N–H bond cleavage of ammonia on graphene-like B36 borophene: DFT studies

The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based machine-learning technique was applied for residue-level prediction of the domain/linker annotations in protein sequences using ordered/disordered regions along protein chains and a set of physicochemical properties. Six different classifiers—decision tree, Gaussian naïve Bayes, linear discriminant analysis, support vector machine, random forest, and multilayer perceptron—were exhaustively explored for the residue-level prediction of domain/linker regions. The protein sequences from the curated CATH database were used for training and cross-validation experiments. Test results obtained by applying the developed PDP-CON tool to the mutually exclusive, independent proteins of the CASP-8, CASP-9, and CASP-10 databases are reported. An n-star quality consensus approach was used to combine the results yielded by different classifiers. The average PDP-CON accuracy and F-measure values for the CASP targets were found to be 0.86 and 0.91, respectively. The dataset, source code, and all supplementary materials for this work are available at https://cmaterju.org/cmaterbioinfo/ for noncommercial use.

     

The H2 dissociation on the BN, AlN, BP and AlP nanotubes: a comparative study

The thermodynamic and kinetic feasibility of H(2) dissociation on the BN, AlN, BP and AlP zigzag nanotubes has been investigated theoretically by calculating the dissociation and activation energies. We determined the BN and AlP tubes to be inert toward H(2) dissociation, both thermodynamically and kinetically. The reactions are endothermic by 5.8 and 3 kcal mol(-1), exhibiting high activation energies of 38.8 and 30.6 kcal mol(-1), respectively. Our results indicated that H(2) dissociation is thermodynamically favorable on both PB and AlN nanotubes. However, in spite of the thermodynamic feasibility of H(2) dissociation on PB types, this process is kinetically unfavorable due to partly high activation energy. Generally, we concluded that among the four studied tubes, the AlN nanotube may be an appropriate model for H(2) dissociation process, from a thermodynamic and kinetic stand point. We also indicated that H(2) dissociation is not homolytic, rather it takes place via a heterolytic bond cleavage. In addition, a comparative study has been performed on the electrical and geometrical properties of the tubes. Our analysis showed that the electrical conductivity of tubes is as follows: BP>AlP>BN>AlN depending on how to combine the electron rich and electron poor atoms.     

Theoretical investigation on the selective detection of SO2 molecule by AlN nanosheets

A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p), cc-pVDZ and cc-pVTZ basis sets were used for the adsorption energy calculation and such energies were corrected for the basis set superposition error. Vertical ionization potential and electron affinity of the investigated system were also computed. The interaction of polypyrrole on the SWCNT surface is characterized by the stacking interaction. Adsorption (binding) energy of pyrrole on the SWCNT surface is weak, but such energy increases with the number of monomer units in the pyrrole oligomer. In the SWCNT-pyrrole complexes, the oxidation and reduction processes will take place only at the SWCNT. The influence of larger unit on the electronic properties of the complex has been detailed.     

DFT studies of acrolein molecule adsorption on pristine and Al- doped graphenes

The ability of pristine graphene (PG) and Al-doped graphene (AlG) to detect toxic acrolein (C₃H₄O) was investigated by using density functional calculations. It was found that C₃H₄O molecule can be adsorbed on the PG and AlG with adsorption energies about ?50.43 and – v30.92 kcal mol^?1 corresponding to the most stable configurations, respectively. Despite the fact that interaction of C₃H₄O has no obvious effects on the of electronic properties of PG, the interaction between C₃H₄O and AlG can induce significant changes in the HOMO/LUMO energy gap of the sheet, altering its electrical conductivity which is beneficial to sensor designing. Thus, the AlG may be sensitive in the presence of C₃H₄O molecule and might be used in its sensor devices. Also, applying an external electric filed in an appropriate orientation (almost stronger than 0.01 a.u.) can energetically facilitate the adsorption of C₃H₄O molecule on the AlG.