Unambiguous Assignment Of Signals Research Articles

Inside Cover: A Single‐Scan Ultraselective Heteronuclear Polarization Transfer Method for Unambiguous Complex Structure Assignment (Angew. Chem. Int. Ed. 32/2023)

The unambiguous assignment of NMR signals to complex organic molecules or mixtures is a challenge. In their Research Article (e202304196), Jin Wook Cha, Min-Seon Kim, and Jin-Soo Park suggest an ultrahigh-resolution single-scan NMR method that enables to acquire a hertz-level signal selectivity in both 1H, 13C and their correlation spectra. The method was applied to compounds with high NMR signal complexity, such as chromopeptide and diastereomeric mixtures, and resulted in complete 1H and 13C NMR signal assignment of individual subunits and epimers.

Innentitelbild: A Single‐Scan Ultraselective Heteronuclear Polarization Transfer Method for Unambiguous Complex Structure Assignment (Angew. Chem. 32/2023)

The unambiguous assignment of NMR signals to complex organic molecules or mixtures is a challenge. In their Research Article (e202304196), Jin Wook Cha, Min-Seon Kim, and Jin-Soo Park suggest an ultrahigh-resolution single-scan NMR method that enables to acquire a hertz-level signal selectivity in both 1H, 13C and their correlation spectra. The method was applied to compounds with high NMR signal complexity, such as chromopeptide and diastereomeric mixtures, and resulted in complete 1H and 13C NMR signal assignment of individual subunits and epimers.

Simulation and Analysis of the Transient Absorption Spectrum of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Acetonitrile.

4-(N,N-Dimethylamino)benzonitrile (DMABN) is a well-known model compound for dual fluorescence—in sufficiently polar solvents, it exhibits two distinct fluorescence emission bands. The interpretation of its transient absorption (TA) spectrum in the visible range is the subject of a long-standing controversy. In the present study, we resolve this issue by calculating the TA spectrum on the basis of nonadiabatic molecular dynamics simulations. An unambiguous assignment of spectral signals to specific excited-state structures is achieved by breaking down the calculated spectrum into contributions from twisted and nontwisted molecular geometries. In particular, the much-discussed excited-state absorption band near 1.7 eV (ca. 700 nm) is attributed to the near-planar locally excited (LE) minimum on the S1 state. On the technical side, our study demonstrates that the second-order approximate coupled cluster singles and doubles (CC2) method can be used successfully to calculate the TA spectra of moderately large organic molecules, provided that the system in question does not approach a crossing between the lowest excited state and the singlet ground state within the time frame of the simulation.

Facilitated structure verification of the biopharmaceutical peptide exenatide by 2D heteronuclear NMR maps

Exenatide is a peptide based anti-diabetic prescription medication. Until now, the literature has lacked a comprehensive atom-specific molecular characterization for this complex large peptide by NMR spectroscopy that can be effortlessly and rapidly utilized for biopharmaceutical structural veracity. Peptide structure verification by NMR is challenging and cumbersome when reliant on traditional proton-based methodology (through-bond and through-space proton connectivity) alone due to increasing complexity, low signal dispersion, and overlap. These challenges are overcome by using 2D heteronuclear (1H-13C and 1H-15N) maps that not only allow unambiguous signal assignment, but also condense the structural verification information within simplified peptide amide and carbon fingerprint maps. Here we report such simplified amide and carbon fingerprint maps for exenatide; made possible by the first ever comprehensive heteronuclear (1H,13C, and 15N) atom specific assignment of exenatide. These heteronuclear assignments were obtained without any isotopic enrichments i.e. at natural abundance, and hence are easily deployable as routine procedures. Furthermore, we compare the 2D heteronuclear maps of exenatide to a chemically identical peptide differing only in the isomerism of the Cα position of the first amino acid, [dHis1]-exenatide, to demonstrate the uniqueness of these maps. We show that despite deliberate changes in pH, temperature, and concentrations, the differences between the amide maps of exenatide and [dHis1]-exenatide are retained. The work presented here not only provides a facilitated structure verification of exenatide but also a framework for heteronuclear NMR data acquisition and signal assignment of large peptides, at natural abundance, in creating their respective unique 2D fingerprint maps.

NNN‐Cobalt(II) Pincer Complexes: Paramagnetic NMR Spectroscopy in Solution and Application as Hydrosilylation Catalysts

The tridentate, monoanionic bis(oxazolinylmethylidene)‐isoindolate pincer ligand was utilized for the synthesis of various cobalt(II) high‐spin complexes. Employing standard complexation procedures, the corresponding acetato and chlorido complexes were isolated in good yields and thoroughly characterized in the solid‐state and in solution. In particular, a density functional theory (DFT) supported paramagnetic NMR analysis revealed a strong correlation between observed 13C NMR shifts and calculated spin‐density distributions, allowing for an unambiguous signal assignment in all 1H and 13C NMR spectra. An acetato‐bridged trinuclear cobalt species as well as the hexacoordinate “homoleptic” complex [(Rboxmi)2Co] were further identified as side products generated in the complex synthesis. The chlorido complexes were applied as catalysts for the cobalt‐catalyzed hydrosilylation of acetophenone, producing the chiral secondary alcohol with moderate enantioselectivities.

Multinuclear NMR Studies and Spin System Analyses on Dibenzo[c.e][1,2]Oxaphosphorine 2‐Oxides

ABSTRACT2H‐Dibenzo[c.e][1,2]oxaphosphorine 2‐oxide (HDOPO), 2‐(N,N‐diethylamino)‐dibenzo[c.e][1,2]oxaphosphorine 2‐oxide (DEADOPO), and 2‐ethoxy‐dibenzo[c.e][1,2]oxaphosphorine 2‐oxide (EtODOPO) are fully characterized in CDCl3 by 1H, 13C, 31P, and 15N NMR spectroscopy on 800‐ and 500‐MHz instruments. A strategy enabling their unambiguous signal assignment is presented, with special emphasis on 2D 1H,13C HMBC spectra. Additional line‐shape iterations of the aromatic 1H multiplets (ABCDX and ABCDEX spin systems) provided all long‐range nJH,H and nJP,H coupling constants with utmost precision. The experimental results augmented with those of the model compound phenylphosphonous acid clearly demonstrate that nJH,H couplings of the PH proton as well as the nJP,C values do not decrease in a monotonic manner with the number of intervening bonds from the phosphorus atom. This fact may potentially lead signal misassignments, if the analysis starts out from the coupling constants, as it occurred for HDOPO in the recent publication by Wagner et al. (Phosphorus, Sulfur and Silicon, 187, 2012, 781–798). The corrected assignment will be given in the present paper. Finally, the A2M3X or ABM3X type 1H spectral patterns of ethyl groups are also analyzed and explicit equations are derived to evaluate the strongly coupled ABM3X multiplets in EtODOPO.

Comparison of spike parameters from optically identified GABAergic and glutamatergic neurons in sparse cortical cultures

Primary neuronal cultures share many typical features with the in vivo situation, including similarities in distinct electrical activity patterns and synaptic network interactions. Here, we use multi-electrode array (MEA) recordings from spontaneously active cultures of wildtype and glutamic acid decarboxylase 67 (GAD67)-green fluorescent protein (GFP) transgenic mice to evaluate which spike parameters differ between GABAergic interneurons and principal, putatively glutamatergic neurons. To analyze this question we combine MEA recordings with optical imaging in sparse cortical cultures to assign individual spikes to visually-identified single neurons. In our culture system, excitatory and inhibitory neurons are present at a similar ratio as described in vivo, and spike waveform characteristics and firing patterns are fully developed after 2 weeks in vitro. Spike amplitude, but not other spike waveform parameters, correlated with the distance between the recording electrode and the location of the assigned neuron’s soma. Cluster analysis of spike waveform properties revealed no particular cell population that may be assigned to putative inhibitory or excitatory neurons. Moreover, experiments in primary cultures from transgenic GAD67-GFP mice, which allow optical identification of GABAergic interneurons and thus unambiguous assignment of extracellular signals, did not reveal any significant difference in spike timing and spike waveform parameters between inhibitory and excitatory neurons. Despite of our detailed characterization of spike waveform and temporal spiking properties we could not identify an unequivocal electrical parameter to discriminate between individual excitatory and inhibitory neurons in vitro. Our data suggest that under in vitro conditions cellular classifications of single neurons on the basis of their extracellular firing properties should be treated with caution.

Unambiguous assignment of 13C NMR signals in epimeric 4,5-epoxy-3-oxo-steroids assisted by X-ray diffraction and gauge invariant atomic orbitals calculation of absolute isotropic shieldings

Complete assignments of the 13 C signals of diastereomeric 4,5-epoxy-3-oxo steroids based on a combination of 1D and 2D NMR techniques are described The assignments were corroborated or corrected by calculation of the absolute isotropic 13 C NMR shieldings using the Gauge Invariant

NMR methods for structural studies of large monomeric and multimeric proteins.

NMR structural studies of large monomeric and multimeric proteins face distinct challenges. In large monomeric proteins, the common occurrence of frequency degeneracies between residues impedes unambiguous assignment of NMR signals. To overcome this barrier, nonuniform sampling (NUS) is used to measure spectra with optimal resolution within reasonable time, new correlation maps resolve previous impasses in assignment strategies, and novel selective methyl labeling schemes provide additional structural probes without cluttering NMR spectra. These advances push the limits of NMR studies of large monomeric proteins. Large multimeric and multidomain proteins are studied by NMR when individual components can also be studied by NMR and have known structures. The structural properties of large assemblies are obtained by identifying binding surfaces, by orienting domains, and employing limited distance constraints. Segmental labeling and the combination of NMR with other methods have helped popularize NMR studies of such systems.

“Perfect Echo” HMQC: Sensitivity and resolution enhancement by broadband homonuclear decoupling

Homonuclear 1H–1H J-modulation leads to J-multiplets in F1 dimension of 2D 1H–13C HMQC spectra. This hampers unambiguous signal assignment for overcrowded 13C spectra. Broadband homonuclear decoupling has been achieved in the indirect t1 evolution period by incorporating blocks of perfect echo. This method of perfect echo HMQC demonstrates better resolution and sensitivity than conventional HMQC spectra. The results on Cyclosporine demonstrate that the method is very efficient for refocusing geminal couplings in weakly coupled –13CH2 groups. Partial refocusing of vicinal couplings is also observed for –13CH and –13CH3 groups. Interpretation of the result based on product operator formalism is also given. Comparison of pe-HMQC, HMQC and HSQC reveals that the F1 linewidth of pe-HMQC is much narrower than HMQC and very close to that of HSQC for CH2 groups.

1H‐NMR Fingerprinting of Vaccinium vitis‐idaea Flavonol Glycosides

The fruits of Vaccinium vitis-idaea L. are a valuable source of biologically active flavonoid derivatives. For studies focused on the purification of its quercetin glycosides (QGs) and related glycosides from plants and for the purpose of biological studies, the availability of numeric datasets from computer-assisted ¹H iterative full spin analysis (HiFSA), that is, ¹H-NMR fingerprinting, can replace and assist the repetitive and tedious two-dimensional NMR identification protocol required for both known and new compounds, respectively. To fully interpret the complex ¹H-NMR fingerprints of eight QGs obtained from the berries of V. vitis-idaea and provide complete and unambiguous signal assignments. Vaccinium vitis-idaea QGs were purified in a single run by long-bed gel permeation chromatography and identified by comparison with commercially available compounds using LC-MS combining ion-trap and time-of-flight detection and one- or two-dimensional NMR. The HiFSA analysis yielded full sets of ¹H chemical shifts and proton-proton coupling constants, allowing for field-independent spectral simulation. Signal assignments were achieved for the reference standards and the QGs that dominated in purified fractions. However, even mixtures of two to three QGs could be fitted using the HiFSA approach. In the case of the overlapped sugar resonances, the initial fitting of the ¹H spectra of reference compounds, together with values extracted from the two-dimensional NMR data and literature data, assisted in the process. The HiFSA method revealed for the first time the presence of Q-3-O-β-glucopyranoside and Q-3-O-β-glucuronopyranoside in the berries of V. vitis-idaea, and unambiguously confirmed the structures of Q-3-O-[4″-(3-hydroxy-3-methylglutaroyl)]-α-rhamnopyranoside, Q-3-O-α-rhamnopyranoside, Q-3-O-β-galactopyranoside, Q-3-O-α-arabinofuranoside, Q-3-O-β-xylopyranoside and Q-3-O-α-arabinopyranoside.

Broadband homodecoupled heteronuclear multiple bond correlation spectroscopy

A general concept for removing proton–proton scalar J couplings in 2D NMR spectroscopy is proposed. The idea is based on introducing an additional J resolved dimension into the pulse sequence of a conventional 2D experiment to design a pseudo 3D NMR experiment. The practical demonstration is exemplified on the widely used gradient coherence selected heteronuclear long-range correlation spectroscopy (HMBC). We refer to this type of pulse sequence as tilt HMBC experiment. For every 13C chemical shift evolution increment, a homonuclear J resolved experiment is recorded. The long-range defocusing delay of the HMBC pulse sequence is exploited to implement this building block. The J resolved evolution period is incremented in a way very similar to ACCORDION spectroscopy to accommodate the buildup of heteronuclear long-range antiphase magnetisation as well. After Fourier transformation in all dimensions the spectra are tilted in the J resolved dimension. Finally, a projection along the J resolved dimension is calculated leading to almost disappearance of proton–proton spin multiplicities in the 2D tilt HMBC spectrum. The tilt HMBC experiment combines sensitivity with simple experimental setup and can be recorded with short recycle delays, when combined with Ernst angle excitation. The recorded spectra display singlet proton signals for long-range correlation peaks making an unambiguous signal assignment much easier. In addition to the new experiment a simple processing technique is applied to efficiently suppress the noise originating from forward linear prediction in the indirect evolution dimensions. In case of issues with fast repetition times, probe heating and RF power handling most of the RF pulses can be replaced by broadband, frequency swept pulses operating at much lower power.

GIAO chemical shifts calculations of some polycyclic cage compounds: Unambiguous assignment of NMR signals and stereoisomers

Abstract GIAO model at DFT/B3LYP level of theory using the cc-pVTZ basis set was employed for calculations of 1H and 13C NMR chemical shifts (δ) for various rigid polycyclic compounds. The data obtained were used as an auxiliary tool to an unequivocal assignment of all 1H and 13C NMR signals and the endo/exo stereochemistry of the strained compounds studied. For these compounds the theoretical model adopted was sufficient to obtain a good description of chemical shifts.

4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins

A four-dimensional (4D) APSY (automated projection spectroscopy)-HBCB(CG)CDHD experiment is presented. This 4D experiment correlates aromatic with aliphatic carbon and proton resonances from the same amino acid side chain of proteins in aqueous solution. It thus allows unambiguous sequence-specific assignment of aromatic amino acid ring signals based on backbone assignments. Compared to conventional 2D approaches, the inclusion of evolution periods on (1)H(β) and (13)C(δ) efficiently removes overlaps, and provides two additional frequencies for consequent automated or manual matching. The experiment was successfully applied to three proteins with molecular weights from 6 to 13 kDa. For the complementation of the assignment of the aromatic resonances, TOCSY- or COSY-based versions of a 4D APSY-HCCH(aro) sequence are proposed.

High-Resolution Solid-State NMR Structure of a 17.6 kDa Protein

The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.

Experimental access to HSQC spectra decoupled in all frequency dimensions

A new operator called RESET “Reducing nuclEar Spin multiplicitiEs to singuleTs” is presented to acquire broadband proton decoupled proton spectra in one and two dimensions. Basically, the homonuclear decoupling is achieved through the application of bilinear rotation pulses and delays. A [BIRD] r,x pulse building block is used to selectively invert all proton magnetization remotely attached to 13C isotopes, which is equivalent to a scalar J decoupling of the protons directly attached to 13C from all other protons in the spin system. In conjunction with an appropriate data processing technique pure shift proton spectra are obtained. For this purpose, the concept of constant time acquisition in the observe dimension is exploited. Both ideas were merged together producing superior HSQC based pseudo 3D pulse sequences. The resulting HSQC spectra show cross peaks with collapsed multiplet structures and singlet responses for the proton chemical shift frequencies. An unambiguous assignment of signals from overcrowded spectra becomes much easier. Finally, the recently introduced SHARC technique is exploited to enhance the capability of the scalar J decoupling method. A significant reduction of the total measurement time is achieved. The time is saved by reducing the number of 13C chemical shift evolution increments and working with superimposed narrow spectral bandwidths in the 13C indirect domain.

DFT studies of the structure and vibrational and NMR spectra of 1-(2-methylpropenyl)-2-methylbenzimidazole

Synthesis of two new 1-(2-methylpropenyl)-2-methylbenzimidazoles by reaction of 2-methylbenzimidazole with 3-chloro-2-methylpropene using a strong base as a catalyst is described. Gas chromatography–mass spectrometry (GC–MS) allowed the characterization of the structural isomers: the slightly more stable 1-(2-methyl-1-propenyl)-2-methylbenzimidazole (51%) and a less stable 1-(2-methyl-2-propenyl)-2-methylbenzimidazole (49%). The results of theoretical calculations indicate that the difference in the energy between the two structural isomers is 3.21 kcal mol −1 at the B3LYP/6-311+G ∗∗ level. The structures were confirmed by 1H and 13C Nuclear Magnetic Resonance, elemental analysis and spectroscopic methods such as FT-Raman, FT-IR and UV–VIS. The experimental results were supported by performing DFT calculations for energies, geometries, vibrational frequencies and shieldings constants using 6-311+G ∗∗ basis sets and B3LYP functional. The theoretical data have satisfactorily reproduced the experimental results. The consistency and efficiency of the GIAO method used to calculate absolute shielding of the studied compounds were checked by the analysis of statistical parameters and were found to be in excellent agreement with experimental values. This correlation has been used for unambiguous NMR signal assignments for studied compounds.

C [sbnd]N bond rotation and E– Z isomerism in some N-benzyl- N-methylcarbamoyl chlorides: A DFT study

The current report presents the first theoretical study of the restricted C N bond rotation in carbamoyl chlorides. Several N-benzyl- N-methylcarbamoyl chlorides were investigated, with varying pattern of substitution in the aromatic ring. Optimizations and frequency calculations were conducted employing DFT at the B3LYP/6-31+G(d) level of theory. Each of the studied structures exhibits a pair of rotamers (s- Z and s- E), generated upon rotation around the C( O) N bond. The s- E isomer is the global minimum in every case, but the preference for it is usually less than 1 kcal/mol. Two possible transition state structures were identified for the rotamer interconversion: TS syn and TS anti , in close analogy to other related compounds, such as amides and carbamates. In contrast to the two latter types, however, the preferred transition state in the case of carbamoyl chlorides is TS syn , which we attribute to a stabilizing gauche effect. The optimized minima structures of the studied carbamoyl chlorides were subjected to GIAO B3LYP/6-311+G(2d,p) calculations, and the resultant isotropic shifts were found to be in excellent agreement with available experimental values. This has allowed us to provide unambiguous NMR signal assignments for the s- E and s- Z isomers of the studied compounds.

Unambiguous Assignment of NMR Protein Backbone Signals with a Time-shared Triple-resonance Experiment

An experiment that provides a simple procedure to assign backbone nuclei in proteins is presented. The method relies on time-shared evolution of the coherences present in the (HN)NCAHA and (HA)CANNH experiments. By exploiting the fact that some of the coherences are common to both experiments the alpha and amide protons that are simultaneously detected are correlated with each other and with nitrogen and carbon nuclei. Thus, simultaneous assignment of Halpha, H(N), Calpha and N signals is achieved in a single 3D spectrum. The experiment was tested on the streptococcal protein G B1 domain (GB1) which was easily assigned using a "stairway" procedure and on an 11 kDa domain of the yeast transcriptional co-activator Gal11.

Synthesis and Resolution of the Atropisomeric 1,1'-Bi-2-naphthol: An Experiment in Organic Synthesis and 2-D NMR Spectroscopy

The synthesis and resolution of the atropisomeric 1,1'-bi-2-naphthol illustrates several important concepts in organic chemistry and serves as a good experiment for organic chemistry laboratory course of intermediate to advanced levels. Racemic 1,1'-bi-2-naphthol is synthesized by the oxidative coupling of 2-naphthol and is resolved into the enantiopure form by the selective inclusion compound formation of the R enantiomer with (−)-N-benzylcinchonidinium chloride. The enantiomeric excess of the products are determined by chiral HPLC. The naphthol unit of 1,1'-bi-2-naphthol is composed of a benzene and a phenol fused together. Both 1H and 13C NMR spectra show complicated and overlapping signals in the aromatic region and complete signal assignment is extremely difficult. Unambiguous signal assignment is made possible with the help of various 2-D NMR techniques such as COSY, HMQC, and COLOC. It serves as an advanced exercise for spectroscopic structural identification of organic compounds.