On the average orientation of molecules undergoing large-amplitude conformational changes in anisotropic liquids

Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints

Residual dipolar couplings (RDCs) and other residual anisotropic NMR parameters provide valuable structural information of high quality and quantity, bringing detailed structural models of flexible molecules in solution in reach. The corresponding data interpretation so far is directly or indirectly based on the concept of a molecular alignment tensor, which, however, is ill-defined for flexible molecules. The concept is typically applied to a single or a small set of lowest energy structures, ignoring the effect of vibrational averaging. Here, we introduce an entirely different approach based on time averaged molecular dynamics with dipolar couplings as tensorial orientational restraints that can be used to solve structural problems in molecules of any size without the need of introducing an explicit molecular alignment tensor into the computation. RDC restraints are represented by their full 3D interaction tensor in the laboratory frame, for which pseudo forces are calculated using a secular dipolar Hamiltonian as the target. The resulting rotational averaging of each individual tensorial restraint leads to structural ensembles that best fulfil the experimental data. Using one-bond RDCs, the approach has been implemented in the force field procedures of the program COSMOS and extensively tested. A concise theoretical introduction, including the special treatment of force fields for stable and fast MD simulations, as well as applications regarding configurational analyses of small to medium-sized organic molecules with different degrees of flexibility, is given. The observed results are discussed in detail.

Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules

The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility. The independence of the initial structure or any a priori assumption as well as the possibility to combine different experimental constraints represent features, which make the COSMOS software a promising tool for the investigation of torsional angle distributions of flexible molecules, regardless of their size and degree of freedom.

Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone

To understand the properties and/or reactivity of an organic molecule, an understanding of its three-dimensional structure is necessary. Simultaneous determination of configuration and conformation often poses a daunting challenge. Thus, the more information accessible for a given molecule, the better. Additionally to (3)J-couplings, two sources of information, quantitative NOE and more recently also RDCs, are used for conformational analysis by NMR spectroscopy. In this paper, we compare these sources of conformational information in two molecules: the configurationally well-characterized strychnine 1, and the only recently configurationally and conformationally characterized α-methylene-γ-butyrolactone 2. We discuss possible sources of error in the measurement and analysis process, and how to exclude them. By this means, we are able to bolster the previously proposed flexibility for these two molecules.

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations

Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.

NMR discrimination in nonrigid prochiral solutes dissolved in chiral liquid crystals: symmetry considerations

Enantiodiscrimination in the NMR spectra of flexible prochiral solutes dissolved in chiral liquid crystals (CLCs) is reviewed and compared with the analog phenomenon in such rigid solutes. In rigid prochiral solutes, the discrimination is brought about by the cancellation of improper symmetry elements upon dissolving in CLC within the frame of solute-solvent ordering mechanisms. If this reduction in symmetry renders the ordering of enantiotopic sites dissimilar, spectral discrimination may be observed. Symmetry considerations indicate that this is only possible for improper nonaxial groups lacking inversion symmetry. Nonrigid prochiral solutes consist of rapidly (on the NMR timescale) interconverting enantiomers, in which the racemization is accompanied by exchange of nonequivalent sites. These sites become, on the average, enantiotopically related, and in CLC, they exhibit spectral discrimination. The mechanism of the effect and the symmetry selection rules are different for the two cases. Specifically, the discrimination in flexible prochiral compounds results from the different ordering of the interchanging enantiomers in CLC. Using Altman's definition of average symmetry (Proc. R. Soc. A, 1967, 298, 184), selection rules for the phenomenon are derived. It follows that chiral discrimination in nonrigid prochiral solutes is much more abundant and can occur in all symmetry types except those possessing inversion. In particular, contrary to earlier thoughts, the effect can occur in compounds with axial symmetry. Illustrative examples of such studies with particular emphasis on compounds with average axial symmetry of the type D(3h), C(3v) and C(3h) are reviewed in this contribution.

Challenge of large-scale motion for residual dipolar coupling based analysis of configuration: the case of fibrosterol sulfate A

Fibrosterol sulfate A is a polysulfated bis-steroid with an atypical side chain. Due to the flexibility of the linker, large-scale motions that change dramatically the shape of the entire molecule are expected. Such motions pose major challenges to the structure elucidation and the correct determination of configuration. In this study, we will describe the determination of the relative configuration of fibrosterol sulfate A through a residual dipolar coupling based multiple alignment tensor analysis complemented by molecular dynamics. For completeness, we applied also the single tensor approach which is unreliable due to the large-scale motions and compare the results.

Chiral Discrimination in the 13C and 2H NMR of the Crown and Saddle Isomers of Nonamethoxy-Cyclotriveratrylene in Chiral Liquid-Crystalline Solutions

We report 2H and 13C NMR spectra of the crown and saddle isomers of nonamethoxy-tribenzocyclononene (1), dissolved in lyotropic achiral and chiral liquid-crystalline solutions based on poly-gamma-benzyl-glutamate and poly-gamma-benzyl-L-glutamate (PBG and PBLG). The 2H-[1H] measurements include spectra of compound 1 deuterated in the ring methylene and in the aromatic sites as well as of the methyl groups in natural abundance. Carbon-13 spectra were recorded in natural abundance as well as in two isotopomers enriched in the ring methylene and one of the methoxy groups. The crown isomer (c-1) is rigid with C3 symmetry and can be separated into its enantiomers using a chiral high-performance liquid chromatography column. The NMR spectra of racemic c-1 in PBLG solutions exhibit two sets of lines due to the enantiomers. The peaks were identified by comparing the spectra with those of the neat enantiomers. Analysis of the 2H quadrupolar splittings and the 13C residual chemical shift anisotropies shows that the dominant factor determining the chiral discrimination is the difference in the ordering of the two enantiomers in the chiral liquid crystals. The saddle isomer (s-1) is highly flexible, undergoing fast pseudorotation between six conformers. The "frozen" conformers have C1 symmetry and are therefore chiral. Three of these comprise one enantiomer, and the other three the second one. However, the rapidly interconverting species has, on the average, a C3h symmetry and is therefore achiral. The methylene groups in the latter are, however, prostereogenic, and their hydrogen/deuterium-carbon bonds constitute enantiotopic pairs. The 2H NMR spectra of the s-1 methylene-deuterated in PBLG solutions exhibit, in fact, enantio-discrimination with two quadrupolar doublets. This is in contrast to rigid prochiral molecules with a threefold symmetry axis, which normally do not show such discrimination. A detailed analysis of the effect is presented, and it is argued that the discrimination observed for s-1 reflects the different ordering of its enantiomers during the pseudorotation cycle.

NMR Determination of Smectic Ordering of Probe Molecules

The NMR spectra of the three solutes ortho-, meta-, and para-dichlorobenzene in the nematic and smectic A phases of the liquid crystals 8CB and 8OCB are analyzed to yield two orientational order parameters for each solute. Extrapolation of the asymmetry in the energy parameters that describe the orientational ordering in the nematic phase are used to provide estimates of the strength of the nematic potential in the smectic A phase. The experimentally determined asymmetry of the orientational order parameters in the smectic A phase is then used in conjunction with Kobayashi-McMillan theory applied to solutes to give information about the smectic A layering and the nematic/smectic A coupling. In both smectic A solvents, the solute smectic coupling constant, tau, is negative (with the origin fixed at the center of the smectic layer) for all solutes. The signs and relative values of tau indicate that the ortho and para solutes favor the interlayer region while the meta solute is more evenly distributed throughout the layers.

Chain dynamics in a chiral C phase by deuteron spin relaxation study

Molecular reorientations and internal conformational transitions of an aligned chiral liquid crystal (LC) 10B1M7 are studied by means of deuterium spin-lattice relaxation in its smectic A (SmA) and smectic C* (SmC*) phase. The motional model which is applicable to uniaxial phases of many LCs is found to be adequate even when the phase is a tilted SmC* phase. The deuterium NMR spectrum in this phase cannot discern rotations of the molecular director about the pitch axis. The basic assumption is that the phase biaxiality is practically unobservable. However, the relaxation rates can be accounted for by the tilt angle between the molecular director and the layer normal in the SmC* phase. The tumbling motion appears to show a higher activation energy upon entering from the uniaxial SmA into the SmC* phase.

NMR as a tool in the investigation of fundamental problems in ordered liquids

An overview is presented of modern NMR techniques and a variety of experimental and theoretical tools employed in the study of solutes dissolved in liquid crystals. The NMR techniques involve multiple quantum and spectral subtraction methods. In addition, various experimental and theoretical tools are discussed, including: the theoretical background of observed order parameters; the use of 'magic mixtures' to separate orientational contributions; the reorientation-vibration interaction; the use of model calculations based on size and shape of the various solutes; and the use of computer simulations. Applications to the benchmark probe molecules hydrogen, methane, ethane, and butane and their isotopomers are treated.

A theory of orientational ordering in uniaxial liquid crystals composed of molecules with alkyl chains

The constituent molecules of thermotropic liquid crystals invariably contain an aromatic core to which is attached one and often two n -alkyl chains. Nuclear magnetic resonance investigations have revealed that the chain does not exist entirely in an all- trans configuration and that the orientational order of the methylene groups varies markedly along the chain. In this paper we develop a theory to explain these variations for a uniaxial phase at a given temperature and pressure. Our theory contains two distinct parts: one is a model for the conformational distribution of the alkyl chains while the other is for the potential of mean torque experienced by a conformer and which is responsible for its alignment with respect to the director. We use the rotameric state model developed by Flory to describe the conformations adopted by the alkyl chain. The potential of mean torque presents a more difficult problem and we assume that it may be represented by a sum of contributions from each rigid group in the molecule. The order parameters for the methylene and methyl groups in the alkyl chains of the 4- n -pentyl and 4- n -octyl-4'-cyanobiphenyls predicted by the theory are found to be in good accord with those obtained experimentally. We have also used the theory to predict the conformational distributions for both the isotropic and nematic phases of these mesogens; the calculated distributions are contrasted with those assumed by other models. In addition we have obtained the ordering matrices for the various conformers adopted by the two 4- n -alkyl-4'-cyanobiphenyls. The results of these calculations do not support the notion that the orientational order of such molecules can be described by a single, cylindrically symmetric ordering matrix.