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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...
Cyclohexenones via Michael Addition and Aldol Condensation: The Robinson Annulation01:27

Cyclohexenones via Michael Addition and Aldol Condensation: The Robinson Annulation

Robinson annulation is a base-catalyzed reaction for the synthesis of 2-cyclohexenone derivatives from 1,3-dicarbonyl donors (such as cyclic diketones, β-ketoesters, or β-diketones) and α,β-unsaturated carbonyl acceptors. Named after Sir Robert Robinson, who discovered it, this reaction yields a six-membered ring with three new C–C bonds (two σ bonds and one π bond).
Olefin Metathesis Polymerization: Acyclic Diene Metathesis (ADMET)00:53

Olefin Metathesis Polymerization: Acyclic Diene Metathesis (ADMET)

Acyclic diene metathesis polymerization or ADMET polymerization involves cross-metathesis of terminal dienes, such as 1,8-nonadiene, to give linear unsaturated polymer and ethylene. As ADMET is a reversible process, the formed ethylene gas must be removed from the reaction mixture to complete the polymerization process.
Similar to cross-metathesis, ADMET also involves the formation of metallacyclobutane intermediate by [2+2] cycloaddition of one of the double bonds of a terminal diene with...
Diels–Alder Reaction Forming Cyclic Products: Stereochemistry01:28

Diels–Alder Reaction Forming Cyclic Products: Stereochemistry

The Diels–Alder reaction is one of the robust methods for synthesizing unsaturated six-membered rings. The reaction involves a concerted cyclic movement of six π electrons: four π electrons from the diene and two π electrons from the dienophile.
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...
Alkenes via Reductive Coupling of Aldehydes or Ketones: McMurry Reaction01:22

Alkenes via Reductive Coupling of Aldehydes or Ketones: McMurry Reaction

The radical dimerization of ketones or aldehydes gives vicinal diols through a pinacol coupling reaction. However, the behavior of titanium metals used for the reaction as a source of electrons is unusual. When the reaction is carried out in the presence of titanium, diols can be isolated at low temperatures. Else titanium further reacts with diols, forming alkenes through the McMurry reaction.

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Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
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Conformational sampling of macrocyclic alkenes using a Kennard-Stone-based algorithm.

Diederica D Claeys1, Toon Verstraelen, Ewald Pauwels

  • 1Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium.

The Journal of Physical Chemistry. A
|June 10, 2010
PubMed
Summary

This study introduces a new algorithm to efficiently select diverse molecular conformations for computational chemistry. This method aids in accurately predicting molecular properties by optimizing calculations at higher theoretical levels.

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Discovery and Synthesis Optimization of Isoreticular Al(III) Phosphonate-Based Metal-Organic Framework Compounds Using High-Throughput Methods

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Biophysics

Background:

  • Molecular conformations dictate biomolecule properties and functions.
  • Low-level theory can sample conformational space, but higher accuracy requires costly computations.
  • Efficiently selecting representative conformations is crucial for accurate molecular modeling.

Purpose of the Study:

  • To present a novel Kennard-Stone-based algorithm for selecting diverse molecular conformations.
  • To reduce computational cost by optimizing a selected subset of conformations at higher theoretical levels.
  • To validate the algorithm's effectiveness in studying macrocyclic alkenes.

Main Methods:

  • Conformational ensemble generation using molecular dynamics (MD) simulations.
  • Analysis of MD trajectories with the MD-Tracks code.
  • Application of a Kennard-Stone algorithm utilizing a distance matrix for diverse conformation selection.

Main Results:

  • The algorithm successfully selects a diverse set of conformations from a larger ensemble.
  • Accurate thermodynamic stability of double-bond isomers in flexible macrocyclic alkenes was reproduced.
  • Chirality of stereocenters significantly impacts macrocycle conformation, more than double-bond configuration.

Conclusions:

  • The developed algorithm provides an efficient strategy for selecting diverse conformations.
  • This approach enables accurate high-level theoretical studies of complex molecules like macrocyclic alkenes.
  • Understanding conformational preferences is key to predicting molecular behavior and function.