Journal of Theoretical and Computational Chemistry

The stability and electronic structures of fluorinated Janus MoSSe (MoSSe-F_x, x = 0–16) were investigated by the first-principles method. Energetically, the Se_top site of Janus MoSSe is the most favorable site for F-adsorption. Based on the adsorption, binding and formation energy analysis, it seems the fluorinated Janus MoSSe is stable. The analysis of the electronic density distribution and orbital hybrid shows that the fluorinated Janus MoSSe forms stable structure as well. Then, the electronic structure and work function change with the concentration of F atoms analyzed. With the increase of adsorbed F atoms, the bandgap of Janus MoSSe-F_x decreases from 1.456 (pristine case, $x=0$) to 1.073eV (semi-fluorinated case, $x=16$), and changes from direct to indirect bandgap semiconductor. It is noteworthy that there are some additional doping levels near the valence band after F adsorbed, which originated from the F 2$p$ doping states. The charge population analysis shows that electrons transfer was from Se to F atoms. It is worth noting that the charge on F atom (MoSSe-F₁₆) is two times more than Se atoms in pristine Janus MoSSe (MoSSe-F₀). As a result, the built-in electric field pointed from Mo to F atoms is enhanced, resulting in the tremendous increase of the work function for fluorinated Janus MoSSe. The work function changes from 5.22eV ($x=0$) in pristine case to 8.30eV after semi-fluorinated ($x=16$). Therefore, due to the adjustable work function and built-in electric field, the fluorinated Janus MoSSe monolayer shows better properties for applications in the piezoelectric device, optoelectronic device or photocatalyst.

To explore the excellent sensor for detecting the pollution gas $S{O}_2$, the adsorptions of $S{O}_2$ molecule on the surfaces of Fe/Co-doped carbon nanotubes (CNTs) and single vacancy defected (8, 0) CNTs were investigated by using density functional theory (DFT). In addition, the adsorption energies, geometries, energy gaps and electronic structures were analyzed. The results showed that Fe/Co-doping and single-vacancy-defected can improve the adsorption and sensitiveness of CNTs toward $S{O}_2$. Considering the changes of energy gap before and after the $S{O}_2$ molecule adsorbed on each modified CNTs and its adsorption strength, Fe-doped CNTs (Fe-CNTs) and Co-doped site-2 single-vacancy-defected CNTs performed better for detecting $S{O}_2$ molecule. With the decreasing number of electrons of the doped atom (Fe, Co, Ni), the adsorption became more stable. The results of this paper are profound and meaningful for designing $S{O}_2$ sensing devices.

Experimental study and quantum chemical calculations have been used to study the adsorption of Cu²⁺ and Mg²⁺ on silica gel derived from rice hulls ash. XRD measurements showed that the silica obtained has amorphous structure with BET of 250.1m²/g and pzc at pH 2. Adsorption of Cu²⁺ and Mg²⁺ on silica at 28^∘C showed maximum capacities of 0.26 and 0.20mmol/g, respectively. In both cases of metal ions, the interaction was explained to proceed via hydrogen bonding through the outer hydration shell. Using density functional theory (DFT), interactions of hydrated metal ions with naked, mono- and di-hydrated silanol have been investigated. Calculations at the used level predict an increase of the entropy upon adsorption interaction with dehydrated silanol. Adsorption of hydrated Cu²⁺ and hydrated/un-hydrated Mg²⁺ on silanol is an exothermic process as predicted by B3LYP/6-31+G(d)//HF/6-31+G(d). This, in turn, leads to more negative free energy of reaction compared to experiment, $-$59.8 versus $-$25.8kJ/mol for Cu²⁺ and $-$53.8 versus $-$22.6kJ/mol for Mg²⁺. However, the strength of interaction between silica and both ions was reproduced correctly by theory.

Water plays a significant role in determining the protein–ligand binding modes, especially when water molecules are involved in mediating protein–ligand interactions, and these important water molecules are receiving more and more attention in recent years. Considering the effects of water molecules has gradually become a routine process for accurate description of the protein–ligand interactions. As a free docking program, Autodock has been most widely used in predicting the protein–ligand binding modes. However, whether the inclusion of water molecules in Autodock would improve its docking performance has not been systematically investigated. Here, we incorporate important bridging water molecules into Autodock program, and systematically investigate the effectiveness of these water molecules in protein–ligand docking. This approach was evaluated using 18 structurally diverse protein–ligand complexes, in which several water molecules bridge the protein–ligand interactions. Different treatment of water molecules were tested by using the fixed and rotatable water molecules, and a considerable improvement in successful docking simulations was found when including these water molecules. This study illustrates the necessity of inclusion of water molecules in Autodock docking, and emphasizes the importance of a proper treatment of water molecules in protein–ligand binding predictions.