The seventh blind test of crystal structure prediction: structure generation methods.

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern.

Cocrystal Synthesis through Crystal Structure Prediction.

Crystal structure prediction (CSP) is an invaluable tool in the pharmaceutical industry because it allows to predict all the possible crystalline solid forms of small-molecule active pharmaceutical ingredients. We have used a CSP-based cocrystal prediction method to rank ten potential cocrystal coformers by the energy of the cocrystallization reaction with an antiviral drug candidate, MK-8876, and a triol process intermediate, 2-ethynylglyclerol. For MK-8876, the CSP-based cocrystal prediction was performed retrospectively and successfully predicted the maleic acid cocrystal as the most likely cocrystal to be observed.

Selecting a stable solid form of remdesivir using microcrystal electron diffraction and crystal structure prediction.

Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations.

Virtual Coformer Screening by Crystal Structure Predictions: Crucial Role of Crystallinity in Pharmaceutical Cocrystallization.

One of the most popular strategies of the optimization of drug properties in the pharmaceutical industry appears to be a solid form changing into a cocrystalline form. A number of virtual screening approaches have been previously developed to allow a selection of the most promising cocrystal formers (coformers) for an experimental follow-up. A significant drawback of those methods is related to the lack of accounting for the crystallinity contribution to cocrystal formation.

Additive and Photochemical Manufacturing of Copper.

In recent years, 3D printing technologies have been extensively developed, enabling rapid prototyping from a conceptual design to an actual product. However, additive manufacturing of metals in the existing technologies is still cost-intensive and time-consuming. Herein a novel platform for low-cost additive manufacturing is introduced by simultaneously combining the laser-induced forward transfer (LIFT) method with photochemical reaction.

Photochemical Copper Coating on 3D Printed Thermoplastics.

3D printing using thermoplastics has become very popular in recent years, however, it is challenging to provide a metal coating on 3D objects without using specialized and expensive tools. Herein, a novel acrylic paint containing malachite for coating on 3D printed objects is introduced, which can be transformed to copper via one-step laser treatment. The malachite containing pigment can be used as a commercial acrylic paint, which can be brushed onto 3D printed objects.

Self-consistent field for fragmented quantum mechanical model of large molecular systems.

Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions.

Single layer of MX₃ (M = Ti, Zr; X = S, Se, Te): a new platform for nano-electronics and optics.

A serial of two-dimensional titanium and zirconium trichalcogenides nanosheets MX3 (M = Ti, Zr; X = S, Se, Te) were investigated based on first-principles calculations. The evaluated low cleavage energy indicates that stable two-dimensional monolayers can be exfoliated from their bulk crystals in the experiment. Electronic studies reveal the very rich electronic properties in these monolayers, including metallic TiTe3 and ZrTe3, direct band gap semiconductor, TiS3, and indirect band gap semiconductors, TiSe3, ZrS3 and ZrSe3.

Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.

Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods.

Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum-mechanical and molecular-mechanical subsystems. Instead, classical Lennard-Jones (LJ) potentials between QM and MM nuclei are used to model electronic Pauli repulsion and long-range London dispersion, despite the fact that the latter two are inherently of quantum nature. Use of the simple LJ potential in QM/MM methods can reproduce minimal geometries and energies of many molecular clusters reasonably well, as compared to full QM calculations.

Liquid water simulations with the density fragment interaction approach.

We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys.

Nearly free electron superatom states of carbon and boron nitride nanotubes.

By first-principles theory we study the nearly free electron (NFE) states of carbon and boron nitride nanotubes. In addition to the well-known π bands, we found a series of one-dimensional (1D) NFE bands with on-axis spatial distributions, which resemble atomic orbitals projected onto a plane. These bands are 1D counterparts of the recently discovered superatom orbitals of 0D fullerenes.

Power-law strength-degree correlation from resource-allocation dynamics on weighted networks.

Many weighted scale-free networks are known to have a power-law correlation between strength and degree of nodes, which, however, has not been well explained. We investigate the dynamic behavior of resource-traffic flow on scale-free networks. The dynamical system will evolve into a kinetic equilibrium state, where the strength, defined by the amount of resource or traffic load, is correlated with the degree in a power-law form with tunable exponent.