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Volumn 113, Issue 13, 2009, Pages 4425-4434

Solvent reorganization energies in A-DNA, B-DNA, and rhodamine 6G-DNA complexes from molecular dynamics simulations with a polarizable force field

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DYNAMICS; ELECTROMAGNETIC WAVE POLARIZATION; ELECTRON TRANSITIONS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; POSITIVE IONS; SOLVENTS;

EID: 65249144636     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp809774q     Document Type: Article
Times cited : (19)

References (87)
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    • Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem. 1999, 111, 991. Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem. Int. Ed. 1999, 38, 941.
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    • Toukmaji, A.; Sagui, C.; Board, J. A.; Darden, T. J. Chem. Phys. 2000, 113, 10913.
    • Toukmaji, A.; Sagui, C.; Board, J. A.; Darden, T. J. Chem. Phys. 2000, 113, 10913.
  • 48
    • 84906357497 scopus 로고    scopus 로고
    • For ET between chemically different donor and acceptor moieties, the reorganization energy can be obtained by averaging the potential energy gaps ΔV of forward
    • For ET between chemically different donor and acceptor moieties, the reorganization energy can be obtained by averaging the potential energy gaps ΔV of forward
  • 49
    • 84906400724 scopus 로고    scopus 로고
    • and backward
    • (i) and backward
  • 50
    • 84906372075 scopus 로고    scopus 로고
    • processes: λ s, δV i-δV f)/2. Here, ΔV is the difference between two potential energies, calculated at the same solvent configuration, but with the hole located at the initial and final states of each of the two reactions. For such nonsymmetric ET at the shortest distances, 3.4 and 6.8 Å, the standard deviations S i and S f of the corresponding potential energy gaps were averaged according to S 2, S i 2, S f 21/2/2; for details, see ref 33
    • (f) processes: λ s ) (δV i-δV f)/2. Here, ΔV is the difference between two potential energies, calculated at the same solvent configuration, but with the hole located at the initial and final states of each of the two reactions. For such nonsymmetric ET at the shortest distances, 3.4 and 6.8 Å, the standard deviations S i and S f of the corresponding potential energy gaps were averaged according to S 2) (S i 2 + S f 2)1/2/2; for details, see ref 33.
  • 52
    • 84906357498 scopus 로고    scopus 로고
    • The result, 1.77 0.27 eV, of this latter setup should be treated with caution because the DNA solute is artificially underpolarized. Therefore, this perturbation cannot be considered as small, as the energetics is notably affected.
    • The result, 1.77 ( 0.27 eV, of this latter setup should be treated with caution because the DNA solute is artificially underpolarized. Therefore, this perturbation cannot be considered as small, as the energetics is notably affected.
  • 55
    • 0003998388 scopus 로고    scopus 로고
    • Lide, D. R, Ed, 81st ed, CRC Press: Boca Raton, FL
    • (a) Lide, D. R., Ed. Handbook of Chemistry and Physics, 81st ed.; CRC Press: Boca Raton, FL, 2000.
    • (2000) Handbook of Chemistry and Physics
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    • Oki, M, et al, Eds, 4th ed, Maruzen: Tokyo
    • (b) Oki, M., et al., Eds. Kagaku Binran, 4th ed.; Maruzen: Tokyo, 1993.
    • (1993) Kagaku Binran
  • 61
    • 84906357499 scopus 로고    scopus 로고
    • Edge effects are indeed negligible. For instance, we obtained λ s 1.23 ( 0.24 eV for the sequence 5-GG +GG GG-3(R DA ) 6.8 Å) and 1.43 ( 0.24 eV for the sequence 5-GG +GGG G-3(R DA ) 10.1 Å), both for B-DNA. The terminal sequences are different from the standard cases of the present work (Table 3), but the λ s values are essentially the same within standard deviations: 1.17 ( 0.22 eV (R DA ) 6.8 Å, X(3) ) T) and 1.51 ( 0.25 eV (R DA ) 6.8 Å, X(4) ) TT).
    • Edge effects are indeed negligible. For instance, we obtained λ s ) 1.23 ( 0.24 eV for the sequence 5-GG +GG GG-3(R DA ) 6.8 Å) and 1.43 ( 0.24 eV for the sequence 5-GG +GGG G-3(R DA ) 10.1 Å), both for B-DNA. The terminal sequences are different from the standard cases of the present work (Table 3), but the λ s values are essentially the same within standard deviations: 1.17 ( 0.22 eV (R DA ) 6.8 Å, X(3) ) T) and 1.51 ( 0.25 eV (R DA ) 6.8 Å, X(4) ) TT).
  • 63
    • 84906400723 scopus 로고    scopus 로고
    • Such corrections increase the value of λ by 5-20% as shown by studies of the temperature dependence of ET rates in DNA duplexes; e.g, see ref 21
    • Such corrections increase the value of λ by 5-20% as shown by studies of the temperature dependence of ET rates in DNA duplexes; e.g., see ref 21.
  • 73
    • 84906386204 scopus 로고    scopus 로고
    • The derivative is approximated as finite difference, ?λ s/?R DA ̃ (λi +1-λi )/ΔR DA with ΔR DA ) 3.4 Å in all cases.
    • The derivative is approximated as finite difference, ?λ s/?R DA ̃ (λi +1-λi )/ΔR DA with ΔR DA ) 3.4 Å in all cases.
  • 76
    • 84906386203 scopus 로고    scopus 로고
    • We refer to the earlier results of F. D. Lewis (see refs 66 and 67) despite the fact that they were recently reconsidered:
    • We refer to the earlier results of F. D. Lewis (see refs 66 and 67) despite the fact that they were recently reconsidered:
  • 84
    • 84906386205 scopus 로고    scopus 로고
    • Dissertation, Technische Universität, München
    • (a) von Feilitzsch, T. Dissertation, Technische Universität, München, 2002.
    • (2002)
    • von Feilitzsch, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.