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Structural Determination of a DNA Oligomer for a Molecular Spin Qubit Lloyd Model of Quantum Computers

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Published/Copyright: December 28, 2016
Zeitschrift für Physikalische Chemie
From the journal Zeitschrift für Physikalische Chemie Volume 231 Issue 2

Abstract

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 MM searched 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.

Keywords: conformational search; DNA; ESR; molecular mechanics; spin labelling

Dedicated to: Kev Salikhov on the occasion of his 80th birthday.

Acknowledgments

We acknowledge Professor Kazuhiko Nakatani and Dr. Hiroshi Atsumi, Institute of Scientific Industrial Research (ISIR), Osaka University for providing us with the sample for the pulsed ELDOR experiments and valuable discussions, and Professor Masahiro Kitagawa, Division of Advanced Electronics and Optical Science, Department of System Innovation, Graduate School of Engineering Science, Osaka University for his valuable discussions. This work has been supported by Grants-in-Aid for Scientific Research on Innovative Areas “Quantum Cybernetics” and Scientific Research (B) from MEXT, Japan and by JSPS KAKENHI Grant Number 25410098. The support for the present work by the FIRST Project on “Quantum Information Processing” from The Cabinet Office, JSPS, Japan and by the AOARD Project on “Quantum Properties of Molecular Nanomagnets” (Award No. FA2386-13-1-4030) is also acknowledged.

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Supplemental Material:

The online version of this article (DOI: 10.1515/zpch-2016-0799) offers supplementary material, available to authorized users.

Received: 2016-5-10
Accepted: 2016-11-22
Published Online: 2016-12-28
Published in Print: 2017-2-1

©2017 Walter de Gruyter GmbH, Berlin/Boston

Articles in the same Issue

  1. Frontmatter
  2. Preface
  3. Editorial Review
  4. From Free Radicals and Spin-Chemistry Over Spin-Dynamics and Hyperpolarization to Biology and Materials Science
  5. On Relations Between Singlet and Triplet Recombination Yields for Singlet and Triplet Precursors
  6. The Quantum Dynamical Basis of a Classical Kinetic Scheme Describing Coherent and Incoherent Regimes of Radical Pair Recombination
  7. Reaction Operators for Radical Pairs. The Exactly Solvable Model
  8. Estimation of the Fraction of Spin-Correlated Radical Ion Pairs in Irradiated Alkanes using Magnetosensitive Recombination Luminescence from Exciplexes Generated upon Recombination of a Probe Pair
  9. Theoretical Description of Pulsed RYDMR: Refocusing Zero-Quantum and Single Quantum Coherences
  10. A Transient EPR Study of Electron Transfer in Tetrathiafulvalene-Aluminum(III) Porphyrin-Anthraquinone Supramolecular Triads
  11. Solvent Radical Anions in Irradiated Aliphatic Ketones and Esters as Observed Using Time-Resolved Magnetic Field Effects in the Recombination Fluorescence
  12. Effect of Dehydrated Trehalose Matrix on the Kinetics of Forward Electron Transfer Reactions in Photosystem I
  13. Photo-CIDNP in the Reaction Center of the Diatom Cyclotella meneghiniana Observed by 13C MAS NMR
  14. Light-Stimulated Generation of Free Radicals by Quinones-Chelators
  15. Influence of C2-Methylation of Imidazolium Based Ionic Liquids on Photoinduced Spin Dynamics of the Dissolved ZnTPP Studied by Time-Resolved EPR
  16. ESR Study of Electron States in Ge/Si Heterostructures with Nanodisc Shaped Quantum Dots
  17. Novel Anthrathiophene-Based Small Molecules as Donor Material for Organic Photovoltaics: Synthesis and Light-Induced EPR Study
  18. Structural Determination of a DNA Oligomer for a Molecular Spin Qubit Lloyd Model of Quantum Computers
https://doi.org/10.1515/zpch-2016-0799
Keywords for this article
conformational search; DNA; ESR; molecular mechanics; spin labelling

Articles in the same Issue

  1. Frontmatter
  2. Preface
  3. Editorial Review
  4. From Free Radicals and Spin-Chemistry Over Spin-Dynamics and Hyperpolarization to Biology and Materials Science
  5. On Relations Between Singlet and Triplet Recombination Yields for Singlet and Triplet Precursors
  6. The Quantum Dynamical Basis of a Classical Kinetic Scheme Describing Coherent and Incoherent Regimes of Radical Pair Recombination
  7. Reaction Operators for Radical Pairs. The Exactly Solvable Model
  8. Estimation of the Fraction of Spin-Correlated Radical Ion Pairs in Irradiated Alkanes using Magnetosensitive Recombination Luminescence from Exciplexes Generated upon Recombination of a Probe Pair
  9. Theoretical Description of Pulsed RYDMR: Refocusing Zero-Quantum and Single Quantum Coherences
  10. A Transient EPR Study of Electron Transfer in Tetrathiafulvalene-Aluminum(III) Porphyrin-Anthraquinone Supramolecular Triads
  11. Solvent Radical Anions in Irradiated Aliphatic Ketones and Esters as Observed Using Time-Resolved Magnetic Field Effects in the Recombination Fluorescence
  12. Effect of Dehydrated Trehalose Matrix on the Kinetics of Forward Electron Transfer Reactions in Photosystem I
  13. Photo-CIDNP in the Reaction Center of the Diatom Cyclotella meneghiniana Observed by 13C MAS NMR
  14. Light-Stimulated Generation of Free Radicals by Quinones-Chelators
  15. Influence of C2-Methylation of Imidazolium Based Ionic Liquids on Photoinduced Spin Dynamics of the Dissolved ZnTPP Studied by Time-Resolved EPR
  16. ESR Study of Electron States in Ge/Si Heterostructures with Nanodisc Shaped Quantum Dots
  17. Novel Anthrathiophene-Based Small Molecules as Donor Material for Organic Photovoltaics: Synthesis and Light-Induced EPR Study
  18. Structural Determination of a DNA Oligomer for a Molecular Spin Qubit Lloyd Model of Quantum Computers
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