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Water
Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
X-ray and neutron scattering experiments on ice have led to the “tridymite ice I” structure shown in Figure 4.2. Water molecules are approximately tetrahedrally arranged, with each water involved (potentially) in four hydrogen bonds and the H–O–H angle 109.4°. Oxygen atoms show approximate sp3 orbital hybridization, with two “lone-pair” orbitals and two bonds to H atoms. This ice structure, with its rigid lattice, is more open than the liquid water structure, resulting in the familiar observation that ice floats on water. We will come back to this in a moment. The “rigid lattice” does not imply that ice cubes from your freezer are single crystals: this would be rare indeed. Many defects occur, owing to impurities, air bubbles, cracks, and other molecule misorientations, and X-ray or neutron diffraction measurements on ice generally imply polycrystalline samples.
Microscopic Analysis of Impurity Solubility in Semiconductors
Published in Victor I. Fistul, Impurities in Semiconductors, 2004
Therefore, the sp-hybrid chemical bonding of d-impurities to silicon atoms is very unlikely because of the great energy requirements for the electron shell restructuring of the d-atom. More feasible is the formation of tetrahedral bonds between an impurity atom and silicon atoms by involving d-electrons into the chemical bonding. With the concept of atomic orbital hybridization, one can suggest the production of d3s-hybrids geometrically equivalent to a tetrahedron, similar to the sp3-hybrid. Electronic configurations producing d3s-hybrids are illustrated in Figure 4.9. It should be noted that d-atoms with the Me0(d7s2) and Me0(d8s2) configurations in the free state may have the d2sp bond which represents a distorted tetrahedron. In this case, the lattice distortions around the impurity atom must be appreciable, and the d-atom displacement from the lattice site is likely to occur (the Yan-Teller effect).
Effect of doping and vacancy defect on the sensitivity of stanene toward HCN
Published in Molecular Physics, 2022
Shumin Yan, Qingxiao Zhou, Weiwei Ju, Xiangyang Li
First, the influence of the adsorption of HCN molecule on the band structures is analysed (Figure 7). It is worth noting that the band gap of the Ti-VSn substrate changes from 0 to 0.035 eV after the adsorption of HCN. The relationship between conductivity and band gap conforms to the following formula [43]: where σ is the electric conductivity of the configurations, k is the Boltzmann's constant and T is the thermodynamic temperature. The conductivity of the material is observed to be lower after adsorption. Interestingly, the Cr-VSn substrate behaved as a conductor. After the adsorption of HCN molecule, the HCN/Cr-VSn system displays a half-metal property; it behaves like a conductor in spin up and like a semiconductor in spin down [44]. To further understand the electron interaction between HCN molecule and the doped substrate, DOS diagrams have been illustrated in Figure 8. Taking the HCN/Ti-VSn system as an example, the d orbital of the Ti atom underwent orbital hybridisation with the s orbital of the HCN molecule (between −19 eV to −17 eV and −11 eV to −9 eV). This significant orbital hybridisation led to the largest adsorption energy (−1.852 eV) for doped stanene.
Adsorption properties of NH3, NO, and O2 molecules over the FeO (100) and oxygen-defected FeO (100) surfaces: a density functional theory study
Published in Molecular Physics, 2021
Chaoyue Xie, Yunlan Sun, Baozhong Zhu, Weiyi Song, Minggao Xu
To study the adsorption mechanism, the PDOS results of NO adsorbed on the Fe-top sites of the FeO (100) and oxygen-defected FeO (100) surfaces were studied, respectively. The results are shown in Figure 5. As shown in Figure 5(a), the PDOS analysis displays the orbitals change of N and Fe atoms on the FeO (100) surface. The p-orbital of N and d-orbital of Fe occurs hybridisation at −7.71, −6.95, −1.72, and 1.09 eV, respectively, indicating that the adsorption of NO on the Fe-top site of the FeO (100) surface is chemisorption. Figure 5(b) also shows the PDOS results of NO adsorption on the oxygen-defected FeO (100) surface. N’s p-orbital and Fe’s d-orbital produces hybridisation at −7.70, −6.88, −1.72, and 1.09 eV, respectively, implying that the electron commutativity in Fe–N configuration is strong, which proves the chemisorption of NO on the Fe-top site of the oxygen-defected FeO (100) surface. Compared with the adsorption of NO on the Fe-top of the FeO (100) surface at approximately −1.72, −5.23, and −6.88 eV, the d-orbital hybridisation level of Fe atom on the O-defected FeO (100) surface is reduced, indicating that the adsorption of NO molecule on the Fe-top site of FeO (100) surface is more stable than that on the Fe-top site of the oxygen-defected FeO (100) surface.
Exploring the sensitivity of Hf2CO2 towards H2S: a DFT study
Published in Molecular Physics, 2023
Tongwei Li, Jing Chen, Kai Tian, Qingxiao Zhou, Mengjie Li, Weiwei Ju
To further exploring the electronic characteristics, the partial density of states (PDOS) of the H2S molecule, TM-dopants and neighbouring Hf (O) atoms were calculated and shown in Figure 7. For H2S/Ti-Hf2CO2 system, the PDOS carves of H2S hybridised with Ti-d orbital above the Fermi level (EF). According to above discussions, chemical bonds formed between Ti-dopant and adjacent O-atoms, and then the PDOS of O were illustrated. Furthermore, hybridisation between O and Ti-d orbital was observed below and above Fermi level. Same as Ti-doped system, apparent orbital hybridisation between H2S molecule and Cr (Ni) existed around the EF, suggesting the enhancement of adsorption stability was mainly contributed by TM-dopants (Ti, Cr and Ni). The magnetism was also considered, and spin-up and spin-down DOS programmes were unsymmetric for Cr-doped Hf2CO2. The total magnetic moments (µtotal) of H2S/Cr-Hf2CO2 was 5.2 µB (Table 2), and the DOS result indicated that Cr-d orbital dominated the magnetic state of system. To better understand the charge transfer between the H2S and substrate, the charge density differences (CDD) diagram was observed in Figure 8. The yellow region around the H2S molecule was larger than the blue region, indicating that the H2S molecule acted as an electron donor, which was agreement with the positive value of Q1 in Table 2. It can be found that charge transfer mainly occurred between the H2S molecule and the transition metal dopants.