Complexity Science Mini-Project, 2009
Nucleation of Different Polymorphs: Emergent Behaviour in the Self Assembly of
Metal-Organic Frameworks.
Supervisor: P.M. Rodger
Suitable for either 1st or 2nd mini-project
Metal organic framework materials (MOFs) are a class of crystalline materials that
incorporate a nanometer sized pores and channels into their crystal structure. The excitement
in these materials comes from the wide variety of pore geometries that can be formed from
relatively simple building blocks, since this raises the possibility of creating materials that
can act as highly selective molecular sieves for purifying compounds such as pharmaceutical
drugs. A major challenge with these materials arises from the fact that a number of different
crystal structures, with different framework topologies, can be formed from a given set of
building blocks. At present there is little understanding of the factors that will cause any
particular network structure to emerge from the reaction mixture; nor is there much
understanding of the factors that will cause a particular structure to propagate itself once it
does nucleate.
At one level, MOFs are relatively simple to describe: they consist of two or more secondary
building units, each with a well defined shape and connectivity. However, there are many
different networks that can be formed from a given set of secondary building blocks.
Characterising the way different networks emerge from an initial random assembly is a
challenging problem for complexity science.
This project will use dynamical simulation methods (molecular dynamics) to model the
emergence of different network topologies from a given mixture. Within the confines of this
miniproject, the models employed will be relatively simple, yet still lead to a variety of
different structures. Thus, coarse-grained particle models of various secondary building units
(tetrahedral or octahedral nodes, linked by 2- or 3-connected units) will be used, and the
potential structures allowed to emerge by following the equations of motion of a mixture of
such units. Simulations will also be performed with accelerated sampling molecular dynamics
methods, such as metadynamics, to facilitate the rapid emergence of different network
structures from a random, dynamical mixture. The simulations will then be analyzed to
characterise the structural features that signal the nucleation and lifetime of different
framework topologies, and how these are influenced by the range and nature of the
interactions between the secondary building units.
These coarse-grained models can incorporated into existing molecular dynamics computer
programs for both molecular dynamics and metadynamics, though there is also scope for
students to develop their own code to perform these simulations where that is desirable. The
project will enable students to develop their skills in dynamical simulation, statistical
mechanics and the analysis of complex data.
Background Reading
For MOF structures and uses: Ferey, G Chemical Society Reviews 2008, 37, 191-214; Tanaka, D.; Kitagawa, S.
Chemistry of Materials 2008, 20, 922-931
For simulations with sticky-patch models: Doye, J. P. K.; Louis, A. A.; Lin, I. C.; Allen, L. R.; Noya, E. G.;
Wilber, A. W.; Kok, H. C.; Lyus, R. Physical Chemistry Chemical Physics 2007, 9, 2197-2205
For metadynamics: Martonak, R.; Laio, A.; Bernasconi, M.; Ceriani, C.; Raiteri, P.; Zipoli, F.; Parrinello, M.
Zeitschrift fur Kristallographie 2005, 220, 489-498; Quigley, D.; Rodger, P. M. J. Chem. Phys. 2008, 128,
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