scholarly journals Ditregra – an auxiliary program for structural determination of diterpenes

1997 ◽  
Vol 13 (3) ◽  
pp. 227-249 ◽  
Author(s):  
Sandra A. Vestri Alvarenga ◽  
Jean Pierre Gastmans ◽  
Gilberto do Vale Rodrigues ◽  
Vicente de Paulo Emerenciano
Keyword(s):  
Expert System ◽  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Heuristic Approach ◽  
Structural Determination ◽  
The Creation ◽  
Auxiliary Program ◽  
C Nmr

This work describes the creation of heuristics rules based on13C-NMR spectroscopy that characterize several skeletal types of diterpenes. Using a collection of 2745 spectra we built a database linked to the expert system SISTEMAT. Several programs were applied to the database in order to discover characteristic signals that identify with a good performance, a large diversity of skeletal types. The heuristic approach used was able to differentiate groups of skeletons based firstly on the number of primary, secondary, tertiary and quaternary carbons, and secondly the program searches, for each group, if there are ranges of chemical shifts that identifies specific skeletal type. The program was checked with 100 new structures recently published and was able to identify the correct skeleton in 65 of the studied cases. When the skeleton has several hundreds of compounds, for example, the labdanes, the program employs the concept of subskeletal, and does not classify in the same group labdanes with double bounds at different positions. The chemical shift ranges for each subskeletal types and the structures of all skeletal types are given. The consultation program can be obtained from the authors.

Determination of chemical shifts in 6-condensed syringylic lignin model compounds

Holzforschung ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Lucas Lagerquist ◽  
Jani Rahkila ◽  
Patrik Eklund
Keyword(s):  
Chemical Shift ◽  
Methoxy Group ◽  
Chemical Shifts ◽  
Model Compounds ◽  
Correlation Peak ◽  
Lignin Model Compounds ◽  
Benzylic Alcohols ◽  
Lignin Model ◽  
C Nmr

Abstract A small library of 6-substituted syringyl model compounds with aliphatic, carboxylic, phenylic, benzylic alcohols and brominated substituents were prepared. The influence of the substituents on the chemical shifts of the compounds was analyzed. All of model compounds showed a characteristic increase in the 13C NMR chemical shift of the methoxy group vicinal to the substitution. This 13C NMR peak and its corresponding correlation peak in HSQC could potentially be used to identify 6-condensation in syringylic lignin samples.

Determination of the configuration of ribitol in the C-polysaccharide of Streptococcus pneumoniae using a synthetic approach

1999 ◽  
Vol 77 (4) ◽  
pp. 481-494 ◽  
Author(s):  
Huiping Qin ◽  
T Bruce Grindley
Keyword(s):  
Streptococcus Pneumoniae ◽  
Chemical Shift ◽  
Spectral Data ◽  
Chemical Shifts ◽  
Natural Material ◽  
Synthetic Approach ◽  
Average Difference ◽  
Natural Polysaccharide ◽  
C Nmr

The C-polysaccharide is an antigen common to all known serotypes of Streptococcus pneumoniae bacteria and is a potential target for vaccine preparation. The final uncertainty in the structure of its repeating unit, a pentasaccharide phosphate containing two phosphorylcholine side chains, has been resolved by determining the configuration of ribitol. Assignment of configuration was performed by synthesis of the two trisaccharide phosphate fragments that have either D- or L-ribitol at their centers and comparison of their 1H and 13C NMR spectral data with that of the natural polysaccharide. The syntheses employed common synthons added in different orders to an asymmetrically substituted chiral ribitol derivative to obtain opposite chiralities in the ribitol segments. The data for the trisaccharide containing D-ribitol was almost identical to that of the natural material while that for the trisaccharide containing L-ribitol differed significantly. In particular, the chemical shift differences between the two protons of the primary carbons of ribitol units directly attached to the β-2-acetamido-2-deoxy-galactopyranosyl residue were 0.10, 0.12, and 0.33 ppm, in the natural polysaccharide, the D-ribitol-containing trisaccharide, and the L-ribitol-containing trisaccharide, respectively. The average difference between the 13C NMR chemical shifts of corresponding ribitol carbons from the natural polysaccharide and the D-ribitol-containing trisaccharide phosphate was 0.034 ppm. This evidence indicates that ribitol in the C-polysaccharide has the D-configuration and that a very similar mixture of conformations in the ribitol portions is present for the natural polysaccharide and the D-ribitol-containing trisaccharide phosphate.Key words: C-polysaccharide, Streptococcus pneumoniae, ribitol, dibutylstannylene acetal, determination of configuration.

Determination of the preferred tautomeric form of histamine by 13C nmr spectroscopy

1977 ◽  
Vol 55 (5) ◽  
pp. 576-578 ◽  
Author(s):  
William F. Reynolds ◽  
Chau W. Tzeng
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
13C Nmr ◽  
Tautomeric Form ◽  
Chemical Shifts ◽  
13C Nmr Spectroscopy ◽  
Imidazole Ring ◽  
Shift Method ◽  
Ph Dependent

The pH-dependent 13C chemical shifts for histamine indicate an approximate 4:1 preference for the Nτ-H tautomer of the imidazole ring, similar to that previously deduced for L-histidine. It is concluded that the 13C chemical shift method is a complimentary technique to the method of determining tautomer preference from pK values. Factors determining the tautomer preference in histamine and L-histidine are discussed.

MONOREG – an expert system for structural elucidation of monoterpenes

2001 ◽  
Vol 79 (12) ◽  
pp. 1915-1925 ◽  
Author(s):  
Marcelo J Ferreira ◽  
Gilberto V Rodrigues ◽  
Vicente P Emerenciano
Keyword(s):  
Expert System ◽  
Nmr Spectra ◽  
Structural Elucidation ◽  
Structural Determination ◽  
Systematic Data ◽  
Data Analyses ◽  
Nmr Data ◽  
Living Organisms ◽  
C Nmr

This paper describes a new expert system denominated MONOREG for structural determination of monoterpenes. This system is composed of five programs capable of performing 13C NMR spectra data analyses and analyses of systematic data from living organisms. At the end of this procedure, it shows the likely skeletons of the compound in question as well as the substructures compatible with the 13C NMR data. The system was tested on the skeleton elucidation of 40 monoterpenes from a wide variety of structure types and exhibited excellent results in the skeleton prediction process.

Structural Determination of the Hydrofullerene C60D36 by Neutron Diffraction

1998 ◽  
Vol 54 (3) ◽  
pp. 345-350 ◽  
Author(s):  
L. E. Hall ◽  
D. R. McKenzie ◽  
R. L. Davis ◽  
M. I. Attalla ◽  
A. M. Vassallo
Keyword(s):  
Neutron Diffraction ◽  
Density Function ◽  
Diffraction Data ◽  
Fourier Transformation ◽  
Structural Determination ◽  
Molecular Models ◽  
Reduced Density ◽  
C Nmr

A mixture of C60D36 with 24.5 \pm 4.5% C60 by weight has been analysed by neutron diffraction techniques. The diffraction data was converted to a reduced density function G(r) by Fourier transformation. The C60 component of the G(r) was subtracted out. This enabled a comparison for five molecular models of C60D36, with symmetries T, Th , S 6 and two D 3 d isomers, with the experimental G(r). This specimen of C60D36 was found to be best described by a T symmetry isomer, in agreement with 13C NMR and IR data for C60H36 [Attalla et al. (1993). J. Phys. Chem. pp. 6329–6331].

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

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