Dynamics of ligand binding from 13C NMR relaxation dispersion at natural abundance

We show that Carr-Purcell-Meiboom-Gill (CPMG) 13Calpha NMR relaxation dispersion measurements are a viable means for profiling mus-ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Calpha nuclei that experience mus-ms modulation of their chemical shifts due to binding. 13Calpha shifts are dominated by local torsion angles , psi, chi1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The mus-ms dynamic information gained helps establish flexibility-activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.     

(13)C natural abundance in the British diet: implications for (13)C breath tests

Surprisingly little information is available on the natural abundance of the minor isotope of carbon, (13)C, in common foodstuffs in the British diet. This study therefore aimed to examine the (13)C natural abundance of foodstuffs from a small cross-section of the British diet. The isotopic abundance, delta per mil, was calculated by measurement of the isotope ratio (13)C:(12)C by isotope ratio mass spectrometry. Results from this study were also compared with results from a North American study to highlight the difference in isotopic abundance between Northern European foodstuffs and North American foodstuffs. Such data should prove useful to those planning tracer studies using the stable isotope (13)C where enrichment is measured against a large and variable natural abundance in the body. Minimisation of this basal variation, for example in breath CO(2), can be achieved by controlling dietary intake of foods naturally abundant in (13)C.     

High-resolution magic-angle spinning (13)C spectroscopy of brain tissue at natural abundance

High-resolution magic-angle spinning (MAS) (1)H and (13)C magnetic resonance spectroscopy (MRS) has recently been applied to study the metabolism in intact biological tissue samples. Because of the low natural abundance and the low gyromagnetic ratio of the (13)C nuclei, signal enhancement techniques such as cross-polarization (CP) and distortionless enhancement by polarization transfer (DEPT) are often employed in MAS (13)C MRS to improve the detection sensitivity. In this study, several sensitivity enhancement techniques commonly used in liquid- and solid-state NMR, including CP, DEPT and nuclear Overhauser enhancement (NOE), were combined with MAS to acquire high-resolution (13)C spectra on intact rat brain tissue at natural abundance, and were compared for their performances. The results showed that different signal enhancement techniques are sensitive to different classes of molecules/metabolites, depending on their molecular weights and mobility. DEPT was found to enhance the signals of low-molecular weight metabolites exclusively, while the signals of lipids, which often are associated with membranes and have relatively lower mobility, were highly sensitive to CP enhancement.     

1H Indirect detected 13C Low-Abundance Single-transition correlation Spectroscopy (HICLASS)-13C homonuclear correlation at natural abundance

A novel proton-detected (13)C homonuclear correlation experiment is reported at natural abundance, viz., (1)H Indirect detected (13)C Low-Abundance Single-transition correlation Spectroscopy (HICLASS). HICLASS is based on the evolution of (13)C single-quantum single transitions, followed by their mixing, and (1)H detection subsequent to heteronuclear transfer. Reduced relaxation losses during the evolution time and partial selectivity in the (1)H multiplet structure result in enhanced sensitivity of HICLASS. The superior performance of HICLASS is demonstrated for (1)H-detected (13)C correlation work.     

Measurement of long-range 29Si,13C spin-spin coupling at natural abundance

Schemes for sensitive measurements of spin-spin coupling constants between rare nuclei with low magnetogyric ratios are considered and two combinations of INEPT with gradient versions of (X,Y)HMQC and (X,Y)COSY are suggested as particularly suitable for 29Si,13C couplings. It is demonstrated that the (H,Si)INEPT-(Si,C,Si)gHMQC combination (with 29Si detection) produces excellent results even though it is theoretically inferior to the (H,Si)INEPT-(Si,C)gCOSY combination (with 13C detection).     

H(C)P and H(P)C triple-resonance experiments at natural abundance employing long-range couplings

Modified two-dimensional (2D) triple-resonance H(C)P and H(P)C experiments based on INEPT/HMQC and double-INEPT schemes are applied to the study of organophosphorus compounds at natural abundances. The implementation of effective (1)H--(13)C gradient selection, additional purging pulsed field gradients, spinlock pulses, and improved phase cycling is demonstrated to allow weak correlation signals based on long-range couplings to be readily observed. Through the combination of two heteronuclear long-range coupling constants, (n)J(CH) and (n)J(PC) in H(C)P experiments or (n)J(PH) and (n)J(PC) in H(P)C experiments, protons can be correlated to a second heteronucleus through 4-7 chemical bonds. These experiments thus overcome the inherit limitations of classical (1)H-X HMBC experiments, which require a nonzero value of the heteronuclear coupling constant (n)J(XH). Ultra-broadband inversion composite pulses are successfully employed in the H(P)C INEPT/HMQC and H(P)C double-INEPT pulse sequences to increase the utility of the experiments and the quality of obtained spectra. This work extends and completes a set of 2D phase-sensitive triple-resonance experiments applicable at natural abundances, and also offers insight into the methodology of triple-resonance experiments and the application of pulsed field gradients. A one-dimensional triple-resonance experiment employing carbon detection is suggested for accurate determination of small (n)J(PC).     

Determination of (13)C natural abundance of amino acid enantiomers in soil: methodological considerations and first results

The application of a combined gas chromatography-combustion/isotope ratio mass spectrometry (GC-C/IRMS) method for stable carbon isotope analysis of amino acid enantiomers in soil samples is presented. Triplicate delta(13)C analyses of pentafluoropropionyl (PFP) isopropyl ester derivatives of 27 amino acid enantiomers revealed that discrimination of (13)C during derivatization is different for different amino acid enantiomers and different amounts. Injection of increasing amounts of amino acid derivatives showed that the isotopic signal varied up to 10 per thousand for D-aspartic acid. Correction for the delta(13)C signal of underivatized amino acid enantiomers is possible for all investigated amino acid enantiomers using logarithmic functions. Operating the GC-C/IRMS system in the split-mode (split ratio 1:12) is possible but resulted in a higher isotopic discrimination. The detection limit approached 3 ng for some amino acid enantiomers in the splitless mode, while the lower limit of routine determination exceeded 10 ng injection amount. The upper limit at which accurate stable isotope values were obtained was 200 ng injection amount. Compound-specific delta(13)C analysis of alanine, valine, aspartic and glutamic acid showed that the D-forms were enriched in (13)C relative to the L-forms, suggesting that microbes significantly contributed to the formation of the D-enantiomers in soil.     

Carbon-13 kinetic isotope effects in the decarbonylations of lactic acid containing13C at the natural abundance level

The¹³C kinetic isotope fractionation in the decarbonylation of lactic acid of natural isotopic composition by sulfuric acid has been studied in the temperature range of 20–80°C. The¹³C₍₁₎ isotope separation in the decarbonylation of lactic acid by concentrated sulfuric acid depends strongly on the temperature above 40°C. Below this temperature the¹³C isotope effect in the decarbonylation of lactic acid by concentrated sulfuric acid is normal similarly as has been found inthe decarbonylation of lactic [1-¹⁴C] acid. The experimental values of k(¹²C)/k(¹³C) ratios of isotopic rate constants for¹²C and¹³C are close to, but slightly higher than theoretical¹³C-kinetic isotope effects calculated (neglecting tunneling) under the asumption that the C₍₁₎-OH bond is broken in the rate-controlling step of the dehydration reaction. Dilution of concentrated sulfuric acid with water up to 1.4 molar (H₂O)/(H₂SO₄) ratio caused the increase of the¹³C isotope fractionation from 1.0273 found in concentrated sulfuric acid at 80.5°C to 1.0536±0.0008 (at 80.6°C). A discussion of the abnormally high temperature dependence of¹⁴C and¹³C isotope fractionation in this reaction and the discussion of the problem of relative¹⁴C/¹³C kinetic isotope effects is given.     

Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance

Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons.     

1H, 13C and 77Se NMR study of tetraselenafulvalene derivatives supported by novel H(Se)C and H(C)Se triple-resonance experiments at natural abundance

A series of substituted tetraselenafulvalenes (TSeFs) was studied in solution using 1H, 13C and 77Se NMR spectroscopy. Chemical shifts and heteronuclear coupling constant values were determined and assigned. Novel two-dimensional H(Se)C and H(C)Se triple-resonance correlation experiments were applied at natural abundance in order to accomplish 13C and 77Se signal assignments. Using this approach, all the signals were unambiguously assigned and atom connectivity was established in the studied TSeF derivatives. These experiments, allowing signal assignments of quaternary carbons, may find wide application in the study of substituted TSeF and other organoselenium compounds. To the best of our knowledge, triple-resonance experiments with proton detection have been applied to organoselenium compounds for the first time.     

Polymeric adducts of rhodium(II) tetraacetate with aliphatic diamines: natural abundance 13C and 15N CPMAS NMR investigations

Complexation properties of dimeric rhodium(II) tetracarboxylates have been utilised in chemistry, spectroscopy and organic synthesis. Particularly, the combination of these rhodium salts with multifunctional ligands results in the formation of coordination polymers, and these are of interest because of their gas‐occlusion properties. In the present work, the polymeric adducts of rhodium(II) tetraacetate with flexible ligands exhibiting conformational variety, ethane‐1,2‐diamine, propane‐1,3‐diamine and their N,N′‐dimethyl‐ and N,N,N′,N′‐tetramethyl derivatives, have been investigated by means of elemental analysis, ¹³C CPMAS NMR, ¹⁵N CPMAS NMR and density functional theory modelling. Elemental analysis and NMR spectra indicated the axial coordination mode and regular structures of (1 : 1)_n oligomeric chains in the case of adducts of ethane‐1,2‐diamine, N,N′‐dimethylethane‐1,2‐diamine N,N,N′,N′‐tetramethylethane‐1,2‐diamine and N,N,N′,N′‐tetramethylpropane‐1,3‐diamine. Propane‐1,3‐diamine and N,N′‐dimethylpropane‐1,3‐diamine tended to form heterogeneous materials, composed of oligomeric (1 : 1)_n chains and the additive of dirhodium units containing equatorially bonded ligands. Experimental findings have been supported by density functional theory modelling of some hypothetical structures and gauge‐invariant atomic orbital calculations of NMR chemical shifts. Copyright © 2013 John Wiley & Sons, Ltd.     

Through-bond 13C-13C correlation at the natural abundance level: refining dynamic regions in the crystal structure of vitamin-D3 with solid-state NMR

Recently, we presented a novel nuclear magnetic resonance experiment for establishing through-bond connectivity in disordered solids using scalar coupling-driven correlation. This method, a variant of the popular double-quantum-filtered correlation spectroscopy experiment in liquids, is robust under fast magic-angle-spinning conditions and in the presence of dynamics. Here, we show that this new experiment, the UC2QF COSY, can be extended to 13C natural abundance correlation in moderately sized molecules, allowing the assignment of the 54 peaks of the solid-state NMR spectrum of microcrystalline vitamin-D3. In this case, comparison between the assigned peaks and ab initio calculations of the chemical shifts based on the crystal coordinates permits a refinement of the average structure in dynamic regions reported as disordered in the crystal structure.     

Simple organofluorine compounds giving field-dependent 13C and 19F NMR spectra with complex patterns: higher order effects and cross-correlated relaxation

The CF(3) signals in the (13)C{(1)H} spectrum of 1,1,1,3,3,3-hexafluoroisopropyl alcohol and the (CF(3))(2) CH signals in the corresponding triflate exhibit much greater complexity than might first be expected. The same holds for the (13)C satellites in the (19)F spectra. Complex patterns appear because of higher order effects resulting from the combination of a relatively large four-bond (19)F-(19)F J coupling in the ((13)CF(3))(12)CH((12)CF(3))-containing isotopomer and a typical large one-bond (13)C/(12)C isotope effect on the (19)F chemical shift. This complexity cannot be eliminated at very high magnetic field strengths. The triflate (CF(3))(2)CH-O-SO(2)CF(3) presents still additional complexity because of the presence of two different types of CF(3) groups exhibiting (6)J(FF) in any of the isotopomers and the chemical shift differences in hertz between the various (19)F signals in the two different (13)CF(3)-containing isotopomers. In addition, the presence of a small (5)J(CF) in the ((13)CF(3))((12)CF(3))(12)CH-O-SO(2) (12)CF(3) isotopomer is revealed only through simulations. The hexafluoroisopropyl CF(3) groups in the alcohol and triflate and the SO(2)CF(3) group in the triflate apparently provide the first examples of cross-correlated relaxation in (13)CF(3) groups. An analysis of the spectra in the context of previously reported work highlights the novel aspects of our findings. In particular, for each part of the complex hexafluoroisopropyl CF(3) quartet, peak height and linewidth variations resulting from cross-correlated relaxation are observed. These variations within a group of (13)C signals reflect different spin-lattice and spin-spin relaxation rates for the transitions within that group arising from higher order coupling effects.     

Identifying guanosine self assembly at natural isotopic abundance by high-resolution 1H and 13C solid-state NMR spectroscopy

By means of the (1)H chemical shifts and the proton-proton proximities as identified in (1)H double-quantum (DQ) combined rotation and multiple-pulse spectroscopy (CRAMPS) solid-state NMR correlation spectra, ribbon-like and quartet-like self-assembly can be identified for guanosine derivatives without isotopic labeling for which it was not possible to obtain single crystals suitable for diffraction. Specifically, characteristic spectral fingerprints are observed for dG(C10)(2) and dG(C3)(2) derivatives, for which quartet-like and ribbon-like self-assembly has been unambiguously identified by (15)N refocused INADEQUATE spectra in a previous study of (15)N-labeled derivatives (Pham, T. N.; et al. J. Am. Chem. Soc.2005, 127, 16018). The NH (1)H chemical shift is observed to be higher (13-15 ppm) for ribbon-like self-assembly as compared to 10-11 ppm for a quartet-like arrangement, corresponding to a change from NH···N to NH···O intermolecular hydrogen bonding. The order of the two NH(2)(1)H chemical shifts is also inverted, with the NH(2) proton closest in space to the NH proton having a higher or lower (1)H chemical shift than that of the other NH(2) proton for ribbon-like as opposed to quartet-like self-assembly. For the dG(C3)(2) derivative for which a single-crystal diffraction structure is available, the distinct resonances and DQ peaks are assigned by means of gauge-including projector-augmented wave (GIPAW) chemical shift calculations. In addition, (14)N-(1)H correlation spectra obtained at 850 MHz under fast (60 kHz) magic-angle spinning (MAS) confirm the assignment of the NH and NH(2) chemical shifts for the dG(C3)(2) derivative and allow longer range through-space N···H proximities to be identified, notably to the N7 nitrogens on the opposite hydrogen-bonding face.     

Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13C-13C dipolar couplings

Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed ¹H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using ¹³C-¹³C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although ¹³C-¹³C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions.     

Improved pulse sequences for measurement of small long‐range couplings between heteronuclei (29Si?13C) at natural abundance

The gradient pulse sequences for measurement of small long‐range couplings between heteronuclei (²⁹Si? ¹³C) in natural abundance reported to date (INEPT‐(Si,C)gCOSY and INEPT‐(Si,C,Si)HMQC) suffer from significant signal loss when these nuclei (²⁹Si, ¹³C) are coupled through one‐bond couplings to protons. This negative effect can be completely eliminated by using non‐gradient versions (INEPT‐(Si,C)COSY) or by switching proton decoupling off during gradient pulses (modified INEPT‐(Si,C,Si)gHMQC pulse sequence). The beneficial effects of these two approaches on the quality of the spectra are demonstrated here. Copyright © 2009 John Wiley & Sons, Ltd.     

Asymmetric NMR spectra of weakly coupled nuclei: A common characteristic in the 13C NMR spectra of [U-13C]-labeled molecules and in natural abundance protoncoupled 13C spectra

Typically encountered proton-decoupled spectra of [U-¹³C]-labeled molecules or proton-coupled spectra of natural abundance or singly labeled molecules contain many nuclei which satisfy the weak coupling approximation. The spectra of such nuclei are frequently highly asymmetric and often appear to exhibit the skewed intensity distribution characteristic of strongly coupled spins. Analysis of typical cases indicates that such effects arise in the presence of at least one moderately strong coupling interaction in the spin system (Jδν ～ 1/3), and the apparent intensity asymmetry reflects small differences in the spacing of unresolved components of the observed resonance. This effect is analogous to the case of ‘virtual coupling’ in which weakly coupled spins cannot be analyzed as first order spectra; however; the ABX spin system which generally serves as a model for such systems does not predict the existence of spectral asymmetry for the X resonances. Prediction of this asymmetry requires a spin system of at least four spins with at least ABMX complexity, and can be treated generally using the effective Hamiltonian approach of Poeple and Schaefer.     

3D Heteronuclear long‐range 1H–13C scalar correlation at natural abundance: application to oligosaccharide analysis

A 3D ¹H–¹³C–¹H refocused INEPT transfer experiment is proposed in which the initial coherence transfer of ¹H longitudinal to ¹³C transverse magnetization is tuned to the long‐range ¹H, ¹³C couplings while the reverse INEPT component transfers the magnetization to the directly bonded ¹H. Integration of a constant time ¹H evolution period into the long‐range coherence transfer interval provides absorption mode signals for each dimension. A ¹³C purge component at the beginning of the sequence selects for ¹²C‐bound ¹H magnetization that is then transferred to a ¹³C‐bound hydrogen, thus strongly suppressing the diagonal signals. This experiment is expected to be of particular value for situations in which resonance overlap in the ¹³C dimension renders 2D long‐range heteronuclear correlation data ambiguous. In combination with a diagonal‐suppressed 3D ¹H–¹³C–¹H TOCSY‐HSQC experiment, complete assignment of the ring resonances of the Lewis‐b hexasaccharide was obtained on a 4.2 mM sample using a conventional 500 MHz probe (0.1% ethylbenzene signal‐to‐noise ratio of 600), suggesting its applicability to sub‐millimolar samples using cryoprobe technology. Copyright © 2002 John Wiley & Sons, Ltd.