Ab initio simulations of reactions occurring in molecular crystals
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Although the solid state may not usually be thought of as an environment suitable for chemical reactions under mild conditions, a growing number of organic compounds are known to undergo interesting and, in many cases, practically useful chemistry in the molecular crystal phase. Of particular interest are photochemical reactions occurring in molecular crystals, which possess a number of characteristic features that make them attractive to study using the methods of theoretical chemistry. Firstly, molecular packing and steric effects strongly influence the mechanistic course of reactions in the crystal phase, which in some cases enables clean and controllable chemistry, including synthetic reactions as well as reversibly switchable isomerisations accompanied by a change of the macroscopic properties of the crystal, such as shape and colour. Secondly, in part due to their fast (subpicosecond) timescales and relatively low conversion rates (of the order of a few per cent), many of these reactions present challenges to experimental techniques, which computer simulation methods are uniquely positioned to overcome. Finally, these systems lend themselves well to simulation using a hybrid combination of two ab initio electronic structure methods, one of which is used to describe the electronic excitation of a reactive molecule while the other is applied to the surrounding bulk lattice. This thesis describes the computational modelling of two such reactions: the syn-anti photoisomerisation of 7-(2-pyridyl)indole and the reversible cis-enol⇄trans-keto photoisomerisation of N-salicylidene-2-chloroaniline. The solid-state mechanisms and rates of both reactions are computed using the TD-DFT/DFT hybrid method, in the latter case validating a previously postulated reaction mechanism. Furthermore, the thermal (ground-state) tautomerisation reaction in the photochromic and non-photochromic polymorphs of N-salicylidene-2-chloroaniline is investigated through calculations at the DFT level of theory. The results of these calculations indicate that both polymorphs are thermochromic, but tautomeric equilibrium in the non-photochromic polymorph is more sensitive to temperature than in the photochromic polymorph. Additionally, a critical assessment is presented of the accuracy of the various emphab initio methods employed throughout this work.