Fundamental and practical aspects of molecular dynamics using tensorial orientational constraints

ABSTRACT

Residual Dipolar Couplings are important structural parameters in high resolution NMR spectroscopy that allow the determination of configuration and conformation of small-to-medium-sized molecules even in difficult cases. The data interpretation for flexible molecules, however, is demanding and several downfalls are associated with established methods. With the Molecular Dynamics using Orientational tensorial Constraints (MDOC) approach, only recently a promising method for interpreting RDCs has been reported. Here, a fundamental derivation of the key equations of MDOC and the most commonly used alignment tensor concept is given, highlighting the profound differences of the two approaches. Next to the mathematical derivation, also the validity of resulting structural and orientational ensembles, the setting of important simulation parameters, the specific effect of tensorial constraints, and the nature of the expected outcomes are discussed in detail.

Graphical abstract

KEYWORDS:

• Alignment tensor
• order tensor
• Saupe matrix
• MDOC
• orientational tensorial constraints
• structural and orientational ensemble

Acknowledgments

The authors gratefully acknowledge financial support by the Deutsche Forschungsgemeinschaft (LU 835/11-1, SFB 1176 project C3 and instrumentation facility Pro²NMR) and by the HGF programme BIFTM. M.E.D.P. thanks the Alexander von Humboldt Foundation for a postdoctoral fellowship.

Disclosure statement

U. Sternberg is the developer of the program COSMOS used for the MDOC simulations. The computational COSMOS Backend for HPC systems is freely available and the COSMOS Frontend with GUI is commercially distributed (http://www.cosmos-software.de). For any inquiries please contact the author.

Additional information

Funding

This work was supported by the Alexander von Humboldt-Stiftung [postdoctoral fellowship]; Deutsche Forschungsgemeinschaft [LU 835/11-1; SFB 1176 project C3; instrumentation facility PRO2NMR]; Helmholtz-Gemeinschaft [HGF programme BIFTM].