Theories of scanning probe microscopes at the atomic scale

Significant progress has been made both in experimentation and in theoretical modeling of scanning probe microscopy. The theoretical models used to analyze and interpret experimental scanning probe microscope (SPM) images and spectroscopic data now provide information not only about the surface, but also the probe tip and physical changes occurring during the scanning process. The aim of this review is to discuss and compare the present status of computational modeling of two of the most popular SPM methods—scanning tunneling microscopy and scanning force microscopy—in conjunction with their applications to studies of surface structure and properties with atomic resolution. In the context of these atomic-scale applications, for the scanning force microscope (SFM), this review focuses primarily on recent noncontact SFM (NC-SFM) results. After a brief introduction to the experimental techniques and the main factors determining image formation, the authors consider the theoretical models developed for the scanning tunneling microscope (STM) and the SFM. Both techniques are treated from the same general perspective of a sharp tip interacting with the surface—the only difference being that the control parameter in the STM is the tunneling current and in the SFM it is the force. The existing methods for calculating STM and SFM images are described and illustrated using numerous examples, primarily from the authors' own simulations, but also from the literature. Theoretical and practical aspects of the techniques applied in STM and SFM modeling are compared. Finally, the authors discuss modeling as it relates to SPM applications in studying surface properties, such as adsorption, point defects, spin manipulation, and phonon excitation.Peer reviewe

Efficient parametrization of complex molecule-surface force fields

We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. © 2015 Wiley Periodicals, Inc

Nature of intrinsic and extrinsic electron trapping in SiO 2

Using classical and ab initio calculations we demonstrate that extra electrons can be trapped in pure crystalline and amorphous SiO2 (a-SiO2) in deep band gap states. The structure of trapped electron sites in pure a-SiO2 is similar to that of Ge electron centers and so-called [SiO4/Li]0 centers in α quartz. Classical potentials were used to generate amorphous silica models and density functional theory to characterize the geometrical and electronic structures of trapped electrons in crystalline and amorphous silica. The calculations demonstrate that an extra electron can be trapped at a Ge impurity in α quartz in six different configurations. An electron in the [SiO4/Li]0 center is trapped on a regular Si ion with the Li ion residing nearby. Extra electrons can trap spontaneously on pre-existing structural precursors in amorphous SiO2, while the electron self-trapping in α quartz requires overcoming a barrier of about 0.6 eV. The precursors for electron trapping in amorphous SiO2 comprise wide (≥132∘) O–Si–O angles and elongated Si–O bonds at the tails of corresponding distributions. Using this criterion, we estimate the concentration of these electron trapping sites at ≈4×1019 cm−3

Identification of intrinsic electron trapping sites in bulk amorphous silica from ab initio calculations

Using ab initio calculations we demonstrate that extra electrons in pure amorphous SiO2 can be trapped in deep band gap states. Classical potentials were used to generate amorphous silica models and density functional theory to characterise the geometrical and electronic structures of trapped electrons. Extra electrons can trap spontaneously on pre-existing structural precursors in amorphous SiO2 and produce ≈≈3.2 eV deep states in the band gap. These precursors comprise wide (⩾⩾130°°) O–Si–O angles and elongated Si–O bonds at the tails of corresponding distributions. The electron trapping in amorphous silica structure results in an opening of the O–Si–O angle (up to almost 180°°). We estimate the concentration of these electron trapping sites to be View the MathML source≈5×1019cm-3

Modelling charge self-trapping in wide-gap dielectrics: Localization problem in local density functionals

We discuss the adiabatic self-trapping of small polarons within the density functional theory (DFT). In particular, we carried out plane-wave pseudo-potential calculations of the triplet exciton in NaCl and found no energy minimum corresponding to the self-trapped exciton (STE) contrary to the experimental evidence and previous calculations. To explore the origin of this problem we modelled the self-trapped hole in NaCl using hybrid density functionals and an embedded cluster method. Calculations show that the stability of the self-trapped state of the hole drastically depends on the amount of the exact exchange in the density functional: at less than 30% of the Hartree-Fock exchange, only delocalized hole is stable, at 50% - both delocalized and self-trapped states are stable, while further increase of exact exchange results in only the self-trapped state being stable. We argue that the main contributions to the self-trapping energy such as the kinetic energy of the localizing charge, the chemical bond formation of the di-halogen quasi molecule, and the lattice polarization, are represented incorrectly within the Kohn-Sham (KS) based approaches.Comment: 6 figures, 1 tabl

Calculating the entropy loss on adsorption of organic molecules at insulating surfaces

Although it is recognized that the dynamic behavior of adsorbing molecules strongly affects the entropic contribution to adsorption free energy, detailed studies of the adsorption entropy of large organic molecules at insulating surfaces are still rare. We compared adsorption of two different functionalized organic molecules, 1,3,5-tri(4-cyano-4,4-biphenyl)benzene (TCB) and 1,4-bis(cyanophenyl)-2,5-bis(decyloxy)benzene (CDB), on the KCl(001) surface using density functional theory (DFT) and molecular dynamics (MD) simulations. The accuracy of the van der Waals corrected DFT-D3 was benchmarked using Møller–Plesset perturbation theory calculations. Classical force fields were then parametrized for both the TCB and CDB molecules on the KCl(001) surface. These force fields were used to perform potential of mean force (PMF) calculations of adsorption of individual molecules and extract information on the entropic contributions to adsorption energy. The results demonstrate that entropy loss upon adsorption are significant for flexible molecules. Even at relatively low temperatures (e.g., 400 K), these effects can match the enthalpic contribution to adsorption energ

Defects in WS2 monolayer calculated with a nonlocal functional: any difference from GGA?

Density Functional Theory (DFT) with Generalized Gradient Approximation (GGA) functionals is commonly used to predict defect properties in 2D transition metal dichalcogenides (TMDs). Since GGA functionals often underestimate bandgaps of semiconductors and incorrectly describe the character of electron localization in defects and their level positions within the band-gap, it is important to assess the accuracy of these predictions. To this end, we used the non-local density functional PBE0-TC-LRC to calculate the properties of a wide range of intrinsic defects in monolayer WS2. The properties, such as geometry, in-gap states, charge transition levels, electronic structure and the electron/hole localization of the lowest formation energy defects are discussed in detail. They are broadly similar to those predicted by the GGA PBE functional but exhibit numerous quantitative differences caused by the degree of electron and hole localization in charged states. For some anti-site defects, more significant differences are seen, with both changes in defect geometries (differences of up to 0.5 Å) as well as defect level positions within the band gap of WS2. This work provides an insight into the performance of functionals chosen for future DFT calculations of transition metal dichalcogenides with respect to the desired defect properties