Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc–sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc–sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited.

No abstract

structure structure (organic substances) K 9000 -046The out,out to out,in Transition for 1,(n + 2)-Diazabicyclo(n.3.1) alkanes.-The borderline for changeover from "out,out" to "out,in" structures for a homologous series of bicyclic systems is defined for the first time for the title compounds (I)-(VI). The "out,out" (axial,axial) and "out,in" (axial,equatorial) structures represent isomers of different configurations. The borderline is at (IV) in the gas phase, but at (V) in CDCl3 solution; this solvent effect is attributed to better solvation of "out" lone pairs. The experimental data of photoelectron spectra are correlated with force field (MM2) calculations. Related tricyclic systems having 10-and 12-membered rings are also studied. -(ALDER, R. W.; HEILBRONNER, E.; HONEGGER, E.; MCEWEN, A. B.; MOSS, R. E.; OLEFIROWICZ, E.; PETILLO, P. A.; SESSIONS, R. B.; WEISMAN, G. R.; WHITE, J. M.; YANG, Z.