Exceptionally low shear modulus in a prototypical imidazole-based metal-organic framework.

Using Brillouin scattering, we measured the single-crystal elastic constants (C(ij)'s) of a prototypical metal-organic framework (MOF): zeolitic imidazolate framework (ZIF)-8 [Zn(2-methylimidazolate)(2)], which adopts a zeolitic sodalite topology and exhibits large porosity. Its C(ij)'s under ambient conditions are (in GPa) C(11)=9.522(7), C(12)=6.865(14), and C(44)=0.967(4). Tensorial analysis of the C(ij)'s reveals the complete picture of the anisotropic elasticity in cubic ZIF-8. We show that ZIF-8 has a remarkably low shear modulus G(min) < or approximately 1 GPa, which is the lowest yet reported for a single-crystalline extended solid. Using ab initio calculations, we demonstrate that ZIF-8's C(ij)'s can be reliably predicted, and its elastic deformation mechanism is linked to the pliant ZnN(4) tetrahedra. Our results shed new light on the role of elastic constants in establishing the structural stability of MOF materials and thus their suitability for practical applications

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.Comment: 16 pages, 5 figure

Modelling of functional hybrid organic-inorganic materials: from structure to properties

Computational modelling of porous hybrid organic-inorganic materials is a challenging task. The dual nature and flexibility of frameworks require the delicate description of systems. In addition, the absence of reliable force-fields and the size of systems makes the density functional theory (DFT) the best choice. The poor description of long-range dispersion interactions, a crucial deficiency of DFT, has been circumvented by introducing the dispersion correction schemes. Zeolitic imidazolate frameworks (ZIF), extended analogues of inorganic zeolites by topological similarity, are the focal point of this thesis. Their prospective applications in gas adsorption/separation and catalysis are driving the search of new not-yet-syntesised structures and methods to tune their properties. A set of new hypothetical ZIF has been explored, including lightweight LiB-based frameworks. To establish structure-property relationship, the impact of topologies and linker has been analysed. It has been revealed the crucial role of linker-linker interaction and packing for the thermodynamics stability of frameworks. Furthermore, the mechanical properties of ZIFs have been explored. Close collaboration with experimentalist groups has allowed the cross-linked analysis and rationalization of the observed of phenomena. Finally, an empirical force-field fitting protocol from ab initio data has been improved. The idea is to exploit the redundant internal coordinates in fitting as it makes the problem more linear, but an existing code was able to handle non-periodic models only. The periodicity has been implemented to allow fitting force-field for material, which could not be partitioned into non-periodic models, including ZIFs. The new protocol has been tested with several systems

Mechanical properties of dense zeolitic imidazolate frameworks (ZIFs): a high-pressure X-ray diffraction, nanoindentation and computational study of the zinc framework Zn(Im)2, and its lithium-boron analogue, LiB(Im)4.

The dense, anhydrous zeolitic imidazolate frameworks (ZIFs), Zn(Im)(2) (1) and LiB(Im)(4) (2), adopt the same zni topology and differ only in terms of the inorganic species present in their structures. Their mechanical properties (specifically the Young's and bulk moduli, along with the hardness) have been elucidated by using high pressure, synchrotron X-ray diffraction, density functional calculations and nanoindentation studies. Under hydrostatic pressure, framework 2 undergoes a phase transition at 1.69 GPa, which is somewhat higher than the transition previously reported in 1. The Young's modulus (E) and hardness (H) of 1 (E≈8.5, H≈1 GPa) is substantially higher than that of 2 (E≈3, H≈0.1 GPa), whilst its bulk modulus is relatively lower (≈14 GPa cf. ≈16.6 GPa). The heavier, zinc-containing material was also found to be significantly harder than its light analogue. The differential behaviour of the two materials is discussed in terms of the smaller pore volume of 2 and the greater flexibility of the LiN(4) tetrathedron compared with the ZnN(4) and BN(4) units

PSI4 1.4 : Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.Peer reviewe