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2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does...

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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conserved Binding Sites

Conserved Binding Sites

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: Variable-Temperature NMR

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Related Experiment Video

Updated: Oct 26, 2025

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Multiple Conformer Descriptors for QSAR Modeling.

Aleksandra Nikonenko¹, Dmitry Zankov², Igor Baskin³

¹Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic.

Molecular Informatics

|August 3, 2021

Summary

This study introduces a novel quantitative structure-activity relationship (QSAR) modeling approach using chirality-aware 3D pharmacophore descriptors and latent variables. This method enhances predictive accuracy by considering molecular flexibility and stereochemistry, outperforming traditional 2D and 3D QSAR methods.

Keywords:

3D pharmacophore descriptors 4D QSAR multiple instance learning

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Area of Science:

Computational Chemistry
Cheminformatics
Drug Discovery

Background:

Traditional quantitative structure-activity relationship (QSAR) methods often neglect crucial molecular properties like stereoconfiguration and conformational flexibility.
Existing 3D QSAR approaches struggle with selecting representative conformers, while some 4D QSAR methods ignore stereochemistry or require complex conformer alignment.

Purpose of the Study:

To develop a novel QSAR modeling approach that effectively incorporates stereochemistry and conformational flexibility.
To represent entire conformer sets of molecules using latent variables derived from 3D pharmacophore descriptors.
To overcome limitations of existing 2D, 3D, and 4D QSAR methods.

Main Methods:

A new QSAR approach was developed using chirality-aware 3D pharmacophore descriptors for individual conformers.
Conformers of training set compounds were clustered to generate a latent variable representation.
The final molecular representation was a bit string encoding cluster membership, utilized with Random Forest and other machine learning methods.

Main Results:

The proposed approach demonstrated superior performance compared to conventional 2D and 3D QSAR methods across multiple datasets.
The method effectively captures stereochemical information and conformational diversity.
Sensitivity analysis indicated the impact of parameter tuning, such as the number of conformers and clusters.

Conclusions:

The developed QSAR modeling strategy offers a robust and accurate method for predicting molecular activity by integrating 3D pharmacophore information and conformational space.
This approach provides a significant advancement over existing QSAR techniques, particularly for complex molecules with stereochemical considerations.
The latent variable representation based on conformer clustering offers a versatile framework for various machine learning applications in drug discovery.