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Photodissociation of a ruthenium(II) arene complex and its subsequent interactions with biomolecules: a density functional theory study

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Abstract

The piano-stool RuII arene complex [(η6-benz)Ru(bpm)(py)]2+ (benz = benzene, bpm = 2,2′-bipyrimidine, and py = pyridine), which is conventionally nonlabile (on a timescale and under conditions relevant for biological reactivity), can be activated by visible light to selectively photodissociate the monodentate ligand (py). In the present study, the aquation and binding of the photocontrolled ruthenium(II) arene complex [(η6-benz)Ru(bpm)(py)]2+ to various biomolecules are studied by density functional theory (DFT) and time-dependent DFT (TDDFT). Potential energy curves (PECs) calculated for the Ru–N (py) bonds in [(η6-benz)Ru(bpm)(py)]2+ in the singlet and triplet state give useful insights into the photodissociation mechanism of py. The binding energies of the various biomolecules are calculated, which allows the order of binding affinities among the considered nuleic-acid- or protein-binding sites to be discerned. The kinetics for the replacement of water in the aqua complex with biomolecules is also considered, and the results demonstrate that guanine is superior to other biomolecules in terms of coordinating with the RuII aqua adduct, which is in reasonable agreement with experimental observations.

Photoinduced aquation and biomolecules replacement reaction for the complex

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Abbreviations

bpm:

2,2′-Bipyrimidine

Ru-bpm:

[(η6-benz)RuII(bpm)]2+

p-cym:

p-Cymene

benz:

Benzene

G:

Guanine

py:

Pyridine

A:

Adenine

met:

(CH3)2S

cys:

CH3SH

cym-Ru-py:

[(η6-p-cym)RuII(bpm)(py)]2+

Ru-py:

[(η6-benz)RuII(bpm)(py)]2+

Ru-H2O:

[(η6-benz)RuII(bpm)(H2O)]2+

Ru-G:

[(η6-benz)RuII(bpm)(G)]2+

Ru-A:

[(η6-benz)RuII(bpm)(A)]2+

Ru-hist:

[(η6-benz)RuII(bpm)(hist)]2+

Ru-cys:

[(η6-benz)RuII(bpm)(cys)]2+

Ru-met:

[(η6-benz)RuII(bpm)(met)]2+

hist:

5-Methyl-1H-imidazole

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (nos. 20725103, 20831006, 20821001, 20973204, 21172274, 21173273), the Guangdong Provincial Natural Science Foundation (no. 9351027501000003), and the National Basic Research Program of China (973, program no. 2007CB815306). It was partially sponsored by the high-performance grid computing platform of Sun Yat-sen University.

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Authors and Affiliations

  1. MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Hanlu Wang, Xiting Zhang, Cunyuan Zhao, Liangnian Ji & Zong-Wan Mao

  2. Department of Chemistry, The University of Memphis, Memphis, TN, 38152-3550, USA

    Nathan J. DeYonker

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  1. Hanlu Wang
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  2. Nathan J. DeYonker
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  3. Xiting Zhang
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  4. Cunyuan Zhao
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Correspondence to Cunyuan Zhao or Zong-Wan Mao.

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Wang, H., DeYonker, N.J., Zhang, X. et al. Photodissociation of a ruthenium(II) arene complex and its subsequent interactions with biomolecules: a density functional theory study. J Mol Model 18, 4675–4686 (2012). https://doi.org/10.1007/s00894-012-1467-3

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