Crystal structure prediction molecular dynamics

When applying a SA approach to crystal structure prediction, a Metropolis Monte Carlo scheme [20], rather than molecular dynamics [28], is usually chosen to sample the configurational space (different possible candidate structures). In practice, this scheme proceeds by comparing the quality (value of the cost function) of a new candidate structure with the current candidate structure. The new candidate is either rejected or used to replace the current candidate struc-... 

In an oligonucleotide-drug hydrate complex, the appearance of a clathrate hydrate-like water structure prompt a molecular dynamics simulation (40). Again the results were only partially successful, prompting the statement, "The predictive value of simulation for use in analysis and interpretation of crystal hydrates remains to be established." However, recent molecular dynamics calculations have been more successful in simulating the water structure in Ae host lattice of a-cyclodextrin and P-cyclodextrin in the crystal structures of these hydrates (41.42). 

After the formulation of defect thermodynamics, it is necessary to understand the nature of rate constants and transport coefficients in order to make practical use of irreversible thermodynamics in solid state kinetics. Even the individual jump of a vacancy is a complicated many-body problem involving, in principle, the lattice dynamics of the whole crystal and the coupling with the motion of all other atomic structure elements. Predictions can be made by simulations, but the relevant methods (e.g., molecular dynamics, MD, calculations) can still be applied only in very simple situations. What are the limits of linear transport theory and under what conditions do the (local) rate constants and transport coefficients cease to be functions of state When do they begin to depend not only on local thermodynamic parameters, but on driving forces (potential gradients) as well Various relaxation processes give the answer to these questions and are treated in depth later. 

Fig. 11.1. Two predicted binding conformations of an HIV-1 integrase inhibitor to a molecular dynamics (MD) snapshot of the protein. The green conformation is similar to that in the crystal structure and the magenta is in a secondary predicted binding trench that opened during an MD simulation of the protein [24]...

The behavior of real component powders may be estimated using a yield criterion (1), which requires a knowledge of the magnitudes of the directional response to stress of the particle and knowledge of the particle size distribution and particle orientation. Much of this information is not readily available for molecular organic solids and is the subject increasing attention of academic materials scientists. Even knowing the crystal structure, the dynamic response to mechanical stresses is not currently predictable without exhaustive effort (3). However, yield behavior may be measured and correlated to the... 

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