CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. In addition, the CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This paper provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM paper in 1983.

Most P2-type layered oxides suffer from multiple voltage plateaus, due to Na+/vacancy-order superstructures caused by strong interplay between Na–Na electrostatic interactions and charge ordering in the transition metal layers. Here, Mg ions are successfully introduced into Na sites in addition to the conventional transition metal sites in P2-type Na0.7[Mn0.6Ni0.4]­O2 as new cathode materials for sodium-ion batteries. Mg ions in the Na layer serve as “pillars” to stabilize the layered structure, especially for high-voltage charging, meanwhile Mg ions in the transition metal layer can destroy charge ordering. More importantly, Mg ion occupation in both sodium and transition metal layers will be able to create “Na–O–Mg” and “Mg–O–Mg” configurations in layered structures, resulting in ionic O 2p character, which allocates these O 2p states on top of those interacting with transition metals in the O-valence band, thus promoting reversible oxygen redox. This innovative design contributes smooth voltage profiles and high structural stability. Na0.7Mg0.05[Mn0.6Ni0.2Mg0.15]­O2 exhibits superior electrochemical performance, especially good capacity retention at high current rate under a high cutoff voltage (4.2 V). A new P2 phase is formed after charge, rather than an O2 phase for the unsubstituted material. Besides, multiple intermediate phases are observed during high-rate charging. Na-ion transport kinetics are mainly affected by elemental-related redox couples and structural reorganization. These findings will open new opportunities for designing and optimizing layer-structured cathodes for sodium-ion batteries.

The Escherichia coli type III effector Map belongs to a large family of bacterial virulence factors that activate host Rho GTPase signaling pathways through an unknown molecular mechanism. Here we report direct evidence that Map functions as a potent and selective guanine-nucleotide exchange factor (GEF) for Cdc42. The 2.3-Å structure of the Map–Cdc42 complex revealed that Map mimics the GEF strategy of the mammalian Dbl family but has a three-dimensional architecture that is nearly identical to the bacterial GEF Salmonella spp. SopE. A comparative analysis between human and bacterial GEFs revealed a previously uncharacterized pairing mechanism between Map and the variable β2–3 interswitch region of Cdc42. We propose a GTPase selection model that is experimentally validated by the preferential activation Rac1 and RhoA by the Shigella spp. effectors IpgB1 and IpgB2, respectively. These results significantly expand the repertoire of bacterial GEF mimics and unify a GEF selection mechanism for host GTPase substrates.

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