Element Mis-identification in X-ray Crystallography: A Series of Case Studies

Friday, September 8, 2017

Dr. James Donahue

Department of Chemistry

Tulane University

Hand Lab 1144, 3:30 PMJames Donahue

X-ray crystallography is sometimes described as a definitive technique in identifying a compound. As a stand-alone technique, the certainty offered by X-ray crystallography is limited to a description of atom connectivity, as opposed to atom identity, because elements with similar atomic number have similar diffracting power. In this talk, a series of examples are considered in which coordination compounds of the transition metals are incorrectly formulated on the basis of a crystal structure. First, a set of reports describing the syntheses and structures of [MCl2(diazadiene)] (M = Cr, Mo, W) complexes is reassessed in the context of known chemistry of low-valent Group VI metal complexes, crystallographic trends such as M–Cl bond lengths and unit cell volumes, and calculated metal-ligand bond lengths. Crystallographic data and computational results are inconsistent with any of these species being second or third row transition metal complexes. The crystallographic information files accompanying the [MCl2(diazadiene)] (M = Mo, W) published structures reveal that the metal atoms were refined with partial site occupancy factors (0.775 for Mo; 0.4005 and 0.417 for W), the effect of which was to produce lighter-element behavior and better refinement in accord with the metal atoms’ correct identity, which is Zn2+. Divalent zinc originates from zinc metal employed as a reducing agent. A similar case involving [(Me3P)2ZnCl2] misidentified as [(Me3P)2MoCl2] is noted. A third case of element mis-assignment involves a tetrametallic species, [M(iPr2Pipdt)]4[BF4]4 (iPr2Pipdt = diisopropylpiperazine-2,3-dithione), that is created by treatment of [MoOCl(iPr2Pipdt)2]+ with AgBF4. The metal atom is identified as Mo1+, but a variety of chemical considerations is strongly indicative of Ag+ as the more chemically plausible metal ion. Finally in our own work, attention is given to considerable confusion caused by the inability to distinguish Cl- from SH- as a ligand in Cu1+ complexes on the basis of crystallography. Offered in conclusion are thoughts on some preemptive practices that guard against element mis-identification in the crystal structure determination process.


James P. Donahue was born and raised in northern Indiana. He did his undergraduate studies at M.I.T., earning a B.S. in chemistry in 1991. With the support of a DoD fellowship, he did his doctoral work with Richard Holm at Harvard University, earning his Ph.D. in 1998 with a dissertation about the synthesis and properties of small molecule analogues of the active sites on molybdo- and tungstoenzymes. In 1999, he began a postdoctoral study with F. A. Cotton at Texas A&M with the support of an NIH fellowship. In 2004, he assumed a tenure track assistant professor position at Tulane University, and in 2011 he was promoted to his current rank of associate professor.

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