Total Line Shape Analysis Research Articles

Bayesian analysis of 1D [formula omitted]H-NMR spectra

Extracting spin system parameters from 1D high resolution 1H-NMR spectra can be an intricate task requiring sophisticate methods. With a few exceptions methods to perform such a total line shape analysis commonly rely on local optimization techniques which for increasing complexity of the underlying spin system tend to reveal local solutions. In this work we propose a full Bayesian modeling approach based on a quantum mechanical model of the spin system. The Bayesian formalism provides a global optimization strategy which allows to efficiently include prior knowledge about the spin system or to incorporate additional constraints concerning the parameters of interest. The proposed algorithm has been tested on synthetic and real 1D 1H-NMR data for various spin systems with increasing complexity. The results show that the Bayesian algorithm provides accurate estimates even for complex spectra with many overlapping regions, and that it can cope with symmetry induced local minima. By providing an unbiased estimate of the model evidence the proposed algorithm furthermore offers a way to discriminate between different spin system candidates.

Complete 1H and 13C NMR chemical shift assignments of mono-to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER

Carbohydrate structure can be elucidated or confirmed by using NMR spectroscopy as the prime technique. Prediction of 1H and 13C NMR chemical shifts by computational approaches makes this assignment process more efficient and the program CASPER can perform this task rapidly. It does so by relying on chemical shift data of mono-, di-, and trisaccharides. In order to improve accuracy and quality of these predictions we have assigned 1H and 13C NMR chemical shifts of 30 monosaccharides, 17 disaccharides, 10 trisaccharides and one tetrasaccharide; in total 58 compounds. Due to different rotamers, ring forms, α- and β-anomeric forms and pD conditions this resulted in 74 1H and 13C NMR chemical shift data sets, all of which were refined using total line-shape analysis for the 1H resonances in order to obtain accurate chemical shifts. Subsequent NMR chemical shift predictions for three sialic acid-containing oligosaccharides, viz., GD1a, a disialyl-LNnT hexasaccharide and a polysialic acid-lactose decasaccharide, and NMR-based structural elucidations of two O-antigen polysaccharides from E. coli O174 were performed by the CASPER program (http://www.casper.organ.su.se/casper/) resulting in very good to excellent agreement between experimental and predicted data thereby demonstrating its utility for carbohydrate compounds that have been chemically or enzymatically synthesized, structurally modified or isolated from nature.

Cis Versus trans-Azobenzene: Precise Determination of NMR Parameters and Analysis of Long-Lived States of 15N Spin Pairs

We provide a detailed evaluation of nuclear magnetic resonance (NMR) parameters of the cis- and trans-isomers of azobenzene (AB). For determining the NMR parameters, such as proton–proton and proton–nitrogen J-couplings and chemical shifts, we compared NMR spectra of three different isotopomers of AB: the doubly 15N labeled azobenzene, 15N,15N′-AB, and two partially deuterated AB isotopomers with a single 15N atom. For the total lineshape analysis of NMR spectra, we used the recently developed ANATOLIA software package. The determined NMR parameters allowed us to optimize experiments for investigating singlet long-lived spin states (LLSs) of 15N spin pairs and to measure LLS lifetimes in cis-AB and trans-AB. Magnetization-to-singlet-to-magnetization conversion has been performed using the SLIC and APSOC techniques, providing a degree of conversion up to 17 and 24% of the initial magnetization, respectively. Our approach is useful for optimizing the performance of experiments with singlet LLSs; such LLSs can be exploited for preserving spin hyperpolarization, for probing slow molecular dynamics, slow chemical processes and also slow transport processes.

Gas-phase nuclear magnetic resonance study of internal isomerization in perfluoro-2-azapropene: Comparison of experimental and computed kinetic parameters

Rate constants obtained from total line-shape analysis of five temperature-dependent gas-phase NMR spectra of perfluoroazapropene yielded the kinetic barrier to internal isomerization: G‡298 = 66.9 (0.4) kJ mol−1. Five temperature-dependent liquid spectra (5 mol% in CDCl3) yielded G‡298 = 67.4 (0.8) kJ mol−1. Ab initio calculations performed using the compound methods Complete Basis Set (CBS-4M, QB3, APNO), Gaussian (G1-4), and Weizmann (W1U, WBD) gave results consistent with a transition state corresponding to nitrogen inversion. The values that best matched the experimental G‡298 value for each compound method were 63.9 kJ mol−1 (CBS-APNO), 66.1 kJ mol−1 (G2), and 65.6 kJ mol−1 (W1BD).

Total lineshape analysis of high-resolution NMR spectra powered by simulated annealing

The novel algorithm for a total lineshape analysis of high-resolution NMR spectra has been developed. A global optimization by simulated annealing has been applied that has allowed to overcome the main trouble of common approaches which had frequently returned solutions for local minima rather than for global ones. The algorithm has been verified for the four-spin test systems ABCD, and has been successfully used for analysis of experimental NMR spectra of proline. The approach has allowed to avoid a sophisticated manual setup of initial parameters and to conduct the analysis of complicated high-resolution NMR spectra nearly automatically.

Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligosaccharides using the computer program CASPER

1H and 13C NMR chemical shift data are used by the computer program CASPER to predict chemical shifts of oligo- and polysaccharides. Three types of data are used, namely, those from monosaccharides, disaccharides, and trisaccharides. To improve the accuracy of these predictions we have assigned the 1H and 13C NMR chemical shifts of eleven monosaccharides, eleven disaccharides, twenty trisaccharides, and one tetrasaccharide; in total 43 compounds. Five of the oligosaccharides gave two distinct sets of NMR resonances due to the α- and β-anomeric forms resulting in 48 1H and 13C NMR chemical shift data sets. In addition, the pyranose ring forms of Neu5Ac were assigned at two temperatures, due to chemical shift displacements as a function of temperature. The 1H NMR chemical shifts were refined using total line-shape analysis with the PERCH NMR software. 1H and 13C NMR chemical shift predictions were subsequently carried out by the CASPER program (http://www.casper.organ.su.se/casper/) for three branched oligosaccharides having different functional groups at their reducing ends, namely, a mannose-containing pentasaccharide, and two fucose-containing heptasaccharides having N-acetyllactosamine residues in the backbone of their structures. Good to excellent agreement was observed between predicted and experimental 1H and 13C NMR chemical shifts showing the utility of the method for structural determination or confirmation of synthesized oligosaccharides.

Studies on the conformational flexibility of α-l-rhamnose-containing oligosaccharides using 13C-site-specific labeling, NMR spectroscopy and molecular simulations: implications for the three-dimensional structure of bacterial rhamnan polysaccharides

Bacterial polysaccharides are comprised of a variety of monosaccharides, L-rhamnose (6-deoxy-L-mannose) being one of them. This sugar is often part of α-(1 → 2)- and/or α-(1 → 3)-linkages and we have therefore studied the disaccharide α-L-Rhap-(1 → 2)-α-L-Rhap-OMe to obtain information on conformational preferences at this glycosidic linkage. The target disaccharide was synthesized with (13)C site-specific labeling at C1' and at C2', i.e., in the terminal group. 2D (1)H,(13)C-HSQC-HECADE and (1)H,(13)C-J-HMBC NMR experiments, 1D (13)C and (1)H NMR spectra together with total line-shape analysis were used to extract conformationally dependent hetero- and homonuclear spin-spin coupling constants. This resulted in the determination of (2)J(C2',H1'), (3)J(C1',C1), (3)J(C1',C3), (3)J(C2',C2), (2)J(C1',C2), (1)J(C1',C2'), and (1)J(C1',H1'). These data together with previously determined J(CH) and (1)H,(1)H NOEs result in fourteen conformationally dependent NMR parameters that are available for analysis of glycosidic linkage flexibility and conformational preferences. A 100 ns molecular dynamics (MD) simulation of the disaccharide with explicit water molecules as solvent showed a major conformational state at φ(H)≈ 40° and ψ(H)≈-35°, consistent with experimental NMR data. In addition, MD simulations were carried out also for α-L-Rhap-(1 → 3)-α-L-Rhap-OMe and a rhamnan hexasaccharide. The gathered information on the oligosaccharides was used to address conformational preferences for a larger structure, a 2- and 3-linked nonasaccharide, with implications for the 3D structure of rhamnan polysaccharides, which should be regarded as flexible polymers.

Complete 1H and 13C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program casper

The computer program casper uses 1H and 13C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the 1H and 13C, as well as 31P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and β-anomeric forms. In total 35 1H and 13C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D 1H, 13C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t 1 incremented 1H, 13C-HSQC experiment and a 1D 1H, 1H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3 Hz apart. The 1H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program ( http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental 1H and 13C NMR chemical shifts.

NMR-based metabolomics of mammalian cell and tissue cultures

NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized to quantify 30 metabolites such as amino acids, Krebs cycle intermediates, activated sugars, cofactors, and others in both media and cell extracts. The impact of bioreactor scale and addition of anti-apoptotic agents to the media on the extracellular and intracellular metabolome indicated changes in metabolic pathways of energy utilization. These results shed light into culture parameters that can be manipulated to optimize growth and protein production. Second, metabolomic analysis was performed on the superfusion media in a common model used for drug metabolism and toxicology studies, in vitro liver slices. In this study, it is demonstrated that two of the 48 standard media components, choline and histidine are depleted at a faster rate than many other nutrients. Augmenting the starting media with extra choline and histidine improves the long-term liver slice viability as measured by higher tissues levels of lactate dehydrogenase (LDH), glutathione and ATP, as well as lower LDH levels in the media at time points out to 94h after initiation of incubation. In both models, media components and cellular metabolites are measured over time and correlated with currently accepted endpoint measures.

NMR analysis of conformationally dependent nJC, H and nJC, C in the trisaccharide α‐L‐Rhap‐(1 → 2)[α‐L‐Rhap‐(1 → 3)]‐α‐L‐Rhap‐OMe and a site‐specifically labeled isotopologue thereof

An array of NMR spectroscopy experiments have been carried out to obtain conformationally dependent (1)H,(13)C- and (13)C,(13)C-spin-spin coupling constants in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe. The trisaccharide was synthesized with (13)C site-specific labeling at C2' and C2″, i.e. in the rhamnosyl groups in order to alleviate (1)H spectral overlap. This facilitated the measurement of a key trans-glycosidic proton-proton cross-relaxation rate using 1D (1)H,(1)H-T-ROESY experiments as well as a (3)J(C, H) coupling employing 1D (1)H,(13)C-long-range experiments, devoid of potential interference from additional J coupling. By means of both the natural abundance compound and the (13)C-labeled sample 2D (1)H,(13)C-J-HMBC and (1)H,(13)C-HSQC-HECADE NMR experiments, total line-shape analysis of (1)H NMR spectra and 1D (13)C NMR experiments were employed to extract (3)J(C, H) , (2)J(C, H), (3)J(C, C), and (1)J(C, C) coupling constants. The (13)C site-specific labeling facilitates straightforward determination of (n)J(C, C) as the splitting of the (13)C natural abundance resonances. This study resulted in eight conformationally dependent coupling constants for the trisaccharide and illustrates the use of (13)C site-specific labeling as a valuable approach that extends the 1D and 2D NMR methods in current use to attain both hetero- and homonuclear spin-spin coupling constants that subsequently can be utilized for conformational analysis.

Oxygenation of Zinc Dialkyldithiocarbamate Complexes: Isolation, Characterization, and Reactivity of the Stoichiometric Oxygenates

S-oxygenation of dithiocarbamate (DTC) complexes has been implicated in their function as industrial anti-oxidants, as well as in their use as pesticides and most recently in their cumulative toxicity, but little is known of the species generated. Several S-oxygenated derivatives of N,N-disubstituted DTCs have been synthesized, characterized by a variety of methods, and their structure and reactivity examined. Low-temperature reaction of bis(N,N-diethyldithiocarbamato)zinc(II), Zn(deDTC)2 1, with oxygenating reagents (hydrogen peroxide, m-chloroperbenzoic acid, urea hydrogen peroxide) yields mono-oxygenated DTC complexes (N,N-peroxydiethyldithiocarbamato)(N,N-diethyldithiocarbamato)zin(II), Zn(O-deDTC)(deDTC), 2 and bis(N,N-peroxydiethyldithiocarbamato)zinc(II), Zn(O-deDTC)2, 3. The tetraoxygenated derivative bis(N,N-diethylthiocarbamoylsulfinato)zinc(II), Zn(O(2)-deDTC)2, 4, was cleanly obtained by initial reaction of the DTC salts with stoichiometric oxidant prior to complexation with Zn(II). X-ray crystallographic analysis of 2, 3, and 4 show that the peroxydithiocarbamate ligands are S,O-bound. Similar derivatives were obtained from the homoleptic dimethyl and pyrollidine DTC Zn complexes. These oxygenated species display unique 1H and 13C NMR variable-temperature spectra, as the symmetry of DTC ligand is broken upon oxygenation; total line shape analysis (TLSA) was used to compare the energetic parameters for rotation about the C-N bond in several derivatives. Compounds 2, 3, and 4 were deoxygenated by alkyl phosphine, regenerating the parent dithiocarbamate 1. The peroxydithiocarbamate complexes were susceptible to base-catalyzed hydrolytic decomposition, giving ligand-based products indicative of S-oxidation and S-extrusion.

Measurement of Olefin Bond Rotation Barriers in a Series of Vinylaniline Complexes of the Cyclopentadienyliron(II) Dicarbonyl Cation and Their Correlation to Metal−Olefin Bond Asymmetry

1H NMR techniques (selective inversion, total line shape analysis, and T1ρ measurement) have been used to measure the olefin bond rotation rates in a series of compounds of the general formula CpFe(CO)2[η2-CH2C(H)NH(p−C6H4X)], where X = OMe (4), H (6), CN (9), NO2 (10), Cl (11), COOMe (12). Complexes 4, 6, 11, and 12 enabled the use of all three methods to yield data sets that spanned a wide temperature range and allowed for reliable determination of the thermodynamic activation parameters for olefin bond rotation. When these three methods were combined with a bootstrap statistical analysis of the Eyring plots, it was possible to resolve the small differences in the ΔH⧧ values between three of the four complexes. A clear trend is established between increasing electron donation from the aniline ligand and the facilitation of olefin bond rotation. These results are placed in the context of previous work, providing additional experimental evidence that electronic control from the para position of the anilin...

Complexation of Cu(II) with L- and DL-threonine: An ESR study

Complexation of Cu(II) ions with L- and DL-threonine in aqueous solution was studied. Treatment of the ESR spectra of solutions containing Cu(II) and threonine in various ratios and having various pH, involving total line shape analysis, revealed formation of geometric isomers of the complex ions [Cu(thrH−1)2]2− differing in the mutual arrangement of the N and O atoms in the equatorial plane; the complexation and isomerization equilibrium constants were determined.

Compensation of steric demand by cation-pi interactions, cobaltocenium cations as guests in tetraurea calix[4]arene dimers.

The affinities of ferrocene (2) and the cobaltocenium cation (3+), which have roughly the same size and differ in their charge, towards the inner cavity of the dimeric capsule formed by tetraurea calix[4]arene (1) were studied in C2D4Cl2 solutions. While 3+, which occupies more than 75% of the internal volume of the dimer, is readily encapsulated this is not the case for 2. This is probably due to cation-pi interactions, which operate only between 3+ and the aromatic rings of the calix[4]arene dimer. We found that the affinity of the cobaltocenium cation is higher than that of the tropylium cation (4+) and is only 2-3 times less than that of the tetraethylammoniun cation (5+). From the variable temperature 1H NMR spectra of this capsule, the free energy of activation at 298 K (deltaGdouble dagger(298K)) for the reorientation of the hydrogen bonded belt between the two parts of the dimer could be determined by total line shape analysis for the aromatic protons of the calixarene. The value of 14.3 +/- 0.2 kcal mol(-1) for the dimeric capsules of 3+ PF6- is very similar to the free activation energy found for dimeric capsules of 1 with 4+ PF6- and 5+ PF6- in C2D4Cl2. It becomes significantly lower, if PF6- is replaced by BF4-. We also found that ten times more DMSO is needed to disrupt the capsule 1 x 3+ x 1 than the corresponding 1 x 1 dimer containing benzene as guest. This demonstrates again the importance of the cation-pi interactions for the stability of such hydrogen-bonded dimeric capsules.

1H and 13C NMR study of 2‐hydroxyglutaric acid and its lactone

AbstractDetermination of the level and absolute configuration of 2‐hydroxyglutaric acid in a patient's urine is a method of diagnosing two metabolic diseases. Such a determination can be done with the aid of NMR spectroscopic methods. In this paper the careful interpretation of 1H and 13C NMR spectra of this metabolite and its lactone measured under conditions used in biomedical assays is reported. The 1H chemical shifts and spin–spin coupling constants were derived using the total lineshape analysis method. Copyright © 2002 John Wiley & Sons, Ltd.

VALISA: a new procedure for total lineshape analysis of NMR spectra. Conformational analysis of trans-1,2-dibromocyclopentane

A new strategy of total lineshape analysis of the multiplet structure of NMR spectra was proposed and a VALISA program was developed to implement the computational procedure. Evaluation of the new technique taking a solution of several test problems and the complete analysis of the 1H NMR spectrum of trans-1,2-dibromocyclopentane as examples showed its high efficiency. Using a complete set of vicinal spin-spin coupling constants, detailed conformational analysis of this molecule was carried out and a more correct model for the description of conformational interconversions of the five-membered cycles was proposed. Conformational behavior of trans-1,2-dibromocyclopentane molecule can be reasonably described assuming large-amplitude molecular vibrations along a sector of the pseudorotation path, containing mostly diequatorial conformations.

Tropylium cation capsule of hydrogen-bonded tetraurea calix[4]arene dimers

The interaction between tropylium salts and tetraurea calix[4]arene derivatives (such as 1 and 2) was studied in solution using 1D, 2D, diffusion, VT NMR and UV–visible spectroscopy. It was found that tropylium salts form charge transfer complexes with both the monomers and dimers of the tetraurea calix[4]arene derivatives depending on the experimental conditions. Compound 1 increases dramatically the solubility of tropylium salts in apolar solvents such as C2D4Cl2, CDCl3 and CD2Cl2 by forming the molecular capsule 1·C7H7+·1. In contrast to the benzene capsule of 1, in 1·C7H7+·1 the hydrogen bonds in the equatorial region that hold together the two parts of the dimer change their directionality faster than the NMR time scale (at 400 MHz) at temperatures higher than 298 K. Interestingly, the free energy barrier for this dynamic process at 298 K (ΔG‡298), depends on the nature of the counter-anion. Free energies of activation of 14.3 ± 0.2 kcal mol−1 and 12.6 ± 0.2 kcal mol−1 were found by total lineshape analysis for the dimeric capsules of C7H7+PF6− and C7H7+BF4−, respectively. The affinity of the tropylium cation toward the dimer's cavity is much higher than that of neutral organic guests. Although exact quantitative values are not available due to the low solubility of tropylium salts in apolar solvents, a rough estimation in CD2Cl2 shows that the tropylium cation affinity is several orders of magnitude higher than that of benzene, which is known to be a good guest. These results show that once the steric requirements are met, electronic effects may serve as an additional driving force for the formation of such molecular capsules demonstrating the importance of cation–π interactions in such systems.

Rotational Isomerism Involving an Acetylenic Carbon II : Effect of 1-Halogen Substituents on Rotamer Population and Rotational Barrier around C(sp)-C(sp3) Bonds in Bis(9-triptycyl)ethynes

Abstract A series of (1,4-dimethyl-9-triptycyl)(1-halo-9-triptycyl)ethynes were synthesized to examine the effect of halogen substituents on the rotational isomerism about C(sp)-C(sp3) bonds. The kinetic and thermodynamic data of the isomerization between the ap and sc rotamers were determined by the total lineshape analysis and the intensity of the 1H NMR signals, respectively. The rotational barriers are enhanced with the steric size of halogen atoms from 11.6 (F) to 17.3 (I) kcal mol-1, and there is a linear correlation between the barrier height and van der Waals radius of the 1-substituent. Although large halogen atoms decrease the ratio of the sterically congested sc form, its population tends to be larger than that expected from the steric effect. This finding is attributable to the C-H…X(halogen) interactions between the 1-Me and X groups in the sc form. The possibility of the weak interactions is discussed on the basis of molecular structures optimized by the MM2 calculations.

Rotational Isomerism Involving an Acetylenic Carbon: Synthesis of and Barrier to Rotation around C(sp)-C(sp3) Bonds in Bis(1,4-disubstituted 9-triptycyl)ethynes

Abstract The substituent effect on the rotational barriers of acetylenic to tetrahedral C-C bonds was studied for the title compounds carrying Me or OMe substituents at the 1,4-positions in the 9-triptycyl groups. These compounds were prepared by use of the Diels-Alder and the Sonogashira reactions from a 9-ethynylanthracene derivative. The kinetic parameters were determined by the total lineshape analysis of the signals observed by the variable temperature 1H NMR for five compounds. The rotational barriers are in the range of 9—15 kcal mol-1, and are enhanced as the steric size of the substituents is increased (H < OMe < Me). This substituent effect is attributed to the destabilization of the transition state of the rotation process, where the two triptycyl groups are almost eclipsed about the central axis, by the steric interactions between the peri substituents. The acetylenic carbons are significantly deformed from the linear geometry in the X-ray structure of the tetramethyl compound. The substituent effect on the rotamer population is also discussed with the aid of the MM calculation.

Gas-Phase Nuclear Magnetic Resonance Study of (15N)Trifluoroacetamide: Comparison of Experimental and Computed Kinetic Parameters

Rate constants obtained from total line-shape analysis of 11 temperature-dependent gas-phase NMR spectra of (15N)trifluoroacetamide yielded the following kinetic parameters: ΔG⧧298 = 15.1(0.36) kcal mol-1, ΔH⧧ = 13.3(1.3) kcal mol-1, and ΔS⧧ = −5.9(4.5) cal mol-1 K-1. Ab initio calculations performed at the MP2 level using the 6-311++G(d,p) basis set calculated ΔG⧧298 = 15.19 kcal mol-1, ΔH⧧ = 14.35 kcal mol-1, and ΔS⧧ = −2.82 cal mol-1 K-1 in reasonable agreement with experiment. Hartree−Fock calculations using that basis set were also in reasonable agreement with experiment, yielding ΔG⧧298 = 16.03 kcal mol-1, ΔH⧧ = 14.35 kcal mol-1, and ΔS⧧ = −5.62 cal mol-1 K-1. DFT calculations (B3-PW91) using the same basis set gave results that were considerably less accurate.