Structural features of diastereomeric oxazolidin-2-ones

Model diastereomeric oxazolidinones containing various substituents at positions 3 and 5 were synthesized. Several individual diastereomers bearing methyl groups at positions 4 and 5 in cis-and trans orientations were isolated. The TLC and ¹H NMR spectroscopic data suggest that diastereomers, particularly those containing the aryl substituent at position 5, are substantially different in the physical and spectral properties. The configurations of some diastereomers were established by X-ray diffraction and NOESY spectroscopy. For these compounds, the reliable assignment of the characteristic ¹H NMR signals of individual groups was made, which provided evidence for the cis or trans orientation of the methyl groups at positions 4 and 5. The scope of the method as applied to the determination of the cis and trans isomers from their ¹H NMR spectra is discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 133–139, January, 2007.     

Molecular aspects of polymer network deformation - small angle neutron scattering and NMR studies

Poly(1,4-butadiene) networks obtained by a 4-functional random cross-linking reaction over a broad range of polymer concentration were studied by small angle neutron scattering(SANS), ²H NMR and Monte Carlo(MC) simulation in the isotropic and uniaxially deformed state. The defect structure of the networks has been characterized by MC simulation of the cross-linking reaction. The anisotropy of the radius of gyration in deformed networks determined from SANS has been analyzed by the theory of Ullman. It was found that the number of active cross-links per chain is in agreement with MC and that the chain deformation follows phantom behaviour. The local orientation as measured by ²H NMR is related to the global anisotropy of the network by a MC calculation of oriented chains. The ²H NMR line shape of the deformed network is analyzed in terms of two relaxation processes arising from interior parts of the chains and from segments at chain ends. The mobility of both decrease with strain. It was found that the orientation connected to the first process shows the classical strain dependence of rubber elasticity, whereas the second exhibits a weaker dependence on strain.     

Magic-Angle-Pulse Driven Separation of Degenerate 1H Transitions in Methyl Groups of Proteins: Application to Studies of Methyl Axis Dynamics

Dynamics of protein side chains is one of the principal determinants of conformational entropy in protein structures and molecular recognition events. We describe NMR experiments that rely on the use of magic-angle pulses for efficient isolation of degenerate ¹H transitions of the I=3/2 manifold of ¹³CH₃ methyl groups, and serve as ‘building blocks’ for the measurement of transverse spin relaxation rates of the fast- and slow-relaxing ¹H transitions – the primary quantitative reporters of methyl axis dynamics in selectively {¹³CH₃}-methyl-labelled, highly deuterated proteins. The magic-angle-pulse driven experiments are technically simpler and, in the absence of relaxation, predicted to be 2.3-fold more sensitive than previously developed analogous schemes. Validation of the methodology on a sample of {¹³CH₃}-labeled ubiquitin demonstrates quantitative agreement between order parameters of methyl three-fold symmetry axis obtained with magic-angle-pulse driven experiments and other established NMR techniques, paving the way for studies of methyl axis dynamics in human DNAJB6b chaperone, a protein that undergoes exchange with high-molecular-weight oligomeric species.     

Three-dimensional structures of 2-alkyl-4-formyltetrahydropyrans

The three-dimensional structures of a number of diastereomeric 2-alkyl-4-formyltetrahydropyrans were studied by means of ¹H and ¹³C NMR spectroscopy. It is shown that the 2,2-dialkyl derivatives are mixtures of two configurational isomers in which the formyl group is equatorially oriented. 2-Monoalkyl-4-formyltetrahydropyrans exist in the form of mixtures of two diastereomeric forms that have different orientations (axial and equatorial) of the formyl group; the alkyl group in both isomers is equatorially oriented.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 311–314, March, 1979.     

A Common Conformation of Stabilized Triphenyl Phosphonium Ylidic Diesters with Bulky Alkoxy Groups

The phosphonium ylidic diesters, methyl and ethyl isopropyl and, methyl and ethyl t-butyl triphenylphosphoranylidene malonates, 1a,b and 2a,b , respectively, have the syn-anti conformation in solution, as in the crystal, and the bulkier alkoxy group is oriented towards phosphorus. The ¹ H NMR spectra show that in 1a,b , the isopropyl group is oriented towards the face of a phenyl group, consistent with π shielding in the ¹ H signals, and examination of the ¹ H coupled ¹³ C NMR spectra allows assignment of the acyl carbon signals. Computed bond lengths and angles for isolated molecules are similar to those in the crystal, and the geometry and the NMR spectra indicate extensive ylidic resonance. Estimated partial atomic charges on the ester oxygens are more negative when they are oriented towards, rather than away from, phosphorus.     

13C chemical shielding tensor orientations in a phosphoenolpyruvate moiety from 13C rotational-resonance MAS NMR lineshapes

The absolute orientations of the three ¹³C chemical shielding tensors in the phosphoenolpyruvate (PEP) moiety in a PEP-model compound with known crystal structure are reported. The study uses a fully ¹³C-enriched polycrystalline sample of triammonium phosphoenolpyruvate monohydrate, (NH₄)₃(PEP)⋅H₂O, and ¹³C MAS NMR experiments fulfilling various different ¹³C rotational-resonance conditions. The absolute ¹³C chemical shielding tensor orientations are derived by iterative fitting, employing numerically exact simulations, of various rotational-resonance ¹³C MAS NMR lineshapes of the three-¹³C-spin system in fully ¹³C-enriched (NH₄)₃(PEP)⋅H₂O. The implications of the results of this study for future, biochemically oriented solid-state NMR studies on the PEP moiety are outlined.     

A Methyl‐TROSY‐Based 1H Relaxation Dispersion Experiment for Studies of Conformational Exchange in High Molecular Weight Proteins

Molecular complexes often sample conformational states that direct them to specific functions. These states can be difficult to observe through traditional biophysical approaches but they can be studied using a variety of different NMR spin relaxation experiments. However, these applications, when focused on moderate to high molecular weight proteins, are complicated by fast relaxing signals that negatively affect the sensitivity and resolution of spectra. Here a methyl ¹H CPMG‐based experiment for studies of excited conformational states of protein machines is described that exploits a TROSY‐effect to increase signal‐to‐noise. Complexities from the multiplicity of methyl ¹H transitions are addressed to generate a robust pulse scheme that is applied to a 320 kDa homeostasis protein, p97.     

Two-Dimensional NMR Studies of Polyene Systems. I. All-trans-Retinal

Two-dimensional (2-D) NMR results are presented for all-trans-retinal. 2-D J-resolved ¹H-NMR separated the multiplets of the olefinic protons and accurately determined their chemical shifts. 2-D shift-correlated ¹H-NMR gave the connectivities between scalar coupled protons. From the observed H,H long-range couplings the assignment of the methyl resonances was possible. 2-D J-resolved ¹³C-NMR separated overlapping C,H-multiplets and allowed analysis of the C,H long-range couplings, 2-D shift-correlated ¹³C-NMR related each directly bonded C,H-pair in this molecule. The potential of 2-D NMR in resolving and identifying individual resonances in polyene spectra is discussed.     

An Accurate Method for Cholesterol Analysis in Bile

Abstract

An accurate method for quantitative analysis of cholesterol in human bile is presented. Bile cholesterol was extracted in a single solvent (chloroform) in single step and ¹H NMR spectra of the extract were obtained by suppressing chloroform signal by presaturation. Cholesterol was quantitatively estimated through integral area of its H‐18 methyl signal which invariably appears distinctly in the nuclear magnetic resonance (NMR) spectrum. Precision and accuracy were determined from the recovery of added cholesterol from bile. Excellent correlation was observed between added and recovered cholesterol (R²=1). Direct and accurate analysis of cholesterol following simple extraction method as presented here may have important implications.     

1H NMR analysis of O‐methyl‐inositol isomers: a joint experimental and theoretical study

Density functional theory (DFT) calculations of ¹H NMR chemical shifts for l ‐quebrachitol isomers were performed using the B3LYP functional employing the 6‐31G(d,p) and 6‐311 + G(2d,p) basis sets. The effect of the solvent on the B3LYP‐calculated NMR spectrum was accounted for using the polarizable continuum model. Comparison is made with experimental ¹H NMR spectroscopic data, which shed light on the average uncertainty present in DFT calculations of chemical shifts and showed that the best match between experimental and theoretical B3LYP ¹H NMR profiles is a good strategy to assign the molecular structure present in the sample handled in the experimental measurements. Among four plausible O‐methyl‐inositol isomers, the l ‐quebrachitol 2a structure was unambiguously assigned based only on the comparative analysis of experimental and theoretical ¹H NMR chemical shift data. The B3LYP infrared (IR) spectrum was also calculated for the four isomers and compared with the experimental data, with analysis of the theoretical IR profiles corroborating assignment of the 2a structure. Therefore, it is confirmed in this study that a combined experimental/DFT spectroscopic investigation is a powerful tool in structural/conformational analysis studies. Copyright © 2012 John Wiley & Sons, Ltd.     

Solid-state 2H NMR structure of retinal in metarhodopsin I

The structural and photochemical changes in rhodopsin due to absorption of light are crucial for understanding the process of visual signaling. We investigated the structure of trans-retinal in the metarhodopsin I photointermediate (MI), where the retinylidene cofactor functions as an antagonist. Rhodopsin was regenerated using retinal that was (2)H-labeled at the C5, C9, or C13 methyl groups and was reconstituted with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. Membranes were aligned by isopotential centrifugation, and rhodopsin in the supported bilayers was then bleached and cryotrapped in the MI state. Solid-state (2)H NMR spectra of oriented rhodopsin in the low-temperature lipid gel state were analyzed in terms of a static uniaxial distribution (Nevzorov, A. A.; Moltke, S.; Heyn, M. P.; Brown, M. F. J. Am. Chem. Soc. 1999, 121, 7636-7643). The line shape analysis allowed us to obtain the methyl bond orientations relative to the membrane normal in the presence of substantial alignment disorder (mosaic spread). Relative orientations of the methyl groups were used to calculate effective torsional angles between the three different planes that represent the polyene chain and the beta-ionone ring of retinal. Assuming a three-plane model, a less distorted structure was found for retinal in MI compared to the dark state. Our results are pertinent to how photonic energy is channeled within the protein to allow the strained retinal conformation to relax, thereby forming the activated state of the receptor.     

Structure and dynamics of silk fibroin studied with 13C, 15N and 2H solid state NMR

[1-¹³C]Gly, L-[1-¹³C]Ala, [¹⁵N]Gly, L-[¹⁵N]Ala, [2,2-²H₂]Gly, L-[3,3-²H₂]Ser and [3,3,3-²H₃]Ala labeled silk fibroin fibers from Bombyx mori and Samia cynthia ricini silkworms were prepared in order to analyze structure of backbone and dynamics of side chain. The torsion angles ϕ and Ψ were determined from the angular dependent ¹³C and ¹⁵N solid state NMR spectra for uniaxially oriented fiber samples. In addition, the characteristic side chain dynamics of Ser residue determined from solid state ²H NMR measurements was compared with those of Ala and Gly residues.     

A NMR method for the analysis of mixtures of alkanes with different deuterium substitutions

¹³C NMR at 125.76 MHz with ¹H and ²H decoupling, ²H NMR at 76.77 MHz with ¹H decoupling, and ¹H NMR at 500.14 MHz with ²H decoupling were employed as analytical tools to study the complex mixtures of deuterated ethanes resulting from the catalytic H–D exchange of normal ethane with gas-phase deuterium in the presence of a platinum foil. Reference samples consisting of 1:1 binary mixtures of pure normal ethane and ethane-d_n (n=1–6) were used to identify the peak positions in the ¹³C, ²H, and ¹H NMR spectra due to each individual isotopomer, and the effect of isotopic substitution on the chemical shifts was determined in each case. While the NMR of all three nuclei worked well for the identification of the individual components of the 1:1 standard mixtures, both ¹H and ²H NMR suffered from inadequate resolution when studying complex reaction mixtures because of the broadening of the lines due to ¹H–¹H (¹H NMR) and ²H–²H (²H NMR) couplings. ¹³C NMR was therefore determined to be the method of choice for the quantitative analysis of the reaction mixtures. Using the ¹³C NMR results, a correlation that takes into account the primary and secondary isotope substitution effects on chemical shifts was deduced. This equation was used for the identification of the individual components of the mixtures, and integration of the individual observed resonances was then employed for quantification of their composition. This study shows that ¹³C NMR with ¹H and ²H decoupling is a viable procedure for studying mixtures of deuterated ethanes. Furthermore, the additivity of the isotopic effects on chemical shifts and the transferability of the values obtained with ethane to other molecules makes this approach general for the analysis of other isotopomer mixtures.     

A fast MAS 1H NMR study of amino acids and proteins

Fast sample spinning (up to 32 kHz) in tandem with delayed acquisition enabled resolved ¹H NMR spectra of solid amino acids to be recorded. The resulting spectra are, however, significantly dependent on sample crystallinity and on sample preparation conditions, e.g. sample drying. Sample heating leads to a marked increase in signal to noise ratio and enables groups with different dynamic properties to be identified. In addition, the observation of peak shifts as a function of heating allows the identification of hydrogen bonded sites. Spectral assignment of the ¹H MAS spectra is proposed for some examples based on relaxation properties, study of deuteriated samples and 2D NMR. The effects of molecular weight and sample complexity on the ¹H MAS spectra were investigated using tetraglycine, polyglycine and two proteins: a small protein (lysozyme) and a much larger protein (a cereal storage protein named high molecular weight subunit 1Dx5). Moderate spectral resolution was achieved for the peptides and lysozyme, but for 1Dx5, significant resolution enhancement was obtained enabling the identification of resonances in all regions of the spectra including the alpha region, the aromatic region and the NH backbone region.     

Dynamic rheo-optical characterization of uniaxially oriented polyamide 11

Dynamic mechanical analysis, coupled with polarized step-scan FTIR transmission spectroscopy, has been used to monitor the submolecular motional behavior of uniaxially oriented polyamide 11. The dynamic in-phase spectra depend upon the morphology of the samples as well as on the polarization direction of the infrared radiation. The lineshape features of the dynamic in-phase spectra and their relationship to sample deformation are analyzed on the basis of changes of the internal coordinates, the reorientation movement of several functional groups, and the thickness change of the film during the stretching cycle. Dynamic infrared spectra are helpful for deconvolution of overlapping bands on the basis of their different responses to the external perturbation, which sometimes cannot be resolved well by derivative spectroscopy or curve-fitting analysis. The lineshape features have been used to follow microstructural changes after isothermal heat treatment. Near the N H stretching frequency, two bands at 3270 cm⁻¹ and 3200 cm⁻¹ are resolved and analyzed in terms of Fermi resonance between the N H stretching fundamental mode and the overtone and combination modes of the amide I and II vibrations. The dynamic response of the N H stretching mode correlates with the modulation of hydrogen bond strength in uniaxially oriented PA-11. After thermal treatment at the highest temperature (190°C), the dynamic response in this region is mainly caused by the modulation of crystals. In amide I region, three bands at 1680 cm⁻¹, 1648 cm⁻¹, and 1638 cm⁻¹ are separated and assigned to hydrogen bond-free, hydrogen-bonded amorphous, and hydrogen-bonded crystalline regions, respectively. The dynamic responses of the hydrogen-bonded regions are more sensitive to external perturbation. Two components are found in the amide II region, and the band at 3080 cm⁻¹ is assigned to the overtone resonance of the component with perpendicular polarization. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 2895–2904, 1998     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.     

Investigations of polypeptide rotational diffusion in aligned membranes by 2H and 15N solid-state NMR spectroscopy

Transmembrane and in-plane oriented peptides have been prepared by solid-phase peptide synthesis, labeled with 3,3,3-2H3-alanine and 15N-leucine at two selected sites, and reconstituted into oriented phophatidylcholine membranes. Thereafter, proton-decoupled 15N and 2H solid-state NMR spectroscopy at sample orientations of the membrane normal parallel to the magnetic field direction have been used to characterize the tilt and rotational pitch angle of these peptides in some detail. In a second step the samples have been tilted by 90 degrees . In this setup the spectral line shapes are sensitive indicators of the rate of rotational diffusion. Whereas monomeric transmembrane peptides exhibit spectral averaging and well-defined resonances, larger complexes are characterized by broad spectral line shapes. In particular the deuterium line shape is sensitive to association of a few transmembrane helices. In contrast, the formation of much larger complexes affects the 15N chemical shift spectrum. The spectra indicate that in liquid crystalline membranes an amphipathic peptide of 14 amino acids exhibits fast rotational diffusion on both the 2H and 15N time scales (>10(-5) s). Extending the sequences to 26 amino acids results in pronounced changes of the 2H solid-state NMR spectrum, whereas the signal intensities of 15N solid-state NMR spectra degrade. Below the phase transition temperature of the phospholipid bilayers, motional averaging on the time scale of the 2H solid-state NMR spectrum ceases for transmembrane and in-plane oriented peptides. Furthermore at temperatures close to the phase transition the total signal intensities of the deuterium solid-state NMR spectra strongly decrease.     

NMR Spectroscopy for Protein Higher Order Structure Similarity Assessment in Formulated Drug Products

Peptide and protein drug molecules fold into higher order structures (HOS) in formulation and these folded structures are often critical for drug efficacy and safety. Generic or biosimilar drug products (DPs) need to show similar HOS to the reference product. The solution NMR spectroscopy is a non-invasive, chemically and structurally specific analytical method that is ideal for characterizing protein therapeutics in formulation. However, only limited NMR studies have been performed directly on marketed DPs and questions remain on how to quantitively define similarity. Here, NMR spectra were collected on marketed peptide and protein DPs, including calcitonin-salmon, liraglutide, teriparatide, exenatide, insulin glargine and rituximab. The 1D ¹H spectral pattern readily revealed protein HOS heterogeneity, exchange and oligomerization in the different formulations. Principal component analysis (PCA) applied to two rituximab DPs showed consistent results with the previously demonstrated similarity metrics of Mahalanobis distance (D_M) of 3.3. The 2D ¹H-¹³C HSQC spectral comparison of insulin glargine DPs provided similarity metrics for chemical shift difference (Δδ) and methyl peak profile, i.e., 4 ppb for ¹H, 15 ppb for ¹³C and 98% peaks with equivalent peak height. Finally, 2D ¹H-¹⁵N sofast HMQC was demonstrated as a sensitive method for comparison of small protein HOS. The application of NMR procedures and chemometric analysis on therapeutic proteins offer quantitative similarity assessments of DPs with practically achievable similarity metrics.     

The assignment of the 1H NMR signals to the methine bridge H-atoms in chlorophyll derivatives

Experiments are described which prove the assignments of the α- and β-protons in the ¹H NMR spectra of methyl phaeophorbide a ( 1 ) and methyl pyrophaeophorbide a ( 2 ). Because of the structural relationship between derivatives of the bacteriochlorophylls d ( 5 ) and 2 , dehydration of 5 results in a homologue mixture [2-(des-α-hydroxyethyl)-2-vinyl-bacteriomethyl phaeophorbide] d ( 6 ) of 2. Since the homologue substituents in 6 are located at C-4 and C-5 surrounding the β-H position, and since only one broad signal appears in its ¹H NMR spectrum, this is assigned to the β-proton. This experiment proves that the sequence of increasing shielding is β, α and δ in 6 ; and, therefore, the same sequence applies to the ¹H NMR spectra of 1 and 2 . This knowledge reveals that the product of electrochemical reduction of 1 in deuteromethanol is exclusively an α-chlorin-phlorin ( 8 ). In addition, the ¹H NMR spectrum of the 2-vinyl derivatives of the bacteriomethyl phaeophorbides c ( 7 ) shows the same broad signal at lowest field as does that of 6 . The sequence of increasing shielding is therefore, β, α. The influence of the additional δ-methyl group in 7 on the ring current is explained.     

Fluorinated Carbohydrates as Lectin Ligands: Dissecting Glycan–Cyanovirin Interactions by Using 19F NMR Spectroscopy

NMR spectroscopy and isothermal titration calorimetry (ITC) are powerful methods to investigate ligand–protein interactions. Here, we present a versatile and sensitive fluorine NMR spectroscopic approach that exploits the ¹⁹F nucleus of ¹⁹F‐labeled carbohydrates as a sensor to study glycan binding to lectins. Our approach is illustrated with the 11 kDa Cyanovirin‐N, a mannose binding anti‐HIV lectin. Two fluoro‐deoxy sugar derivatives, methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside and methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside were utilized. Binding was studied by ¹⁹F NMR spectroscopy of the ligand and ¹H–¹⁵N HSQC NMR spectroscopy of the protein. The NMR data agree well with those obtained from the equivalent reciprocal and direct ITC titrations. Our study shows that the strategic design of fluorinated ligands and fluorine NMR spectroscopy for ligand screening holds great promise for easy and fast identification of glycan binding, as well as for their use in reporting structural and/or electronic perturbations that ensue upon interaction with a cognate lectin.