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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...
Radical Chain-Growth Polymerization: Chain Branching01:17

Radical Chain-Growth Polymerization: Chain Branching

The skeletal structure of polymers synthesized via radical polymerization is always branched. For example, the polymerization of ethylene by radical polymerization results in a low-density grade of polyethylene with a heavily branched skeletal structure. Here, the radical site abstracts hydrogen from the growing chain, and the radical site shifts from the end (a primary carbon center) to anywhere within the growing chain (a secondary carbon center). Consequently, the part of the chain from the...
Protein Denaturation01:28

Protein Denaturation

The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...
Conformations of Cyclohexane02:11

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 tetrahedral value,...
Free-Radical Chain Reaction and Polymerization of Alkenes02:35

Free-Radical Chain Reaction and Polymerization of Alkenes

The conversion of alkenes to macromolecules called polymers is a reaction of high commercial importance. The structure of the polymer is defined by a repeating unit, while the terminal groups are considered insignificant. The average degree of polymerization represents the number of repeating units in the polymer molecule and is denoted by the subscript n.
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...

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Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization
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Published on: November 12, 2014

Charge renormalization of helical macromolecules.

D J Lee1

  • 1Max-Planck Institute für Physik Komplexer Systeme, Nöthnizter Strasse 38, Dresden D-01187, Germany. domolee@hotmail.com

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|March 10, 2011
PubMed
Summary

This study rigorously grounds the Kornyshev-Leikin (KL) theory for helical macromolecule electrostatic interactions using statistical mechanics. The KL theory accurately predicts long-range forces, incorporating ion condensation and hard-core effects for DNA-like structures.

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Area of Science:

  • Physical Chemistry
  • Statistical Mechanics
  • Biophysics

Background:

  • The Kornyshev-Leikin (KL) theory describes electrostatic interactions between helical macromolecules.
  • A rigorous statistical mechanical foundation for the KL theory is needed.

Purpose of the Study:

  • To provide a rigorous statistical mechanical grounding for the KL theory.
  • To analyze the long-range electrostatic forces between helical macromolecules.
  • To investigate the role of ion condensation and hard-core effects.

Main Methods:

  • Derivation of free energy from a grand partition function.
  • Self-consistent calculation of ion distribution.
  • Application to a DNA-like surface charge distribution.

Main Results:

  • The KL theory's long-range force prediction is validated.
  • The formalism incorporates corrections due to ion hard-core radius.
  • KL parameters are calculated for a DNA model with ions in grooves.

Conclusions:

  • The statistical mechanical approach confirms the KL theory's long-range behavior.
  • The model allows for calculating electrostatic contributions to ion binding potentials.
  • This work provides a framework for understanding ion-macromolecule interactions.