Pyridinedicarboxamide Strands Form Double Helices via an Activated Slippage Mechanism

• Published in: Journal of the American Chemical Society Vol. 126; no. 8; pp. 2362 - 2367
• Main Authors: Acocella, Angela, Venturini, Alessandro, Zerbetto, Francesco
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 03.03.2004
• Subjects: Amides - chemistry; Applied sciences; Biomimetic Materials - chemistry; Biopolymers - chemistry; Crystallography, X-Ray; Exact sciences and technology; Models, Molecular; Molecular Conformation; Nucleic Acid Conformation; Organic polymers; Physicochemistry of polymers; Properties and characterization; Pyridines - chemistry; Structure, morphology and analysis; Surface Properties; Thermodynamics; Nitrogen heterocycle polymer; Pyridine derivative polymer; Double helical structure; Conformational dynamics; Supramolecular structure; Molecular dynamics method; Theoretical study; Potential energy surfaces; Carboxamide; Oligomer; Intramolecular interaction
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja038103f

The intertwining process of two strands of oligo-pyridinecarboxamides to form a double helix (Nature 2000, 407, 720) is found to consist of a series of discrete steps, where the tail of one of the strands proceeds inside the other single helix in an eddy-like process. While a plethora of minima can be located along the pathway, they exist only for a few, well-defined supramolecular arrangements of the two molecules. The initial transition state for the introduction of one molecule in the pitch of the other has the largest barrier and is therefore the rate-determining step of an activated slippage mechanism, which is characterized by a series of roller-coasting hills. Along the entire pathway, the intramolecular energy that stabilizes the single helices is slowly transformed into intermolecular energy that finally provides the necessary stabilization only near the end of the entwining process. Solvent or other chemical factors, such as the presence of ions, able to destabilize the full formation of the double helix may therefore drastically affect its formation.