Exploring supramolecular space

Chemical space is a framework used to describe the vast amounts of known molecules of natural or synthetic origin. The main premise is that similar structures have similar properties (e.g., SAR), and thus, can be clustered in groups (‘galaxies’) using such properties as criteria (parameters) for their classification. The concept is primarily used in the field of drug discovery and to a lesser degree in materials development.

Supramolecules are not explicitly excluded from the working definition of chemical space, nor are they implicitly included. Thus, the term of supramolecular space in meant to specifically target the study of how intrinsic parameters (i.e., spatial covalent connectivity) determine the properties of the resulting supramolecules. It can be distinguished from the standard definition of chemical space by the explicit inclusion of extrinsic parameters (e.g., media, co-solutes, temperature, pH), which very often dictate the very existence of the supramolecule in the first place.

Since supramolecular space is very vast, and just like our outer universe, continues to expanding at an accelerated rate. So, this blog will focus primarily on selected “galaxies” (topics) that are most related to our research interests. The following is a partial list of topics that will be discussed in this site:

1. Assemblies of molecules: Not simple aggregates, but groups of molecules interacting via specific non-covalent interactions (NCIs) (although some interesting cases are at the edge of this definition) with atomic/molecular precision.
2. NCIs and reversible covalent interactions: Reversibility and timescale are of the essence here
3. Complex molecular systems (e.g., hierarchical, dynamic libraries): With emphasis on synthetic systems, but with with specific interest in combinations of synthetic and natural systems
4. Molecular information transfer
5. Design and synthesis of molecular machinery

If you think we should expand this list of topics leave your suggestions in the comments.

This week we will discuss the first two articles related to supramolecular space. In one of them Jean discusses a recent article by the groups of Wheeler, Houk and Kool dealing with a quantitative assessment on the nature of hydrogen bonds within the context of base-pairing in DNA. Hydrogen bonding interactions are arguably the most studied of all NCIs, yet there are still important details to be found out as Jean explains in his post. Andrew, on the other hand, discusses a recent article by the groups of Rastrelli and Prins where they report the advantages of using ¹³C labeling strategies for the NMR analysis of a complex supramolecular dynamic library. I’m looking forward to a lively discussion both in the comments and on Friday’s GM.

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