Important factors stabilizing stacking interaction between 3-nitropyrrole and natural nucleobases revealed by ab initio calculations | Zendy

Kohji Seio | Zendy; Hisashi Ukawa | Zendy; Koh-ichiroh Shohda | Zendy; Mitsuo Sekine | Zendy

Open Access

Important factors stabilizing stacking interaction between 3-nitropyrrole and natural nucleobases revealed by ab initio calculations

Author(s) -

Kohji Seio,

Hisashi Ukawa,

Koh-ichiroh Shohda,

Mitsuo Sekine

Publication year - 2003

Publication title -

nucleic acids symposium series

Language(s) - English

Resource type - Journals

eISSN - 1746-8272

pISSN - 0261-3166

DOI - 10.1093/nass/3.1.49

Subject(s) - nucleobase , stacking , ab initio , computational chemistry , chemistry , ab initio quantum chemistry methods , interaction energy , base pair , molecular orbital , chemical physics , crystallography , molecular physics , dna , molecule , organic chemistry , biochemistry

Stacking energies between canonical nucleobases and a universal base, 3-nitropyrrole (3-NP), were estimated by use of molecular orbital (MO) and molecular mechanics (MM) calculations. The detailed analysis of the energy profiles revealed the importance of the London dispersion energy to stabilize the stacked dimers and electrostatic interactions to determine the orientation of 3-NP to the nucleobases in the dimers. Although the energy profiles of 3-NP/natural base dimers obtained by the MO and MM calculations were qualitatively correlated with each other, the correlations were poorer than those obtained for the stacking between natural bases. The origin of the difference between 3-NP and natural bases will be discussed to understand the possibility and limitation of the current MM calculations for the simulation and design of other universal bases.

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