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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.6K
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.
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Conformations of Cyclohexane02:11

Conformations of Cyclohexane

14.9K
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...
14.9K
Thermal Strain01:19

Thermal Strain

2.7K
Thermal strain is a concept that arises when we consider how temperature changes affect structures. Unlike the conventional assumption that structures remain constant under load, real-world scenarios often involve temperature fluctuations that can significantly impact these structures. Consider a homogeneous rod with a uniform cross-section resting freely on a flat horizontal surface. If the rod's temperature increases, the rod elongates. This elongation is proportional to the temperature...
2.7K
Thermal expansion and Thermal stress: Problem Solving01:27

Thermal expansion and Thermal stress: Problem Solving

2.0K
San Francisco's Golden Gate Bridge is exposed to temperatures ranging from -15 °C to 40 °C. At its coldest, the main span of the bridge is 1275 m long. Assuming that the bridge is made entirely of steel, what is the change in its length between these temperatures?
To solve the problem, first, identify the known and unknown quantities. The initial length (L) of the bridge is 1275 m, the coefficient of linear expansion (α) for steel is 12 x 10-6/°C, and the change in temperature (ΔT) is 55...
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Thermal Sigmatropic Reactions: Overview01:16

Thermal Sigmatropic Reactions: Overview

2.4K
Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in 1,5-hexadiene, referred...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis.

Tadeo E Saldaño1, Victor M Freixas1, Silvio C E Tosatto2

  • 1Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD Bernal, Argentina.

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Summary

This study introduces an iterative method to explore protein dynamics and conformational changes. It successfully models protein flexibility and conformational selection between different states, aiding drug design.

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Area of Science:

  • Structural Biology
  • Computational Biophysics
  • Protein Dynamics

Background:

  • Proteins exist as dynamic ensembles of conformers in equilibrium.
  • Thermal fluctuations drive transitions between these protein conformers.
  • Normal-modes analysis (NMA) with elastic network models (ENMs) explores protein global dynamics.

Purpose of the Study:

  • To develop an iterative approach for exploring protein conformational spaces.
  • To enable unbiased exploration or guided pathways between protein conformations (e.g., apo and holo forms).
  • To investigate protein conformational selection and dynamics.

Main Methods:

  • An iterative method introducing structural distortions based on equilibrium dynamics.
  • Application to four proteins with varying ligand-binding induced structural changes.
  • Testing strategies for efficient conformational change and exploration of protein conformational multiplicity.

Main Results:

  • The iterative approach successfully explored conformational spaces between apo and holo forms.
  • The conformational selection model was consistently confirmed across tested proteins.
  • Different strategies impacted the efficiency of achieving desired conformational changes.

Conclusions:

  • The developed iterative approach effectively models protein conformational ensembles and dynamics.
  • It validates the conformational selection mechanism in ligand binding.
  • The method offers flexibility for both unbiased and targeted exploration of protein conformational landscapes.