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Being a program written primarily in Python that strictly adheres to modern object-oriented software engineering and parallel programming practices, VeloxChem is shown to be suitable for the development of (semi)automatized workflows that extend its scope from first-principles quantum chemical purism to hybrid quantum–classical interoperability and some degree of semiempiricism. Methods are presented for building complex systems such as metal–organic frameworks, constructing molecular mechanics and interpolation mechanics force fields, conformer searches, system solvation, determining free energies of solvation, and determining free energy profiles of reaction pathways using the empirical valence bond method. The implementations are made intuitive with opportunities for interactive plotting and 3D molecular structure illustrations through the use of Jupyter notebooks.

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VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software wh...

The bacterial mechanosensitive channel, MscL, opens in response to elevated membrane tension during osmotic shock. Some mutations, like L17A and V21A, can reduce the activation tension threshold, thus...

Easily tunable and processable, porous organic polymers (POPs) have found increasing utility in various applications. Molecular modeling and simulations are invaluable tools in polymer science but remain under-reported in the POP literature. Accurate modeling and simulation of these materials could boost the discovery of high-performance POPs and allow for a more thorough contribution to big data. These polymers contain free volume-promoting structural units, such as iptycenes, and exhibit high glass-transition temperatures, excellent thermal stability, and tunable functionality. However, popular transferable force fields utilized in all-atomistic molecular dynamics (MD) simulations are not fully parametrized for intrinsically porous thermoplastic materials. We present a streamlined workflow for all-atomistic MD simulations of nonporous and porous amorphous polymer materials. In conjunction with the programs ORCA, Q-Force, Assemble!, and GROMACS, a highly accessible methodology is established for force field (FF) parametrization, creation of initial configurations, and simulation of various nonporous and porous polymers. This protocol can reproduce experimental bulk densities and fractional free volume values for amorphous polymeric materials with excellent accuracy and has been made available as a Python package, called PolyPal. As an example, we present our results using PolyPal on a series of nonporous and porous polymers that were previously synthesized and experimentally characterized. FF accuracy was also validated through solid-state NMR studies. These simulations will not only open new avenues for the rational design of high-performance POPs through the contribution of improved insight but also provide a streamlined pathway for simulating previously unexplored porous polymeric materials.

We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum e...