Crystal polymorphism in pendimethalin herbicide is driven by electronic delocalization and changes in intramolecular hydrogen bonding. A crystallographic, spectroscopic and computational study

Abstract

Pendimethalin, N-(1-ethylpropyl)-3,4-dimethyl-2,6-dinitrobenzenamine, is a potent herbicide that exists in two differently coloured polymorphic crystal habits. Triclinic pendimethalin I (P 1̄) is the orange-coloured thermodynamically stable form, whereas monoclinic pendimethalin II (P 2₁/c) is a bright-yellow metastable form. The latter is normally produced first upon cooling the molten chemical, whereas the orange form is formed by a polymorphic phase transition which occurs slowly upon long term storage of the yellow form at temperatures below its melting point. Such phase transitions are rapidly revealed by calorimetry. The crystal structures of the polymorphs have been determined using single crystal X-ray diffraction. Solid state NMR spectroscopy, vibrational spectroscopy and UV–VIS spectroscopy were applied to further study the nature of the polymorphism in terms of intra- and inter-molecular properties. Solid state CP-MAS ¹³C NMR spectroscopy was shown to be the method of choice for quantitative analysis of polymorphic mixtures. The differences in spectral properties and crystal habits were investigated by computational methods which included molecular exciton, molecular orbital and molecular mechanics calculations. The dramatic colour change from yellow to orange-red during the polymorphic transition is discussed in terms of competing inter- and intra-molecular electronic effects. The driving force for the yellow (II) to orange (I) polymorphic transition is attributed to the change in the electronic delocalization achieved from shortening, strengthening, and partially straightening the ‘bent’ hydrogen bond between the secondary amino hydrogen and an oxygen of the 6′-nitro group. This results in increased overlap between the amino nitrogen’s lone pair and the π-electron orbitals of the aromatic ring. The calculated lattice stabilization energy due to this process is 4 to 5 kcal mol^–1, and the relative lattice energies are consistent with the observed stabilities of the polymorphs. The slow kinetics of the polymorphic transition are largely governed by the steric interaction of the 1-ethylpropyl side chain and the two nitro groups. During crystallization, the more compact side chain conformation required to form the energetically more stable orange (I) polymorph appears to be more difficult to achieve than that required for the yellow (II) polymorph.

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