Residual dipolar couplings as a tool in determining the structure of organic molecules

RDC-based determination of the relative configuration of the fungicidal cyclopentenone 4,6-diacetylhygrophorone A12

The hygrophorones, a class of cyclopentenones isolated from fruiting bodies of the genus Hygrophorus (basidiomycetes), show promising antifungal activity. While the constitution of 4,6-diacetylhygrophorone A(12) (3) and the relative configuration of the stereogenic centers in the cyclopentenone ring were elucidated using standard NMR and MS techniques, the relative configuration of the exocyclic stereogenic center could not be assigned. By introducing a sample of 3 into an alignment medium and measuring anisotropic NMR parameters, namely, residual dipolar couplings, we were able to unambiguously determine the relative configuration of all three stereogenic centers in 4,6-diacetylhygrophorone A(12) simultaneously by fitting several structure proposals to the experimental data.

Configuration verification via RDCs on the example of a tetra-substituted pyrrolidine ring

The configurational analysis of organic compounds is an important application for high resolution NMR spectroscopy. In the present study, a tetra-substituted pyrrolidine with four chiral carbon atoms is analyzed using classical methods based on (3) J and NOE data in solution and compared and verified with recently introduced alternative approaches via residual dipolar couplings (RDCs) in two weak anisotropic alignment media. The molecule shows sufficient rigidity in the five-membered ring for the configurational characterization with the various techniques. However, the flexibility caused by the many freely rotating bonds potentially poses problems for the interpretation of data. It is shown that RDCs measured in poly-γ-benzyl-l-glutamate and a stretched polydimethylsiloxane gel provide useful information for the distinction of diastereomers, but the success varies with the data interpretation strategy used. Although a general improvement of corresponding correlation factors is observed when limiting data to a subset of dipolar couplings directly connected to the central ring, the distinction power is reduced because of the smaller number of RDCs available for potential model falsification. Singular value decomposition for fitting experimental RDCs is able to distinguish in most cases the correct from incorrect configurations, but the differences in correlation factors can be relatively small. Surprisingly, predicting RDCs using the rod model as implemented in PALES gives best results in distinguishing the eight possible diastereomers. It is also found that the use of proton-phosphorus and carbon-phosphorus RDCs helps with the configurational analysis of the model compound.

A systematic approach for optimizing the robustness of pulse sequence elements with respect to couplings, offsets, and B1-field inhomogeneities (COB)

Robust experiments that cover a wide range of chemical shift offsets and J-couplings are highly desirable for a multitude of applications in small molecule NMR spectroscopy. Many attempts to improve individual aspects of the robustness of pulse sequence elements based on rational and numerical design have been reported, but a general optimization strategy to cover all necessary aspects for a fully robust sequence is still lacking. In this article, a viable optimization strategy is introduced that covers a defined range of couplings, offsets, and B(1)-field inhomogeneities (COB) in a time-optimal way. Individual components of the optimization strategy can be optimized in any adequate way. As an example for the COB approach, we present the (1)H -(13)C-COB-INEPT with transfer of approximately 99% over the full carbon and proton bandwidth and (1)J(CH) -couplings in the range of 120-250 Hz, which have been optimized using efficient algorithms derived from optimal control theory. The theoretical performance is demonstrated in a number of corresponding COB-HSQC experiments.

Review: Use of residual dipolar couplings to determine the structure of carbohydrates

Solution nuclear magnetic resonance spectroscopy is especially useful in the carbohydrate field. The measurement of residual dipolar couplings provides long-range structural information, a valuable complement for the structural study of carbohydrates either in its free form or in the bound state to proteins. They permit to deduce the geometry and the flexibility of the glycosidic linkages, which have a major influence on the conformation of carbohydrates and their overall shape. This article reviews the current application of the residual dipolar couplings methodology to carbohydrates.

Influence of solvent and salt concentration on the alignment properties of acrylamide copolymer gels for the measurement of RDC

The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration.

HR-HSBC: Measuring heteronuclear one-bond couplings with enhanced resolution

Heteronuclear one-bond couplings have a variety of applications, and their accurate determination is the basis for obtaining specific structural information of mostly small organic compounds. In this context, it is of utmost importance to reduce signal overlap to a minimum, and a number of techniques has been introduced during the last decades. Here, we introduce a modified version of the HR-HMBC (Magn. Reson. Chem. 2010, 48, 179-183) for heteronuclear one-bond coupling measurements with improved resolution because of the J-resolved-like tilt of corresponding multiplet patterns. The pulse sequence is introduced, and its performance is compared with a standard ω(2)-coupled HSQC experiment. Example spectra on glucose and maltose demonstrate that signals can be resolved that overlap otherwise. The approach is discussed in detail.

Phenylalanine-based polyarylacetylenes as enantiomer-differentiating alignment media

Lyotropic liquid crystalline phases of a phenylalanine-based polyacetylene are introduced as new enantiodifferentiating alignment media. Based on the unusual temperature dependence of the quadrupolar splitting of the (2)H-signal of the solvent (CDCl(3)), three distinct states of the phase with different orientational properties can be identified. This offers the opportunity to measure multiple alignment data sets without changing the sample. Unexpectedly, the largest difference in the orientation of the enantiomers of isopinocampheol was found in the high temperature domain of the phase. This is even more astonishing because the helical structure of the polymer backbone seems to break down at temperatures above approximately 10 °C, leaving the stereogenic centers of the amino acid moieties in the repeating units as the only reason for the enantiodifferentiation.

Noncovalently and covalently cross-linked polyurethane gels as alignment media and the suppression of residual polymer signals using diffusion-filtered spectroscopy

With polyurethane (PU), a novel alignment medium for organic solvents is introduced and characterized, which is very robust and easy to produce on a large scale. Linear PU already constitutes an elastomer gel with several solvents based on its ability to form hydrogen bonds. Covalent cross-linking of the polymer with accelerated electrons provides an alignment medium with different properties. However, PU exhibits a number of undesired polymer signals in corresponding spectra, which ideally have to be removed spectroscopically. Within this context, we demonstrate the applicability of diffusion-filtered experiments for removal of the polymer signals. Example spectra for the usefulness of PU alignment media are provided for the common test molecules strychnine and norcamphor.

Speeding up the measurement of one-bond scalar (1J) and residual dipolar couplings (1D) by using non-uniform sampling (NUS)

The accurate and precise measurement of one-bond scalar and residual dipolar coupling (RDC) constants is of prime importance to be able to use RDCs for structure determination. If coupling constants are to be extracted from the indirect dimension of HSQC spectra a significant saving of measurement time can be achieved by non-uniform sampling (NUS). Coupling constants can either be obtained with the same precision as in traditionally acquired spectra in a fraction of the measurement time or the precision can be significantly improved if the same amount of measurement time as for traditionally acquired spectra is invested. The application of NUS for the measurement of (1)J (scalar coupling constants) and (1)T (total couplings constants) from different kinds of ω(1)-coupled spectra (including also J-scaled ones) is examined in detail and the possible gains in time or resolution are discussed. When using the newly proposed compressed sensing (CS) algorithm for processing, the quality of the spectra is comparable to the traditionally sampled ones.

Determination of size and sign of hetero-nuclear coupling constants from 2D 19F-13C correlation spectra

Fluorinated organic compounds have become increasingly important within the polymer and the pharmaceutical industry as well as for clinical applications. For the structural elucidation of such compounds, NMR experiments with fluorine detection are of great value due to the favorable NMR properties of the fluorine nucleus. For the investigation of three fluorinated compounds, triple resonance 2D HSQC and HMBC experiments were adopted to fluorine detection with carbon and/or proton decoupling to yield F-C, F-C{H}, F-C{C(acq)} and F-C{H,C(acq)} variants. Analysis of E.COSY type cross-peak patterns in the F-C correlation spectra led, apart from the chemical shift assignments, to determination of size and signs of the J(CH), J(CF), and J(HF) coupling constants. In addition, the fully coupled F-C HMQC spectrum of steroid 1 was interpreted in terms of E.COSY type patterns. This example shows how coupling constants due to different nuclei can be determined together with their relative signs from a single spectrum. The analysis of cross-peak patterns, as presented here, not only provides relatively straightforward routes to the determination of size and sign of hetero-nuclear J-couplings in fluorinated compounds, it also provides new and easy ways for the determination of residual dipolar couplings and thus for structure elucidation. The examples and results presented in this study may contribute to a better interpretation and understanding of various F-C correlation experiments and thereby stimulate their utilization.

The products of 5-fluorouridine by the action of the pseudouridine synthase TruB disfavor one mechanism and suggest another

The pseudouridine synthase TruB handles 5-fluorouridine in RNA as a substrate, converting it into two isomeric hydrated products. Unexpectedly, the two products differ not in the hydrated pyrimidine ring but in the pentose ring, which is epimerized to arabinose in the minor product. This inversion of stereochemistry at C2' suggests that pseudouridine generation may proceed by a mechanism involving a glycal intermediate or that the previously proposed mechanism involving an acylal intermediate operates but with an added reaction manifold for 5-fluorouridine versus uridine. The arabino product strongly disfavors a mechanism involving a Michael addition to the pyrimidine ring.

1H and 13C NMR studies of glycine in anisotropic media: double-quantum transitions and the effects of chiral interactions

The (1)H NMR spectrum of glycine in stretched gelatin gel and in cromolyn liquid crystal displays a well-resolved doublet due to (1)H-(1)H dipolar interaction. Multiple spectra were obtained within a wide range of offset frequencies of partially saturating radio-frequency (RF) radiation to generate steady-state irradiation envelopes or z-spectra of glycine. Maximal suppression of the doublet occurred when the irradiation was applied exactly at the centre frequency, between the two glycine peaks. This phenomenon is due to double-quantum transitions and is similar to our previous work on quadrupolar nuclei (2)H (HDO) and (23)Na(+). When the (13)C isotopomer glycine-2-(13)C was used, the same effect was found in twice, split by (1)J(CH)+2D(CH). Additional signals in (1)H and (13)C NMR due to prochiral-chiral interactions were found when glycine-2-(13)C was dissolved in chiral anisotropic gelatin and κ-carrageenan gels. The NMR spectra were successfully simulated assuming a (2)J(HH) coupling constant of -16.5Hz and two distinct dipolar coupling constants for the -(13)CH(2)- group (D(C,HA), and D(C,HB)).

Naturally Occurring Biodegradable Polymers as the Basis of Chiral Gels for the Distinction of Enantiomers by Partially Oriented Nmr Spectroscopy

Introduction

In modern, high resolution NMR spectroscopy, anisotropic parameters play an important role. They can be measured with the help of liquid crystalline mesophases or stretched polymer gels as so-called alignment media. Biologically occurring chiral polymers are of special interest as alignment media for this technique because they allow enantiomers to be distinguished.

Methods

Biopolymers have been studied by deuterium 1D and J-BIRDd,X-HSQC NMR experiments with respect to their ability to distinguish enantiomers and a summary of existing biopolymers for the task is given.

Results

Gelatin is shown to distinguish D-proline from L-proline and next to already known biopolymers, gellan gum is introduced as a novel biologically derived polymer that is able to partially align solute molecules.

Conclusions

Biologically occurring and biodegradable polymers are well suited as alignment media and in many cases are able to distinguish enantiomers. As the orienting properties are different for different media and solute molecules, the bandwidth of corresponding polymers will be further increased in the future.

Variable angle NMR spectroscopy and its application to the measurement of residual chemical shift anisotropy

The successful measurement of anisotropic NMR parameters like residual dipolar couplings (RDCs), residual quadrupolar couplings (RQCs), or residual chemical shift anisotropy (RCSA) involves the partial alignment of solute molecules in an alignment medium. To avoid any influence of the change of environment from the isotropic to the anisotropic sample, the measurement of both datasets with a single sample is highly desirable. Here, we introduce the scaling of alignment for mechanically stretched polymer gels by varying the angle of the director of alignment relative to the static magnetic field, which we call variable angle NMR spectroscopy (VA-NMR). The technique is closely related to variable angle sample spinning NMR spectroscopy (VASS-NMR) of liquid crystalline samples, but due to the mechanical fixation of the director of alignment no sample spinning is necessary. Also, in contrast to VASS-NMR, VA-NMR works for the full range of sample inclinations between 0° and 90°. Isotropic spectra are obtained at the magic angle. As a demonstration of the approach we measure ¹³C-RCSA values for strychnine in a stretched PDMS/CDCl₃ gel and show their usefulness for assignment purposes. In this context special care has been taken with respect to the exact calibration of chemical shift data, for which three approaches have been derived and tested.

Macromolecular NMR spectroscopy for the non-spectroscopist

NMR spectroscopy is a powerful tool for studying the structure, function and dynamics of biological macromolecules. However, non-spectroscopists often find NMR theory daunting and data interpretation nontrivial. As the first of two back-to-back reviews on NMR spectroscopy aimed at non-spectroscopists, the present review first provides an introduction to the basics of macromolecular NMR spectroscopy, including a discussion of typical sample requirements and what information can be obtained from simple NMR experiments. We then review the use of NMR spectroscopy for determining the 3D structures of macromolecules and examine how to judge the quality of NMR-derived structures.