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Fischer Projections

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

Conformations of Cyclohexane

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...

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

Conformations of Cycloalkanes

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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...

Conformations of Ethane and Propane

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In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
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Interactive Molecular Model Assembly with 3D Printing

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Published on: August 13, 2020

BFMP: a method for discretizing and visualizing pyranose conformations.

Spandana Makeneni¹, B Lachele Foley, Robert J Woods

¹Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States.

Journal of Chemical Information and Modeling

|October 8, 2014

Summary

A new method, Best-fit, Four-Membered Plane (BFMP), classifies pyranose ring conformations. This approach accurately characterizes all ring shapes and quantifies conformational distortion.

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Area of Science:

Carbohydrate Chemistry
Structural Biology
Computational Chemistry

Background:

Pyranose rings are fundamental in biochemistry and medicinal chemistry.
Accurate characterization of pyranose ring conformations is crucial for understanding their function.
Existing methods may lack comprehensive coverage or ease of interpretation.

Purpose of the Study:

To introduce a novel and robust classification method for pyranose ring conformations.
To provide a tool that is automated, interpretable, and maps to IUPAC nomenclature.
To offer a qualitative measure of ring distortion.

Main Methods:

Development of the Best-fit, Four-Membered Plane (BFMP) method.
Utilizing reference planes defined by four atoms for classification.
Application to analyze data from crystal structures and molecular dynamics simulations.

Main Results:

The BFMP method successfully characterizes all asymmetrical and symmetrical pyran ring shapes.
The method provides a qualitative measurement of ring distortion.
BFMP is readily automated and easy to interpret.

Conclusions:

The BFMP method offers a significant advancement in the classification of pyranose ring conformations.
This method is versatile and applicable to various structural datasets.
BFMP facilitates a deeper understanding of carbohydrate structure-activity relationships.