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Related Concept Videos

Cycloalkanes02:28

Cycloalkanes

14.7K
Cycloalkanes are saturated cyclic hydrocarbons with carbon atoms arranged in the form of rings. They have two fewer hydrogen atoms than the corresponding acyclic alkane; therefore, their general formula is CnH2n. The structural formulas of cycloalkanes are simplified using the line-angle representation. The regular polygons are used to represent the cycloalkane rings, with each side representing a carbon-carbon bond.
The IUPAC nomenclature of cycloalkanes follows similar rules that apply to...
14.7K
Frost Circles for Different Conjugated Systems01:18

Frost Circles for Different Conjugated Systems

3.4K
The inscribed polygon method is consistent with Hückel’s 4n + 2 rule and helps to learn whether the given cyclic compound is aromatic or not. The compound is stable and aromatic if every bonding molecular orbital (MO) is completely filled with a pair of electrons. However, if the non-bonding or antibonding orbitals are filled with electrons, the compound is unstable and not aromatic. Consider the Frost circle diagrams for cycloalkenes containing 4 to 8 carbons.
3.4K
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

13.6K
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...
13.6K
Molecular Shapes01:18

Molecular Shapes

60.1K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
60.1K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

14.5K
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...
14.5K
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

17.2K
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...
17.2K

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Benchmark of Generic Shapes for Macrocycles.

Atilio Reyes Romero1, Angel Jonathan Ruiz-Moreno1,2,3, Matthew R Groves1

  • 1Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands.

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Summary

Moloc, a shape-guided algorithm, efficiently generates diverse macrocycle conformations for drug discovery. It offers high sampling efficiency and exhaustiveness, outperforming other computational tools in benchmarking studies.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • Macrocycles are crucial for targeting undruggable proteins with limited binding pockets.
  • Computational methods are essential for overcoming conformational challenges in macrocycle design.
  • Moloc is an interactive, shape-guided algorithm developed by Roche biostructural community since 1986.

Purpose of the Study:

  • To benchmark the Moloc algorithm's performance.
  • To quantify accuracy, diversity, speed, exhaustiveness, and sampling efficiency.
  • To compare Moloc against commercial and open-access conformational analysis tools.

Main Methods:

  • Benchmarking using a dataset of 208 structurally complex macrocycles.
  • Automated quantification of key performance metrics.
  • Comparison with eight other software packages (four commercial, four open-access).

Main Results:

  • Moloc demonstrated superior sampling efficiency and exhaustiveness.
  • The algorithm processed three-quarters of the database below high ring accuracy thresholds.
  • Moloc produced diverse conformations without excessive output or ring splitting, comparable to leading commercial software.

Conclusions:

  • Moloc is a highly efficient and effective tool for macrocycle conformation generation.
  • Its performance makes it a valuable asset for drug discovery targeting challenging proteins.
  • The algorithm and automation scripts are freely available for academic research.