How to simulate x-ray pattern in materials studio

#How to simulate x ray pattern in materials studio code
#How to simulate x ray pattern in materials studio plus

1 в–ё gives an impression of the dimensions of the simulation box. This can be achieved by constructing a simulation box containing 12 Г— 12 Г— 12 = 1728 molecules, because 12 is a multiple of 1, 2, 3, 4 and 6, allowing a phase transition to virtually all of the 230 possible space groups. Furthermore, the number of molecules in each direction of the simulation cell must be commensurate with the number of molecules in the starting structure and the unknown target structure.

The cut-off distance for both types of non-bonded interaction was 25вЂ…Г… and each side-to-side distance of the supercell was not less than 50вЂ…Г… (twice the cut-off distance). To allow the use of a relatively large cut-off distance for non-bonded interactions (electrostatic and van der Waals) and to reduce the self-interactions introduced by the periodic boundary conditions, relatively large supercells must be used.

#How to simulate x ray pattern in materials studio plus

The Forcite Plus module in Materials Studio was used, periodic boundary conditions were applied, the time step was 1вЂ…fs and the space group of all the simulation cells was P1. The DFT-D crystal structure was energy-optimized, with an unrestrained unit cell, with the COMPASS force field to yield a structure corresponding to TВ =В 0вЂ…K, the temperature of which was then slowly increased. DFT-D is too computationally expensive to be used for MD, and the COMPASS force field (Sun, 1998 в–ё) was used for classical MD simulations. This is the crystal structure that would have been obtained from a modern-day crystal structure prediction study (Reilly et al., 2016 в–ё), even in the absence of experimental data, provided the study had been successful in locating the most experimentally stable polymorph. To ensure that our calculations could have been performed even in the absence of any experimental data, to allow for the possibility of a true prediction, the experimental crystal structure was first energy minimized with an unrestrained unit cell and dispersion-corrected density functional theory (DFT-D).

#How to simulate x ray pattern in materials studio code

The crystal structure of the low-temperature phase was taken from the Cambridge Structural Database (Groom et al., 2016 в–ё reference code KOFHOC). A TLS (translation, libration, screw) refinement of the experimental data confirmed the phase-transition mechanism observed in the MD simulations. The success of our approach was subsequently verified by temperature-dependent powder diffraction experiments. The crystal structure of the initial phase ( P2 1/ c, ZвЂІ = 2 Г— ВЅ) was reported in 1991, and the crystals are reported to jump and shatter at 344.5вЂ…K (Ding et al., 1991 в–ё). In other words, when the known (or predicted) starting structure is heated in silico with MD, we expect to observe a phase transition, the product of which hopefully corresponds to the phase of interest.ДЄs a model system, we used a jumping crystal for which the crystal structure of the initial phase is known, whereas that of the post-salient phase is not: trans, trans, anti, trans, trans-perhydroВpyrene ( I).

The known starting structure can be recreated computationally by means of molecular modelling (or, in the ideal case, by crystal structure prediction), whereas the process can be recreated computationally by means of molecular dynamics (MD). This led us to consider a computational approach to the determination of the structure of the new phase based on the two pieces of information that are known: the structure of the starting phase and the preparation process of the new phase. Indeed, in these cases the crystal structure of the resulting phase, which is often the phase of interest, must be determined from powder diffraction data (Trask et al., 2005 в–ё Bond et al., 2014 в–ё Panda et al., 2014 в–ё). These cases have in common that the structures of the starting phases and the preparation processes are known, but the structures of the end products are difficult to determine because the crystals tend to shatter in the process, leaving nothing but a sample in powder form to work with. Examples are the preparation of co-crystals by solid-state grinding (Trask & Jones, 2005 в–ё), the dehydration of hydrates to prepare anhydrates (Fujii et al., 2012 в–ё) or the heating of crystals to make them вЂjumpвЂ™ (Sahoo et al., 2013 в–ё). Occasionally, interesting crystal structures can be prepared by applying temperature or pressure to a crystalline phase in order to trigger a phase transition and obtain a different solid phase.

How to simulate x-ray pattern in materials studio