TiOPc molecule is adsorbed on Ag(111) in an oxygen-up configuration with the molecular pi-conjugated backbone oriented parallel to the surface. The commensurate phase reveals a high packing density, containing two molecules at inequivalent adsorption sites within the unit cell. Both molecules assume different…
We report first-principles studies of electronic transport in monolayers of Tour wires functionalized with different side groups. An analysis of the scattering states and transmission eigenchannels suggests that the functionalization does not strongly affect the resonances responsible for current flow through the monolayer. However, functionalization has a significant effect on the interactions within the monolayer, so that monolayers with NO$_2$ side groups exhibit local minima associated with twisted conformations of the molecules. We use our results to interpret observations of negative dif…
We have combined scanning tunneling microscopy with inelastic electron tunneling spectroscopy (IETS) and density functional theory (DFT) to study a tetracyanoethylene monolayer on Ag(100). Images show that the molecules arrange in locally ordered patterns with three non-equivalent, but undeterminable, adsorption sites. While scanning tunneling spectroscopy only shows subtle variations of the local electronic structure at the three different positions, we find that vibrational modes are very sensitive to the local atomic environment. IETS detects sizeable mode frequency shifts of the molecules …
The magnetic properties of a monolayer of Fe4 single molecule magnets grafted onto a Au (111) thin film have been investigated using low energy muon spin rotation. The properties of the monolayer are compared to bulk Fe4. We find that the magnetic properties in the monolayer are consistent with those measured in the bulk, strongly indicating that the single molecule magnet nature of Fe4 is preserved in a monolayer. However, differences in the temperature dependencies point to a small difference in their energy scale. We attribute this to a ~60% increase in the intramolecular magnetic interacti…
We have investigated the influence of the substrate on the fluorescence of adsorbed organic molecules. Monolayer films of perylene-3,4,9,10-tetracarboxylic-3,4,9,10-diimide (PTCDI), a supramolecular network formed from PTCDI and melamine, and perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) have been deposited on hexagonal boron nitride (hBN). The principal peaks in the fluorescence spectra of these films were red-shifted by up to 0.37 eV relative to published measurements for molecules in helium droplets. Smaller shifts (~0.03 eV) arising from interactions between neighbouring m…
Using first-principles calculations we show that the work function of noble metals can be decreased or increased by up to 2 eV upon the adsorption of self-assembled monolayers of organic molecules. We identify the contributions to these changes for several (fluorinated) thiolate molecules adsorbed on Ag(111), Au(111) and Pt(111) surfaces. The work function of the clean metal surfaces increases in this order, but adsorption of the monolayers reverses the order completely. Bonds between the thiolate molecules and the metal surfaces generate an interface dipole, whose size is a function of the me…
We have investigated the impact of toxic N2O gas upon structural and electronic properties of 2D MoSe2 monolayer using DFT approach. In this work, as a result of N2O gas absorption, charge transfer, band gap and density of states (DOS) are changed and these parameters are extracted as electronic properties of 2D MoSe2 monolayer nano-gas sensor. Moreover, the band gap is tunable upon the N2O gas absorption for pristine and adsorbed MoSe2 in both Top Mo (Top Se) structures. Also, the spin up and down states in the DOS results considerable magnetic moment altering the magnetic property of the 2D …
We present a first-principles investigation of the electronic and optical properties of hybrid organic-inorganic interfaces consisting of MoS$_2$ monolayer and the $π$-conjugate molecules pyrene and pyridine. For both hybrid systems, the quasi-particle band structure obtained from the $G_0W_0$ approximation shows -- in contrast to density-functional theory -- level alignment of type II, owing to the mutual dynamical screening of the interface constituents. $\textit{Ab initio}$ calculations of the absorption spectrum based on the Bethe-Salpeter equation reveal besides intra-layer excitons on th…
The surface a thin-film is attached to and the surrounding monolayer causes geometrical confinement of a interrogated molecule; we look at the base case of a SC$_{18}H_{37}$ in a SC$_{18}H_{37}$ monolayer on Au[111]. Normal mode analysis was used to get vibrations, and these are analysed using mode character indicators which can quantify: how active an element is in a mode; the overall direction of the mode; and which chemical coordinates are relevant. We examined the 4 possible packing structures. We find that the more thermodynamically stable structures were less perturbed by the surface and…
Using molecular manipulation in a cryogenic scanning tunneling microscope, the structure and rearrangement of sexiphenyl molecules at the buried interface of the organic film with the Cu(110) substrate surface have been revealed. It is shown that a reconstruction of the first monolayer of flat lying molecules occurs due to the van der Waals pressure from subsequent layers. In this rearrangement, additional sexiphenyl molecules are forced into the established complete monolayer and adopt an edge-on configuration. Incorporation of second layer molecules into the first layer is also demonstrated …
We report a post-growth aging mechanism of Bi$_2$Te$_3$(111) films with scanning tunneling microscopy in combination with density functional theory calculation. It is found that a monolayered structure with a squared lattice symmetry gradually aggregates from surface steps. Theoretical calculations indicate that the van der Waals (vdW) gap not only acts as a natural reservoir for self-intercalated Bi and Te atoms, but also provides them easy diffusion pathways. Once hopping out of the gap, these defective atoms prefer to develop into a two dimensional BiTe superstructure on the Bi$_2$Te$_3$(11…
Chiral-Induced Spin Selectivity Effect in a 1 nm Thin 1,1'-Binaphthyl-2,2'-diyl Hydrogenphosphate Self-Assembled Monolayer on Nickel Oxide
Technical University of Darmstadt（达姆施塔特工业大学）；Technical University of Munich（慕尼黑工业大学）；Weizmann Institute of Science（魏茨曼科学研究所）；Chemnitz University of Technology（开姆尼茨工业大学）；Heidelberg University（海德堡大学）；Merck Electronics KGaA（默克电子股份公司）；University of Freiburg（弗赖堡大学）
We have performed a density functional theory study of the possible layered geometries occurring after dehydrogenation of a self-assembled monolayer (SAM) of biphenyl-thiol molecules (BPTs) adsorbed on a Au(111), as it has been experimentally observed for low energy electron irradiated SAMs of 4'-nitro-1,1'-biphenyl-thiol adsorbed on a Au(111) surface. [Eck, W. et al., Advanced Materials 2000, 12, 805] Cross-link formation between the BPT molecules has been analyzed using different models with different degrees of complexity. We start by analyzing the bonding between biphenyl (BP) molecules in…
Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglecte…
We present the results of molecular dynamics (MD) studies of hexane physisorbed onto graphite for eight coverages in the range $0.875 \le ρ\le 1.05$ (in units of monolayers). At low temperatures the adsorbate molecules form a uniaxially incommensurate herringbone (UI-HB) solid. At high coverages the solid consists of adsorbate molecules that are primarily rolled on their side perpen-dicular to the surface of the substrate. As the coverage is decreased, the amount of molecular rolling diminishes until $ρ$ = 0.933 where it disappears (molecules become primarily parallel to the surface). If the d…
Pairs of electrodes with nanometer separation (nano-gap) are achieved through an electromigration-induced break-junction (EIBJ) technique at room temperature. Lithographically defined gold (Au) wires are formed by e-beam evaporation over oxide coated silicon substrates silanized with (3-Mercaptopropyl)trimethoxysilane (MPTMS) and then subjected to electromigration at room temperature to create a nanometer scale gap between the two newly formed Au electrodes. The Si-O-Si covalent bond at the SiO$_2$ surface and the Au-sulphur (Au-S) bond at the top evaporated Au side, makes MPTMS as an efficien…
Here we a present a density functional theory study of pentacene ultra-thin films on flat [(111)] and vicinal [(455)] Au surfaces. We have performed crystal and electronic structure calculations by using PBE and optB86b-vdW functionals and investigated the effects of long range Van der Waals interactions for different coverages starting from a single isolated molecule up to 4 monolayers of coverage. For an isolated molecule both functionals yield the hollow site as the most stable one with bridge-60 site being very close in energy in case of optB86b-vdW. Binding strength of an isolated pentace…
Electrically stimulated switching of a charge injection barrier at the interface between an organic semiconductor and an electrode modified with a disordered monolayer (DM) is studied by using various benzenethiol derivatives as DM molecules. The switching behavior is induced by a structural change in the DM molecules, and is manifested as a reversible inversion of the polarity of DM-modified Au electrode/rubrene/DM-modified Au electrode diodes. The switching direction is found to be dominantly determined by the push-back effect of the thiol bonding group, while the terminal group modulates th…
We present microscopic investigations on the two-dimensional arrangement of cobalt phthalocyanine molecules on a graphite (HOPG) substrate in the low coverage regime. The initial growth and ordering of molecular layers is revealed in high resolution scanning tunneling microscopy (STM). On low coverages single molecules orient mostly along one of the substrate lattice directions, while they form chains at slightly higher coverage. Structures with two different unit cells can be found from the first monolayer on. A theoretical model based on potential energy calculations is presented, which rela…
We have fabricated a variety of novel molecular tunnel junctions based on self-assembled-monolayers (SAM) of two-component solid-state mixtures of molecular wires (1,4 methane benzene-dithiol; Me-BDT with two thiol anchoring groups), and molecular insulator spacers (1-pentanethiol; PT with one thiol anchoring group) at different concentration ratios, r of wires/spacers, which were sandwiched between two metallic electrodes such as gold and cobalt. FTIR spectroscopy and surface titration were used, respectively to verify the formation of covalent bonds with the electrodes, and obtain the number…
We report the synthesis and characterization of molecular rectifying diodes on silicon using sequential grafting of self-assembled monolayers of alkyl chains bearing a pi group at their outer end (Si/sigma-pi/metal junctions). We investigate the structure-performance relationships of these molecular devices and we examine to what extent the nature of the pi end-group (change in the energy position of their molecular orbitals) drives the properties of these molecular diodes. For all the pi-groups investigated here, we observe rectification behavior. These results extend our preliminary work usi…
The formation of interface dipoles in self-assembled monolayers (SAMs) of --CH$_3$ and --CF$_3$ terminated short-chain alkanethiolates on Ag(111) is studied by means of density functional theory calculations. The interface dipoles are characterized by monitoring the change in the surface work function upon adsorption of the SAM. We compare results obtained for SAMs in structures with a different packing density of molecules, i.e. {$(\sqrt{7}\times\sqrt{7}) R19.1^{\circ}$}, {$(\sqrt{3}\times\sqrt{3}) R30^{\circ}$}, and {p(2$\times$2)}. The work function of alkanethiolate SAMs on silver depends …
