Can I use Complex Build to assemble a transition metal or an actinide metal complex?
At present Complex Build only supports, with high accuracy, lanthanide complexes. We are working on extending it to other metals as well.
However, in the meantime, Complex Build can still be very helpful from a purely stereochemical point of view, even for other metal complexes. So, If you find your ligands of interest in the software database, we would suggest you build your complex as follows: for a transition metal complex, please, assemble your complex in Complex Build as a lutetium complex; for an actinide complex, please, assemble your complex as a lanthanum complex. This will approximate the bond lengths to closer to the experimental ones in these cases. If your correct oxidation state is either +2 or +3, please use the correct one in either Lutetium or Lanthanum, otherwise use either one. After you generate the file with the geometry, you can then replace Lutetium or Lanthanum by your metal. Remember to update the charge and multiplicity to the actual values for your complex. If you are going to run ab initio/DFT calculations, please make sure to update the pseudopotentials as well (as the ones in the files are for the lanthanides only). And if you are going to run semiempirical calculations, please note that RM1 will only tackle lanthanides. The other models, such as PM7 or PM6, will probably be able to handle your metal.
I am an experimentalist. What can Complex Build do for me?
A lot. Just for comparison, when looking at a tetrahedral carbon atom, it suffices to know if its is bound, or not, to four different ligands to know whether it will be a chiral center, or not. If chiral it will have two stereoisomers, otherwise only one. Easy. However, with metal complexes, the situation is much more complicated. Frequently, even with repeating ligands, the coordination polyhedron may be chiral. So, by assembling your metal complex in Complex Build, you will know what the coordination polyhedron point groups could possibly be, and how many stereoisomers there will be in each one. You will also know if your stereoisomer is chiral or not. You will also be able to look at the spatial arrangements in each case and better interpret, for example, spectroscopic NMR results. Finally, information such as these, may also help you in the design of more luminescent lanthanide complexes, since asymmetry of the coordination polyhedron is linked to boosts in its quantum yield of luminescence.
Why do Lumpac mop files created by Complex Build have .lumpac extensions?
Lumpac .mop files are different from the usual MOPAC input files because they must use the ALLVEC keywords so that they can calculate the chemical partition of the decay rate of luminescence, as described in the following article: https://www.nature.com/articles/srep21204. Prior to using them in LUMPAC, just change the .lumpac extension of the file to .mop.
Why do GAMESS .inp files created by Complex Build have .gamess extensions?
GAMESS input files have extension .inp. However, .inp files are used by many softwares. So, to avoid confusion, Complex Build creates these files with the .gamess extension. Prior to using them in GAMESS, just change the .gamess extension of the file to .inp, and GAMESS will run seamlessly.
When I build a complex, either with coordination numbers 11 and 12, or when I attach ligands of higher denticities, such as tridentates, Complex Build does not present me with options to control the stereochemistry of the complex.
Indeed. We are still working on the mathematical details of the stereochemistry of coordinations 11 and 12, as well as of ligands of higher denticities. As they become available, they will be implemented in future versions. In the meantime, Complex Build will present you with one stereoisomer of its choice, that it obtained while attempting to minimize the Crowding function (with no guarantee that it will be the one with the lesser crowding).
Optimizations do not work in Windows installations with Russian locale and regional settings.
Sometimes, when Complex Build is installed in a Windows computer with Russian regional settings, the optimization part of Complex Build will not proceed. Only a red statement "Optimizing…" will appear without any visible changes in the main window or in the "Optimization progress" window. We are working on resolving this issue. In the meantime, we suggest that you create a temporary Windows account and set its locale to another country. Complex Build should then work.
Where was Complex Build developed?
Complex Build was developed in the city of Recife, state of Pernambuco, Brazil.