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Simulations were based on the Dreiding 2.1 force field given in Mayo, S. L.; Olafson, B. D.; Goddard, W. A. J. Phys. Chem. 1990, 94, 8897. The charge distribution is calculated with the charge equilibration method as described in Rappe, A. K.; Goddard, W. A. J. Phys. Chem. 1991, 95, 3358. The classical molecular dynamics package used was Cerius2 V2.5 by Molecular Simulation Inc.
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note
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For Pt, the Lennard-Jones parameters were missing and were replaced by those of Ru that has a similar van der Waals radius.
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45
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85088171602
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note
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1 (a = 31.326 Å, b = 35.679 Å, c = 19.504 Å, α = β = γ = 90.00°).
-
-
-
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47
-
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0026742978
-
-
Entry DDB004 in the nucleic acid database (Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S.-H.; Srinivasan, A. R.; Schneider, B. Biophys. J. 1992, 63, 751).
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Schneider, B.9
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48
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0346634053
-
-
note
-
The major difference between this monostrand adduct and double-strand cis-platin-DNA adducts is represented by the orientation of the purine bases, which is modified by the presence of the Watson-Crick base-pair H-bond interaction. In fact, the base/base dihedral angle is reduced from ∼80° to 50-60°. Also the planarity of the platinum first environment is partially lost (the Pt position is displaced by 0.4 Å from the best-fit plane of the four ligands).
-
-
-
-
49
-
-
0346002918
-
-
note
-
The most important intermolecular interaction among the complexes are the guanine-guanine stacking interactions (minimum G-G distance 3.4 Å) and H-bond interactions, namely, ammonia-phosphate, ammonia-O6 guanine, phosphate-guanine amino, and imino group interactions. H-bond interactions are also formed between the biomolecule and the 27 detected water molecules. The majority of the water molecules belong to the first solvation shell of the ammonia ligands, the phosphate group, the heteroatoms of the nucleobases. The four symmetry-related tetrameric aggregates comprising the unit cell are separated by water channels.
-
-
-
-
50
-
-
0347894236
-
-
note
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The volume of the system being kept constant during the simulations, F indicates the Helmholtz free energy.
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52
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0347263908
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The statistical error is estimated to be about 2 kcal/mol
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The statistical error is estimated to be about 2 kcal/mol.
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59
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