A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data

Phase-transition-induced jumping, bending, and wriggling of single crystal nanofibers of coronene

For decades, it has been reported that some organic crystals suddenly crack, break, or jump when they are heated from room temperature. Recently, such crystals have been intensively studied both in fundamental science and for high-speed mechanical device applications. According to these studies, the sudden crystal motions have been attributed to structural phase transitions induced by heating. Stress created by the phase transition is released through the sudden and rapid motion of the crystals. Here we report that single crystal nanofibers of coronene exhibit a new type of ultrafast motion when they are cooled from room temperature and subsequently heated to room temperature. The nanofibers make centimeter-scale jumps accompanied by surprisingly unique behaviors such as sharp bending and wriggling. We found that the motions are caused by a significantly fast structural phase transition between two polymorphs of coronene. A theoretical investigation revealed that the sudden force generated by the phase transition together with the nanoscale dimensions and elastic properties create dynamical instability in the nanofibers that results in the motions. Our finding demonstrates the novel mechanism that leads to ultrafast, large deformation of organic crystals.

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

The CLP-dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal-oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non-rigid and hydrogen-bonded compounds for the reproduction of radial distribution functions and of crystal-specific collective orientational variables against X-ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X-ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

Computational and materials structural science

This Editorial discusses recent development in computational and materials structural science as exemplified by recent articles published in IUCrJ.