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Abstract
An aminoborane side product from the nicergoline manufacture process was identified by single-crystal X-ray diffraction. As boranes of pharmaceutical molecules are quite rare, the binding potential of the BH3 group was investigated and compared with similar compounds using Cambridge Structural Database (CSD). Surprisingly, the packing was stabilized by a dihydrogen bond, which triggered a false alert for too-short contact of hydrogen atoms in IUCR checkCIF. As the dihydrogen bond concept is not widely known, such an alert might mislead crystallographers to force –CH3 optimal geometry to –BH3 groups. The B–H distances equal to or less than 1.0 Å (17% of the CSD structures) are substantially biased when analyzing the structures of aminoborane complexes in CSD. To conduct proper searching, B–H bond length normalization should be applied in the CSD search.
Highlights
Sodium borohydride is widely used as a reducing agent in the synthesis of many active pharmaceutical substances
Please note that the systematic ergoline numbering N6 corresponds to N2 in the current crystal structure)
A Cambridge Structural Database (CSD) user who is aware of the problem can handle it with an optional normalization of B–H lengths to at least 1.15 Å as available in the Conquest search
Summary
Sodium borohydride is widely used as a reducing agent in the synthesis of many active pharmaceutical substances. In the course of the reaction of daunomycin with sodium borohydride, various borate esters were observed. In this case, the coordination of boron to the drug proceeded via an oxygen atom [1]. Aminoboranes [3] are usually known as hydrogenation agents They offer some advantages over sodium borohydride, such as good solubility in organic solvents. They are less sensitive to acids and can serve as chiral reducing agents [4,5,6]. Despite their popularity, very few crystal structures of boranes of alkaloids or pharmaceutical molecules have been described. The crystal structures of several borane complexes of cinchona alkaloids have been reported [7]
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