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Is Cobalt Joining the σ‑/π-Hole Crown? Exploring Noncovalent Interactions in Cobalamin
Sergi Burguera1, Antonio Bauzá1
1Universitat de Les Illes Balears, Ctra. de Valldemossa, Km. 7.5, Palma de Mallorca, Islas Baleares 07122, Spain.
JACS Au
|November 28, 2025
Summary
This study reveals σ-/π-hole interactions involving cobalt (Co) in biological systems for the first time, using Cobalamin (Cbl) as a model. These findings impact chemical biology and supramolecular chemistry.
Area of Science:
- Biochemistry
- Computational Chemistry
- Supramolecular Chemistry
Background:
- Cobalamin (Cbl) is crucial in biological systems.
- Noncovalent interactions (NCIs) involving cobalt (Co) are often overlooked in biological contexts.
- Understanding these interactions is key to advancing chemical biology and biotechnology.
Purpose of the Study:
- To computationally investigate σ-/π-hole chemistry of Co within a biological framework.
- To analyze the prevalence and structural characteristics of L···Co interactions in Cbl-containing structures.
- To explore the role of σ-hole interactions in stabilizing Co coordination.
Main Methods:
- Protein Data Bank (PDB) survey to identify Cbl structures.
- Statistical analysis of noncovalent interactions involving the Co atom.
- Quantum chemical calculations (BP86-D3/def2-TZVP) on selected examples.
- Characterization of σ-hole interactions with various electron donor molecules.
Main Results:
- Identified 67 out of 111 Cbl structures with NCIs involving the Co atom.
- Revealed trends in the abundance and structural features of L···Co interactions (L = C, N, O).
- Discovered a σ-hole complex involving 5,6-dimethylbenzimidazole (DMB) stabilizing a pre-Co coordination state.
- Characterized local noncovalent energy minima based on σ-hole interactions.
Conclusions:
- This study provides the first computational evidence of σ-/π-hole interactions involving Co in biological systems.
- These interactions are significant in Cbl and likely other biological Co complexes.
- Findings offer new insights for supramolecular chemistry and biotechnology applications.
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