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Cambridge MedChem Consulting

Molecular interactions

More on hydrogen bonding interactions

Studies of hydrogen bond strength and directionality are largely based on crystal structures which can be biased by crystal packing forces. In a systematic QM study of a wide range of hydrogen bonding groups by Diogo Santos-Martins, Stefano Forli, 34 donors and 67 acceptors DOI they showed there is no correlation between the strength of the hydrogen bond and directionality.

Results demonstrate that there are very strong HB acceptors (e.g.,DMSO) with nearly isotropic interactions, and weak ones (e.g.,thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity, but be very distant in the strength spectrum (e.g., thioacetone and pyridine).

This work also includes a fabulous sheet in the supplementary information giving details of interaction energies for various groups.

I've updated the molecular interactions page.

Molecular Interactions page updated

The Molecular Interactions page has been updated to include a section on anion-aryl interactions.

anion_aryl

Molecular Interactions page updated

I've updated the molecular interactions page to add more details on halogens.

Halogens are present in around 25% of drugs, calculated using data from Guide to Pharmacology Database and often used as bioisosteric replacements for H, Methyl, OH and NH2.

Bonds to halogen are significantly weaker than hydrogen bonds but there are many examples in the PDB of carbonyls interacting with halogens with bonds to I, and Br predominating. It is perhaps worth noting that halogens have been introduced into ligands to aid X-ray analysis, but they may also influence binding. Based on the observed bond angles the interaction is between the halogen and pi-cloud of the carbonyl rather than the lone pair with a clear clustering of X--O=C-N dihedral angles of 90° associated with interactions that involve primarily the pi-system of the carbonyl.

Molecular Interactions page updated

I've updated the Molecular Interactions page expanding the section on hydrogen bonds.

Molecular Interactions Updated

I’ve just updated the page on molecular interactions, expanding the section on halogen bonding interactions.

Molecular Interactions

I’ve just updated the molecular interactions page in the drug discovery resources, expanding the section on bonding to halogen.