Abstract
BackgroundThe advent of combinatorial chemistry has revived the interest in five-membered heterocyclic rings as scaffolds in pharmaceutical research. They are also the target of modifications in nucleic acid chemistry. Hence, the characterization of their conformational features is of considerable interest. This can be accomplished from the analysis of the 3JHH scalar coupling constants.ResultsA freely available program including an easy-to-use graphical user interface (GUI) has been developed for the calculation of five-membered ring conformations from scalar coupling constant data. A variety of operational modes and parameterizations can be selected by the user, and the coupling constants and electronegativity parameters can be defined interactively. Furthermore, the possibility of generating high-quality graphical output of the conformational space accessible to the molecule under study facilitates the interpretation of the results. These features are illustrated via the conformational analysis of two 4'-thio-2'-deoxynucleoside analogs. Results are discussed and compared with those obtained using the original PSEUROT program.ConclusionA user-friendly Matlab interface has been developed and tested. This should considerably improve the accessibility of this kind of calculations to the chemical community.
Highlights
The advent of combinatorial chemistry has revived the interest in five-membered heterocyclic rings as scaffolds in pharmaceutical research
We propose an integrated, user-friendly Matlab program, including a self-explanatory graphical user interface (GUI), to facilitate the set-up, execution and subsequent analysis of pseudorotation calculations for five-membered ring systems decorated with a variety of substituents
In the main window of the GUI, both the coupling data and additional parameters required by equations 1 and 6 can be interactively defined, using a simplified representation of the cycle
Summary
Program features Only the main features of the program, fully described in the manual available together with the program, are discussed. Comparison to PSEUROT To test the performance of the computational core and the input/output handling using the GUI and compare the results with respect to PSEUROT (version 6.2), a set of two 4'-thio-2'-deoxynucleoside analogs [32] was used For both molecules, depicted, literature [32] provides a full set of five coupling constants measured at five different temperatures as well as Diez-parameters for each endocyclic bond. For both compounds, two conformations were fit to the experimental data using our Matlab GUI and PSEUROT 6.2. This gives a more realistic view of the conformational behavior of compound 1
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