Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that was based on the...
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...
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

The molecular ions of linear alkanes prefer to fragment at the carbon-carbon bond away from the end of the chain since the cleavage of an inner bond creates a stable carbocation and a stable radical. Consequently, the mass signals of linear alkanes feature intense peaks in the middle of the mass-to-charge ratio plot with weaker peaks on either end. The fragmentation of each carbon-carbon bond with the release of a methyl group in each splitting leads to prominent peaks in the mass spectra...
Nomenclature of Alkanes02:22

Nomenclature of Alkanes

In the late 19th-century, the number of new chemical compounds discovered increased tremendously. Hence, the necessity arose to develop a naming system for the systematic nomenclature of these newly discovered compounds. IUPAC (International Union for Pure and Applied Chemistry), established in 1919, sets rules for the nomenclature.
The alkane nomenclature considers the length of the carbon chain, the number, and the location of the substituent to arrive at its systematic name. The IUPAC...
Structure of Alkanes02:23

Structure of Alkanes

The formation of carbon-carbon bonds leading to the creation of the carbon chain is the basis of organic chemistry. August Kekulé and Archibald Scott Couper independently developed this idea of carbon chain formation.
Hydrocarbons are the simplest organic compounds composed of carbons and hydrogens. Based on the bond order between carbons, the hydrocarbons are further classified into alkanes, alkenes, and alkynes. 
Alkanes are the simplest hydrocarbons with sp3 hybrid carbon atoms. These sp3...
Stereoisomerism of Cyclic Compounds02:33

Stereoisomerism of Cyclic Compounds

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,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Calculating Nonbonded Potentials for Classical Simulations of Atoms in Molecules and Metal Surfaces.

Journal of chemical theory and computation·2025
Same author

Effective Ion Exclusion Requires Hydration Shell Stripping.

The journal of physical chemistry. B·2025
Same author

Tuning partial charges of alkyl alcohols to improve simulated fluid properties.

The Journal of chemical physics·2025
Same author

Reconciling Chain Orientation in Polymer-Grafted Nanoparticles between Coarse-Grained Models and Resonant Soft X-ray Scattering.

ACS nano·2025
Same author

Efficient simulations of mobility matrices for electrolytes by applying forces.

Chemical science·2024
Same author

Crystalline and Amorphous Interface Simulations of Donor-Acceptor Blends.

Journal of chemical theory and computation·2024

Related Experiment Video

Updated: May 31, 2026

Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics
13:58

Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics

Published on: September 28, 2016

Simulation of multiple ordered phases in C23 n-alkane.

Nathaniel Wentzel1, Scott T Milner

  • 1Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

The Journal of Chemical Physics
|June 21, 2011
PubMed
Summary

Simulations reveal normal alkanes

Area of Science:

  • Materials Science
  • Physical Chemistry
  • Solid-State Physics

Background:

  • Normal alkanes exhibit distinct ordered phases: orthorhombic (X) and rotator phases (RI, RII).
  • Rotator phase transitions are weakly first-order and may influence crystalline polyethylene nucleation.
  • Understanding these transitions is crucial for materials science and polymer physics.

Purpose of the Study:

  • To investigate the phase behavior and transitions of normal alkanes using computational methods.
  • To characterize the structural and thermodynamic properties of different alkane phases.
  • To develop order parameters for quantifying local and global phase order.

Main Methods:

  • All-atom isothermal, isostress (NσT) simulations of pure C(23) alkane solid.

More Related Videos

On-line Analysis of Nitrogen Containing Compounds in Complex Hydrocarbon Matrixes
07:49

On-line Analysis of Nitrogen Containing Compounds in Complex Hydrocarbon Matrixes

Published on: August 5, 2016

Preparation of a Corannulene-functionalized Hexahelicene by Copper(I)-catalyzed Alkyne-azide Cycloaddition of Nonplanar Polyaromatic Units
09:35

Preparation of a Corannulene-functionalized Hexahelicene by Copper(I)-catalyzed Alkyne-azide Cycloaddition of Nonplanar Polyaromatic Units

Published on: September 18, 2016

Related Experiment Videos

Last Updated: May 31, 2026

Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics
13:58

Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics

Published on: September 28, 2016

On-line Analysis of Nitrogen Containing Compounds in Complex Hydrocarbon Matrixes
07:49

On-line Analysis of Nitrogen Containing Compounds in Complex Hydrocarbon Matrixes

Published on: August 5, 2016

Preparation of a Corannulene-functionalized Hexahelicene by Copper(I)-catalyzed Alkyne-azide Cycloaddition of Nonplanar Polyaromatic Units
09:35

Preparation of a Corannulene-functionalized Hexahelicene by Copper(I)-catalyzed Alkyne-azide Cycloaddition of Nonplanar Polyaromatic Units

Published on: September 18, 2016

  • Heating and cooling scans to identify phase transitions and properties.
  • Development of Potts- and Ising-like order parameters to measure phase order.

    • Main Results:

    • Simulations identified a phase sequence consistent with experiments, with a more stable monoclinic crystal than the experimental orthorhombic structure.
    • The RI phase is an orthorhombic crystal with molecular rotations; RII is a hexagonal packing of chain stems.
    • Pretransitional fluctuations in local RI order were observed in the RII phase near the RI-RII transition.

    Conclusions:

    • The study provides a detailed molecular-level understanding of normal alkane phase transitions.
    • Computational findings offer insights into the nature of rotator phases and their relationship to crystalline structures.
    • The developed order parameters are valuable tools for analyzing phase transitions in molecular solids.