Modern nanotechnology research has generated numerous experimental data for various nanomaterials. However, the few nanomaterial databases available are not suitable for modeling studies due to the way they are curated. Here, we report the construction of a large nanomaterial database containing annotated nanostructures suited for modeling research. The database, which is publicly available through http://www.pubvinas.com/, contains 705 unique nanomaterials covering 11 material types. Each nanomaterial has up to six physicochemical properties and/or bioactivities, resulting in more than ten endpoints in the database. All the nanostructures are annotated and transformed into protein data bank files, which are downloadable by researchers worldwide. Furthermore, the nanostructure annotation procedure generates 2142 nanodescriptors for all nanomaterials for machine learning purposes, which are also available through the portal. This database provides a public resource for data-driven nanoinformatics modeling research aimed at rational nanomaterial design and other areas of modern computational nanotechnology.

We designed novel nanodescriptors that can characterize the nanostructure diversity and also be quickly calculated in batches, to profile nanoparticles.

Nanoparticle structural parameters, such as size, surface chemistry, and shape, are well-recognized parameters that affect biological activities of nanoparticles. However, whether the core material of a nanoparticle also plays a role remains unknown. To answer this long-standing question, we synthesized and investigated a comprehensive library of 36 nanoparticles with all combinations of three types of core materials (Au, Pt, and Pd), two sizes (6 and 26 nm), and each conjugated with one of six surface ligands of different hydrophobicity. Using this systematic approach, we were able to identify cellular perturbation specifically attributed to core, size, or surface ligand. We discovered that core materials exhibited a comparable regulatory ability as surface ligand on cellular ROS generation and cytotoxicity. Pt nanoparticles were much more hydrophilic and showed much less cell uptake compared to Au and Pd nanoparticles with identical size, shape, and surface ligands. Furthermore, diverse core materials also regulated levels of cellular redox activities, resulting in different cytotoxicity. Specifically, Pd nanoparticles significantly reduced cellular H2O2 and promoted cell survival, while Au nanoparticles with identical size, shape, and surface ligand induced higher cellular oxidative stress and cytotoxicity. Our results demonstrate that nanoparticle core material is as important as other structural parameters in nanoparticle–cell interactions, making it also a necessary consideration when designing nanomedicines.

Molecular dynamics simulations have been performed to investigate the transport properties of a single Ca(2+), K(+), and Na(+) in a water-filled transmembrane cyclic peptide nanotube (CPNT). Two transmembrane CPNTs, i.e., 8×(WL)n=4,5/POPE (with uniform lengths but various radii), were applied to clarify the dependence of ionic transport properties on the channel radius. A huge energy barrier keeps Ca(2+) out of the octa-CPNT, while Na(+) and K(+) can be trapped in two CPNTs. The dominant electrostatic interaction of a cation with water molecules leads to a high distribution of channel water around the cation and D-defects in the first and last gaps, and significantly reduces the axial diffusion of channel water. Water-bridged interactions were mostly found between the artificially introduced Ca(2+) and the framework of the octa-CPNT, and direct coordinations with the tube wall mostly occur for K(+) in the octa-CPNT. A cation may drift rapidly or behave lazily in a CPNT. K(+) behaves most actively and can visit the whole deca-CPNT quickly. The first solvation shells of Ca(2+) and Na(+) are basically saturated in two CPNTs, while the hydration of K(+) is incomplete in the octa-CPNT. The solvation structure of Ca(2+) in the octa-CPNT is most stable, while that of K(+) in the deca-CPNT is most labile. Increasing the channel radius induces numerous interchange attempts between the first-shell water molecules of a cation and the ones in the outer region, especially for the K(+) system.