Software
We have developed software to help with the analysis of dynamic combinatorial libraries. We are happy to make the programs available free of charge to anyone working in academia. For more information contact Sijbren Otto.
DCL Mass List Generator – Version 1.0
Runs under Windows 98 or higher
Overview
This program calculates the masses that are expected in a mass spectrum of a combinatorial library of oligomers of building blocks. It requires input of the masses of the (uncharged) monomer units as they appear in the oligomers. It generates a scrollable list of m/z values (z can be upto 3) and compositions of oligomers, which can be saved as a text file or printed.
Options
1 - Ionisation mode. The program can deal with both positive and negative ions, assuming that ionisation occurs through, respectively, protonation or deprotonation. Hence, the masses that are generated correspond to M+1 or M-1 (for singly charges species), respectively.
2 - Oligomer range. The user can choose between limiting the output to masses below a certain maximum or to oligomers up to a given size.
3 - Mass accuracy. The user can specify the number of decimals required in the list of oligomer masses.
4 - Include multiple charged species. Double and triply charged species can be included when required.
5 – Sorting. The user can choose between sorting of the list of oligomers on the basis of mass or of size of the oligomer.
6 – Similar masses. The program allows for quick assessment of whether different oligomers turn out to have masses that are within a user-specified range from one another (and therefore likely to be indistinguishable in the mass spectrum). This option is only available when the list of oligomers is sorted on the basis of mass!
Limitations
Version 1.0 can cope with up to 20 different building blocks and is able to calculate the masses for oligomers not larger than 20-mers. The program does not allow for limitation of the oligomers to certain architectures, i.e. all building blocks are allowed to combine with each other in all possible ratios.
DCLSim – Version 1.1
DCLSim is a tool designed for the simulation of Dynamic Combinatorial Libraries (DCLs) under a variety of conditions. It randomly generates DCLs according to a statistical model and a set of user-specified parameters, calculates the distribution of library members at equilibrium, and performs statistical analyses of the results.
This entails the calculation of the equilibrium distribution of products, given a set of equilibrium constants and initial building block concentrations. This method has more general applications than the simulation of DCLs, and so a separate interface has been provided for this.
The workings of DCLSim are explained in more detail in:
Corbett, P. T.; Otto, S.; Sanders, J. K. M. Chem. Eur. J. 2004, 10 , 3139.
The programme has been written by Peter Corbett (pcorbett@chiark.greenend.org.uk)
DCLFit
DCLFit can fit host-guest binding constants and the equilibrium constants for formation of library members from experimental data on the concentrations of the various library members under varying conditions (building block and template concentrations). The workings of DCLSim are explained in more detail in:
Ludlow, R. F., Liu, J., Li, H., Roberts, S. L., Sanders, J. K. M., Otto, S. Angew. Chem., Int. Ed. 2007, 46, 5762.
