Structural characterization and quantitation of compound loading of disubstituted benzoates bound to Wang resin through high-resolution magic angle spinning NMR spectroscopy

The combination of 1D and 2D high-resolution magic angle spinning NMR experiments led to the assignment of the proton and carbon resonances for several disubstituted benzoates bound to a polystyrene resin through a Wang linker. It is shown that the signal corresponding to the methylene protons of the linker can be utilized to monitor the solid-phase reactions and determine the loading of the compounds on the resin.     

Application of HR‐MAS NMR in the solid‐phase synthesis of a glycopeptide using Sieber amide resin

The solid‐phase synthesis (SPS) of a structurally complex glycopeptide, using Sieber amide resin, was monitored by high resolution magic angle spinning NMR, demonstrating the further application of this technique. A synthetic peptidoglycan derivative, a precursor of a biologically active PGN, known to be involved in the cellular recognition, was prepared by SPS. The synthesis involved the preparation of an N‐alloc glucosamine moiety and the synthesis of a simple amino acid sequence L ‐Ala‐D ‐Glu‐L ‐Lys‐D ‐Ala‐D ‐Ala. Last step consisted the coupling, on solid‐phase, of the protected muramyl unit to the peptide chain. Proton spectra with good suppression of the polystyrene signals in swollen resin samples were obtained in DMF‐d₇ as a solvent and by using a nonselective 1D TOCSY/DIPSI‐2 scheme, thus allowing to follow the SPS without losses of compound and cleavage from the resin. The assignment of the proton spectra of the resin‐bound amino acid sequence and of the bound glycopeptide was achieved through the combination of MAS COSY, TOCSY and NOESY. Copyright © 2010 John Wiley & Sons, Ltd.     

Characterization of the 310-helix in model peptides by HRMAS NMR spectroscopy

A tetra- and a hepta-homopeptide from the C(alpha)-tetrasubstituted Aib (alpha-aminoisobutyric acid) residue were covalently linked to the POEPOP resin by the fragment-condensation approach. The conformational preferences of the two model peptides were determined for the first time on a solid support by means of high-resolution magic angle spinning NMR spectroscopy. The results obtained indicate that the Aib homopeptides adopt a regular 3(10)-helical structure even when they are covalently bound to a polymeric matrix, and thus confirm the remarkable conformational stability of the peptides rich in this amino acid. An ATR-FTIR spectroscopic investigation, performed in parallel, also confirmed that these polymer-bound peptides do indeed adopt a helical conformation. The results of this study open the possibility to exploit the peptide-resin conjugates based on C(alpha)-tetrasubstituted alpha-amino acids as helpful, structurally organized templates in molecular recognition studies or as catalysts in asymmetric synthesis.     

DEUSS: a perdeuterated poly(oxyethylene)-based resin for improving HRMAS NMR studies of solid-supported molecules

A novel resin called DEUSS (perdeuterated poly(oxyethylene)-based solid support) has been prepared by anionic polymerization of deuterated [D4]ethylene oxide, followed by cross-linking with deuterated epichlorohydrin. DEUSS can be suspended in a wide range of solvents including organic and aqueous solutions, in which it displays a high swelling capacity. As measured by proton HRMAS of the swollen polymer, the signal intensity of the oxyethylene protons is reduced by a factor of 110 relative to the corresponding nondeuterated poly(oxyethylene)poly(oxypropylene) (POEPOP) resin, thus facilitating detailed HRMAS NMR studies of covalently linked molecules. This 1H NMR invisible matrix was used for the solid-phase synthesis of peptides, oligoureas, and a series of amides as well as their characterization by HRMAS NMR spectroscopy. On-bead NMR spectra of high quality and with resolution comparable to that of liquid samples were obtained and readily interpreted. The complete absence of the parasite resin signals will be of great advantage, for example, for the optimization of multistep solid-phase stereoselective reactions, and for the conformational study of resin-bound molecules in a large variety of solvents.     

Evidence of secondary structure by high-resolution magic angle spinning NMR spectroscopy of a bioactive peptide bound to different solid supports.

The structure of the 19-amino acid peptide epitope, corresponding to the 141-159 sequence of capsid viral protein VP1 of foot-and-mouth disease virus (FMDV), bound to three different resins, namely, polystyrene-MBHA, PEGA, and POEPOP, has been determined by high-resolution magic angle spinning (HRMAS) NMR spectroscopy. A combination of homonuclear and heteronuclear bidimensional experiments was used for the complete peptide resonance assignment and the qualitative characterization of the peptide folding. The influence of the chemicophysical nature of the different polymers on the secondary structure of the covalently attached FMDV peptide was studied in detail. In the case of polystyrene-MBHA and polyacrylamide-PEGA resins, the analysis of the 2D spectra was hampered by missing signals and extensive overlaps, and only a propensity toward a peptide secondary structure could be derived from the assigned NOE correlations. When the FMDV peptide was linked to the polyoxyethylene-based POEPOP resin, it was found to adopt in dimethylformamide a helical conformation encompassing the C-terminal domain from residues 152 to 159. This conformation is very close to that of the free peptide previously analyzed in 2,2,2-trifluoroethanol. Our study clearly demonstrates that a regular helical structure can be adopted by a resin-bound bioactive peptide. Moreover, a change in the folding was observed when the same peptide-POEPOP conjugate was swollen in aqueous solution, displaying the same conformational features as the free peptide in water. The possibility of studying solid-supported ordered secondary structures by the HRMAS NMR technique in a wide range of solvents can be extended either to other biologically relevant peptides and proteins or to new synthetic oligomers.     

Multistep synthesis of 2,5-diketopiperazines on different solid supports monitored by high resolution magic angle spinning NMR spectroscopy

The solid-phase synthesis of 2,5-diketopiperazines containing the trans-4-hydroxy-L-proline amino acid residue (Hyp) was performed on Ellman polystyrene, polyoxyethylene-polyoxypropylene (POEPOP), polystyrene-polyoxyethylene NovaSyn, and Wang resins, respectively. The reaction pathway allowed the introduction of different functional groups around the bicyclic scaffold in a combinatorial approach, and it generated mixtures of isomers. A detailed characterization of the single reaction steps by high resolution magic angle spinning (HRMAS) NMR spectroscopy was performed. The NMR spectral resolution of the resin-bound intermediates and final products was greatly influenced by the polymer matrix. The POEPOP resin permitted to obtain HRMAS NMR spectra with a resolution comparable with that of the spectra of the molecules in solution. Moreover, configurational and conformational isomers formed during the solid-phase reaction steps could be detected and easily assigned. Therefore, the combination of the HRMAS NMR technique with the use of nonaromatic resins may become an extremely powerful tool in solid-phase organic synthesis. This approach will allow the monitoring of multistep reactions and the conception of on-bead structural studies either on small molecules or on natural and/or synthetic oligomers.     

Characterization of signals in the solution 1H NMR spectrum of poly(isobutylene‐co‐p‐methylstyrene) and their utility

Poly(isobutylene‐co‐p‐methylstyrene) is an important precursor to Exxpro™ elastomers. A previous report detailed the characterization of both the proton and the carbon NMR spectra of the copolymer. 1 However, several resonances in the proton NMR spectrum of the copolymer were not assigned. Specifically, the proton methine resonance of the BSB triad sequence is now identified and used to calculate BSB triad contribution to the copolymer microstructure. This report describes the assignment of this resonance and other resonances associated with microstructural sequence distribution around p‐methylstyrene. The proton NMR signals of interest resonate at 2.8 ppm and 2.5 ppm in a typical spectrum for poly(isobutylene‐co‐p‐methylstyrene). The nature of these resonances were determined by preparation and characterization of specifically deuterated poly(isobutylene‐co‐p‐methylstyrene)s employing both one and two dimensional NMR techniques. The 2.8 ppm signal is assigned as the methine proton of a p‐methylstyrene incorporated between two isobutylene units (the BSB triad). The signal at 2.5 ppm is assigned to the meso‐BSS triad. Determination of these resonances allows for rapid evaluation of isolated p‐methylstyrene units (BSB triads) present in the copolymer using only ¹H NMR. The utility of this technique is demonstrated by comparing BSB triad values determined by ¹H and ¹³C NMR analysis. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1680–1686, 2000     

Photo‐induced cross‐linking mechanism in azide–novolac negative photoresists: molecular level investigation using NMR spectroscopy

Negative photoresists are composed of a photoactive component (aromatic azides/bisazides) and cyclized rubber or novolac resin dissolved in an organic solvent. Hydrogen abstraction and/or insertion reaction of the reactive nitrene intermediate formed during photoirradiation of the azide result in a cross‐linked network of the novolac resin. The molecular weight of novolac resin in the exposed part of the photoresist film thus increases compared with that of the unexposed part. This makes the exposed part insoluble in the alkaline developer. Exploiting this change in physical property, a pattern can be transferred to a substrate from a mask. A better understanding of the exact mechanism of cross‐linking reactions is very important to the design of a high‐performing negative photoresist. A quinone–imine‐type complex has been proposed earlier involving the aromatic moiety of novolac resin as the reaction site. A more recent study focuses the attack of nitrene on the methylenic bridge and hydroxyl group of novolac resins, which were found to be responsible for the cross‐linking reaction along with the aromatic moiety of novolac resin. However, in our study no evidence was found for the involvement of a methylenic hydrogen or aromatic moiety of novolac resin in the cross‐linking reaction. The ¹H NMR, ¹³C NMR and DEPT‐135 spectra before and after photolysis indicate that the cross‐linking site is predominantly the hydroxyl group of novolac resin. Multiple reaction sites of attack for the nitrene intermediate have been demonstrated in cashew nut shell liquid (CNSL)‐based novolac resin by ¹H NMR spectroscopy, which in turn further increases the cross‐linked network in the exposed part of a negative photoresist. Copyright © 2003 John Wiley & Sons, Ltd.     

Pure Isotropic Proton NMR Spectra in Solids using Deep Learning

The resolution of proton solid-state NMR spectra is usually limited by broadening arising from dipolar interactions between spins. Magic-angle spinning alleviates this broadening by inducing coherent averaging. However, even the highest spinning rates experimentally accessible today are not able to completely remove dipolar interactions. Here, we introduce a deep learning approach to determine pure isotropic proton spectra from a two-dimensional set of magic-angle spinning spectra acquired at different spinning rates. Applying the model to 8 organic solids yields high-resolution ¹H solid-state NMR spectra with isotropic linewidths in the 50–400 Hz range.     

Receptor‐Bound Conformation of Cilengitide Better Represented by Its Solution‐State Structure than the Solid‐State Structure

The X‐ray crystal and NMR spectroscopic structures of the peptide drug candidate Cilengitide (cyclo(RGDf(NMe)Val)) in various solvents are obtained and compared in addition to the integrin receptor bound conformation. The NMR‐based solution structures exhibit conformations closely resembling the X‐ray structure of Cilengitide bound to the head group of integrin αvβ3. In contrast, the structure of pure Cilengitide recrystallized from methanol reveals a different conformation controlled by the lattice forces of the crystal packing. Molecular modeling studies of the various ligand structures docked to the αvβ3 integrin revealed that utilization of the solid‐state conformation of Cilengitide leads—unlike the solution‐based structures—to a mismatch of the ligand–receptor interactions compared with the experimentally determined structure of the protein–ligand complex. Such discrepancies between solution and crystal conformations of ligands can be misleading during the structure‐based lead optimization process and should thus be taken carefully into account in ligand orientated drug design.     

Filaggrin Peptides with β‐Hairpin Structure Bind Rheumatoid Arthritis Antibodies

In the early detection of rheumatoid arthritis (RA) synthetic filaggrin peptides serve as antigens for rheumatoid‐specific autoantibodies (anti‐citrullinated peptide antibody, ACPA) in ELISA tests. In this work we present a peptide that exhibits the binding epitope of ACPA in the form of a stable folding β‐hairpin. The homogeneity of the peptide folding was confirmed by NMR spectroscopy and might lead to the first proposed structure of the antibody‐bound conformation of the epitope.     

Surface‐initiated ring‐opening polymerization of p‐dioxanone on Wang resin bead

Biodegradable poly(p‐dioxanone) (PPDO) was formed on Wang resin surface by surface‐initiated ring‐opening polymerization (SI‐ROP). The SI‐ROP of p‐dioxanone (PDO) was achieved by heating a mixture of Tin(II) bis(2‐ethylhexanoate) [Sn(Oct)₂], hydroxyl functionalized Wang resin, and PDO in anhydrous toluene at 80 °C. The resultant polymer‐grafted Wang resin (Wang‐g‐PPDO) was characterized by fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), optical microscopy (OM), and field‐emission scanning electron microscopy (FE‐SEM). The FTIR spectra of Wang‐g‐PPDO show peak characteristic of PPDO at 2943 cm^?1 (? C? H stretch), at 1741 cm^?1 (? C?O stretch), and 1136 cm^?1 (C? O? C stretch) indicating the formation of ester linkage between PPDO and hydroxyl terminated Wang resin. The DSC thermogram show melting peak corresponding to PPDO polymer on Wang resin surface. Thermogravimetric investigation shows increase in PPDO content on the Wang resin surface in terms of percentage of weight loss with increase in reaction time. The OM and SEM photographs clearly show the formation of PPDO polymer on the Wang resin surface without altering the spherical nature of Wang resin bead. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1178–1184, 2008     

2D NMR analysis for unambiguous structural elucidation of phenolic compounds formed through reaction between (+)‐catechin and glyoxylic acid

Various phenolic compounds were synthesized in an aqueous–alcoholic solution containing (+)‐catechin and glyoxylic acid which was used as a model of fruit‐derived food browning that usually occurs during aging. After purification by semi‐preparative HPLC, the isolated compounds were subjected to homo‐ and heteronuclear proton and carbon NMR analysis including COSY, TOCSY, ROESY, HSQC and HMBC techniques. These experiments allowed the structural elucidation and complete ¹H and ¹³C NMR assignment of the isolated compounds. The strategies followed for the assignment of all proton and carbon resonances in addition to the linkage site determination are discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Hydroacridines: Part 23. 1H and 13C NMR spectra of sym‐octahydroacridine,its 9‐(3‐pyridyl) and 9‐(4‐pyridyl) derivatives and the corresponding N(10)‐oxides. An experimental approach to the diamagnetic anisotropy of the pyridine nucleus

The complete ¹H NMR chemical shift assignments of 1,2,3,4,5,6,7,8‐octahydroacridine ( 1 ), 1,2,3,4,5,6,7,8‐octahydro‐9‐(3‐pyridyl)acridine ( 2 ), 1,2,3,4,5,6,7,8‐octahydro‐9‐(4‐pyridyl)acridine ( 3 ) and the corresponding N(10)‐oxides 1a , 2a and 3a , respectively, were achieved on the basis of 400 MHz ¹H NMR spectra and proton–proton decoupling, HMQC and NOEDIFF experiments. The spectral data for the above compounds provided the first experimental evidence of the difference in the anisotropy effect of the two non‐symmetrical moieties of the pyridine nucleus, and allowed us to ascertain that the shielding effect of the moiety defined by the C(2′)—N—C(6′) atoms is weaker than that of the C(3′)—C(4′)—C(5′) moiety. The ¹³C NMR spectra of 1 – 3 and 1a – 3a and the effect of N(10)‐oxidation on the ¹³C NMR chemical shifts are also discussed. The N‐oxidation of 2 and 3 with m‐chloroperbenzoic acid occurred regiospecifically, affording the N(10)‐oxides 2a and 3a free of N(1′)‐oxide isomers. Copyright © 2002 John Wiley & Sons, Ltd.     

Modern proton‐detected 1D 1H–15N NMR experiments. Application to the measurement of 1H,15N coupling constants at natural abundance

Non‐selective and selective versions of several proton‐detected 1D NMR experiments to be applied to ¹⁵N are proposed. Clean, artifact‐free 1D spectra are easily obtained by the effective coherence selection by pulsed‐field gradients and the attainable sensitivity is maximized using modern pulse schemes. Despite the low sensitivity inherent to ¹⁵N NMR spectroscopy, the successful application of these experiments is demonstrated for resonance assignments and accurate measurement of both one‐bond and long‐range proton–nitrogen coupling constants on a model tripeptide at natural abundance. Copyright © 2001 John Wiley & Sons, Ltd.     

A relationship between the half‐width of 73Ge NMR signals and hypercoordination in some phenylgermanes

⁷³Ge NMR spectra of some phenylgermanes were determined. The chemical shifts and half‐widths are discussed in terms of structure and in relation to hypercoordination of germanium atoms. It appears that linewidths can be a measure of hypercoordination. Copyright © 2002 John Wiley & Sons, Ltd.     

Isolation and spectral study of 4‐methyl‐6,8‐dihydroxy‐7H‐benz[de]anthracen‐7‐one

4‐Methyl‐6,8‐dihydroxy‐7H‐benz[de]anthracen‐7‐one was isolated from the sap of Aloe by column chromatography. Its ¹H and ¹³C NMR spectra were completely assigned by utilizing two‐dimensional ¹H‐detected heteronuclear one‐bond (HMQC) and multiple‐bond (HMBC) chemical shift correlation experiments together with ¹H–¹H COSY and DEPT techniques. These techniques were also valuable in assigning the protons and carbons of those benzanthrone compounds which were previously incompletely reported because of the overlap of proton signals. The molecular structure was elucidated by 2D NMR analysis. The spectral properties (MS, IR and UV) are also presented. Copyright © 2003 John Wiley & Sons, Ltd.     

Design,Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid‐State 19F NMR Spectroscopy

A conformationally restricted monofluorinated α‐amino acid, (3‐fluorobicyclo[1.1.1]pentyl)glycine (F‐Bpg), was designed as a label for the structural analysis of membrane‐bound peptides by solid‐state ¹⁹F NMR spectroscopy. The compound was synthesized and validated as a ¹⁹F label for replacing natural aliphatic α‐amino acids. Calculations suggested that F‐Bpg is similar to Leu/Ile in terms of size and lipophilicity. The ¹⁹F NMR label was incorporated into the membrane‐active antimicrobial peptide PGLa and provided information on the structure of the peptide in a lipid bilayer.     

Investigation of the binding of a carbohydrate-mimetic peptide to its complementary anticarbohydrate antibody by STD-NMR spectroscopy and molecular-dynamics simulations

Saturation transfer difference (STD)‐NMR spectroscopy was used to probe experimentally the bioactive solution conformation of the carbohydrate mimic MDWNMHAA 1 of the O‐polysaccharide of Shigella flexneri Y when bound to its complementary antibody, mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD? Molecular Dynamics platform were also undertaken to give a more accurate picture of the conformational flexibility and the possibilities for bound ligand conformations. The ligand topology, or the dynamic epitope, was mapped with the CORCEMA‐ST (COmplete Relaxation and Conformational Exchange Matrix Analysis of Saturation Transfer) program that calculates a total matrix analysis of relaxation and exchange effects to generate predicted STD‐NMR intensities from simulation. The comparison of these predicted STD enhancements with experimental data was used to select a representative binding mode. A protocol that employed theoretical STD effects calculated at snapshots during the entire course of a molecular dynamics (MD) trajectory of the peptide bound to the Fv portion of the antibody, and not the averaged atomic positions of receptor–ligand complexes, was also examined. In addition, the R factor was calculated on the basis of STD (fit) to avoid T1 bias, and an effective R factor, R_eff, was defined such that if the calculated STD (fit) for proton k was within error of the experimental STD (fit) for proton k, then that calculated STD (fit) for proton k was not included in the calculation of the R factor. This protocol was effective in deriving the antibody‐bound solution conformation of the peptide which also differed from the bound conformation determined by X‐ray crystallography; however, several discrepancies between experimental and calculated STD (fit) values were observed. The bound conformation was therefore further refined with a simulated annealing refinement protocol known as STD‐NMR intensity‐restrained CORCEMA optimization (SICO) to give a more accurate representation of the bound peptide epitope. Further optimization was required in this case, but a satisfactory correlation between experimental and calculated STD values was obtained. Attempts were also made to obtain STD enhancements with a synthetic pentasaccharide hapten, corresponding to the O‐polysaccharide, while bound to the antibody. However, unfavorable kinetics of binding in this system prevented sufficient STD build‐up, which, in turn, hindered a rigorous analysis via full STD build‐up curves.     

NMR analysis of mono‐ and difructosyllactosucrose synthesized by 1F‐fructosyltransferase purified from roots of asparagus (Asparagus officinalis L.)

Two novel oligosaccharides, mono‐ and difructosyllactosucrose {[O‐β‐D ‐fructofuranosyl‐(2 → 1)]_n‐β‐D ‐fructofuranosyl‐O‐[β‐D ‐galactopyranosyl‐(1 → 4)]‐α‐D ‐glucopyranoside, n = 1 and 2} were synthesized using 1^F‐fructosyltransferase purified form roots of asparagus (Asparagus officinalis L.). Their ¹H and ¹³C NMR spectra were assigned using several NMR techniques. The spectral analysis was started from two anomeric methines of aldose units, galactose and glucose, since they showed separate characteristic signals in their ¹H and ¹³C NMR spectra. After assignments of all the ¹H and ¹³C signals of two units of aldose, they were discriminated as galactose and glucose using proton–proton coupling constants. The HMBC spectrum revealed the galactose residue attached to C‐4 of glucose, fructose residue attached to the C‐1 of glucose, and further fructosyl fructose linkage extended from the glucosyl fructose residues. Copyright © 2002 John Wiley & Sons, Ltd.