Journal
ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS
Volume 231, Issue 2, Pages 439-458Publisher
WALTER DE GRUYTER GMBH
DOI: 10.1515/zpch-2016-0799
Keywords
conformational search; DNA; ESR; molecular mechanics; spin labelling
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Funding
- MEXT, Japan
- JSPS KAKENHI [25410098]
- FIRST Project on Quantum Information Processing
- Cabinet Office, JSPS, Japan
- AOARD Project on Quantum Properties of Molecular Nanomagnets [FA2386-13-1-4030]
- Grants-in-Aid for Scientific Research [15K13681, 17K05840, 25410098] Funding Source: KAKEN
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The global molecular and local spin-site structures of a DNA duplex 22-oligomer with site-directed four spin-labeling were simulated by molecular mechanics (MM) calculations combined with Q-band pulsed electron-electron double resonance (PELDOR) spectroscopy. This molecular-spin bearing DNA oligomer is designed to give a complex testing ground for the structural determination of molecular spins incorporated in the DNA duplex, which serves as a platform for 1D periodic arrays of two or three non-equivalent electron spin qubit systems, (AB) n or (ABC) n, respectively, enabling to execute quantum computing or quantum information processing (Lloyd model of electron spin versions): A, B and C designate non-equivalent addressable spin qubits for quantum operations. The non-equivalence originates in difference in the electronic g-tensor. It is not feasible to determine the optimal structures for such DNA oligomers having molecular flexibility only by the MM calculations because there are many local minima in energy for their possible molecular structures. The spin-distance information derived from the PELDOR spectroscopy helps determine the optimal structures out of the possible ones acquired by the MM calculations. Based on the MMsearched structures, we suggest the optimal structures for semi-macromolecules having site-directed multi-spin qubits. We emphasize that for our four molecular spins embedded in the DNA oligomer the Fajer's error analysis in PELDOR-based distance measurements was of essential importance.
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