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Physical Properties of Alkanes02:33

Physical Properties of Alkanes

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Alkanes are nonpolar molecules due to the presence of only carbon and hydrogen atoms. The electronegativity difference between carbon and hydrogen is minimal, and hence alkanes have a zero dipole moment. This leads to the presence of only dispersion forces between the molecules. The strength of dispersion forces is dependent on the surface area of the molecules on which they act. Since the surface area increases with the molecular length for straight-chain alkanes, the dispersion forces also...
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Structure of Alkanes02:23

Structure of Alkanes

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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....
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Nomenclature of Alkanes02:22

Nomenclature of Alkanes

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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...
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Relative Stabilities of Alkenes01:59

Relative Stabilities of Alkenes

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The relative stability of alkenes can be determined by comparing their heats of hydrogenation. The lower heat of hydrogenation indicates the more stable alkene.  The three main factors determining the relative stability of alkenes are i) the number of substituents attached to the double-bond carbon atoms, ii) hyperconjugation, and iii) the stereochemistry of the double bond.
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Constitutional Isomers of Alkanes02:18

Constitutional Isomers of Alkanes

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Organic compounds of the same molecular formula can have different structural formulas called constitutional isomers, and the phenomenon is known as constitutional isomerism. Alkanes with four or more carbons showing multiple structures with the same molecular formula thereby exhibit constitutional isomerism.
The linear isomer of an alkane is prefixed by the term “n”; hence a linear isomer of pentane is known as n-pentane. Based on the type of branching, some of the...
18.7K
Inductive Effects on Chemical Shift: Overview01:27

Inductive Effects on Chemical Shift: Overview

2.3K
The protons in unsubstituted alkanes are strongly shielded with chemical shifts below 1.8 ppm. Methine, methylene, and methyl protons appear at approximately 1.7, 1.2 and 0.7 ppm, while the proton signal from methane appears at 0.23 ppm. An electronegative substituent, such as chlorine, withdraws the electron density from the protons, increasing their chemical shift. Progressive substitution of the hydrogens in methane by chlorine shifts the proton signals increasingly downfield, to 3.05 ppm in...
2.3K

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A new AMBER-compatible force field parameter set for alkanes.

Alexei M Nikitin1, Yury V Milchevskiy, Alexander P Lyubartsev

  • 1Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, 119991, Russia, agilemolecule@gmail.com.

Journal of Molecular Modeling
|February 20, 2014
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A new alkane force field parameter set offers universal simulation of linear, branched, and cyclic alkanes. This method improves conformational and thermodynamic property descriptions for biomolecules like amino acids and lipids.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Biomolecular Simulation

Background:

  • Accurate simulation of alkanes is crucial for biomolecular modeling.
  • Existing force fields may lack universal applicability for diverse alkane structures.

Purpose of the Study:

  • To develop a new, unified force field parameter set for alkanes.
  • To ensure compatibility with the AMBER force field family.

Main Methods:

  • Modification of Lennard-Jones parameters for sp3 carbons.
  • Reduction of Lennard-Jones radius to 1.75Å for all sp3 carbons.
  • Separate optimization of Lennard-Jones well depths based on carbon substitution.

Main Results:

  • The new parameter set successfully describes conformational and thermodynamic properties of various alkanes.
  • Achieved unification across linear, branched, and cyclic alkane simulations.
  • Demonstrated compatibility with AMBER force fields.

Conclusions:

  • The developed force field parameter set provides a universal description for alkanes.
  • It is suitable for simulating alkyl residues in biomolecules, including amino acids and lipids.
  • This advancement can enhance the accuracy of molecular dynamics simulations in biochemistry.