1H NMR assignment and secondary structure of recombinant RGD-hirudin

The conformation of a new recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, was investigated by multi-dimensional NMR spectroscopy. The 1H NMR spectra of this protein are assigned in a sequential manner by using a combination of 2D NMR techniques to demonstrate through-bond and through-space (<5 A) connectivities. The secondary structure of recombinant RGD-hirudin was deduced from chemical shift indices, sequential NOEs and 3J(HNalpha) coupling constants. The results show that the recombinant RGD-hirudin has two anti-parallel beta-sheets and no alpha-helix, and also that the Arg-Gly-Asp (RGD) binding motif of this protein is located at the end of a long arm, which consists of two anti-parallel beta-strands (residues 26-31 and 36-41). As the strands are connected by a beta-turn, the recombinant RGD-hirudin acquires high flexibility and inhibits platelet aggregation more effectively.     

1H NMR and UV-visible data fusion for determining Sudan dyes in culinary spices

Two data fusion strategies (variable and decision level) combined with a multivariate classification approach (Partial Least Squares-Discriminant Analysis, PLS-DA) have been applied to get benefits from the synergistic effect of the information obtained from two spectroscopic techniques: UV-visible and ¹H NMR. Variable level data fusion consists of merging the spectra obtained from each spectroscopic technique in what is called “meta-spectrum” and then applying the classification technique. Decision level data fusion combines the results of individually applying the classification technique in each spectroscopic technique. Among the possible ways of combinations, we have used the fuzzy aggregation connective operators. This procedure has been applied to determine banned dyes (Sudan III and IV) in culinary spices. The results show that data fusion is an effective strategy since the classification results are better than the individual ones: between 80 and 100% for the individual techniques and between 97 and 100% with the two fusion strategies.     

Characterization of the measurement error structure in 1D H NMR data for metabolomics studies

NMR-based metabolomics is characterized by high throughput measurements of the signal intensities of complex mixtures of metabolites in biological samples by assaying, typically, bio-fluids or tissue homogenates. The ultimate goal is to obtain relevant biological information regarding the dissimilarity in patho-physiological conditions that the samples experience. For a long time now, this information has been obtained through the analysis of measured NMR signals via multivariate statistics.NMR data are quite complex and the use of such multivariate statistical methods as principal components analysis (PCA) for their analysis assumes that the data are multivariate normal with errors that are identical, independent and normally distributed (i.e. iid normal). There is a consensus that these assumptions are not always true for these data and, thus, several methods have been devised to transform the data or weight them prior to analysis by PCA. The structure of NMR measurement noise, or the extent to which violations of error homoscedasticity affect PCA results have neither been characterized nor investigated.A comprehensive characterization of measurement uncertainties in NMR based metabolomics was achieved in this work using an experiment designed to capture contributions of several sources of error to the total variance in the measurements. The noise structure was found to be heteroscedastic and highly correlated with spectral characteristics that are similar to the mean of the spectra and their standard deviation. A model was subsequently developed that potentially allows errors in NMR measurements to be accurately estimated without the need for extensive replication.     

Determination of the microstructure of polychloroprenes from 1H and 13C NMR data

Commercial samples of chloroprene rubbers were studied by high-resolution NMR spectroscopy (600 MHz). ¹H and ¹³C NMR proved to be efficient in quantitative analysis of the microstructure of polychloroprenes.     

Pore structure of samples of amorphous silica of various origins by data on 1H NMR

Pore structure of amorphous silica obtained from biogenic and mineral raw materials was studied by the nuclear magnetic resonance (¹H NMR) at 200–298 K. As biogenic raw materials were used fruit shells, rice and oats straw, larch needles, horsetail pedicels, and diatomic algae. The pore size distribution in silica samples of various origins was determined.     

Pyrroles from ketoximes and acetylene. 11. Conformation of 1-vinylpyrroles from1H NMR data

A number of 1-vinylpyrroles were studied by PMR spectroscopy. Bulky substituents in the position of the pyrrole ring give rise to deshielding of h_b and a decrease in²J(H_A,H_B) and⁶J(H₃,H_B). The results were interpreted as a decrease in the p, conjugation in the N-vinyl group due to distortion of the coplanarity. The dihedral angle () between the planes of the pyrrole ring and the double bond was estimated (with an accuracy of ±5 °).See [10] for our previous communication [10].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 328–330, March, 1980     

Pseudo-tetrahedral semi-sandwich cycloruthenated compounds: 1H NMR data and DFT-calculations about the racemisation process of the ruthenium atom

The partial substitution of the acetonitrile ligand of compound 1a 〚(η⁶-C₆H₆)Ru(C₆H₄-2-CH₂NMe₂)(NCMe)〛⁺PF₆^– by CD₃OD was observed while running the ¹H NMR spectra of 1a in this solvent, this giving rise to the formation of 1b. In opposition to 1a, the ¹H NMR spectrum of 1b is temperature-dependent, as at T > 40 °C the coalescence of the signals of the –CH₂NMe₂ protons was observed, this being an evidence for the fast racemisation of the Ru centre in 1b at the NMR timescale. DFT-calculations allowed us to envision a likely process for this racemisation. It should take place via the decoordination of the methanol ligand at an early step of the reaction, followed by the inversion of the configuration of the thus-obtained 16 e^– species (2). The transition state (3) for this latter reaction was identified and the total free energy of the racemisation was thus calculated, affording a value close to the activation energy found experimentally by ¹H NMR (∼13 kcal mol^–1 vs ∼15.5 kcal mol^–1, respectively).     

1H and 13C NMR spectral data of new saponins from Cordia piauhiensis

Two new bidesmoside triterpenoid saponins were isolated from stems of Cordia piauhiensis. Their structures, characterized as 3-O-alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl pomolic acid 28-O-beta-D-glucopyranosyl ester (1) and 3-O-alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl oleanolic acid 28-O-beta-D-glucopyranosyl-(1 --> 6)-beta-D-glucopyranosyl ester (2), were unequivocally established after extensive NMR (1H, 13C, DEPT 135 degrees, COSY, HSQC, HMBC, TOCSY, and NOESY) studies.     

Automated structure verification based on 1H NMR prediction

A unique opportunity exists when an experimental NMR spectrum is obtained for which a specific chemical structure is anticipated. A process of Verification--the confirmation of a postulated structure--is now possible, as opposed to Elucidation-the de novo determination of a structure. A method for automated structure verification is suggested, which compares the chemical shifts, intensities and multiplicities of signals in an experimental 1H NMR spectrum with those from a predicted spectrum for the proposed structure. A match factor (MF) is produced and used to classify the spectrum-structure match into one of three categories, correct, ambiguous, or incorrect. The verification result is also augmented by the spectrum assignment obtained as part of the verification process. This method was tested on a set of synthetic spectra and several sets of experimental spectra, all of which were automatically prepared from raw data. Taking into account even the most problematic structures, with many labile protons present and poor prediction accuracy, 50% of all spectra can still be automatically verified without any false positives or negatives. In a blind test on a typical set of data, it is shown that fewer than 31% of the structures would need manual evaluation. This means that a system is possible whereby 69% of the spectra are prepared and evaluated automatically, and never need to be seen or evaluated by a human.     

FICA,a new chiral derivatizing agent for determining the absolute configuration of secondary alcohols by 19F and 1H NMR spectroscopies

Optically active 1-fluoroindan-1-carboxylic acid (FICA) was designed and prepared as its methyl ester for determining the absolute configuration of chiral molecules by both ¹H and ¹⁹F NMR spectroscopies. Enantiomerically pure isomers of FICA methyl esters (FICA Me esters) were obtained by chromatographic separation using HPLC with a Daicel Chiralcel OJ-H column. The absolute configuration of the (+)-FICA Me ester was deduced to be (S) by X-ray crystallographic analysis of the (+)-FICA amide of (R)-α-phenethylamine. Both enantiomers were derived to the diastereomeric esters of chiral secondary alcohols by an ester exchange reaction. In the ¹H NMR spectra, the signs of Δδ_H (δ_R ? δ_S) were consistent on each side of the FICA molecular plane. Therefore, the concept of the modified Mosher’s method could be successfully applied to the FICA-based procedure. Moreover, the consistency in the signs of Δδ_F (δ_R ? δ_S) values suggests that the FICA method would be reliable in assigning the absolute configurations of secondary alcohols based on ¹⁹F NMR spectroscopy.     

Determining the absolute stereochemistry of secondary/secondary diols by 1H NMR: basis and applications

[structures: see text] The absolute configuration of 1,2-, 1,3-, 1,4-, and 1,5-diols formed by two secondary (chiral) hydroxy groups can be deduced by comparison of the NMR spectra of the corresponding bis-(R)- and bis-(S)-MPA esters. The correlation between the NMR spectra of the bis-ester derivatives and the absolute stereochemistry of the diol involves the comparison of the chemical shifts of the signals for substituents R1/R2 and for the hydrogens attached to the two chiral centers [H(alpha)(R1) and H(alpha)(R2)] in the bis-(R)- and the bis-(S)-ester and is expressed as delta deltaRS. Theoretical calculations [energy minimization by semiempirical (AM1), ab initio (HF), DFT (B3LYP), and Onsager methods, and aromatic shielding effect calculations] and experimental data (NMR and CD spectroscopy) indicate that in these bis-MPA esters, the experimental delta deltaRS values are the result of the contribution of the shielding/deshielding effects produced by the two MPA units that combine according to the actual stereochemistry of the diol. The reliability of these correlations is demonstrated with a wide range of diols of known absolute configuration derivatized with MPA and 9-AMA as auxiliary reagents. A simple graphical model that allows the simultaneous assignment of the two asymmetric carbons of a 1,n-diol by comparison of the NMR spectra (delta deltaRS signs) of its bis-(R)- and bis-(S)-AMAA ester derivatives is presented.     

Complete 1H and 13C NMR data assignment of new constituents from Severinia buxifolia

Phytochemical analysis of different organs of the rutaceaeous plant Severinia buxifolia led to the isolation of a new limonoid, a new acridone alkaloid, and a new flavone. Structure elucidation and signal assignment were achieved by the extensive use of 1D and 2D NMR experiments (selective 1D NOE, COSY, NOESY, HSQC, HMBC). Copyright © 2009 John Wiley & Sons, Ltd.     

An unusual spatial structure of di-ortho-substituted hetaryl vinyl ethers according to1H and13C NMR data

According to¹H and¹³C NMR data, 2,6-dimethyl-3,5-dichloro-4-vinyloxy-pyridine and 2-methyl-4-methoxymethyl-5-hydroxymethyl-3-vinyloxypyridine exist predominantly as the sterically hindered s-cis conformation, with the angle between the hetaryl ring and the vinyloxypyridine plane about 60°.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2040–2044, September, 1991.     

Complete 1H and 13C NMR data assignment of protolimonoids from the stem barks of Aphanamixis grandifolia

Seven new protolimonoids, named aphagranins A-G (1-7), along with four known compounds, were isolated from the ethanol extract of the stem barks of Aphanamixis grandifolia. Structure elucidation and signal assignments were achieved on the basis of spectral and chemical evidences.     

Rotational isomerism in 1-vinylpyrazoles and 1-vinylimidazoles from 1H and 13C NMR data and quantum-chemical calculations

A quantitative evaluation of the percentages of rotational isomers of 1-vinylpyrazoles and 1-vinylimidazoles was made on the basis of an analysis of the ¹H and ¹³C NMR spectral parameters and quantum-chemical calculations. It is shown that the populations of the s-cis-(N₍₂₎, N₍₃₎) and s-trans-(N₍₂₎, N₍₃₎) forms in both the 1-vinylpyrazole and in the 1-vinylimidazole are approximately equal.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1346–1351, October, 1990.     

Relative and absolute stereochemistry of secondary/secondary diols: low-temperature 1H NMR of their bis-MPA esters

Comparison of the room- and low-temperature 1H NMR spectra of the bis-(R)- or bis-(S)-MPA ester derivative of an open chain sec,sec-1,2-diol allows the easy determination of its relative stereochemistry and in some cases absolute configuration. If the diol is anti, its absolute configuration can be directly deduced from the signs of DeltadeltaT1T2 for substituents R1/R2, but if the relative stereochemistry of the diol is syn, the assignment of its absolute configuration requires the preparation of two derivatives (both the bis-(R)- and bis-(S)-MPA esters), comparison of their room-temperature 1H NMR spectra, and calculation of the DeltadeltaRS signs for the methines Halpha(R1) and Halpha(R2) and R1/R2 protons. The reliability of these correlations is validated with 17 diols of known absolute configuration used as model compounds.     

Complete assignments of 1H and 13C NMR data of three new dihydrophenanthrofurans from Pleione yunnanensis

Three new dihydrophenanthrofurans, pleionesins A–C (1–3), together with two known dihydrophenanthrenes (4–5) were isolated from the tubers of Pleione yunnanensis (Rolfe). The complete ¹H and ¹³C NMR spectra assignments of these compounds were carried out using 1D and 2D NMR experiments (¹H, ¹³C, selective 1D NOE, HSQC and HMBC). Copyright © 2010 John Wiley & Sons, Ltd.