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

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.Comment: Submitted as a roadmap article to Modelling and Simulation in Materials Science and Engineering; Address any correspondence to Vikram Gavini ([email protected]) and Danny Perez ([email protected]

Détermination de paramètres RMN par la théorie de la fonctionnelle de la densité (application aux éléments 3d en RMN de l'état solide)

La spectroscopie de résonance magnétique nucléaire (RMN) appliquée à l'état solide permet d'observer, outre les perturbations des niveaux Zeeman, un grand nombre d'interactions internes, généralement moyennées à l'état liquide. Lorsque les développements séquentiels expérimentaux ne permettent pas de s'affrranchir de certaines d'entre elles, l'interprétation des spectres est rendue délicate voire impossible. Théorie et méthodes numériques se mettent alors au service de l'expérience pour une meilleure compréhension des bservations. Néanmoins, un dilemme doit être résolu entre précision des calculs, taille des édifices atomiques traités et nature des noyaux sondés. A partir de l'approximation pseudo-potentiel développée dans le formalisme de la théorie de la fonctionnelle de la densité (DFT), il est montré dans ce travail qu'il est possible de prédire avec précision les paramètres de déplacement chimique et de gradient de champ électrique des éléments 3d dans des systèmes étendus. Une étude fine des différentes approximations présentes dans la méthode "gauge-including projector augmented-wave" (GIPAW) a permis le développement d'outils fiables pour l'étude des noyaux 49Ti, 51V et 55Mn. Après validation sur des composés modèles d'oxydes de vanadium, ces outils ont été légitimement appliqués à d'autres systèmes périodiques. Ainsi, l'étude de composés complexes comme un décavanadate de césium ou des phosphovanadates, a permis d'apporter des réponses quant aux indéterminations structurales et aux problèmes d'interprétation des spectres RMN. Quelques problèmes inhérents à l'approche DFT ont été soulevés et discutés.Besides Zeeman levels perturbation, nuclear magnetic resonance spectroscopy (NMR) applied to solid state allows the observation of numerous coupling interactions that are not accessible in liquid state. Despite sequential developments for high resolution measurements, interpretation of resonance spectra remains delicate...NANTES-BU Sciences (441092104) / SudocSudocFranceF

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

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

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

Impact of structural anisotropy on electro-mechanical response in crystalline organic semiconductors

In an effort to gain a fundamental understanding of the electromechanical response in high mobility crystalline organic semiconductors, we have investigated the uniaxial strain-mobility relationships in rubrene and benzothienobenzothiophene crystals. Elastic moduli and Poisson ratios of the materials are evaluated and the strain mobility response of these materials is rationalized using the effective masses and electronic couplings in the framework of hopping and band transport models, giving consistent results. The microscopic origin of the response is investigated in relation to the strain induced variations in the inter- and intra-molecular degrees of freedom. We demonstrate that the strain applied along one of the crystallographic directions in these materials does not only induce mobility variations along the same direction, but also along the other crystallographic directions that are mechanically coupled with large Poisson ratios. A rational design of electronic devices could therefore benefit from the efficient exploitation of this anisotropic strain mobility response in relation to the inherent crystalline anisotropy