Atomistic Simulation Centre School of Mathematics and Physics Queen's University Belfast University Road Belfast BT7 1NN Northern Ireland
AlternativelyDisordered Materials Group
Rutherford Appleton Laboratory
ISIS Disordered Materials
Ionic liquids (ILs) are currently receiving much attention owing to their potential use as replacement solvents in organic synthesis. They are commonly composed of large organic cations (e.g. alkylimidazolium) and poorly coordinating inorganic anions (e.g. hexafluorophosphate, bistrifylamide) and have melting points close to ambient temperatures and wide liquidus ranges. The volatility of typical solvents employed in organic synthesis results in significant emission to the environment, but ILs have negligible vapour pressure making them potentially useful replacements. Furthermore, ILs are able to dissolve both organic and inorganic molecules allowing species to be brought together in one liquid phase forcing reaction homogeneity, and it has been shown that many organic reactions proceed well in ILs and in a significant number of cases are shown to be more selective and/or of higher yield.
Understanding the microscopic liquid structure of these systems is important in order to understand the nature of the interactions existing between ions and dissolved species, and provides data which can further allow the guided design of new ionic liquids targetted for specific applications. In conjunction with QUILL and the School of Chemistry and Chemical Engineering we perform neutron scattering studies in order to probe the liquid phase (using the SANDALS instrument at Rutherford Appleton Laboratory), in conjunction with complementary molecular dynamics simulations.
Aten is a freeware tool available for Linux, Mac, and Windows, designed to be something useful to have to hand if you need to create from scratch some coordinates for your simulations, or edit existing ones. In particular, periodic systems such as liquids, glasses, and crystals are catered for. Along with the necessary rendering of molecular systems, grid data such as surfaces, probability densities can also be viewed at the same time. Aten is entirely written in C++/Qt4 and spare time, and is fully scriptable using its built-in command language.
Will it read or write the coordinate format you need? Most likely. Aten uses filters to drive the input and output of data, which means that if your format isn't supported then with a little effort you can add support for it yourself. As well as this, Aten can read in molecular mechanics forcefield data and write out full forcefield specifications for your systems (again, using filters).
Visit projectaten.net and try it out.
Any classical simulation is limited by the accuracy of the parameters used to represent the interactions present in the system, and for ionic liquids this is no exception. Of course, the predominant interaction in such media is electrostatic, and this can usually be well accounted for in classical simulations by the use of an appropriate set of charges. However, it is known that using charges derived from gas-phase calculations of molecules is not always ideal - for example, the resulting dipole of water in the gas phase is quite different from the actual dipole in the liquid phase. For ionic liquids the assumption of unit positive or negative charges in gas phase calculations on the ions is necessary, and befalls a similar problem since the effects of charge screening are not accounted for. Performing charge derivations based on calculations of the ion pair is an improvement, but in such cases the charge distribution is heavily conformation dependent.
We have shown that the force matching approach can be used to recover an entire forcefield (including intramolecular geometric terms) from ab initio data on the liquid phase that better represents the structural aspects of the liquid. In addition, we have shown that a similar approach suggests that non-integer charges on the ions further improves not only the microscopic structure of the liquid, but also its energetics and dynamics, and without the need for expensive polarisable terms to be included in the forcefield. The conclusion is that such a choice of charges represents an average (i.e. static) picture of charge transfer present in the liquid, existing mostly through hudrogen bonding between ions. This study has so far been performed only for the ionic liquid 1,3-dimethylimidazolium chloride, but further investigations are underway with the hope to extend to systems more widely used in the literature.
It is envisaged that a potential route for the treatment of nuclear waste in order to reduce the length of time required for storage is the transmutation of the most radioactive isotopes into shorter-lived by-products. In this way, the required number of years required for subsequent storage can be reduced by several orders of magnitude. The elemental targets for this transmutation are the minor actinides which possess considerable half-lives - bombardment with thermal neutrons promotes decay into shorter-lived species. However, lanthanides are present in excess in the raw waste material and themselves effectively absorb neutrons preventing efficient transmution of the minor actinides.
The selective separation of the target actinides, therefore, is paramount to the success of the procedure. In this work we examine the ability of multidentate nitrogen donor ligands to fulfil this task, studied by molecular dynamics (to determine likely conformations and partitioning aspects of the candidate ligands), ab initio calculations (to determine the relevant electron properties of known selective extractors), and predictive calculations based on quantitative structure activity relationships (QSARs, in order to determine new structures for study).