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

Temperature-Controllable Liquid Crystalline Medium for Stereochemical Elucidation of Organic Compounds via Residual Chemical Shift Anisotropies

The configuration elucidation of organic molecules continues to pose significant challenges in studies involving stereochemistry. Nuclear magnetic resonance (NMR) techniques are powerful for obtaining such structural information. Anisotropic NMR techniques, such as measurement of residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), complementing isotropic NMR parameters, provide relative configuration information. RCSAs provide valuable structural information, especially for nonprotonated carbons, yet have been severely underutilized due to the lack of an easily operational alignment medium capable of rapid transition from anisotropic to isotropic environments, especially in aqueous conditions. In this study, an oligopeptide-based alignment media (FK)4 is presented for RCSA measurements. Temperature variation manipulates the assembly of (FK)4, yielding tunable anisotropic and isotropic phases without the requirement of any special devices or time-consuming correction procedures during data analysis. Decent observed ΔΔRCSA values from sp3 carbons benefit the utilization of RCSA measurements in the structural elucidation of organic molecules highly composed with sp3 carbons. Moreover, the (FK)4 alignment medium is applicable for both RDC and RCSA measurements in one sample, further advancing the configuration analysis of molecules of interest.

Garbractin A, a Polycyclic Polyprenylated Acylphloroglucinol with a 4,11-dioxatricyclo[4.4.2.01,5]Dodecane Skeleton from Garcinia bracteata Fruits

Garbractin A (1), a structurally complicated polycyclic polyprenylated acylphloroglucinol (PPAP) with an unprecedented 4,11-dioxatricyclo[4.4.2.01,5] dodecane skeleton, was isolated from the fruits of Garcinia bracteata, along with five new biosynthetic analogues named garcibracteatones A-E (2-6). Their structures containing absolute configurations were revealed using spectroscopic data, the residual dipolar coupling-enhanced NMR approach, and quantum chemical calculations. The antihyperglycemic effect of these PPAPs (1-6) was evaluated using insulin-resistant HepG2 cells (IR-HepG2 cells) induced through palmitic acid (PA). Compounds 1, 3, and 4 were found to significantly promote glucose consumption in the IR-HepG2 cells and, therefore, may hold potential as candidates for treating hyperglycemia.

Weakly aligned Ti3C2Tx MXene liquid crystals: measuring residual dipolar coupling in multiple co-solvent systems

Residual Dipolar Coupling (RDC), acquired relying on weakly alignment media, is highly valuable for the structural elucidation of organic molecules. Arising from the striking features of no background signals and low critical concentrations, two-dimensional (2D) liquid crystals (LCs) show the clear advantages of acting as alignment media to measure RDCs. So far, creating multisolvent compatible 2D LC media through a simple and versatile method is still formidably challenging. Herein, we report the rapid creation of aligned media based on the Ti₃C₂T_x MXene, which self-aligned in multiple co-solvents including CH₃OH-H₂O, DMSO-H₂O, DMF-H₂O, and acetone-H₂O. We demonstrated the applicability of these aligned media for the RDC measurement of small organic molecules with different polarities and solubilities. Notably, Ti₃C₂T_x MXene LCs without chemical modification enabled RDC measurements on aromatic molecules. The straightforward preparation of Ti₃C₂T_x media and its compatibility with multiple solvents will push RDC measurement as a routine methodology for structural elucidation. It may also facilitate the investigation of solvation effects on conformational dynamics.

Enantiodiscrimination of Inherently Chiral Thiacalixarenes by Residual Dipolar Couplings

Inherently chiral compounds, such as calixarenes, are chiral due to a nonplanar three-dimensional (3D) structure. Determining their conformation is essential to understand their properties, with nuclear magnetic resonance (NMR) spectroscopy being one applicable method. Using alignment media to measure residual dipolar couplings (RDCs) to obtain structural information is advantageous when classical NMR parameters like the nuclear Overhauser effect (NOE) or J-couplings fail. Besides providing more accurate structural information, the alignment media can induce different orientations of enantiomers. In this study, we examined the ability of polyglutamates with different side-chain moieties─poly-γ-benzyl-l-glutamate (PBLG) and poly-γ-p-biphenylmethyl-l-glutamate (PBPMLG) ─to enantiodifferentiate the inherently chiral phenoxathiin-based thiacalix[4]arenes. Both media, in combination with two solvents, allowed for enantiodiscrimination, which was, to the best of our knowledge, proved for the first time on inherently chiral compounds. Moreover, using the experimental RDCs, we investigated the calix[4]arenes conformational preferences in solution, quantitatively analyzed the differences in the alignment of the enantiomers, and discussed the pitfalls of the use of the RDC analysis.

Sensing Magnetic Field and Intermolecular Interactions in Diamagnetic Solution Using Residual Dipolar Couplings of Zephycandidine

An unusual residual dipolar coupling of methylene protons was recorded in NMR spectra because aromatic zephycandidine has preferential orientation at the external magnetic field. The observed splitting contains contribution from the dipole-dipole D-coupling and the anisotropic component of J-coupling. Absolute values of the anisotropy of magnetic susceptibility |Δχ_ax| are larger for protic solvents because of the hydrogen-bonding compared to aprotic solvents for which polar and dispersion forces are more important. The energy barrier for the reorientation due to hydrogen-bonding is 1.22 kJ/mol in methanol-d_4, 0.85 kJ/mol in ethanol-d₆ and 0.87 kJ/mol in acetic acid-d₆. In dimethyl sulfoxide-d₆, 1.08 kJ/mol corresponds to the interaction of solvent lone pair electrons with π-electrons of zephycandidine. This energy barrier decreases for acetone-d₆ which has smaller electric dipole moment. In acetonitrile-d₃, there is no energy barrier which suggests solvent ordering around the solute due to the solvent-solvent interactions. The largest absolute values of the magnetic anisotropy are observed for aromatic benezene-d₆ and tolune-d₈ which have their own preferential orientation and enhance the order in the solution. The magnetic anisotropy of "isolated" zephycandidine, not hindered by intermolecular interaction could be estimated from the correlation between Δχ_ax and cohesion energy density.

NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2N-1 Diastereomers

Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.

Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D

Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).

Self-Assembled Oligopeptide (FK)4 as a Chiral Alignment Medium for the Anisotropic NMR Analysis of Organic Compounds

Anisotropic NMR parameters have been proven to be powerful for the structural elucidation of organic molecules. Herein, we present an alignment medium based on the self-assembled (FK)₄ oligopeptide, showing excellent properties in measurements of anisotropic NMR parameters in both D₂O and CD₃OD. The preparation of the (FK)₄-based alignment medium is simple and rapid. The low viscosity of the anisotropic phase makes it easy to be transferred to the NMR tube. The alignment of the oligopeptide is fast, stable, and homogeneous, with weak background signals, permitting the acquirement of high-quality NMR spectra. The performance of this alignment medium in residual dipolar coupling measurements and diastereomer discriminations is demonstrated by analyzing several different analytes. The enantiodiscrimination property of the (FK)₄ oligopeptide is revealed by the difference of residual chemical shift anisotropy of the two enantiomers in the 1D ¹³C spectrum, granting its potential use for the quantification and identification of enantiomers of small molecules.

Programmable alignment media from self-assembled oligopeptide amphiphiles for the measurement of independent sets of residual dipolar couplings in organic solvents

NMR spectroscopy in anisotropic media has emerged as a powerful technique for the structural elucidation of organic molecules. Its application requires weak alignment of analytes by means of suitable alignment media. Although a number of alignment media, that are compatible with organic solvents, have been introduced in the last 20 years, acquiring a number of independent, non-linearly related sets of anisotropic NMR data from the same organic solvent system remains a formidable challenge, which is however crucial for the alignment simulations and deriving dynamic and structural information of organic molecules unambiguously. Herein, we introduce a programmable strategy to construct several distinct peptide-based alignment media by adjusting the amino acid sequence, which allows us to measure independent sets of residual dipolar couplings (RDCs) in a highly efficient and accurate manner. This study opens a new avenue for de novo structure determination of organic compounds without requiring prior structural information.

We report a programmable strategy to construct multi-alignment media via peptide self-assembly for the measurement of independent sets of residual dipolar couplings (RDCs).

Self-assembly of Helical Polymers and Oligomers to Create Liquid Crystalline Alignment for Anisotropic NMR Parameters

The measurement of anisotropic residual dipolar couplings (RDCs) parameters for the structure elucidation of organic molecules relies on suitable alignment media. Employment of self-assembled liquid crystalline systems to create anisotropic alignment can be an effective way to realize aligned samples and acquire RDCs. This Mini-review highlights the recent advances on amino acid-based helical polymers and supramolecular oligomers forming rigid, rod-like structures that aggregate into ordered liquid crystalline phases, including amino acid-based helical polyisocyanides, polyacetylenes, polypeptides, and oligopeptides assembled alignment media. The methodology for the determination of anisotropic liquid crystals was briefly discussed, and a summary of recent research progress in the enantiodifferentiation of helical polymers aligned media was followed. In addition, the self-assembled mechanism of oligopeptides and their RDCs structural analysis were also described. This article is protected by copyright. All rights reserved.

NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations

Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.

Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems

The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide ¹⁵N-¹H RDCs, to ¹H-¹H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.

Valine derived poly (acetylenes) as versatile chiral lyotropic liquid crystalline alignment media for RDC-based structure elucidations

Anisotropic samples of lyotropic liquid crystalline (LLC) phases of valine derived polyaryl acetylenes were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of 12 small, chiral, organic molecules. The quadrupolar splitting of the deuterium signal of CDCl₃ can be adjusted by temperature and concentration changes from 0 to 350 Hz. The LLC phases showed excellent orienting properties for all analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±30 Hz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment led to diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with H-bond donors like alcohols and 2° amines.

Single experiment measurement of residual dipolar couplings in aqueous solution using a biphasic bisperylene imide chromonic liquid crystal

The use of the biphasic isotropic/nematic region in a bisperylene imide-based lyotropic liquid crystal system allows the extraction of proton-carbon ¹ D_CH residual dipolar couplings in aqueous solution from a single F1-coupled HSQC experiment. The method was successfully applied to the RDC-based conformational analysis of sucrose.

A Lyotropic Liquid Crystal from a Flexible Oligopeptide Amphiphile in Dimethyl Sulfoxide

Despite the rapid progress in peptide liquid crystals (LCs) due to their prominent properties, our investigation on flexible peptide-based LCs is incomplete, mainly resulted from their unclear formation mechanisms and unexploited applications in organic solvents. Here, we develop a lyotropic LC based on a flexible oligopeptide amphiphile, which aggregates into aligned cylinder-like nanostructures in dimethyl sulfoxide (DMSO). The formation mechanism of lyotropic LC in DMSO was probed by the experimental investigation and molecular dynamics simulation, indicating that the hydrogen bonding and hydrophobic and electrostatic interactions contribute to the formation of ordered nanostructures in the organic solvent. Arising from the orientational order and suitable fluidity, we exploit the application of lyotropic LC as an aligned medium to measure the residual dipolar couplings of bioactive molecules. This study not only offers the understanding of the mechanism to create LC systems without rigid aromatic groups but also expands the applications of ordered bottom-up nanomaterials in organic solvents.

"One-Shot" Measurement of Residual Chemical Shift Anisotropy Using Poly-γ-benzyl-l-glutamate as an Alignment Medium

A method for the measurement of residual chemical shift anisotropy in one experiment using a biphasic isotropic/anisotropic lyotropic liquid crystalline medium based on poly-γ-benzyl-l-glutamate as the alignment medium is presented. This approach is demonstrated on the model compound strychnine and neotricone, a depsidone natural product with a questionable structural assignment based on comparison with the closely related excelsione and in-depth density functional theory calculations.

Practical aspects of oligopeptide AAKLVFF as an alignment medium for the measurements of residual dipolar coupling of organic molecules

Practical aspects of the oligopeptide AAKLVFF as an alignment medium are discussed, including large-scale synthesis of the oligopeptide, detailed description of preparation of the alignment medium, and acquisition of the RDCs. The resulting orienting medium is stable and highly homogeneous with tunable alignment strength in methanol.

Self-Assembly, Nematic Phase Formation, and Organocatalytic Behavior of a Proline-Functionalized Lipopeptide

The self-assembly of the amphiphilic lipopeptide PAEPKI-C₁₆ (P = proline, A = alanine, E = glutamic acid, K = lysine, I = isoleucine, and C₁₆ = hexadecyl) was investigated using a combination of microscopy, spectroscopy, and scattering methods and compared to that of C₁₆-IKPEAP with the same (reversed) peptide sequence and the alkyl chain positioned at the N-terminus and lacking a free N-terminal proline residue. The catalytic activity of these peptides was then compared using a model aldol reaction system. For PAEPKI-C₁₆, the cryo-TEM images showed the formation of micrometer-length fibers, which by small-angle X-ray scattering (SAXS) were found to have radii of 2.5-2.6 nm. Spectroscopic analysis shows that these fibers are built from β-sheets. This behavior is in complete contrast to that of C₁₆-IKPEAP, which forms spherical micelles with peptides in a disordered conformation [Hutchinson J. Phys. Chem. B 2019, 123, 613]. In PAEPKI-C₁₆, spontaneous alignment of fibers was observed upon increasing pH, which was accompanied by observed birefringence and anisotropy of SAXS patterns. This shows the ability to form a nematic phase, and unprecedented nematic hydrogel formation was also observed for these lipopeptides at sufficiently high concentrations. SAXS shows retention of an ultrafine (1.7 nm core radius) fibrillar network within the hydrogel. PAEPKI-C₁₆ with free N-terminal proline shows enhanced anti:syn diastereoselectivity and better conversion compared to C₁₆-IKPEAP. The cytotoxicity of PAEPKI-C₁₆ was also lower than that of C₁₆-IKPEAP for both fibroblast and cancer cell lines. These results highlight the sensitivity of lipopeptide properties to the presence of a free proline residue. The spontaneous nematic phase formation by PAEPKI-C₁₆ points to the high anisotropy of its ultrafine fibrillar structure, and the formation of such a phase at low concentrations in aqueous solution may be valuable for future applications.

Stereochemical Elucidation of Natural Products from Residual Chemical Shift Anisotropies in a Liquid Crystalline Phase

Determination of the stereochemistry of organic molecules still represents one of the major obstacles in the structure elucidation procedure in drug discovery. Although the application of residual dipolar couplings (RDCs) has revolutionized this field, residual chemical shift anisotropies (RCSAs) which contain valuable structural information for nonprotonated carbons have only been scarcely employed so far. In this study, we present a simple but highly effective solution to extract RCSAs of the analytes in a liquid crystalline phase formed by AAKLVFF oligopeptides. This method does not require any special instruments, devices, or correction during postacquisition data analysis and thus can be easily applied in any chemistry laboratory. To illustrate the potential of this method, the relative configurations of four known natural products (1-4) belonging to different structural classes were confirmed. Moreover, we unambiguously elucidated the stereochemistry of spiroepicoccin A (5), a rare thiodiketopiperazine marine natural product whose configuration could not be assigned based on conventional NMR methods.

Lyotropic liquid crystal to measure residual dipolar couplings in dimethyl sulfoxide based on modified cellulose nanocrystals

A novel lyotropic liquid crystal was developed for the measurement of RDCs of organic molecules with no background signals.

Uncommon Polyoxygenated Sesquiterpenoids from South China Sea Soft Coral Lemnalia flava

A detailed chemical investigation of the Chinese soft coral Lemnalia flava yielded four new nardosinane-type sesquiterpenoids (1-4), one new neolemnane-type sesquiterpenoid (5), and one new sesquiterpenoid with an uncommon 6/9 fused bicyclic skeleton (6), together with two known related compounds (7 and 8). The structures and absolute configurations of 1-8 were determined on the basis of extensive spectroscopic data analyses, X-ray diffraction analysis, chemical reactions, and computer-assisted structural elucidation including ¹³C NMR data calculation, residual dipolar coupling based NMR analysis, and time-dependent density functional theoryelectronic circular dichroism calculation. Plausible biogenetic pathways of two uncommon sesquiterpenoids (4 and 6) were proposed.

Directing an oligopeptide amphiphile into an aligned nanofiber matrix for elucidating molecular structures

A novel aligned nanofiber matrix was obtained from the self-assembly of an oligopeptide amphiphile. The alignment properties can be applied to measure residual dipolar couplings (RDCs) for the structural elucidation of molecules by liquid-state NMR.

PBLG as a versatile liquid crystalline medium for anisotropic NMR data acquisition

The chiral nematic phase of poly-γ-benzyl-l-glutamate (PBLG) formed in a chloroform–DMSO co-solvent system can be used as a versatile alignment medium for the acquisition of high quality anisotropic NMR data for molecules of varying polarities.

Cromolyn/gelatin mixtures as aqueous alignment media and utilization of their mechanical stability for a layering technique

In this study, aqueous blends of cromolyn and gelatin ("cromogels") are introduced as anisotropic media. The addition of gelatin enables an advantageous adjustability of the strength, the homogeneity, and the stability of the cromolyn alignment. The mechanical stability of these polymer-dispersed liquid crystals is further utilized by stacking layers of D₂ O/cromolyn/gelatin with varying component ratio. The resulting distinct phases with correspondingly different degrees of alignment can be targeted by spatially resolved NMR techniques. As a case study, we investigated sucrose in a two-phase system with neat D₂ O and analyte layered over the anisotropic medium. A recently presented spatially selective coupled-type HSQC experiment allows the determination of one-bond C-H splitting in both phases.

Residual Dipolar Couplings in Structure Determination of Natural Products

The determination of natural products stereochemistry remains a formidable task. Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for determination of the stereochemistry of organic molecule in solution. This review will provide a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized. This review provides a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized.

Heterologous Expression of a VioA Variant Activates Cryptic Compounds in a Marine-Derived Brevibacterium Strain

A new 14-membered homodimeric macrodiolide, brevidiolide (3), along with four known aromatic compounds (1, 2, 4 and 5) were obtained by heterologous expression of the recombinant plasmid pWLI823 expressing the G231L variant of VioA in the marine-derived Brevibacterium sp. 7002-073. The structures of 1–5 were elucidated on the basis of LC-MS and 2D NMR spectroscopic analyses. In the evaluation for the antibacterial activities of the compounds against multi-drug resistant (MDR) strains, 5 showed notable growth inhibition against Staphylococcus aureus CCARM 3090 and Klebsiella pneumoniae ATCC 13883, with a minimum inhibitory concentration (MIC) value of 3.12 µg/mL.

A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond ¹³C-¹H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH₂ group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.