S(3)E-E.COSY methods for the measurement of (19)F associated scalar and dipolar coupling constants

Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2'-19F probe in nucleic acids

Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as 15N and 13C, which are abundant in biomolecules, fluorine-19 (19F) has recently garnered attention and is being widely used as a site-specific spin probe. While 19F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby 1H spins. In this study, we focused on the ribose 2'-19F spin probe in nucleic acids and investigated the effects of 1H-19F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the 1H-19F dipolar coupling can significantly affect the interpretation of 19F chemical exchange saturation transfer (CEST) experiments when 1H decoupling is applied, while the 1H-19F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various 19F spin systems where 1H-19F interactions are operative, further expanding the utility of 19F relaxation-based NMR experiments.

Pure shift FESTA: An ultra-high resolution NMR tool for the analysis of complex fluorine-containing spin systems

NMR measurements of molecules containing sparse fluorine atoms are becoming increasingly common due to their prevalence in medicinal chemistry. However, the presence of both homonuclear and heteronuclear scalar couplings severely complicates their analysis by NMR. In complex systems, FESTA, a heteronuclear spectral editing method, allows simplified 1 H NMR spectra to be obtained containing only 1 H signals from the same spin system as a chosen 19 F. Despite spectral simplification, signal overlap due to the presence of scalar couplings is often a problem in FESTA spectra. Here, we report a new experiment that combines FESTA and pure shift methods to provide fully decoupled ultra-high resolution FESTA spectra showing a single signal for each 1 H chemical environment. The utility of the method is demonstrated for the analysis of two complex fluorine-containing mixtures of pharmaceutical and biochemical interest.

Pure shift edited NMR methodologies for the extraction of Homo- and heteronuclear couplings with ultra-high resolution

The scalar couplings that result in the splitting of the signals in the NMR spectrum arise due to the interaction of the nuclear spins, whereby the spin polarization is transmitted through chemical bonds. The interaction strengths depend inter alia on the number of consecutive chemical bonds intervening between the two interacting spins and on the molecular conformation. The pairwise interaction of many spins in a molecule resulting in a complex spectrum poses a severe challenge to analyse the spectrum and hence the determination of magnitudes and signs of homo- and heteronuclear couplings. The problem is more severe in the analysis of 1H spectra than the spectra of most of the other nuclei due to the often very small chemical shift dispersion. As a consequence, the straightforward analysis and the accurate extraction of the coupling constants from the 1H spectrum of a complex spin system continues to remain a challenge, and often may be a formidable task. Over the years, the several pure shift-based one-dimensional and two-dimensional methodologies have been developed by workers in the field, which provide broadband homonuclear decoupling of proton spectra, removing the complexity but at the cost of the very informative scalar couplings. To circumvent this problem, several one-dimensional and two-dimensional NMR experiments have been developed for the determination of homonuclear and heteronuclear couplings (nJHX, where n = 1,2,3) while retaining the high resolution obtained by implementing pure shift strategies. This review attempts to summarize the extensive work reported by a large number of researchers over the years for the accurate determination of homo- and heteronuclear scalar couplings.

Selective Nuclear Magnetic Resonance Experiments for Sign-Sensitive Determination of Heteronuclear Couplings: Expanding the Analysis of Crude Reaction Mixtures

State-of-the-art nuclear magnetic resonance (NMR) selective experiments are capable of directly analyzing crude reaction mixtures. A new experiment named HD-HAPPY-FESTA yields ultrahigh-resolution total correlation subspectra, which are suitable for sign-sensitive determination of heteronuclear couplings, as demonstrated here by measuring the sign and magnitude for proton-fluorine couplings (J_HF) from major and minor isomer products of a two-step reaction without any purification. Proton-fluorine couplings ranging from 51.5 to -2.6 Hz could be measured using HD-HAPPY-FESTA, with the smallest measured magnitude of 0.8 Hz. Experimental J_HF values were used to identify the two fluoroketone intermediates and the four fluoroalcohol products. Results were rationalized and compared with the density functional theory (DFT) calculations. Experimental data were further compared with the couplings reported in the literature, where pure samples were analyzed.

High-resolution methods for the measurement of scalar coupling constants

Scalar couplings provide important information regarding molecular structure and dynamics. The measurement of scalar coupling constants constitutes a topic of interest and significance in NMR spectroscopy. However, the measurement of J values is often not straightforward because of complex signal splitting patterns and signal overlap. Many methods have been proposed for the measurement of scalar coupling constants, both for homonuclear and heteronuclear cases. Different approaches to the measurement of scalar coupling constants are reviewed here with several applications presented. The accurate measurement of scalar coupling constants can greatly facilitate molecular structure elucidation and the study of molecule dynamics.

Orchestrated approaches using pure shift NMR: Extraction of spectral parameters, ultra-high resolution, and sensitivity enhancement

The limited chemical shift range of protons and pairwise interaction among all the abundant nuclear spins of a molecule makes ¹ H spectrum too complicated. As a consequence, the straightforward analysis and the accurate extraction of their interaction strengths from the ¹ H spectrum of a complex spin system are formidably difficult or often impossible. This problem persists in the determination of scalar couplings be it between two abundant homonuclear spins or between ¹ H and an abundant heteronuclear spin (viz., ¹⁹ F and ³¹ P). Such problems are encountered in many situations where the determination of homonuclear and heteronuclear couplings is challenging. The several pure shift based one-dimensional and two-dimensional NMR strategies recently developed in our laboratory for the straightforward extraction of homonuclear and heteronuclear interaction parameters in diverse situations are discussed. Initially, the unique application of pure shift technique that paves the way for easy and straightforward extraction of magnitudes of heteronuclear couplings, namely, ⁿ J_HX (where X stands for ¹⁹ F, ³¹ P, etc.), is discussed. Subsequently, several pure shift edited one-dimensional and two-dimensional NMR strategies that are developed for the direct extraction of homonuclear and heteronuclear couplings and for achieving ultra-high-resolved ¹ H spectra with complete eradication of zero frequency peaks and the evolution of unwanted couplings. The enhancement in the sensitivity has also been achieved in the slice-selective pure shift experiments by the rapid acquisition of proton spectrum where the polarization from the adjacent protons is transferred to the selectively excited proton.

Q.E.COSY: determining sign and size of small deuterium residual quadrupolar couplings using an extended E.COSY principle

Residual quadrupolar couplings contain important structural information comparable with residual dipolar couplings. However, the measurement of sign and size of especially small residual quadrupolar couplings is difficult. Here, we present an extension of the E.COSY principle to spin systems consisting of a Spin 1 coupled to a spin ½ nucleus, which allows the determination of the sign of the quadrupolar coupling of the Spin 1 nucleus relative to the heteronuclear coupling between the spins. The so-called Q.E.COSY approach is demonstrated with its sign-sensitivity using variable angle NMR, stretched gels and liquid crystalline phases applied to various CD and CD3 groups. Especially the sign-sensitive measurement of residual quadrupolar couplings that remain unresolved in conventional deuterium 1D spectra is shown.

¹⁹F-Site-Specific-Labeled Nucleotides for Nucleic Acid Structural Analysis by NMR

Naturally occurring RNA lacks fluorine-19 ((19)F), thus, their specifically fluorinated counterparts are particularly well suited to noninvasively monitoring the dynamic conformational properties and ligand-binding interactions of the RNA. For nuclear magnetic resonance (NMR) spectroscopy, (19)F-NMR of fluorine-substituted RNA provides an attractive, site-specific probe for structure determination in solution. Advantages of (19)F include high NMR sensitivity (83% of (1)H), high natural abundance (100%), and the extreme sensitivity of (19)F to the chemical environment leading to a large range of chemical shifts. The preparation of base-substituted 2-fluoropurine and 5-fluoropyrimidine 5'-triphosphates (2F-ATP/5F-CTP/5F-UTP) can be carried out using efficient enzymatic synthesis methods. Both pyrimidine analogs, 5-fluorouridine and 5-fluorocytidine, as well as, 2-fluoroadenosine are readily incorporated into RNA transcribed in vitro using T7 RNA polymerase.

Simultaneous determination of the magnitude and the sign of multiple heteronuclear coupling constants in 19F or 31P-containing compounds

The presence of a highly abundant passive nucleus (Z = 19F or 31P) allows the simultaneous determination of the magnitude and the sign of up to three different heteronuclear coupling constants from each individual cross-peak observed in a 2D 1H-X selHSQMBC spectrum. Whereas J(HZ) and J(XZ) coupling constants are measured from E.COSY multiplet patterns, J(XH) is independently extracted from the complementary IPAP pattern generated along the detected F2 dimension. The incorporation of an extended TOCSY transfer allows the extraction of a complete set of all these heteronuclear coupling constants and their signs for an entire 1H subspin system. 1H-X/1H-Y time-shared versions are also proposed for the simultaneous measurement of five different couplings (J(XH), J(YH), J(XZ), J(YZ), and J(ZH)) for multiple signals in a single NMR experiment.

Homonuclear BIRD-decoupled spectra for measuring one-bond couplings with highest resolution: CLIP/CLAP-RESET and constant-time-CLIP/CLAP-RESET

Heteronuclear one-bond couplings are of interest for various aspects of structural analysis of small organic molecules, including for example the distinction of axial and equatorial protons or the use of RDCs as angular constraints. Such couplings are most easily measured from pure doublets in HSQC-type spectra. Recently, the fully decoupled RESET HSQC experiment was reported and several other so-called pure-shift methods followed that allow for the removal of splittings due to homonuclear scalar interactions in one and two-dimensional NMR. In this work we present broadband homonuclear decoupled CLIP/CLAP-RESET experiments based on an isotope-selective BIRD filter element using a recently reported improved version of Zangger-Sterk data chunking. The concatenated FIDs result in multiplets in which most homonuclear splittings are removed while the heteronuclear one-bond couplings are retained. Couplings can be extracted in an IPAP fashion without scaling of subspectra by the use of optimized coherence transfer elements like the COB-INEPT. The method leads to complete homonuclear decoupling for CH groups and CH3 groups in isotropic samples, but leaves residual splittings with antiphase contributions for e.g. CH2 groups due to (2)JHH coupling evolution that is not affected by the BIRD element. For this case we present a constant-time version of the proposed BIRD decoupling scheme with full homonuclear decoupling. In addition, the effects of strong coupling are discussed. Strong coupling artifacts cannot be circumvented, but the proposed experiments allow their distinct recognition.

Pure shift NMR approach for fast and accurate extraction of heteronuclear couplings

An NMR experiment for the direct determination of heteronuclear couplings from the severely overlapped ¹H NMR spectrum.

Efficient and fast sign-sensitive determination of heteronuclear coupling constants

Two complementary 1D NMR approaches for the fast and easy determination of the magnitude and the sign of heteronuclear J(XH) coupling constants are proposed: The Up&Down technique relies on the direct analysis of anti-phase multiplets whereas the Left&Right technique is based on the relative displacement between separate IPAP components.

GET-SERF, a new gradient encoded SERF experiment for the trivial edition of 1H-19F couplings

A new spatially encoded heteronuclear (1)H-(19)F selective refocusing NMR experiment (GET-SERF) is proposed. This sequence allows editing in one single 2D experiment all couplings between a selected fluorine site and all the proton nuclei of the molecule. Its efficiency is illustrated in the case of diflunisal, a difluorinated anti-inflammatory drug, in isotropic and anisotropic media.

Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA

Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.

Spin state selective Hadamard encoding during transfer periods using multiple selective CW-HCP

Hadamard spectroscopy today represents an alternative to conventional Fourier transform spectroscopy. The selective inversion of several narrow frequency bands is typically achieved by taylored inversion pulses in place of t1-evolution periods. However, band-selective inversion can also be achieved during coherence transfer steps, thereby shortening the period during which the magnetization is in the transverse plane. Using CW heteronuclear cross polarization (CW-HCP) as an example for highly selective coherence transfer, the implementation of Hadamard encoding within a transfer step is presented. Transfer characteristics, the preparation of multiple frequency selective CW-HCP and the possibility of acquiring spin state selective spectra are discussed in detail. The theoretical results are verified on two examples involving a cyclic pentapeptide and ubiquitin.

P.E.HSQC: a simple experiment for simultaneous and sign-sensitive measurement of (1JCH+DCH) and (2JHH+DHH) couplings

The angular information content of residual dipolar couplings between nuclei of fixed distance makes the accurate and sign-sensitive measurement of (1JCH+DCH) and (2JHH+DHH) couplings highly desirable. Experiments published so far are typically highly specialized for the effective measurement of a subset of couplings. The P.E.HSQC presented here, is an E.COSY based experiment which allows the simultaneous measurement of all heteronuclear and homonuclear couplings within CH, CH2, and CH3 groups in a single spectrum with the necessary precision and sign information. The simplicity of the approach and the absence of artefacts like phase distortions due to antiphase evolution make it ideally suited for coupling determination of organic molecules at natural abundance.

J-Spectroscopy in the presence of residual dipolar couplings: determination of one-bond coupling constants and scalable resolution

The access to weak alignment media has fuelled the development of methods for efficiently and accurately measuring residual dipolar couplings (RDCs) in NMR-spectroscopy. Among the wealth of approaches for determining one-bond scalar and RDC constants only J-modulated and J-evolved techniques retain maximum resolution in the presence of differential relaxation. In this article, a number of J-evolved experiments are examined with respect to the achievable minimum linewidth in the J-dimension, using the peptide PA4 and the 80-amino-acid-protein Saposin C as model systems. With the JE-N-BIRDd,X-HSQC experiment, the average full-width at half height could be reduced to approximately 5 Hz for the protein, which allows the additional resolution of otherwise unresolved peaks by the active (J+D)-coupling. Since RDCs generally can be scaled by the choice of alignment medium and alignment strength, the technique introduced here provides an effective resort in cases when chemical shift differences alone are insufficient for discriminating signals. In favorable cases even secondary structure elements can be distinguished.

Measurement of coupling constants in symmetrical spin systems using a full multiple-step cross-polarization-driven NMR pulse scheme

New NMR pulse schemes completely driven under homonuclear and heteronuclear cross-polarization conditions are proposed for the study and the measurement of coupling constants in symmetrical molecules in solution. The appropriate superimposition of independent magnetization components can afford several spin-selective multiplet patterns that are suitable for the determination of the magnitude and the sign of proton-proton and proton-carbon coupling constants with optimum sensitivity levels. A detailed product operator formalism analysis for the proposed doubly selective 1D and nonselective 2D HCP-TOCSY versions is provided and experimental verification for the configurational analysis of symmetric olefinic systems having chemical equivalence is demonstrated.

Spin state selectivity and heteronuclear Hartmann-Hahn transfer

Spin state selectivity can be obtained if inphase and antiphase magnetization can be transformed into each other. Heteronuclear Hartmann-Hahn transfer is usually used for the transfer of inphase magnetization. For a two spin system, however, a building block can be constructed that transfers inphase into antiphase magnetization and vice versa. The article gives a detailed description of the building block as well as experiments with elements similar to spin state selective coherence transfer (S(3)CT) and spin state selective excitation (S(3)E). The possibility of 'sensitivity enhancement' is pointed out and an application in the double selective measurement of coupling constants using a combination of CW-cross-polarization and the S(3)CT-type approach is demonstrated.

Homonuclear Hartmann-Hahn transfer with reduced relaxation losses by use of the MOCCA-XY16 multiple pulse sequence

Homonuclear Hartmann-Hahn transfer is one of the most important building blocks in modern high-resolution NMR. It constitutes a very efficient transfer element for the assignment of proteins, nucleic acids, and oligosaccharides. Nevertheless, in macromolecules exceeding approximately 10 kDa TOCSY-experiments can show decreasing sensitivity due to fast transverse relaxation processes that are active during the mixing periods. In this article we propose the MOCCA-XY16 multiple pulse sequence, originally developed for efficient TOCSY transfer through residual dipolar couplings, as a homonuclear Hartmann-Hahn sequence with improved relaxation properties. A theoretical analysis of the coherence transfer via scalar couplings and its relaxation behavior as well as experimental transfer curves for MOCCA-XY16 relative to the well-characterized DIPSI-2 multiple pulse sequence are given.

JE-TROSY: combined J- and TROSY-spectroscopy for the measurement of one-bond couplings in macromolecules

With the application of RDCs in high-resolution NMR studies of macromolecules, there has been an interest in the development of accurate, sensitive methods for measuring 15N-1H and 13C-1H one-bond coupling constants. Most methods for determining these couplings are based on the measurement of the displacement between cross-peak components in J-coupled spectra. However, for large macromolecules and macromolecular complexes, these methods are often unreliable since differential relaxation can significantly broaden one of the multiplet components (i.e., the anti-TROSY component) and thereby make accurate determination of its position difficult. To overcome this problem, a J-evolved transverse relaxation optimized (JE-TROSY) method is presented for the determination of one-bond couplings that involves J-evolution of the sharpest cross-peak multiplet component selected in a TROSY experiment. Couplings are measured from the displacement of the TROSY component in the additional J-evolution dimension relative to a zero frequency origin. The JE-TROSY method is demonstrated on uniformly labeled 15N, 13C-labeled RNA and peptide samples, as well as with an RNA-protein complex, in which the protein is uniformly 15N, 13C-labeled. In all cases, resolved, sensitive spectra are obtained from which heteronuclear one-bond J-couplings could be accurately and easily measured.