<i>CRYSTALFF</i>– from crystallography to EXAFS multiple-scattering calculations with<i>FEFF</i>

Provost, Karine; Champloy, Frédéric; Michalowicz, Alain

doi:10.1107/s090904950100574x

Cited by 8 publications

(9 citation statements)

References 4 publications

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“…33 FEFF8 input files were prepared with the code CRYSTALFF. 34 As the E 0 energy is fitted, no selfconsistent field was included in the calculation of the potentials. ii The most important single and multiple scattering paths up to 5 Å were sorted with the use of the homemade software Amplitude.…”

Section: Methodsmentioning

confidence: 99%

Coupling CP-MD Simulations and X-ray Absorption Spectroscopy: Exploring the Structure of Oxaliplatin in Aqueous Solution

et al. 2009

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A combined experimental-theoretical approach applying X-ray absorption spectroscopy and ab initio molecular dynamics (CP-MD) simulations is used to get insight into the structural determination of oxaliplatin, a third-generation anticancer drug of the cisplatin family, in aqueous solution. Experimental Pt L(III)-edge EXAFS and XANES spectra of oxaliplatin in water are compared with theoretical XAS spectra. The latter are obtained as statistically averaged spectra computed for a set of selected snapshots extracted from the MD trajectory of ethyldiamineoxalatoplatinum(II) (EDO-Pt) in liquid water. This compound is a simplified structure of oxaliplatin, where the outer part of the cyclohexane ring contained in the cyclohexanediamine ligand of oxaliplatin has been removed. We show that EDO-Pt is an appropriate model to simulate the spectroscopical properties of oxaliplatin given that the cyclohexane ring does not generate particular features in neither the EXAFS nor the XANES spectra. The computation of average EXAFS spectra using structures from the MD simulation in which atoms are selected according to different cutoff radii around the Pt center allows the assignment of spectral features to particular structural motifs, both in k and R-spaces. The outer oxygen atoms of the oxalate ligand (R(Pt-O(II)) = 3.97 +/- 0.03 A) are responsible for a well-defined hump at around 6.5 A(-1) in the k(2)-weighted EXAFS spectrum. The conventional EXAFS analysis data procedure is reexamined by its application to the simulated average EXAFS spectra. The structural parameters resulting from the fit may then be compared with those obtained from the simulation, providing an estimation of the methodological error associated with the global fitting procedure. A thorough discussion on the synergy between the experimental and theoretical XAS approaches is presented, and evidence for the detection of a slight hydration structure around the Pt complex is shown, leading to the suggestion of a new challenge to experimental XAS measurements.

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Section: Methodsmentioning

confidence: 99%

Coupling CP-MD Simulations and X-ray Absorption Spectroscopy: Exploring the Structure of Oxaliplatin in Aqueous Solution

et al. 2009

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“…(ii) Construction of the molecular models using the program Chem3D using crystallographic structures when they are known, or characteristic crystallographic distances and knowledge of the ligands structures. Preparation of the resulting FEFF (Rehr et al, 1992) input files using the code CRYSTALFF (Provost et al, 2001).…”

Section: Xas Measurements and Analysismentioning

confidence: 99%

EXAFS characterization of oxaliplatin anticancer drug and its degradation in chloride media

Bouvet¹,

Michalowicz²,

Crauste–Manciet

et al. 2006

J Synchrotron Radiat

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Oxaliplatin is a second-generation platinum-based anticancer drug. Its degradation is studied in solution, in the presence of chloride ions (in neutral or acidic media) in excess. In both cases the degradation product precipitates immediately. The EXAFS spectra of these products show that they are identical. EXAFS modeling and refinement of the first coordination sphere shows that two light atoms are replaced by two chloride ions. The complete refinement of the local structure is possible by studying the multiple-scattering signal. The results show that the main multiple-scattering contribution is due to the binding oxalato group and that the degradation product is [Cl(2)-(diaminocyclohexane)-Pt(II)].

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“…(ii) Construction of the molecular models with the Chem3D program using characteristic crystallographic distances and the knowledge of the ligand structures. Preparation of the resulting FEFF input files with the code CRYSTALFF …”

Section: Methodsmentioning

confidence: 99%

EXAFS and IR Structural Study of Platinum-Based Anticancer Drugs' Degradation by Diethyl Dithiocarbamate

et al. 2006

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Platinum compounds constitute a discrete class of DNA-damaging anticancer drug agents, including cisplatin, carboplatin, and oxaliplatin. The toxicity of such drugs raises the problem of waste detoxification. Diethyl dithiocarbamate (DDTC) is recommended by the World Heath Organization (WHO) for the destruction of cisplatin, but the degradation product has not been structurally characterized. This paper deals with the extended X-ray absorption fine structure (EXAFS) and IR structural study of the reaction products of DDTC with cisplatin, carboplatin, and oxaliplatin. Cisplatin and carboplatin give the same reaction product: Pt(DDTC)2. In the case of oxaliplatin, we observed the formation of [(diaminocyclohexane)(DDTC)Pt(II)]. In all cases, the replacement of labile ligands by strong ligands should lead to inactive compounds. Our results suggest that the WHO inactivation protocol might be extended to carboplatin and oxaliplatin. Nevertheless, this should be validated by toxicity tests of the degradation products.

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CRYSTALFF– from crystallography to EXAFS multiple-scattering calculations withFEFF

Abstract: CRYSTALFF is an alternative utility to ATOMS containing most of the features of this standard program for converting crystallographic data to FEFF input. In addition, it offers an interface with molecular modelling programs via the PDB format and new coordination sphere analysis options.

Cited by 8 publications

References 4 publications

Coupling CP-MD Simulations and X-ray Absorption Spectroscopy: Exploring the Structure of Oxaliplatin in Aqueous Solution

Coupling CP-MD Simulations and X-ray Absorption Spectroscopy: Exploring the Structure of Oxaliplatin in Aqueous Solution

EXAFS characterization of oxaliplatin anticancer drug and its degradation in chloride media

EXAFS and IR Structural Study of Platinum-Based Anticancer Drugs' Degradation by Diethyl Dithiocarbamate

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