Exemplars of the state of the art in modeling enzymes are reviewed through a selection of works from leading schools using QM-only cluster models, QM/MM models and QM/MM/MD models.A computational protocol is proposed, intended to guide neophytes through the myriad of methodological choices that are necessary for the successful study of chemical reactions in the complex enzymatic environment.

Two low-lying structures are unveiled for the Be B nanocluster system that are virtually isoenergetic. The first, triple-layered cluster has a peripheral B ring as central layer, being sandwiched by two Be rings in a coaxial fashion, albeit with no discernible interlayer Be-Be bonding. The B ring revolves like a flexible chain even at room temperature, gliding freely around the Be prism. At elevated temperatures (1000 K), the Be core itself also rotates; that is, two Be rings undergo relative rotation or twisting with respect to each other. Bonding analyses suggest four-fold (π and σ) aromaticity, offering a dilute and fluxional electron cloud that lubricates the dynamics. The second, helix-type cluster contains a B helical skeleton encompassing a distorted Be prism. It is chiral and is the first nanosystem with a boron helix. Molecular dynamics also shows that at high temperature the helix cluster readily converts into the triple-layered one.

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Herein we introduce a strategy employing lithium atoms as a scaffold to stabilize an embryo for boron tubes.