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

Shedding light on the metal-phthalocyanine EXAFS spectra through classical and ab initio molecular dynamics

Extended X-Ray Absorption Fine Structure (EXAFS) theoretical spectra for some 3d transition metal-phthalocyanines-FePc, NiPc, CuPc, and ZnPc-are presented. Their complexity and rigidity make them a good testbed for the development of theoretical strategies that can complement the difficulties present in the experimental spectrum fitting. Classical and ab initio molecular dynamics trajectories are generated and employed as a source of structural information to compute average spectra for each MPc species. The original ZnPc force field employed in the classical molecular dynamics simulations has been modified in order to improve the agreement with the experimental EXAFS spectrum, and the modification strategy-based on MP2 optimized structures-being extended to the rest of MPcs. Both types of trajectories, classical and ab initio, provide very similar results, showing in all cases the main features present in the experimental spectra despite the different simulation timescales employed. Spectroscopical information has been analyzed on the basis of shells and legs contributions, making possible the comparison with the experimental fitting approaches. According to the simulations results, the simple relationships employed in the fitting process to define the dependence of the Debye Waller factors associated with multiple scattering paths with those of single scattering paths are reasonable. However, a lack of multiple backscattering paths contributions is found due to the intrinsic rigidity of the chemical motif (macrocycle). Its consequences in the Debye Waller factors of the fitted contributions are discussed.

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

The physicochemical properties of the monovalent actinyl cations, PuO₂⁺ and NpO₂⁺, in water have been studied by means of classical molecular dynamic simulations. A specific set of cation-water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The TIP4P water model was adopted. Given the paramagnetic character of these actinyls, the cation-water interaction energies were computed from highly correlated wave functions using the NEVPT2 method. It is shown that the multideterminantal character of the wave function has a relevant effect on the main distances of the hydrated molecular cations. Several structural, dynamical, and energetic properties of the aqueous solutions have been obtained and analyzed. Structural RDF analysis gives An-O_yl distances of 1.82 and 1.84 Å and An-O(water) distances of 2.51 and 2.53 Å for PuO₂⁺ and NpO₂⁺ in water, respectively. Experimental EXAFS spectra from dilute aqueous solutions of PuO₂⁺ and NpO₂⁺ are revisited and analyzed, assuming tetra- and pentahydration of the actinyl cations. Simulated EXAFS spectra have been computed from the snapshots of the MD simulations. Good agreement with the experimental information available is found. The global analysis leads us to conclude that both PuO₂⁺ and NpO₂⁺ cations in water are stable pentahydrated aqua ions.

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

Hydrolysis of the Bi(III) aqua ion under a range of solution conditions has been studied by means of ab initio molecular dynamics simulations. While the Bi(III) aqua ion is stable in pure water, there is an increasing degree of hydrolysis with the number of hydroxide anions in the medium. This is accompanied by a monotonic decrease of the total coordination number to an asymptotic value of ∼6, reached under extreme basicity conditions. Comparison of the simulated Bi(III) hydrolyzed species with the experimental species distribution at different degrees of basicity suggests that, at the PBE/DFT level of theory here employed, liquid water shows an overly acidic character. Predictions of theoretical EXAFS and XANES spectra were generated from the AIMD trajectories for different Bi hydrolyzed species, [Bi(HO)_m(H₂O)_n]^3-m+, m = 0-3 and n = 7-2. Comparison with available experimental spectra is presented. Spectral features joined to the degree of hydrolysis and hydration are analyzed.

Molecular structures and solvation of free monomeric and dimeric ferriheme in aqueous solution: insights from molecular dynamics simulations and extended X-ray absorption fine structure spectroscopy

CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.