EXAFS Debye-Waller factors issued from Car-Parrinello molecular dynamics: Application to the fit of oxaliplatin and derivatives

Abstract

One of the main pitfalls in EXAFS fitting is correlation among parameters, which can lead to unreliable fits. The use of theoretical Debye-Waller factors (DWs) is a promising way to reduce the number of fitted parameters. When working with molecular dynamics, it is not only possible to evaluate DWs from the statistical distributions issued from the trajectory but also to estimate the distribution anharmonicity, and to compute simulated average EXAFS spectra that can be fitted as experimental ones, in order to assess the ability of EXAFS fitting to recover information on DWs, as well as other structural and spectroscopical parameters. The case studied is oxaliplatin, a third generation anticancer drug. The structural information and the simulated average spectra were derived from a Car-Parrinello molecular dynamics (CP-MD) trajectory of a compound closely related to oxaliplatin. We present the DWs issued from this simulation and their use, by taking their theoretical absolute values (no DW fitted) or their ratios (one DW fitted). In this second approach, the fit of oxaliplatin experimental spectra leads to DWs values very close to the theoretical ones. This shows that the CP-MD trajectory provides a good representation of the distance distributions for oxaliplatin. Transferability of oxaliplatin DWs, for all relevant single and multiple scattering paths, to closely related compounds is proven for the case of bis(oxalato)platinum(II) and bis(ethylene diamine)platinum(II).

Effect of Basicity on the Hydrolysis of the Bi(III) Aqua Ion in Solution: An Ab Initio Molecular Dynamics Study

“…This is to say, no experimental information has been used in the XAS spectra building. To double the relationship between an experimental EXAFS spectrum and structure, one may build a set of intermolecular potentials, which produces the same structural parameters as the fitted ones . This is a good test on the influence of other structural and spectroscopical factors on the final signal.…”

“…To double the relationship between an experimental EXAFS spectrum and structure, one may build a set of intermolecular potentials, which produces the same structural parameters as the fitted ones. 54 This is a good test on the influence of other structural and spectroscopical factors on the final signal. To carry out this test we need to develop a trajectory where the basic structural characteristics of the Bi(III) environment given by the experimental fitting are reproduced.…”

EXAFS Spectroscopy of Fractional Mixed-Valence Charge Density Wave Systems

“…To reduce the number of variables in the fits, MSRDs for the Pt−N and Pt−C SS paths were fixed to the values reported by Provost et al, 21 who determined EXAFS MSRDs for bis(ethylenediamine)platinate, which corresponds to the Pt(en) 2 subunit within the chain structure; allowing these values to vary yielded largely similar results. The MSRDs for MS paths were constructed from the SS MSRDs using geometric constraints.…”

“…Four fitting parameters directly related to the CDW properties were allowed to vary: the photoelectron threshold energies of the two inequivalent platinum ions and the MSRDs for the SS paths for the two inequivalent platinum–halide distances along the chain axis. To reduce the number of variables in the fits, MSRDs for the Pt–N and Pt–C SS paths were fixed to the values reported by Provost et al, who determined EXAFS MSRDs for bis­(ethylenediamine)­platinate, which corresponds to the Pt­(en) 2 subunit within the chain structure; allowing these values to vary yielded largely similar results. The MSRDs for MS paths were constructed from the SS MSRDs using geometric constraints.…”

A Coupled EXAFS–Molecular Dynamics Study on PuO2+ and NpO2+ Hydration: The Importance of Electron Correlation in Force-Field Building

“…The combination of XAS spectroscopy and MD simulations has been revealed as an useful strategy 30 − 33 to refine the structural properties of solutions when the standard fitting of the experimental spectra are clouded by different factors as complexity of the system, low concentrations, spectroscopical phenomena as multiexcitations, low signal/noise ratio, and others. 34 The good reproduction of an experimental spectrum by means of the use of the structural information derived from a statistical simulation has a double consequence. 23 On the one hand, it allows access to a direct EXAFS structure assignment provided by the atomistic picture of the statistical trajectory.…”