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Related Concept Videos

Stereoisomerism of Cyclic Compounds02:33

Stereoisomerism of Cyclic Compounds

9.7K
In this lesson, we delve into the role of ring conformation and its stability, which determines the spatial arrangement and, consequently, the molecular symmetry and stereoisomerism of cyclic compounds. 1,2-Dimethylcyclohexane is used as a case study to evaluate the possible number of stereoisomers. Here, given the multiple (n = 2) chiral centers, there are 2n = 4 possible configurations that lack a plane of symmetry, as the ring skeleton exists in a non-planar chair conformation. In addition,...
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Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

16.1K
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...
16.1K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

947
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...
947
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

13.7K
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...
13.7K
Stability of Substituted Cyclohexanes02:30

Stability of Substituted Cyclohexanes

13.5K
This lesson discusses the stability of substituted cyclohexanes with a focus on energies of various conformers and the effect of 1,3-diaxial interactions.
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
13.5K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.2K
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.
1.2K

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Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
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Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

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Conformational preferences induced by cyclization in orbitides: a vibrational CD study.

Maria A S Yokomichi1, Hanyeny R L Silva2, Lorenza E V N Brandao3

  • 1Institute of Science and Technology, Federal University of Sao Paulo (Unifesp), Rua Talim 330, Sao Jose dos Campos, SP 12231-280, Brazil. batista.junior@unifesp.br.

Organic & Biomolecular Chemistry
|January 25, 2022
PubMed
Summary

Vibrational circular dichroism (VCD) reveals new conformations of orbitides, cyclic peptides crucial for medicinal chemistry. This technique offers superior conformational analysis compared to NMR, aiding in drug design.

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Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism
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Area of Science:

  • Biophysical Chemistry
  • Natural Products Chemistry
  • Medicinal Chemistry

Background:

  • Orbitides are plant-derived cyclic peptides with significant bioactivity.
  • Accurate characterization of orbitide solution conformations is vital for medicinal chemistry but challenging.
  • Nuclear Magnetic Resonance (NMR) spectroscopy has limitations in capturing the full conformational ensemble of orbitides.

Purpose of the Study:

  • To investigate the solution-state conformational behavior of the orbitide pohlianin A and its linear precursor using Vibrational Circular Dichroism (VCD).
  • To compare the conformational insights gained from VCD with those from NMR spectroscopy.
  • To explore the utility of VCD in characterizing turn-rich peptidic natural products.

Main Methods:

  • Infrared (IR) and VCD spectroscopy experiments were conducted in acetonitrile-d3 and acetonitrile-d3/D2O mixtures.
  • Density Functional Theory (DFT) calculations were employed at various levels of theory.
  • Conformational analysis was performed on both the linear precursor and the cyclic orbitide.

Main Results:

  • VCD identified inverse γ-turns in the linear precursor and type I/VI β-turns and γ-turns in the cyclic orbitide.
  • Two previously unidentified conformations of the cyclic peptide were discovered, significantly populated in solution.
  • VCD provided enhanced conformational discrimination compared to NMR, revealing a more complete picture of the conformational landscape.

Conclusions:

  • VCD is a powerful tool for stereochemical investigation of orbitides, surpassing NMR in conformational detail.
  • Cyclization of the peptide backbone induces specific turn structures, influencing the overall conformation.
  • The conformational insights from VCD can improve structure-activity relationship studies and guide the design of novel peptide-based therapeutics.