Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid-Crystalline-Based Medium

Residual dipolar coupling (RDC), a robust anisotropic NMR parameter for structural elucidation of organic molecules, is only accessible in an anisotropic environment. Herein, we introduce a novel alignment medium based on the molecular self-assembly of oligopeptide amphiphile (OPA). This medium is compatible with different intermediate and polar solvent systems, such as CD₃OD, [D₆]DMSO, and D₂O. The preparation of the OPA-based medium is simple and rapid, while only very weak background signals were observed from OPAs. Furthermore, we show that the purity of OPA has only a minor influence on the quality of the RDC data. These advantages allow RDC measurements of organic molecules with different polarities and solubilities with high efficiency and accuracy.     

Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium

Residual dipolar coupling (RDC), a robust anisotropic NMR parameter for structural elucidation of organic molecules, is only accessible in an anisotropic environment. Herein, we introduce a novel alignment medium based on the molecular self‐assembly of oligopeptide amphiphile (OPA). This medium is compatible with different intermediate and polar solvent systems, such as CD₃OD, [D₆]DMSO, and D₂O. The preparation of the OPA‐based medium is simple and rapid, while only very weak background signals were observed from OPAs. Furthermore, we show that the purity of OPA has only a minor influence on the quality of the RDC data. These advantages allow RDC measurements of organic molecules with different polarities and solubilities with high efficiency and accuracy.     

A Self‐Assembled Oligopeptide as a Versatile NMR Alignment Medium for the Measurement of Residual Dipolar Couplings in Methanol

Residual dipolar coupling (RDC) is a powerful structural parameter for the determination of the constitution, conformation, and configuration of organic molecules. Herein, we report the first liquid crystal‐based orienting medium that is compatible with MeOH, thus enabling RDC acquisitions of a wide range of intermediate to polar organic molecules. The liquid crystals were produced from self‐assembled oligopeptide nanotubes (AAKLVFF), which are stable at very low concentrations. The presented alignment medium is highly homogeneous, and the size of RDCs can be scaled with the concentration of the peptide. To assess the accuracy of the RDC measurement by employing this new medium, seven bioactive natural products from different classes were chosen and analyzed. The straightforward preparation of the anisotropic alignment sample will offer a versatile and robust protocol for the routine RDC measurement of natural products.     

Residual dipolar coupling measurements of transmembrane proteins using aligned low-q bicelles and high-resolution magic angle spinning NMR spectroscopy

Bicelles are a major medium form to produce weak alignment of soluble proteins for residual dipolar coupling (RDC) measurements. The obstacle to using the same type of bicelles for transmembrane proteins with solution-state NMR spectroscopy is the loss of signals due to the adhesion or penetration of the proteins into large bicelles, resulting in slow protein tumbling. In this study, weak alignment of the second and third transmembrane domains (TM23) of the human glycine receptor (GlyR) was achieved in low-q bicelles (q = DMPC/DHPC). Although protein-free bicelles with such low q would likely show isotropic properties, the insertion of TM23 induced weakly preferred orientations so that the RDC of the embedded protein can be measured. The extent of the alignment increased but the TM23 signal intensity decreased when q was varied from 0.19 to 0.60. A q of 0.50 was found to be an optimal compromise between alignment and the signal-to-noise ratio. In each pair of NMR experiments for RDC measurements, the same sample and pulse sequence were used, with one being performed at high-resolution magic-angle spinning to obtain pure J-couplings without RDC. A meaningful structure refinement in bicelles was possible by iteratively fitting the experimental RDCs to the back-calculated RDCs using the high-resolution NMR structure of GlyR TM23 in trifluoroethanol as the starting template. Combination of this method with the conventional high-resolution NMR in membrane mimicking mixtures of water and organic solvents offers an attractive way to derive structural information for membrane proteins in their native environment.     

Collection of NMR Scalar and Residual Dipolar Couplings Using a Single Experiment

A new DMSO‐compatible aligning gel based on cross‐linked poly(2‐hydroxylethyl methacrylate) (poly‐HEMA) has been developed. Due to a significant difference in bulk magnetic susceptibility between the DMSO inside and outside the gel, it is possible to simultaneously collect isotropic and anisotropic NMR data, such as residual dipolar couplings (RDC), in the same NMR tube. RDC‐assisted structural analysis of menthol and the alkaloid retrorsine is reported as proof of concept.     

Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy

In NMR spectroscopy, residual dipolar couplings (RDCs) have emerged as one of the most exquisite probes of biological structure and dynamics. The measurement of RDCs relies on the partial alignment of the molecule of interest, for example by using a liquid crystal as a solvent. Here, we establish bacterial type 1 pili as an alternative liquid-crystalline alignment medium for the measurement of RDCs. To achieve alignment at pilus concentrations that allow for efficient NMR sample preparation, we elongated wild-type pili by recombinant overproduction of the main structural pilus subunit. Building on the extraordinary stability of type 1 pili against spontaneous dissociation and unfolding, we show that the medium is compatible with challenging experimental conditions such as high temperature, the presence of detergents, organic solvents or very acidic pH, setting it apart from most established alignment media. Using human ubiquitin, HIV-1 TAR RNA and camphor as spectroscopic probes, we demonstrate the applicability of the medium for the determination of RDCs of proteins, nucleic acids and small molecules. Our results show that type 1 pili represent a very useful alternative to existing alignment media and may readily assist the characterization of molecular structure and dynamics by NMR.     

Development of New Supramolecular Lyotropic Liquid Crystals and Their Application as Alignment Media for Organic Compounds

Most alignment media for the residual dipolar coupling (RDC) based molecular structure determination of small organic compounds consist of rod‐like polymers dissolved in organic solvents or of swollen cross‐linked polymer gels. Thus far, the synthesis of polymer‐based alignment media has been a challenging process, which is often followed by a time‐consuming sample preparation. We herein propose the use of non‐polymeric alignment media based on benzenetricarboxamides (BTAs), which self‐assemble into rod‐like supramolecules. Our newly found supramolecular lyotropic liquid crystals (LLCs) are studied in terms of their LLC properties and their suitability as alignment media in NMR spectroscopy. Scalable enantiodifferentiating properties are introduced through a sergeant‐and‐soldier principle by blending achiral with chiral substituted BTAs.     

Reconsideration of the anomalous dielectric behavior of dimethyl sulfoxide in the pure liquid state

Although many vibrational spectroscopic studies using infrared absorption and Raman scattering techniques reveal that dimethyl sulfoxide (DMSO) forms intermolecular associations, such as dimers, in the pure liquid state, the results of many dielectric relaxation studies deny the presence of such associations and claim very little orientational correlation between the dipoles of DMSO molecules because of a Kirkwood correlation factor close to unity in the pure liquid state and in solution. Recently, we found reasons for the inconsistency and elucidated the presence of dimeric DMSO associations via dielectric relaxation measurements from 50 MHz to 50 GHz. The dissociation of DMSO dimers is the major dielectric relaxation process with a relaxation time of 19 ps, while the relaxation of monomeric DMSO is a minor mode with a relaxation time of 4.5 ps at 25 °C and slightly increasing strength with increasing temperature.     

Application of Liquid Crystalline NMR Solvents to a Mixture of Ketones

A series of dilute liquid crystalline solvents are used to study the effect of slight anisotropy caused by partial alignment on chemical shift and residual dipolar coupling (RDC) in small molecules. The residual dipolar couplings between protons in solutes are found to be almost independent of the local environment. It is also found that the chemical shift does not change over the concentration range observed. A linear relationship between residual dipolar coupling and liquid crystal concentration is observed at relatively low concentrations, but is severely violated at high concentrations.     

可溶性聚酰亚胺液晶取向膜的制备与性能

液晶取向膜是液晶显示器中的关键材料,为了制得性能优良的液晶取向膜,我们通过铃木偶联反应制备了3种含有不同末端基团的3,5-二氨基联苯,将制得的3种二胺单体分别与环丁烷四甲酸二酐聚合得到3种新型的聚酰亚胺。 利用核磁氢谱对单体和聚合物的结构进行了表征,测试了聚合物的溶解性、热稳定性以及用作液晶取向膜的性能。 结果表明,所得的聚酰亚胺具有良好的溶解性和热稳定性,经过机械摩擦后,末端带有甲氧基的聚酰亚胺能使液晶分子平行于摩擦方向取向,末端带有苯氧羰基和联苯氧羰基的聚酰亚胺能使液晶分子垂直于摩擦方向取向。 此类可溶性的聚酰亚胺液晶取向膜将简化制备工艺并在柔性显示器件中具有较大的应用价值。     

Poly(ionic liquid)s as phase-transporter for graphene oxide liquid crystals from aqueous to non-polar organic phase via noncovalent functionalization

We synthesise a novel poly(ionic liquid) (PIL) and develop a procedure that allows the phase transfer of graphene oxides (GO) from water to organic solvent, retaining graphene oxide liquid crystal (GOLC) phase in various organic solvents, especially non-polar organic solvents. PIL ([PEP-MIM]DBS) is exploited in this procedure as a noncovalent functional material that is capable of transporting GO from aqueous to non-polar organic phase. PILs can decorate GO noncovalently and keep GO nano-sheets exfoliated in solid-state PILs/GO hybrids, which can well redisperse in organic solvents without any agglomeration. This expands the number of known solvents which can support GOLC phase to dimethyl formamide, dimethyl sulfoxide, acetonitrile, tetrahydrofuran, and a number of other non-polar organic solvents, many of which were not known to afford GOLC phase prior to this report, such as dichloromethane, tetrachloromethane, dichloroethane and tetrachloroethane.     

Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings

The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a strained polyacrylamide gel matrix. Using this composite medium, molecular alignment can be modulated by varying the angle between the directors of ordering for the Pf1 and strained gel matrix, or by varying the ionic strength or concentration of the Pf1 particles. This approach offers significant advantages in that greater experimental control can be exercised over the acquisition of multi-alignment RDC data while a homogeneous chemical environment is maintained across all of the measured RDC data.     

Orientational order of guest molecules in aligned liquid crystal as measured by EPR and UV–vis techniques

Orientational order of guest molecules in aligned liquid crystal 4-cyano-4′-pentylbiphenyl (5CB) is studied via optical dichroism and electron paramagnetic resonance (EPR) spectra measurements. The guest molecules used are bifunctional molecules bearing paramagnetic nitroxide group and photochromic azobenzene moiety. The bifunctional probe with rigidly bonded nitroxide and azobenzene moieties was found to align as a whole, while flexible long spacer between the moieties provides independent alignment for the nitroxide and azobenzene parts. Intermolecular interactions responsible for the alignment of azobenzene and nitroxide moieties of the probe molecules are discussed. The molecules with cis-configuration of azobenzene moiety are able to align in the liquid-crystalline medium, but to a lesser extent than the molecules with trans-configuration. Directions of orientational axes and characteristics of rotational mobility of spin probes are determined. Second, fourth and, in some cases, sixth rank order parameter values are found.     

De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy

We report the de novo determination of 15N-1H bond orientations and motional order parameters for the protein ubiquitin with high accuracy based solely on NMR residual dipolar coupling measurements made in six distinct alignment media. The resulting bond orientations are in agreement with RDC-refined orientations of either solid or solution state coordinates to within approximately 2 degrees , which is also the estimated precision of the resulting orientations. The squared generalized order parameters, which reflect amplitudes of motion spanning the picosecond to millisecond time scales, exhibit a correlation with picosecond time scale order parameters derived from conventional NMR 15N spin relaxation methods. Provided that RDC measurements can be obtained using many different alignment media, this approach (called direct interpretation of dipolar couplings) may significantly impact the attainable accuracy and the molecular weight range accessible to NMR structure determination in the solution state, as well as provide a route for the study of motions occurring on the nanosecond to microsecond time scales, which have been traditionally difficult to study at atomic resolution.     

Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination

Residual dipolar coupling (RDC) provides valuable information about the orientation of each internuclear vector in a macromolecule with respect to the static magnetic field. However, structure determination utilizing RDC still remains challenging without additional restraints such as NOE. In this context, a novel approach has been developed to efficiently extract structural information from RDC by successive application of singular value decomposition (SVD) method in the course of NMR structure determination. Force contribution from the alignment tensor is rigorously formulated in the context of SVD, and assessments have been made to verify its numerical accuracy. The efficacy of this approach is illustrated by showing that RDC restraints alone can restore a distorted beta-hairpin to native-like structure using the replica-exchange molecular dynamics simulations.     

Structural and magnetic modulation of a purely organic open framework by selective guest inclusion

Solvent inclusion/evacuation caused variations in the structural and magnetic characteristics of the purely organic porous magnet based on the tricarboxylic-substituted PTMTC radical. Whereas no inclusion is observed for nonpolar solvents, the exposure of crystals of the alpha-phase of PTMTC to vapors of polar organic solvents with hydrogen acceptor and/or donor functionalities, such as, ethanol, benzoic alcohol, n-decanol, THF, and DMSO results in the inclusion of these solvents in the highly polar tubular channels of the alpha-phase. The resulting inclusion compounds of formula PTMTC.x(guest) show several structural rearrangements, as confirmed by IR and XRPD (X-ray powder diffraction) measurements. The crystal transformations have been studied for a specific case: the PTMTC.EtOH adduct. The crystal structure reveals that included guest solvent molecules participate in the formation of new hydrogen bonds with the carboxylic groups of PTMTC radicals, inducing the disruption of several direct hydrogen bonds among these radicals. As expected, the interruption of direct hydrogen bonds between PTMTC radicals induces large transformations in the magnetic properties. From the ferromagnetic behavior of the alpha-phase, predominant antiferromagnetic interactions are observed for the inclusion adducts. Interestingly, both structural and magnetic changes are reversible after removal of guest solvent molecules.     

RDC‐enhanced structure calculation of a β‐heptapeptide in methanol

Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β‐peptide with proteinogenic side chains in methanol. ¹D_CH, ¹D_NH, and ²D_HH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long‐range definition in the backbone of the resulting 3₁₄‐helix and uncovers side‐chain mobility. Experimental side‐chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three‐state model. Copyright © 2016 John Wiley & Sons, Ltd.     

Orientation Control of Molecularly Functionalized Surfaces Applied to the Simultaneous Alignment and Sorting of Carbon Nanotubes

Self‐assembly has been relied upon for molecular alignment in many advanced technological applications. However, although effective, it is inherently limited in its capability for optimization. Despite the potential benefits, the seemingly fundamental strategy of external orientation control has yet to be realized. Herein we demonstrate an approach that allows control of the orientation of small molecules covalently bound to a surface. The method exploits an alignment relay technique, passing alignment information through a liquid‐crystal medium to small molecules to control surface functionalization events. The method is technically simple and can be carried out on a bench top without the need for specialized equipment. Moreover, we demonstrate the utility of the resulting surfaces to address two long‐standing problems in nanoscience: the sorting and alignment of single‐walled carbon nanotubes. This new method enabled significant alignment of the nanotubes as well as length and diameter sorting.     

Stretched poly(dimethylsiloxane) gels as NMR alignment media for apolar and weakly polar organic solvents: an ideal tool for measuring RDCs at low molecular concentrations

The measurement of residual dipolar couplings (RDCs), meanwhile a standard method for obtaining structural information in biomolecular NMR, requires partial alignment of the sample. Special demands on alignment media so far limit the applicability of this approach to small molecules in organic solvents. Major limitations are the free scalability of alignment and the suppression of residual signals of the alignment medium to allow effective measurement of low-concentration samples. Here, we present stretched poly(dimethylsiloxane) (PDMS) cross-linked by beta-rays as an alignment medium with no visible impurities in 1H NMR spectra but a single signal at approximately 0.1 ppm that can easily be removed by slightly modified water suppression methods. Besides the free scalability, its applicability to the measurement of RDCs in small molecules at low concentration is demonstrated on a approximately 12 mM sample of spiroindene. The induced alignment tensor in this case can be predicted reasonably well by a simplified model on the basis of steric interactions only.     

Determination of Complex Small‐Molecule Structures Using Molecular Alignment Simulation

Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy‐based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule‐specific anisotropic NMR parameters. The quantitative correlation uses an accurate three‐dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ‐benzyl‐l ‐glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.