Functionalization of α-In2Se3 Monolayer via Adsorption of Small Molecule for Gas Sensing.

Based on first-principles calculations, the adsorption of NO and NO2 gas molecules on the α-In2Se3 monolayer have been studied. The adsorption configuration, adsorption energy, electronic structure and charge transfer properties are investigated. It is found that the charge transfer processes of NO and NO2 adsorbed on the surface of α-In2Se3 monolayer exhibit electron donor and acceptor characteristics, respectively. After the adsorption of the molecules, the α-In2Se3 monolayers have new states near the Fermi level induced by NO and NO2, which can trigger some new effects on the conducting and optical properties of the materials, with potential benefits to gas selectivity. The present work provides new valuable results and theoretical foundation for potential applications of the In2Se3-based gas sensor.

Computational study of the one- and two-photon absorption and circular dichroism of (L)-tryptophan.

A density functional theory (DFT) study of the one- and two-photon absorption and circular dichroism spectra of (l)-tryptophan in water is presented. The effects on the simulated spectra of conformational averaging, of solvent as described by the polarizable continuum model (PCM), and of the choice of exchange-correlation (XC) functional are analyzed. Conformational Maxwell-Boltzmann (MB) averaging is carried out at room temperature in the gas phase using the ten lowest-energy conformers in the gas phase, whereas in the solvent, the nine lowest zwitterionic conformers are determined in combination with a PCM continuum model and employed in the calculations. One- and two-photon absorption and circular dichroism spectra are calculated using time-dependent DFT with both the B3LYP and CAM-B3LYP XC functionals, including the 15 lowest excited electronic states in each case. The spectra are shown to be strongly influenced by all parameters of our computational models. Changing the XC functional yields large changes not only in the excitation energies but also in the transition dipole moments and the rotational strengths of each excited state. The inclusion of the effect of water solvation also yields different response properties for each excited state, as well as different ground-state equilibrium geometries for the gas and solvated phases. MB weights change significantly from the gas to the solvated phase, making the effect of conformational averaging strongly phase dependent. The study of all these effects highlights the importance of an accurate and reliable treatment of both ground and excited states when aiming at predicting experimental one- or two-photon spectra. However, the comparison between the MB weighted spectra and experiment for the linear spectroscopies turns out to be rather satisfactory, showing that our approach can yield at least information on the major features of the spectra.

Comprehensive density functional theory study on the mechanism of activation of the nonapeptide hormone oxytocin by metal ions.

The physiological functions of oxytocin (OT) may be activated by bivalent metal ions but not by monovalent ones. However, the reason for this phenomenon is unknown. Thus, in the present study, theoretical calculations were performed to determine the structures and thermochemical properties of OT and related species: OT, [OT+H](+), [OT+2H](2+), [OT+M](+/2+), and [OT+M+H](2+/3+) (M(+) = Na(+) and K(+), M(2+) = Co(2+), Ni(2+), Mg(2+), Zn(2+), and Ca(2+)). Their structures and vibrational frequencies were determined by the density functional theory based method. Their relative electronic energies were determined at the BHandHLYP/6-311G(2df,p) level with proper considerations of the basis set superposition errors. The computed structures were used to explain whether the OT species were physiologically active or not, and the mechanism of the activation of OT by divalent metal ions but not by monovalent metal ions was determined. The relative metal ion affinities of OT were found to be responsible for the relative effectiveness of divalent metal ions for the OT activation, which were in the order of Co(2+) > Ni(2+) > Mg(2+) > Zn(2+), with a minimal effect by Ca(2+). Moreover, the recent observation of the coexistence of [OT+H](+), [OT+2H](2+), and [OT+Na+H](2+) in solution in the absence of a divalent metal ion and their disappearance in the presence of Zn(2+) were also explained by the computed free energy changes of the relevant reactions.

Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers.

Conformations of peptides are the basis for their property studies and the predictions of peptide structures are highly important in life science but very complex in practice. Here, thorough searches on the potential energy surfaces of 13 representative dipeptides by considering all possible combinations of the bond rotational degrees of freedom are performed using the density functional theory based methods. Careful analyses of the conformers of the 13 dipeptides and the corresponding amino acids reveal the connections between the structures of dipeptide and amino acids. A method for finding all important dipeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid conformations is thus proposed. Applying the method to another eight dipeptides carefully examined by others shows that the new approach is both highly efficient and reliable by providing the most complete ensembles of dipeptide conformers and much improved agreements between the theoretical and experimental IR spectra. The method opens the door for the determination of the stable structures of all dipeptides with a manageable amount of effort. Preliminary result on the applicability of the method to the tripeptide structure determination is also presented. The results are the first step towards proving Anfinsen's hypothesis by revealing the relationships between the structures of the simplest peptide and its constituting amino acids. It implies that the structures of peptides are not only determined by their amino acid sequences, but also closely linked with the amino acid conformations.