Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations

Simona, Fabio; Nussbaumer, Alina L.; Häner, Robert; Cascella, Michele (2013). Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations. Journal of physical chemistry - B, 117(8), pp. 2576-2585. Washington, D.C.: American Chemical Society 10.1021/jp310320f

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We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by π- stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Simona, Fabio; Häner, Robert and Cascella, Michele

Subjects:

500 Science > 540 Chemistry
500 Science > 570 Life sciences; biology

ISSN:

1520-6106

Publisher:

American Chemical Society

Language:

English

Submitter:

Robert Häner

Date Deposited:

10 Dec 2013 22:24

Last Modified:

01 Dec 2015 11:17

Publisher DOI:

10.1021/jp310320f

BORIS DOI:

10.7892/boris.39030

URI:

https://boris.unibe.ch/id/eprint/39030

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