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Related Concept Videos

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

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...
Sampling Plans01:23

Sampling Plans

Sampling is a crucial step in analytical chemistry, allowing researchers to collect representative data from a large population. Common sampling methods include random, judgmental, systematic, stratified, and cluster sampling.
Random sampling is a method where each member of the population has an equal chance of being selected for the sample. It involves selecting individuals randomly, often using random number generators or lottery-type methods. For example, when analyzing the properties of a...
Convenience Sampling Method00:55

Convenience Sampling Method

Sampling is a technique to select a portion (or subset) of the larger population and study that portion (the sample) to gain information about the population. Data are the result of sampling from a population. The sampling method ensures that samples are drawn without bias and accurately represent the population.
Convenience sampling is a non-random method of sample selection; this method selects individuals that are easily accessible and may result in biased data. For example, a marketing...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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.
Sampling Methods: Overview01:06

Sampling Methods: Overview

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 sampling...
Sampling Methods: Sample Types01:18

Sampling Methods: Sample Types

Sampling materials are classified into three main types: solid, liquid, and gas.
Solid samples include a variety of substances, such as sediments from water bodies, soil, metals, and biological tissues. Two standard methods for extracting sediments from water bodies are grab sampling and piston coring. Grab sampling involves using a device to collect a discrete sediment sample from the bottom of a water body with minimal disturbance. Grab samples do not always represent the entire area due to...

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Related Experiment Video

Updated: May 8, 2026

Spatial Separation of Molecular Conformers and Clusters
10:37

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

Conformational sampling techniques.

Marcus P D Hatfield, Sándor Lovas1

  • 1Department of Biomedical Sciences, Criss II, Room 313, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA. slovas@creighton.edu.

Current Pharmaceutical Design
|August 17, 2013
PubMed
Summary
This summary is machine-generated.

Understanding a protein's potential energy surface is key to determining its native structure. This involves reducing complexity, calculating energy, and exploring its many possible shapes using diverse computational methods.

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Last Updated: May 8, 2026

Spatial Separation of Molecular Conformers and Clusters
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Area of Science:

  • Computational Biology
  • Biophysics
  • Protein Structure Analysis

Background:

  • The potential energy hyper-surface maps a protein's energy across its conformational space.
  • This surface is crucial for identifying native protein conformations and analyzing statistical ensembles.
  • Key challenges include reducing degrees of freedom, calculating energy for each conformation, and sampling conformational space.

Purpose of the Study:

  • To provide a comprehensive overview of methods for determining a protein's potential energy hyper-surface.
  • To discuss strategies for reducing conformational complexity and accurately calculating energies.
  • To review various computational approaches for sampling protein conformations.

Main Methods:

  • Reducing degrees of freedom: solvent choice, coarse-graining, constraints, periodic boundary conditions.
  • Energy calculation: quantum mechanics vs. molecular mechanics, force field selection.
  • Conformational sampling: deterministic (e.g., homology modeling, eigenvector following) and heuristic (e.g., Monte Carlo, molecular dynamics) approaches.

Main Results:

  • Discusses various techniques for reducing protein complexity and calculating conformational energies.
  • Details deterministic and heuristic computational methods for exploring protein conformational space.
  • Highlights strategies for enhancing conformational searches, such as surface deformation and multi-copy searching.

Conclusions:

  • Determining a protein's potential energy hyper-surface requires careful consideration of dimensionality reduction, energy calculation, and conformational sampling.
  • A wide array of computational methods exist, each with strengths for specific aspects of protein structure analysis.
  • Advanced techniques can improve the efficiency and thoroughness of conformational searches.