Generative ß-hairpin design using a residue-based physicochemical property landscape.

De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the ß-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of ß hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial ß-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.

Investigation of N2 adsorption on Fe3O4(001) using ambient pressure X-ray photoelectron spectroscopy and density functional theory.

Reactions on iron oxide surfaces are prevalent in various chemical processes from heterogeneous catalysts to minerals. Nitrogen (N2) is known to dissociate on iron surfaces, a precursor for ammonia production in the Haber-Bosch process, where the dissociation of N2 is the limiting step in the reaction under equilibrium conditions. However, little is known about N2 adsorption on other iron-based materials, such as iron oxide surfaces that are ubiquitous in soils, steel pipelines, and other industrial materials. An atomistic description is reported for the binding of N2 on the Fe3O4(001) surface using first principles calculations with ambient pressure X-ray photoelectron spectroscopy. Two primary adsorption sites are experimentally identified from N2 dissociation on Fe3O4(001). The electronic signatures associated with the valence band region unambiguously show how the electronic structure of magnetite transforms near ambient pressures due to the binding of atomic nitrogen to different surface sites. Overall, the experimental and theoretical results of our study bridge the gap between ultra-high vacuum studies and reaction conditions to provide insight into other nitrogen-based chemistry on iron oxide surfaces that impact the agriculture and energy industries.

First-Principles Study of a MoS2-PbS van der Waals Heterostructure Inspired by Naturally Occurring Merelaniite.

Vertically stacked, layered van der Waals (vdW) heterostructures offer the possibility to design materials, within a range of chemistries and structures, to possess tailored properties. Inspired by the naturally occurring mineral merelaniite, this paper studies a vdW heterostructure composed of a MoS2 monolayer and a PbS bilayer, using density functional theory. A commensurate 2D heterostructure film and the corresponding 3D periodic bulk structure are compared. The results find such a heterostructure to be stable and possess p-type semiconducting characteristics. Due to the heterostructure's weak interlayer bonding, its carrier mobility is essentially governed by the constituent layers; the hole mobility is governed by the PbS bilayer, whereas the electron mobility is governed by the MoS2 monolayer. Furthermore, we estimate the hole mobility to be relatively high (~106 cm2V-1s-1), which can be useful for ultra-fast devices at the nanoscale.

Tailoring of the electronic property of Zn-BTC metal-organic framework via ligand functionalization: an ab initio investigation.

Metal-organic frameworks (MOFs) are porous materials of recent interest due to their promising properties for technological applications. In this paper, the structure-property relationships of pristine and functionalized Zn-BTC (Zn3(BTC)2) MOFs are investigated. The results based on density functional theory (DFT) find that MOFs with coordinatively saturated secondary building units (SBU) are metallic, and MOFs with coordinatively unsaturated SBU are semi-conducting. The ligand functionalization with electron acceptor (cyano-) and electron donor (amino-) groups appears to tailor the electronic properties of Zn-BTC MOFs; amino-functionalization led to a significant upward shift of the band-edges whereas cyano-functionalization yields shifting of band-edges in the opposite direction, which led to a narrowing of the band gap. Modifying the electronic properties through such ligand functionalization design principles can be useful in engineering MOFs for gas sensing and device applications.