Application of residual dipolar couplings in organic compounds

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. 13C-31P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including 3JH-H-couplings as additional constraints. However, flexible molecules remain a problem.

A supramolecular and liquid crystalline water-based alignment medium based on azobenzene-substituted 1,3,5-benzenetricarboxamides

A supramolecular, lyotropic liquid crystalline alignment medium based on an azobenzene-containing 1,3,5-benzenetricarboxamide (BTA) building block is described and investigated. As we demonstrate, this water-based system is suitable for the investigation of various water-soluble analytes and allows for a scaling of alignment strength through variation of temperature. Additionally, alignment is shown to reversibly collapse above a certain temperature, yielding an isotropic solution. This collapse allows for isotropic reference measurements, which are typically needed in addition to those in an anisotropic environment, to be performed using the same sample just by varying the temperature. The medium described thus provides easy access to anisotropic NMR observables and simplifies structure elucidation techniques based thereon.

Distinct alignment of benzene derivatives in stretched polystyrene and polybutylacrylate gels: Specific polymer-solute interactions

We have measured the alignment of a range of benzene derivatives in cross-linked polystyrene and poly(butyl acrylate) using a small number of residual dipolar couplings and simple geometric considerations. For apolar solutes in polystyrene and protic solutes in poly(butyl acrylate), the preferred molecular orientation does not coincide with the longest molecular axis (steric aligment). This behavior may be explained by specific π-π and hydrogen bonding interactions between solute and polymer, respectively, the latter being confirmed by molecular dynamics simulations.

Insights on the conformational properties of hyaluronic acid by using NMR residual dipolar couplings and MD simulations

The conformational features of hyaluronic acid, a key polysaccharide with important biological properties, have been determined through the combined used of nuclear magnetic resonance (NMR) spectroscopy and molecular modeling techniques. A decasaccharide fragment of sodium hyaluronate (HA) was submitted to 3.5 ns of molecular dynamics in explicit water environment form. The same decasaccharide was prepared by hyaluronidase digestion for the experimental study. The approach consisted in the measurements of NMR residual dipolar coupling (RDC) which were used to filter the molecular dynamics data by retaining those structures which were in agreement with the experimental observations. Further analysis of the new conformer ensemble (HA(RDC)) and clustering the molecules with respect to their overall length led to seven representative structures, which were described in terms of their secondary motifs, namely the best fitting helix geometry. As a result, this protocol permitted the assessment that hyaluronic acid can adopt two different arrangements, which can be described by a three- or four-folded left-handed helix, with a higher occurrence of the first one.

Room-temperature and low-ordered, amphotropic-lyotropic ionic liquid crystal phases induced by alcohols in phosphonium halides

Tri- n-decylmethylphosphonium chloride and bromide ( 1P10X) salts are not liquid crystalline. However, mesophases are induced by adding very small amounts of an alcohol or water. The temperature ranges of the induced smectic A 2 (SmA 2) liquid-crystalline phases can be very broad and the onset temperatures can be below room temperature depending upon the concentration of the alcohol or water and the structure of the alcohol. At least one molar equivalent of hydroxyl groups is necessary to convert the 1P10X completely into a liquid crystal. Strong association between the hydroxyl groups of an alcohol or water and the head groups of the 1P10X is indicated by spectroscopic, diffraction, and thermochemical data. Unlike many other smectic phases, those of the 1P10X/alcohol complexes are easily aligned in strong magnetic fields and the order parameters of selectively deuterated alcohols as measured by (2)H NMR spectroscopy, approximately 10 (-2), are much lower than the values found when the host is a commonly employed thermotropic liquid crystal. The dependence of the specific values of the order parameters on temperature, the nature of the halide anion, and the structure and concentration of the alcohol are reported. In sum, a detailed picture is presented to explain how and why an alcohol or water induces liquid crystallinity in the 1P10X salts. The data also provide a blueprint for designing media with even lower order parameters that can be hosts to determine the conformations and shapes of guest molecules.

Torsion sensitivity in NMR of aligned molecules: study on various substituted biphenyls

To estimate the torsion sensitivity of dipolar coupling, biphenylic molecules were chosen as probes due to their relatively simple structure and the surprisingly high ambiguity of the only flexible parameter-the interring torsion angle. Solution structures of 4,4'-dibromobiphenyl and 4,4'-diiodobiphenyl are reported for the first time in two liquid crystals I52 and ZLI 1695. The comparison of NMR structures of various para-substituted biphenyls (BPs), calculated by the additive potential maximum entropy (APME) approach, shows that the small spread of torsion angle values in case of different solvents and para-substituents is in good agreement with theoretical expectations from hybrid density functional theory (DFT) methods. Furthermore, the real structural changes of interring torsion and the prevalence of solvent effects over para-halosubstitution can be correctly revealed from these small fluctuations.

Dielectric permittivity and temperature effects on spin-spin couplings studied on acetonitrile

Dielectric permittivity (epsilon) and temperature effects on indirect spin-spin coupling constants were studied using acetonitrile as a probe molecule. Experiments were accompanied by hybrid DFT (density functional theory) studies, where the solvent was modeled using the polarization continuum model. Owing to its numerous types of J-couplings, acetonitrile is a very convenient molecule against which various basis sets can be tested or the best basis set can be selected for a given study. The results show reasonable agreement between calculated and experimental values. According to our data, scalar spin-spin coupling constants undergo substantial shifts at lower values of the dielectric constant. Thus J-coupling values are not transferable between measurements made at differing epsilon-conditions, and the assumption of the epsilon-independence of the J-coupling can lead to crucial mistakes in experiments using low-epsilon media. Dielectric permittivity also causes small geometric fluctuations within the molecule, which themselves can affect J-coupling values. Examinations of the results computed with frozen and relaxed geometries show that geometry mediation mostly affects the spin-dipole term of the J-coupling; hence, for accurate evaluation of the latter, frozen geometries are not acceptable. Another interesting fact revealed is the connection between the solvent dielectric properties and the temperature-dependence slopes of J-couplings in corresponding media.

Assessment of solvent effects: do weak alignment media affect the structure of the solute?

Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions.

Measurement of1H–1H Residual Dipolar Coupling Constants for Structural Studies of Medium Size Molecules

Residual dipolar coupling constants (RDCs) are being increasingly applied to elucidate the configuration and conformation of small organic molecules, peptides and oligosaccharides. In this paper we describe a set of robust 1D NMR methods for accurate and precise measurement of proton-proton RDCs of small and medium size molecules. The performance of these techniques is not impeded by the presence of overlapping and broad (1)H multiplets that are typically observed for such molecules in weakly aligned media. The use of these techniques provides access to a large pool of proton-proton RDCs opening new avenues for the solution structure elucidation of medium size molecules by NMR. The techniques are illustrated on the determination of the alignment tensor of the reducing monosaccharide ring of cellobiose and the determination of the relative configuration of sodium cholate.