4.4 Desarrollo Del Modelo
4.4.2 Desarrollo Del Modelo Glaciar
9 Crystal Structures of Chlorothalonil
9.1 Summary
Chlorothalonil is a fungicide commonly used on agricultural products. The experimental crystal structure of chlorothalonil is known, but preliminary experimental data has shown that other polymorphs probably exist. Dr Maryjane Tremayne in Birmingham is conducting an experimental search for these polymorphs. This study seeks to provide a theoretical prediction of possible structures for these polymorphs, which may prove useful in their characterisation. In this chapter, an anisotropic repulsion model has been constructed using the overlap model and compared with empirically fitted isotropic model. This should provide a better description of the anisotropy in the repulsive region that may arise from the non-spherical charge distributions of the atoms. A search for possible crystal structures was carried out using Williams' empirical model potential. The low energy crystal structures were then refined by minimisation using our non-empirical anisotropic model potential. The mechanical and morphological properties of these structures were considered to eliminate low energy structures that were unlikely to be observed. The search was able to find a close approximation to the experimental crystal structure (less than 1 % r.m.s. error in the cell parameters) as the global minimum in the lattice energy. Fourteen hypothetical crystal structures have been found which seem likely to be possible polymorphs. An experimental powder structure was determined and has a /?3m disordered structure and this was confirmed by single crystal structure. One of our PI predicted structures is helpful for Tremayne in characterising this disordered structure.
New Models for Intermolecular Repulsion and their Application to van der W aals Helen H.Y. Tsui
9 Crystal Structures of Chlorothalonil 158
9.2 Introduction
Chlorothalonil is the common name for 2,4,5,6-tetrachloro-1,3-dicyano benzene, Cl4C6(CN)2. It is a widely applied fungicide that has been in production since the 1960's [34] (See Figure 9,1). Britton first determined a crystal structure in 1981 using X-ray diffraction [217], It is monoclinic, space group
P l j a , and was determined at 22(2)°C. The molecular structure is almost symmetrical with only experimentally insignificant deviations from symmetry.
Cl'
I2 r 6 jcr
5|cr
Cl'
Figure 9.1 Chemical diagram of chlorothalonil with numbering labels for atoms.
There is one reported sublimation energy value for chlorothalonil of 109.1 kJ/mol [218] from the NIST Chemistry WebBook [219]. We could use this to test a recent method for estimating the sublimation energy when there is no experimental value available. A recent method of Westwell et al
[220] can predict the sublimation energy based on empirical correlation with the boiling points of the compound. However, this regression was based on a wide range of compounds. Our corresponding regression analysis developed to predict the unknown heat of sublimation of cyanuric chloride, uses 11 chlorinated and other substituted aromatics and heteroaromatics similar to chlorothalonil (See Appendix B). It predicts the sublimation energy of 111.6 kJ/mol for chlorothalonil. O f course, such regression will not always be capable of providing such good predictions, since it is dependent on the choice of data sets used for the analysis.
A recent study by Mitchell et a l on cyanuric chloride and related organic molecules [40] has shown that there is an improvement in reproducing the experimental crystal structure by including atomic anisotropy in the repulsion model. The key feature of their studies is the derivation of anisotropy parameters for the repulsion for the non-spherical atoms. This is vital as the assumption that organic molecules interact with each other as spherical atoms is only for computational convenience. Hence, most simulations of organic molecules in the solid or liquid phase have used mainly isotropic atom-atom model potentials. X-ray deformation density maps show that the charge distribution around an atom in a molecule often has non-spherical features such as lone pairs and n
electron density, which give rise to atomic dipoles, multipoles and higher multipoles. This is the same argument, as in the distributed multipole analysis, that one must include anisotropy in order to represent the molecular charge distribution realistically. If we look at chlorothalonil in Figure 9.2, we
New Models for Intermolecular Repulsion and their Application to van der W aals Com plexes and Crystals of Organic Molecules
Helen H.Y. Tsui August 2001
9 Crystal Structures of Chlorothalonil 159 see that the chlorine and nitrogen atom s are exposed, and hence the need o f anisotropic repulsion is more prom inent.
r
Figure 9.2 Diagram of chlorothalonil volume using spherical van der Waals radii.
N yburg and Faerm an [39] had suggested, from their analysis o f data collected from the CSD that not all atom s are spherical in shape when bonded to carbon. This is in support o f N yburg and W ong's earlier study o f solid chlorine [221], where the chlorine displayed anisotropy and by assum ing polar flattening for the spherical atom -atom potential, the space group o f the crystal structure was predicted correctly. Price et al. [222] have perform ed interm olecular perturbation calculations on the C-C1...C1- C interactions. T hey concluded that the repulsive wall is sufficiently anisotropic to account for the polar flattening observed for the van der W aals contacts o f organic Cl. F urther evidence for atomic anisotropy was shown by an analysis o f the interm olecular interactions betw een halogens and oxygen or nitrogen in the CSD [223]. The results have shown that there is a highly directional and attractive interaction betw een Cl and N atom s. This may also lead to the interpenetration o f the van der W aals volumes. T heir conclusion was that the directionality o f the h alo g en ...o x y g en and halo g en ...n itro g en contacts is prim arily the result o f the anisotropic distribution o f electron density around the halogen nucleus. M aginn et al. [38] suggested that anisotropy in the chlorine-nitrogen interactions accounted for the inability o f isotropic atom -atom potentials to m odel the crystal structure o f cyanuric chloride. Since chlorothalonil also has C1...N interactions, we would expect that an anisotropic repulsion model is also necessary for chlorothalonil.
The non-em pirical repulsion is derived from the m olecular overlap, using a sim ilar approach to the cyanuric chloride (VU G SIZIO) study o f M itchell et al. [40]. The key feature is the derivation o f anisotropy param eters for the non-spherical atom s. A new aspect o f this study is the method o f deriving the proportionality constant betw een the model overlap and the repulsion. T his is necessary because chlorothalonil is too large for the IM PT calculations used in C hapter 4, 6 and 7, and extends the range o f applicability o f the overlap model.
X -ray pow der diffraction patterns have show n that there is the possibility o f a second or even a third polym orph [224]. The form that was determ ined by B ritton [217] is the m ost stable polym orph (Form A) o f chlorothalonil found. T herefore a search for possible polym orphs could shed som e light onto this problem . Since we will have two model potentials, one em pirically fitted isotropic model and our non-em pirical with anisotropic repulsion for the main interactions; it is possible for us to use these
N e w M odels for interm olecular Repulsion a n d their Application to van d er W a a ls C o m p lexes and Crystals of O rg anic M olecules
H e le n H .Y . Tsui August 2001
9 Crystal Structures of Chlorothalonil_________________________________________________ 160 models and perform a search on all the possible polymorphs of chlorothalonil. We used MOLPAK [154,225] to set up possible crystal structures and minimised them in DMAREL [226], first with Williams' empirical repulsion-dispersion [75,77] model because of the efficiency of the model. Then, the low lattice energy minima were minimised with our non-empirical model with anisotropic repulsion. Both the MOLPAK [154,225] and DMAREL [226] programs used are updated version of those used for the blind crystal structure prediction (Chapter 4); therefore we would expect significant improvements in the generation of energetically possible crystal structures. We then calculated the mechanical properties and morphologies of the low energy structures to eliminate some of the 'unlikely' hypothetical structures.
9.3 Molecular model and testing of empirically derived potentials
The geometry of chlorothalonil was ab initio optimised at the SCF level using a 6-3IG* basis set using CADPAC, using bond lengths and angles from the experimental geometry (CSD REFCOD BAWNIW). It is important to use an ab initio molecular structure to search for the other polymorphic forms. If we use the experimental molecular structure in our search, it would favour the crystal structures of Form A. Our lattice energy minimisation method for crystal structure uses a rigid-body, and does not allow intramolecular flexibility.The electrostatic model potential was derived from a distributed multipole analysis (DMA) at the MP2 level with 6-310* basis set in CADPAC for both the ab initio optimised structure and the experimental structure (CSD REFCOD BAWNIW). This was used in the empirical potential with the parameters of Williams [75,77], chosen as the most promising available empirical parameter set (See Equation (4.1) for the form of the potential). We will refer to this combined model as FIT. The FIT model should provide reasonable results, in terms of lattice energy and cell parameters, because the FIT model has been empirically fitted over a range of organic crystal structural data and also thermal data.
Lattice energy minimisations were carried out using the program DMAREL [175], using both the experimental molecular structure, and the ab initio molecular structure. The ab initio molecular structure was pasted into the experimental crystal structure to match the position o f the centre of mass and the direction of the C; to C5 vector and the C2-C5-C3 plane. The use of both experimental and ab
initio optimised molecular structures determines the effects of changes of the intramolecular structure on the predicted crystal structure.
9.4 Derivation of non-empirical model potential
The non-empirical model potential uses the same DMA electrostatic model as used in conjunction with the FIT model above. The dispersion is modelled by a Slater-Kirkwood atom-atom Q dispersion [51] with Miller’s atomic polarizabilities [170]. The anisotropic atom-atom repulsion model was derived by the overlap model, as described below, and so the complete model is referred to as ANI.
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9 Crystal Structures of Chlorothalonil_________________________________________________ 161
9.4.1 The anisotropic atom-atom repulsion model
W e u s e a n a to m - a t o m f o r m f o r th e r e p u ls io n e n e r g y b e tw e e n m o le c u le s A a n d B , w h ic h in th is c a s e a r e tw o c h lo r o t h a l o n i l m o n o m e r s , ^ r e p =