Related Experiment Video
Updated: Jul 1, 2026

Polarization-Sensitive Two-Photon Microscopy for a Label-Free Amyloid Structural Characterization
Published on: September 8, 2023
Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds
Kittusamy Senthilkumar1, Jon I Mujika, Kara E Ranaghan
1Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK.
Abstract:
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transfer due to hydrogen bond formation is studied to assess the severity of spurious polarization of QM atoms by MM point charges close to the QM/MM boundary. The changes in total electron density and natural bond orbital atomic charges due to hydrogen bond formation in selected complexes obtained at the QM/MM level are compared with full QM results. It is found that charge leakage from the QM atoms to MM atomic point charges close to the QM/MM boundary is not a serious problem, at least with limited basis sets. The results are encouraging in showing that important properties of key biomolecular interactions can be treated well at the QM/MM level employing good-quality levels of QM theory.
Related Concept Videos
Molecular Shape and Polarity
Molecular Geometry and Dipole Moments
Bond Polarity, Dipole Moment, and Percent Ionic Character
¹H NMR: Complex Splitting
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
Spin–Spin Coupling Constant: Overview
Qualitatively, any spin plus-half nucleus polarizes the spins of its electrons to the minus-half state. Consequently, the paired electron in the hydrogen–carbon bond must have a...
MO Theory and Covalent Bonding

