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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...

Conformations of Cyclohexane

Conformations of Cyclohexane

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...

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

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

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.

IR Spectroscopy: Molecular Vibration Overview

IR Spectroscopy: Molecular Vibration Overview

When Infrared (IR) radiation passes through a covalently bonded molecule, the bonds transition from lower to higher vibrational levels. The fundamental vibrational motions that result in infrared absorption can be classified as stretching or bending vibrations.
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...

Conformations of Ethane and Propane

Conformations of Ethane and Propane

In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered...

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Related Experiment Video

Updated: Jun 21, 2025

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations.

Souvik Mondal¹, Michael A Sauer¹, Matthias Heyden¹

¹School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States.

The Journal of Physical Chemistry. B

|July 10, 2024

Summary

This summary is machine-generated.

We developed a new method to automatically identify collective variables for biomolecule simulations. This approach uses anharmonic low-frequency vibrations to speed up conformational dynamics analysis.

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Area of Science:

Computational chemistry
Biophysics
Molecular dynamics

Background:

Enhanced sampling simulations are crucial for studying biomolecular conformational dynamics.
Identifying suitable collective variables is a major bottleneck, often requiring user expertise.
Conventional methods struggle with anharmonic, low-frequency vibrations critical for conformational changes.

Purpose of the Study:

To develop an automated method for identifying collective variables.
To utilize anharmonic low-frequency vibrations for enhanced sampling.
To improve the efficiency and accuracy of biomolecular dynamics simulations.

Main Methods:

Developed frequency-selective anharmonic (FRESEAN) mode analysis.
FRESEAN analysis avoids harmonic approximations.
Applied FRESEAN to molecular dynamics simulations of alanine dipeptide.

Main Results:

FRESEAN successfully isolated anharmonic low-frequency vibrations.
Enhanced sampling using these vibrations improved sampling efficiency compared to dihedral angles.
Free energy surfaces showed lower barriers when using anharmonic vibrations.

Conclusions:

Anharmonic low-frequency vibrations are effective collective variables.
FRESEAN analysis enables fully automated enhanced sampling.
This method offers a promising path for efficient biomolecular dynamics simulations.