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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.4K
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Conformations of Cyclohexane02:11

Conformations of Cyclohexane

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Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
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Fischer Projections02:18

Fischer Projections

17.7K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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Conformations of Butane02:20

Conformations of Butane

20.4K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
20.4K
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

21.2K
The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this...
21.2K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.8K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.8K

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Insights into furanose solution conformations: beyond the two-state model.

Xiaocong Wang1, Robert J Woods2

  • 1Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.

Journal of Biomolecular NMR
|March 13, 2016
PubMed
Summary

The two-state model for furanose conformations is generally valid, but molecular dynamics simulations reveal exceptions for specific sugars like methyl α-D-arabinofuranoside, which adopt a wider range of states.

Keywords:
AMBERAnomeric effectGLYCAMMolecular dynamics simulationPotential energy surfacePseudorotation

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Area of Science:

  • Carbohydrate Chemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • The two-state model, using NMR scalar J-coupling constants, is standard for interpreting furanose ring conformations.
  • This model assumes narrow distributions in North and South pseudorotation states.
  • The validity of this simplified approach has been recently questioned.

Purpose of the Study:

  • To rigorously examine the validity of the two-state model for furanose ring conformations.
  • To investigate the influence of force field parameters and simulation methods on conformational analysis.
  • To identify factors contributing to deviations from the two-state model.

Main Methods:

  • Employed molecular dynamics (MD) simulations with a new GLYCAM force field parameter set specifically for furanoses.
  • Calculated theoretical (3) J-coupling constants from unrestrained MD simulations.
  • Compared theoretical coupling constants with experimental data.

Main Results:

  • MD simulations with the new parameters accurately reproduced experimental (3) J-coupling constants (average difference < 1 Hz).
  • The two-state model remains a reasonable approximation for most methyl furanosides.
  • Methyl α-D-arabinofuranoside exhibited a continuum of conformations, deviating from the two-state model.

Conclusions:

  • The study validates the two-state model for most methyl furanosides but highlights exceptions.
  • Deviations arise from destabilization of East/West regions due to the absence of the anomeric effect in α-anomers.
  • Repulsive interactions between hydroxyl groups and ring oxygen in syn-configurations further destabilize certain conformations.