When Can a Computed Pt(II) Substitution Rate Be Trusted? A DFT Framework with Four Reliability Diagnostics Applied to Cisplatin
- 1Department of Organic Chemistry and Pharmaceutical Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211 A, 50-556 Wroclaw, Poland
Abstract
This study presents a DFT protocol for the substitution kinetics of Pt(II) complexes, applied to cisplatin as a case study. We aim to demonstrate that a computed barrier that agrees with experiment does not, by itself, validate the kinetic model, and that further diagnostics are required to assess the reliability of the results. M06-2X/x2c-TZVPall calculations with implicit solvation, explicit treatment of one coordinating water molecule and a set of physical corrections were used to study the aquation, thiolation (with a capped cysteine-thiolate model) and guanine substitution (by 9-methylguanine) pathways. The calculated precomplex-to-transition-state barrier for the first aquation is 2.0 kcal⋅mol−1 below the Eyring barrier inferred from experiment; with the symmetry factor σ = 2 applied, the calculated observed rate constant is 56-fold higher than the experimental value. The formal low-concentration second-order coefficient for thiolation exceeds the reported glutathione rate coefficient by 1.5–1.8 log units, whereas omission of the physical corrections shifts the calculated rate predictions by about 5–8 log units. A direct selectivity descriptor (Sdirect) is introduced and shown to be governed by the precomplex term rather than by the activation step, making it vulnerable to precomplex overstabilization by the implicit solvent. Four diagnostics are proposed that should accompany any computed rate constant or selectivity: the sign of the precomplex free energy, the magnitude of Kpre, the proximity to the diffusion limit, and the decomposition of selectivity into precomplex and activation contributions. These provide a systematic basis for assessing the reliability of computed predictions.
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BibTeX
@article{spiegel2026when,
title = {{When Can a Computed Pt(II) Substitution Rate Be Trusted? A DFT Framework with Four Reliability Diagnostics Applied to Cisplatin}},
author = {Maciej Spiegel and Marcin Mączyński},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = nov,
doi = {10.3390/ijms27219887},
url = {https://www.mdpi.com/1422-0067/27/21/9887},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - When Can a Computed Pt(II) Substitution Rate Be Trusted? A DFT Framework with Four Reliability Diagnostics Applied to Cisplatin
AU - Maciej Spiegel
AU - Marcin Mączyński
PY - 2026
DA - 2026/11/04
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219887
UR - https://www.mdpi.com/1422-0067/27/21/9887
AB - This study presents a DFT protocol for the substitution kinetics of Pt(II) complexes, applied to cisplatin as a case study. We aim to demonstrate that a computed barrier that agrees with experiment does not, by itself, validate the kinetic model, and that further diagnostics are required to assess the reliability of the results. M06-2X/x2c-TZVPall calculations with implicit solvation, explicit treatment of one coordinating water molecule and a set of physical corrections were used to study the aquation, thiolation (with a capped cysteine-thiolate model) and guanine substitution (by 9-methylguanine) pathways. The calculated precomplex-to-transition-state barrier for the first aquation is 2.0 kcal⋅mol−1 below the Eyring barrier inferred from experiment; with the symmetry factor σ = 2 applied, the calculated observed rate constant is 56-fold higher than the experimental value. The formal low-concentration second-order coefficient for thiolation exceeds the reported glutathione rate coefficient by 1.5–1.8 log units, whereas omission of the physical corrections shifts the calculated rate predictions by about 5–8 log units. A direct selectivity descriptor (Sdirect) is introduced and shown to be governed by the precomplex term rather than by the activation step, making it vulnerable to precomplex overstabilization by the implicit solvent. Four diagnostics are proposed that should accompany any computed rate constant or selectivity: the sign of the precomplex free energy, the magnitude of Kpre, the proximity to the diffusion limit, and the decomposition of selectivity into precomplex and activation contributions. These provide a systematic basis for assessing the reliability of computed predictions.
SN - 1422-0067
ER -