Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs

Aquation free energy profiles of neutral cisplatin and cationic monofunctional derivatives, including triaminochloroplatinum(II) and cis-diammine(pyridine)chloroplatinum(II), were computed using state of the art thermodynamic integration, for which temperature and solvent were accounted for explicitly using density functional theory based canonical molecular dynamics (DFT-MD). For all the systems the "inverse-hydration" where the metal center acts as an acceptor of hydrogen bond has been observed. This has motivated to consider the inversely bonded solvent molecule in the definition of the reaction coordinate required to initiate the constrained DFT-MD trajectories. We found that there exists little difference in free enthalpies of activations, such that these platinum-based anticancer drugs are likely to behave the same way in aqueous media. Detailed analysis of the microsolvation structure of the square-planar complexes, along with the key steps of the aquation mechanism are discussed

DFT investigation of 3d transition metal NMR shielding tensors in diamagnetic systems using the gauge-including projector augmented-wave method

We present a density functional theory based method for calculating NMR shielding tensors for 3d transition metal nuclei using periodic boundary conditions. Calculations employ the gauge-including projector augmented-wave pseudopotentials method. The effects of ultrasoft pseudopotential and induced approximations on the second-order magnetic response are intensively examined. The reliability and the strength of the approach for 49Ti and 51V nuclei is shown by comparison with traditional quantum chemical methods, using benchmarks of finite organometallic systems. Application to infinite systems is validated through comparison to experimental data for the 51V nucleus in various vanadium oxide based compounds. The successful agreement obtained for isotropic chemical shifts contrasts with full estimation of the shielding tensor eigenvalues, revealing the limitation of pure exchange-correlation functionals compared to their exact-exchange corrected analogues.Comment: 56 page

Uranyl Carbonate Complexes in Aqueous Solution and Their Ligand NMR Chemical Shifts and ¹⁷O Quadrupolar Relaxation Studied by ab Initio Molecular Dynamics

Dynamic structural effects, NMR ligand chemical shifts, and ¹⁷O NMR quadrupolar relaxation rates are investigated in the series of complexes UO₂²⁺, UO₂(CO₃)₃^4–, and (UO₂)₃(CO₃)₆^6–. Car–Parrinello molecular dynamics (CPMD) is used to simulate the dynamics of the complexes in water. NMR properties are computed on clusters extracted from the CPMD trajectories. In the UO₂²⁺ complex, coordination at the uranium center by water molecules causes a decrease of around 300 ppm for the uranyl ¹⁷O chemical shift. The final value of this chemical shift is within 40 ppm of the experimental range. The UO₂(CO₃)₃^4– and (UO₂)₃(CO₃)₆^6– complexes show a solvent dependence of the terminal carbonate ¹⁷O and ¹³C chemical shifts that is less pronounced than that for the uranyl oxygen atom. Corrections to the chemical shift from hybrid functionals and spin–orbit coupling improve the accuracy of chemical shifts if the sensitivity of the uranyl chemical shift to the uranyl bond length (estimated at 140 ppm per 0.1 Å from trajectory data) is taken into consideration. The experimentally reported trend in the two unique ¹³C chemical shifts is correctly reproduced for (UO₂)₃(CO₃)₆^6–. NMR relaxation rate data support large ¹⁷O peak widths, but remain below those noted in the experimental literature. Comparison of relaxation data for solvent-including versus solvent-free models suggest that carbonate ligand motion overshadows explicit solvent effects

Quadrupolar NMR Relaxation from <i>ab Initio</i> Molecular Dynamics: Improved Sampling and Cluster Models versus Periodic Calculations

Quadrupolar NMR relaxation rates are computed for ¹⁷O and ²H nuclei of liquid water, and of ²³Na⁺, and ³⁵Cl^– in aqueous solution via Kohn–Sham (KS) density functional theory <i>ab initio</i> molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of 2 of experimental results and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling. The latter is found to be the more limiting factor in obtaining good statistical sampling and is improved by averaging over many equivalent nuclei of a system or over several independent trajectories. Further, full periodic plane-wave basis calculations of the EFGs are compared with molecular-cluster atomic-orbital basis calculations. The two methods deliver comparable results with nonhybrid functionals. With the molecular-cluster approach, a larger variety of electronic structure methods is available. For chloride, the EFG computations benefit from using a hybrid KS functional

Communication: Generalized canonical purification for density matrix minimization

A Lagrangian formulation for the constrained search for the N-representable one-particle density matrix based on the McWeeny idempotency error minimization is proposed, which converges systematically to the ground state. A closed form of the canonical purification is derived for which no a posteriori adjustment on the trace of the density matrix is needed. The relationship with comparable methods is discussed, showing their possible generalization through the hole-particle duality. The appealing simplicity of this self-consistent recursion relation along with its low computational complexity could prove useful as an alternative to diagonalization in solving dense and sparse matrix eigenvalue problems

Structure of an Amorphous Boron Carbide Film: An Experimental and Computational Approach

International audienceAn amorphous boron carbide ceramic is prepared via hot wall chemical vapor deposition at 1000 °C using a BCl3/CH4/H2 mixture. Its elemental composition is assessed by electron probe microanalysis (EPMA) and its structure studied by Raman spectroscopy, transmission electron microscopy (TEM), both X-ray diffraction (XRD) and neutron diffraction, 11B magic angle spinning nuclear magnetic resonance (MAS NMR), X-ray absorption spectroscopy (XAS), and ab initio modeling. The atomic structure factor and pair distribution function derived from neutron diffraction data are compared to those deduced from an atomistic model obtained by a liquid quench ab initio molecular dynamics simulation. The good agreement between experimental data and simulation shows that the as-prepared material is essentially made of a random arrangement of icosahedra (B12, B11C, and B10C2) embedded in an amorphous matrix rich in trigonal (BC3 or BC2B) and tetrahedral (CB4) sites. The existence of trigonal boron environments is clearly confirmed by a peak at 50 ppm in both the experimental and simulated 11B MAS NMR spectra, as well as a 190.0 eV component in the XANES-B(1s) spectrum. The intericosahedral linear C–B–C chains observed in crystalline B4C are absent in the as-processed material. Free hexagonal carbon and B4C crystallites appear in the ceramic when heat-treated at 1300 °C/2 h/Ar, as evidenced by high-resolution TEM and Raman spectroscopy. Comparing the pair distribution functions of the heat-treated material with the crystalline B4C model allows confirming the apparition of C–B–C chains in the material. Indeed, two new peaks located at 1.42 and 2.35 Å can only be attributed to a first-neighbor distance between the B and C atoms in the chain and a second-neighbor distance between a chain-boron atom and an icosahedron-boron atom, respectively

From cellulose to kerogen: molecular simulation of a geological process

The process by which organic matter decomposes deep underground to form petroleum and its underlying kerogen matrix has so far remained a no man's land to theoreticians, largely because of the geological (Myears) timescale associated with the process. Using reactive molecular dynamics and an accelerated simulation framework, the replica exchange molecular dynamics method, we simulate the full transformation of cellulose into kerogen and its associated fluid phase under prevailing geological conditions. We observe in sequence the fragmentation of the cellulose crystal and production of water, the development of an unsaturated aliphatic macromolecular phase and its aromatization. The composition of the solid residue along the maturation pathway strictly follows what is observed for natural type III kerogen and for artificially matured samples under confined conditions. After expulsion of the fluid phase, the obtained microporous kerogen possesses the structure, texture, density, porosity and stiffness observed for mature type III kerogen and a microporous carbon obtained by saccharose pyrolysis at low temperature. As expected for this variety of precursor, the main resulting hydrocarbon is methane. The present work thus demonstrates that molecular simulations can now be used to assess, almost quantitatively, such complex chemical processes as petrogenesis in fossil reservoirs and, more generally, the possible conversion of any natural product into bio-sourced materials and/or fuel

Structure of an Amorphous Boron Carbide Film: An Experimental and Computational Approach

An amorphous boron carbide ceramic is prepared via hot wall chemical vapor deposition at 1000 °C using a BCl₃/CH₄/H₂ mixture. Its elemental composition is assessed by electron probe microanalysis (EPMA) and its structure studied by Raman spectroscopy, transmission electron microscopy (TEM), both X-ray diffraction (XRD) and neutron diffraction, ¹¹B magic angle spinning nuclear magnetic resonance (MAS NMR), X-ray absorption spectroscopy (XAS), and ab initio modeling. The atomic structure factor and pair distribution function derived from neutron diffraction data are compared to those deduced from an atomistic model obtained by a liquid quench ab initio molecular dynamics simulation. The good agreement between experimental data and simulation shows that the as-prepared material is essentially made of a random arrangement of icosahedra (B₁₂, B₁₁C, and B₁₀C₂) embedded in an amorphous matrix rich in trigonal (<i><u>B</u></i>C₃ or <i><u>B</u></i>C₂B) and tetrahedral (<i><u>C</u></i>B₄) sites. The existence of trigonal boron environments is clearly confirmed by a peak at 50 ppm in both the experimental and simulated ¹¹B MAS NMR spectra, as well as a 190.0 eV component in the XANES-B­(1s) spectrum. The intericosahedral linear C–B–C chains observed in crystalline B₄C are absent in the as-processed material. Free hexagonal carbon and B₄C crystallites appear in the ceramic when heat-treated at 1300 °C/2 h/Ar, as evidenced by high-resolution TEM and Raman spectroscopy. Comparing the pair distribution functions of the heat-treated material with the crystalline B₄C model allows confirming the apparition of C–B–C chains in the material. Indeed, two new peaks located at 1.42 and 2.35 Å can only be attributed to a first-neighbor distance between the B and C atoms in the chain and a second-neighbor distance between a chain-boron atom and an icosahedron-boron atom, respectively