Core to surface excitations on GaAs(110)

We have carried out ab initio calculations of surface core excitations on finite cluster models of the GaAs(110) surface. For the Ga core excitation we find a localized excited state involving excitation into the empty Ga-4p orbital and bound with respect to the conduction band minimum (CBM) by 0.7 eV. This is in reasonable agreement with experiment (binding energy >~0.8 eV). This transition, which is not analogous to bulk core excitations, is termed a core surfaston to emphasize the character of the state. We find that the As core surfaston is above the CBM by 1.0 eV and hence should be difficult to observe

Chemisorption of Al and Ga on the GaAs (110) surface

We have studied the initial stages of the chemisorption of Al and Ga on the clean GaAs (110) surface by applying quantum chemical methods to small clusters representing Al or Ga on GaAs (110). These calculations suggest that at smallest coverages Al or Ga bind to a surface Ga atom; for higher coverages Al and the surface Ga interchange positions. We have obtained the binding energy, the chemical shifts of the Ga–3d, As–3d and Al–2p states, and the microscopic dipole associated with chemisorption of Al or Ga on GaAs (110). These results are compared to experimental values and further experiments are suggested

Bulk vacancies in CdxHg1–xTe

We report the first theoretical study of vacancies in CdxHg1–xTe alloys. The study employs the tight-binding method for obtaining the Hamiltonian. The Slater–Koster Green's function method is used to obtain the electronic states that result from removing a cation or anion from the virtual crystal used to model the alloys. The primary results are that the anion vacancy levels are far into the conduction band and hence are not likely to produce levels in the gap. In contrast, the cation vacancy is found to produce levels near the valence band edge. We find that spatially these states are very localized on the atoms nearest the vacancy

Geometry of the abrupt (110) Ge/GaAs interface

We have studied the structure relaxation at the abrupt (110) Ge/GaAs interface by applying quantum chemical methods to clusters modeling this interface. Application of this model to bulk Ge and to bulk GaAs leads to theoretical Ge–Ge and Ga–As bond distances of 2.452 and 2.451 Å, respectively, in good agreement with the experimental values of 2.450 and 2.448 Å, respectively. Application of the model to the Ge/GaAs (110) interface indicates that this interface is nearly ideal. We find a very slight reconstruction at the interface leading to a Ge–Ga bond distance which is 0.04 Å longer than the Ge–As bond distance of 2.430 Å. The calculated spacing of the interface layer is 2.3% greater than that of bulk Ge or bulk GaAs

Theoretical studies of the reconstruction of the (110) surface of III–V and II–VI semiconductor compounds

We have studied the reconstruction of the (110) surface of various III–V semiconductor compounds (GaAs, GaP, GaN, AlAs, AlP, AlN, BAs, BP, BN) by applying quantum chemical methods to small clusters representative of these surfaces. Application of these techniques to GaAs (110) leads to a surface shear (0.67 Å) in excellent agreement with experimental values (0.65–0.70 Å). The results lead to trends in the surface distortions and reconstruction consistent with those predicted from local valence considerations. Possibilities for the electronic structure of II–VI semiconductor compounds are also considered

Oxidation of silicon surfaces

We have carried out theoretical studies (generalized valence bond) for chemisorbed O atom and O2 molecule on Si(111) surfaces using clusters of atoms to model the surface. For the perfect surface we find that O2 molecule binds to a single surface Si with an Si–O bond length of 1.68 Å (bulk SiO2RSi–O = 1.61 Å), an Si–O–O angle of 116 °, and an O–O bond distance of 1.32 Å. We have also calculated the shifts in the Si(2p) and O(1s) core level energies for chemisorbed O and O2 on the surface. The Si(2p) shift is +1.1 eV (higher binding energy) for the O atom and +1.5 eV for O2, in agreement with the shifts observed for low oxygen exposure by Spicer and co-workers

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes

Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction-modification (R-M) and CRISPR-Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR-Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR-Cas systems by lowering the affinity of the Cascade and Cas9-crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR-Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems