The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a federation of databases, enhancing the accessibility and discoverability of materials and chemical data.

The crystal structure, cohesive energy, and electronic properties of bulk phases of the fullerene derivative [6, 6]-phenyl-${\text{C}}_{61}$-butyric-acid-methyl-ester (PCBM) have been calculated using ab initio density-functional theory (DFT) techniques. We have only considered cubic and hexagonal crystal lattices with one PCBM molecule per primitive cell. It was found that the cohesive properties of these systems are determined mainly by two types of mechanisms, namely, the van der Waals interaction and the formation of weak hydrogen bonds. Among the considered crystal structures, the most stable one, which is also the most compact structure, is the simple cubic which has a cohesive energy difference of 1.27 eV with respect to the isolated PCBM molecule. Regarding the electronic properties, the simple-cubic PCBM crystal is found to be a semiconductor with an indirect band gap of 1.21 eV. In addition, we have also investigated the electronic contribution of the phenyl-butyric-acid-methyl-ester tail to the electronic states of the entire system. By analyzing the projected density of states (DOS), we found that the states introduced by the tail are too far from the valence and conduction bands, so that the reduction of the band gap of bulk PCBM compared to PCBM molecule results only from the close packing. In addition, the tail introduces a splitting of the degenerate states of the molecule reducing the gap by about 0.2 eV compared to the ${\text{C}}_{60}$ molecule. On the other hand, it is shown that the simple hexagonal structure presents a layered structure with the separation between layers of $12.6\text{Å}$. Furthermore, in the cohesive curve, there is a nonvanishing cohesive energy for noninteracting layers. The study of the hexagonal monolayers shows a stable structure with a cohesive energy of 0.72 eV, which indicates that PCBM can form two-dimensional systems when the PCBM molecules are deposited on the appropriate substrates. The results provided by this work may be important to improve our understanding concerning the mechanisms of formation of PCBM supramolecular structures, and how they can be modified to reach a desired particular property.

Streamlit is an open-source Python coding framework for building web-applications or “web-apps” and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists.

We have studied the dispersion relation of surface plasmon modes in metal cylinders using the Drude model by numerically solving complex eigenfrequencies as a function of the radius. We also studied the quality factor Q of the modes and found that it decays as the radius is increased, and for a small radius there is a maximum value equal to ω s / γ independent of the mode order (where ω s is the Ritchie’s surface plasmon frequency and γ is the damping constant).