scholarly journals Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

2011 ◽  
Vol 7 ◽  
pp. 145-150 ◽  
Author(s):  
Catharine R Jones ◽  
Craig P Butts ◽  
Jeremy N Harvey
Keyword(s):  
Nuclear Overhauser Effect ◽  
Coupling Constants ◽  
Scalar Coupling ◽  
Dynamical Analysis ◽  
Flexible Molecules ◽  
Large Numbers ◽  
Distance Restraints ◽  
Nuclear Overhauser ◽  
Interproton Distances

The determination of accurate NOE-derived interproton distances and confirmation/prediction of relative populations in multi-conformer, flexible small molecules was investigated with the model compound 4-propylaniline. The low accuracy assumed for semi-quantitative NOE distance restraints is typically taken to suggest that large numbers of constraints need to be used in the dynamical analysis of flexible molecules, and this requires, for example, the measurement and Karplus-type analysis of scalar coupling constants (3 J CH and 3 J HH). Herein we demonstrate that, contrary to this common perception, NOE measurements alone are accurate enough to establish interproton distances, and hence conformational detail, in flexible molecules to within a few percent of their ensemble-averaged values, hence reducing the demand for additional restraints in such dynamic analyses.

scholarly journals Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

2017 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Scott D. Kennedy ◽  
Douglas H. Turner ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Overhauser Effect ◽  
Conformational Dynamics ◽  
Maximum Entropy Principle ◽  
Coupling Constants ◽  
Scalar Coupling ◽  
Conformational Ensemble ◽  
Entropy Principle ◽  
Nuclear Overhauser ◽  
Dynamics Simulations

We determine the conformational ensemble of four RNA tetranucleotides by using available nuclear magnetic spectroscopy data in conjunction with extensive atomistic molecular dynamics simulations. This combination is achieved by applying a reweighting scheme based on the maximum entropy principle. We provide a quantitative estimate for the population of different conformational states by considering different NMR parameters, including distances derived from nuclear Overhauser effect intensities and scalar coupling constants. We show the usefulness of the method as a general tool for studying the conformational dynamics of flexible biomolecules as well as for detecting inaccuracies in molecular dynamics force fields.

Time-averaged nuclear overhauser effect distance restraints applied to tendamistat

1990 ◽  
Vol 214 (1) ◽  
pp. 223-235 ◽  
Author(s):  
Andrew E. Torda ◽  
Ruud M. Scheek ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Nuclear Overhauser Effect ◽  
Overhauser Effect ◽  
Distance Restraints ◽  
Nuclear Overhauser

Beiträge zur Chemie des Silieiums und Germaniums, XXIX [1] 29Si-NMR-spektroskopische Untersuchungen von geradkettigen und verzweigten Silanen / Contributions to the Chemistry of Silicon and Germanium, XXIX [1] 29Si NMR Spectroscopic Investigations on Straight and Branched Silanes

1980 ◽  
Vol 35 (3) ◽  
pp. 282-296 ◽  
Author(s):  
Josef Hahn
Keyword(s):  
Nuclear Overhauser Effect ◽  
Empirical Relationship ◽  
Spin Systems ◽  
Coupling Constants ◽  
Complete Analysis ◽  
29Si Nmr ◽  
Overhauser Effect ◽  
Coupling Parameters ◽  
Nuclear Overhauser ◽  
Silicon And Germanium

,The structure of the straight silanes SinH2n+2 (1 ≤ n ≤ 7) and of the branched isomers isotetrasilane, iso- and neopentasilane, 2-silyl- and 3-silylpentasilane, 2,3-disilyltetrasilane as well as 2-silyl- and 3-silylhexasilane could be unambiguously elucidated by 29Si NMR spectroscopy. Systematic trends in the chemical shift and coupling parameters were observed and an empirical relationship between δ(29Si) of a 29Si nucleus and the number of the neighbouring silicon atoms in αβor γposition is given. In 1H decoupled spectra the nuclear Overhauser effect on the 29Si resonance was found to increase with increasing distance of the 29Si nucleus from the end of the chain. A complete analysis of the multi spin systems of disilane, trisilane and isotetrasilane was performed and the signs of the 29Si,H- and H,H-long range coupling constants were determined with regard to the negative sign of 1J(29SiH).

scholarly journals In Silico Modeling of Spirolides and Gymnodimines: Determination of S Configuration at Butenolide Ring Carbon C-4

Toxins ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 685
Author(s):  
Christian Zurhelle ◽  
Tilmann Harder ◽  
Urban Tillmann ◽  
Jan Tebben
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Nuclear Overhauser Effect ◽  
Resonance Spectroscopy ◽  
Functional Theory ◽  
Relative Configuration ◽  
Overhauser Effect ◽  
In Silico Modeling ◽  
Nuclear Overhauser

Only few naturally occurring cyclic imines have been fully structurally elucidated or synthesized to date. The configuration at the C-4 carbon plays a pivotal role in the neurotoxicity of many of these metabolites, for example, gymnodomines (GYMs) and spirolides (SPXs). However, the stereochemistry at this position is not accessible by nuclear Overhauser effect—nuclear magnetic resonance spectroscopy (NOE-NMR) due to unconstrained rotation of the single carbon bond between C-4 and C-5. Consequently, the relative configuration of GYMs and SPXs at C-4 and its role in protein binding remains elusive. Here, we determined the stereochemical configuration at carbon C-4 in the butenolide ring of spirolide- and gymnodimine-phycotoxins by comparison of measured 13C NMR shifts with values obtained in silico using force field, semiempirical and density functional theory methods. This comparison demonstrated that modeled data support S configuration at C-4 for all studied SPXs and GYMs, suggesting a biosynthetically conserved relative configuration at carbon C-4 among these toxins.

scholarly journals Determination of unresolved heteronuclear scalar coupling constants by J(up)-HSQMBC

2016 ◽  
Vol 268 ◽  
pp. 88-94 ◽  
Author(s):  
Simon Glanzer ◽  
Olaf Kunert ◽  
Klaus Zangger
Keyword(s):  
Coupling Constants ◽  
Scalar Coupling

scholarly journals Seven New Cytotoxic and Antimicrobial Xanthoquinodins from Jugulospora vestita

2020 ◽  
Vol 6 (4) ◽  
pp. 188
Author(s):  
Lulu Shao ◽  
Yasmina Marin-Felix ◽  
Frank Surup ◽  
Alberto M. Stchigel ◽  
Marc Stadler
Keyword(s):  
Nuclear Overhauser Effect ◽  
Rhodotorula Glutinis ◽  
Antibacterial Activities ◽  
Coupling Constants ◽  
Biologically Active ◽  
Pichia Anomala ◽  
Spectrometric Data ◽  
Gram Positive Bacteria ◽  
Mammalian Cell Lines ◽  
Nuclear Overhauser

During the course of a screening for novel biologically active secondary metabolites produced by the Sordariomycetes (Ascomycota, Fungi), the ex-type strain of Jugulospora vestita was found to produce seven novel xanthone-anthraquinone heterodimers, xanthoquinodin A11 (1) and xanthoquinodins B10–15 (2–7), together with the already known compound xanthoquinodin B4 (8). The structures of the xanthoquinodins were determined by analysis of the nuclear magnetic resonance (NMR) spectroscopic and mass spectrometric data. Moreover, the absolute configurations of these metabolites were established by analysis of the 1H−1H coupling constants, nuclear Overhauser effect spectroscopy (NOESY) correlations, and Electronic Circular Dichroism (ECD) spectroscopic data. Antifungal and antibacterial activities as well as cytotoxicity of all compounds were tested. Xanthoquinodin B11 showed fungicidal activities against Mucor hiemalis [minimum inhibitory concentration (MIC) 2.1 µg/mL], Rhodotorula glutinis (MIC 2.1 µg/mL), and Pichia anomala (MIC 8.3 µg/mL). All the compounds 1–8 displayed anti-Gram-positive bacteria activity (MIC 0.2–8.3 µg/mL). In addition, all these eight compounds showed cytotoxicity against KB 3.1, L929, A549, SK-OV-3, PC-3, A431, and MCF-7 mammalian cell lines. The six novel compounds (1–3, 5–7), together with xanthoquinodin B4, were also found in the screening of other strains belonging to Jugulospora rotula, revealing the potential chemotaxonomic significance of the compound class for the genus.

Determination of configuration and conformation of isoxazolidines by nuclear Overhauser effect difference spectroscopy

1982 ◽  
Vol 47 (23) ◽  
pp. 4397-4403 ◽  
Author(s):  
Philip DeShong ◽  
C. Michael Dicken ◽  
Ronald R. Staib ◽  
Alan J. Freyer ◽  
Steven M. Weinreb
Keyword(s):  
Nuclear Overhauser Effect ◽  
Difference Spectroscopy ◽  
Overhauser Effect ◽  
Effect Difference ◽  
Nuclear Overhauser ◽  
Configuration And Conformation

Applications of the intermolecular nuclear Overhauser effect. I. Determination of differential solvent effects: the hydration of pyridine

1983 ◽  
Vol 36 (3) ◽  
pp. 493 ◽  
Author(s):  
GR Smith ◽  
B Ternai
Keyword(s):  
Nuclear Overhauser Effect ◽  
Water System ◽  
Lattice Relaxation ◽  
Spin Lattice Relaxation ◽  
Alternative Methods ◽  
Relaxation Rates ◽  
Overhauser Effect ◽  
Nuclear Overhauser ◽  
Intermolecular Relaxation

The intermolecular relaxation rates of the pyridine-water system have been obtained by the measurement of the total spin lattice relaxation rate and the intermolecular nuclear Overhauser effect between pyridine and water, for each pyridine proton. The advantages of this method for the determination of the intermolecular relaxation rates are discussed, and the method is compared with alternative methods. The results indicate that there is a varying degree of hydration about the pyridine molecule, with the nitrogen being the preferred site of water interaction. It is necessary to interpret the results in terms of solute-solute as well as solute-solvent interactions. A model is proposed which takes account of both types of interaction, and is considered in terms of previously proposed models of pyridine-water interactions.

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