Extending molecular dynamics with dipolar NMR tensors as constraints to chiral phosphorus compounds.

Molecular dynamics with orientational constraints (MDOC) simulations use NMR parameters as tensorial constraints in the stereochemical analysis of small molecules. C-P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including -couplings as additional constraints. However, flexible molecules remain a problem.

Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations.

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion.

Residual dipolar couplings as a tool for structural analysis of ionic liquids.

An acrylonitrile/dimethylacrylamide cross-linked polymer could be swollen in different imidazolium ionic liquids. Mechanical compression of the obtained polymer gels inside an NMR tube allowed the measurement of residual dipolar couplings. Conformational analysis of the 1-methyl-3-butyl-imidazolium (BMIM) cation could be performed by including the measured RDCs as restraints in time-averaged molecular dynamics.

Structures Controlled by Entropy: The Flexibility of Strychnine as Example.

To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers.

Statistical evaluation of simulated NMR data of flexible molecules.

A new probability score-named -probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the -probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the -probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility.