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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

924
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

1.2K
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.
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Sampling Methods: Overview01:06

Sampling Methods: Overview

540
A sample refers to a smaller subset representative of a larger population. In analytical chemistry, studying or analyzing an entire population is often impractical or impossible. Therefore, samples are used to draw inferences and generalize the whole population. The sampling method selects individuals or items from a population to create a sample. Standard sampling methods include random, judgemental, systematic, stratified, and cluster sampling. 
In analytical chemistry, the choice of...
540
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

14.8K
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...
14.8K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

13.2K
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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¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.1K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
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Updated: Sep 20, 2025

Spatial Separation of Molecular Conformers and Clusters
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Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods.

Mauricio Bedoya1,2, Francisco Adasme-Carreño1,2, Paula Andrea Peña-Martínez3

  • 1Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile.

Journal of Chemical Information and Modeling
|May 27, 2025
PubMed
Summary

Moltiverse, a new protocol using enhanced sampling molecular dynamics (MD) simulations, accurately predicts small molecule conformations. This method excels in exploring conformational landscapes, especially for flexible molecules like macrocycles, aiding drug discovery.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Accurate prediction of small molecule conformations is vital for drug discovery, especially when protein-ligand interactions are unknown.
  • Existing computational tools face challenges in efficiently exploring vast conformational spaces.

Purpose of the Study:

  • Introduce Moltiverse, a novel protocol for conformer generation using enhanced sampling molecular dynamics (MD) simulations.
  • Evaluate Moltiverse's accuracy and efficiency against established software for small molecules and macrocycles.

Main Methods:

  • Utilized extended adaptive biasing force (eABF) algorithm combined with metadynamics.
  • Employed a single collective variable (radius of gyration, RDGYR) to guide simulations.
  • Benchmarked against RDKit, CONFORGE, Balloon, iCon, and Conformator using Platinum Diverse and Prime datasets.

Main Results:

  • Moltiverse demonstrated comparable accuracy and superior quality in some cases compared to existing methods.
  • Achieved the highest accuracy for macrocycles, which possess high conformational flexibility.
  • Physics-based approach effectively handles diverse molecular complexities.

Conclusions:

  • Moltiverse is a valuable tool for computational drug discovery, offering accurate molecular flexibility representation.
  • The protocol is particularly effective for challenging, flexible systems like macrocycles.
  • Findings provide insights for improving conformer generation algorithms.