A user-friendly Matlab program and GUI for the pseudorotation analysis of saturated five-membered ring systems based on scalar coupling constants

A 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.A user-friendly Matlab interface has been developed and tested. This should considerably improve the accessibility of this kind of calculations to the chemical community.Five-membered heterocyclic ring systems constitute an important part of many biologically relevant molecules. They occur in carbohydrates (furanoses), nucleosides and nucleotides, the amino acid proline and their many derivatives. In addition, they often occur as a moiety in complex natural products. Chemical modifications of nucleic acids, often driven by the needs of antisense research, target in part the five-membered cycle or its analogues in order to tailor their conformation towards the desired needs [1,2].The advent of combinatorial chemistry has also revived the interest in heterocyclic rings and their conformation [3]. As a result, scaffolds containing five-membered heterocycles have received much attention for the rapid generation of potential lead compounds in pharmaceutical research [4-11].Typically, the chemical and conformational space is explored by introducing a diversity of substituents at varying positions around the cycle. Depending on the position and nature of these substituents, the cycle either adopts a single conformation or may be in equili