LiNixMnyCo1−x−yO2 compounds (NMC) are layered oxides widely used in commercial lithium-ion batteries at the positive electrode. Nevertheless surface reactivity of this material is still not well known. As a first step, based on first principle calculations, this study deals with the electronic properties and the surface reactivity of LiMO2 (M = Co, Ni, Mn) compounds, considering the behavior of each transition metal separately in the same α-NaFeO2-type structure, the one of LiCoO2 and NMC. For each compound, after a brief description of the bare slab electronic properties, we explored the acido-basic and redox properties of the (110) and (104) surfaces by considering the adsorption of a gaseous probe. The chemisorption of SO2 produces both sulfite or sulfate species associated respectively to an acido-basic or a reduction process. These processes are localized on the transition metals of the first two layers of the surface. Although sulfate species are globally favored, a different behavior is obtained depending on both the surface and the transition metal considered. We conclude with a simple scheme which describes the reduction processes on the both surfaces in terms of formal oxidation degrees of transition metals.
Vallverdu, G.; Minvielle, M.; Andreu, N.; Gonbeau, D.; Baraille, I. First Principle Study of the Surface Reactivity of Layered Lithium Oxides LiMO2 (M = Ni, Mn, Co). Surface Science 2016, 649, 46–55.
LixPOyNz is an amorphous solid electrolyte widely used in microbattery devices. The present study, based on a confrontation between experiment and theory, aims at providing new knowledge regarding the ionic conductivity model of such systems in correlation with its structure. The computational strategy involved molecular dynamic simulations and first-principle calculations on molecular and periodic models. The experimental target data involve electronic and vibrational properties and were considered through the simulation of Raman and X-ray photoemission spectra in order to identify characteristic patterns of LixPOyNz. In particular, the presence of short phosphate chains is suggested by molecular dynamics calculations, and the simulation of Raman spectra clearly evidenced a new coordination for nitrogen atoms in the amorphous state, not considered until now in the experimental structural model of the electrolyte and initially hypothesized based on core level binding energy computations. Monovalent nitrogen atoms together with short phosphate chains were used to build a structural model of the electrolyte and appeared to lead to a better reproduction of the target experimental results, while it implies a necessary refinement of the diffusion schemes commonly considered for lithium ions.
Guille, É.; Vallverdu, G.; Tison, Y.; Bégué, D.; Baraille, I. Possible Existence of a Monovalent Coordination for Nitrogen Atoms in LixPOyNz Solid Electrolyte: Modeling of X-Ray Photoelectron Spectroscopy and Raman Spectra. J. Phys. Chem. C 2015.
We present first-principle calculations of core-level binding energies for the study of insulating, bulk phase, compounds, based on the Slater-Janak transition state model. Those calculations were performed in order to find a reliable model of the amorphous LixPOyNz solid electrolyte which is able to reproduce its electronic properties gathered from X-ray photoemission spectroscopy (XPS) experiments. As a starting point, Li2PO2N models were investigated. These models, proposed by Du et al. on the basis of thermodynamics and vibrational properties, were the first structural models of LixPOyNz. Thanks to chemical and structural modifications applied to Li2PO2N structures, which allow to demonstrate the relevance of our computational approach, we raise an issue concerning the possibility of encountering a non-bridging kind of nitrogen atoms (=N-) in LixPOyNz compounds.
Guille, É.; Vallverdu, G.; Baraille, I. First-Principle Calculation of Core Level Binding Energies of LixPOyNz Solid Electrolyte. The Journal of Chemical Physics 2014, 141, 244703.
Using periodic density functional theory approaches, the thermodynamic stability of solid-solid interfaces generated during the conversion reaction of copper oxide which is a promising electrode material is investigated. Previous experimental results showed that conversion reactions generate a huge proportion of solid-solid interfaces among Cu2O-Cu, Li2O-Cu and Cu2O-Li2O. Interface grand potentials as a function upon the voltage against a Li|Li+ were computed in order to determine the chemical composition of the most stable interfaces. Then a structural model of the electrode material is proposed, based on the work of adhesion of the most stable systems identified in the first step.
L. Martin, G. Vallverdu, H. Martinez, F. Lecras & I. Baraille; First-principles calculations of solid-solid interfaces : application to conversion materials for lithium-ion batteries; Journal of Materials Chemistry, 2012, DOI: 10.1039/C2JM35078E
An extension of the model described in a previous work (see Maillet J. B. et al., EPL, 78 (2007) 68001) based on Dissipative Particle Dynamics is presented and applied to a liquid high explosive (HE), with thermodynamic properties mimicking those of liquid nitromethane. Large scale nonequilibrium simulations of reacting liquid HE with model kinetic under sustained shock conditions allow a better understanding of the shock-to-detonation transition in homogeneous explosives. Moreover, the propagation of the reactive wave appears discontinuous since ignition points in the shocked material can be activated by the compressive waves emitted from the onset of chemical reactions.
Maillet, J.; Bourasseau, E.; Desbiens, N.; Vallverdu, G. & Stoltz, G. Mesoscopic simulations of shock-to-detonation transition in reactive liquid high explosive EPL, 2011, 96, 68007
We have introduced a new algorithm in the parallel processing PMEMD module of the AMBER suite that allows MD simulations with a potential involving two coupled torsions. We have used this modified module to study the green fluorescent protein. A coupled torsional potential was adjusted on high accuracy quantum chemical calculations of the anionic chromophore in the first excited state, and several 15-ns-long MD simulations were performed. We have obtained an estimate of the fluorescence lifetime (2.2 ns) to be compared to the experimental value (3 ns), which is, to the best of our knowledge, the first theoretical estimate of that lifetime.
Jonasson, G.; Teuler, J.-M.; Vallverdu, G.; Mérola, F.; Ridard, J.; Lévy, B. & Demachy, I. Excited state dynamics of the green fluorescent protein on the nanosecond time scale Journal of Chemical Theory and Computation, 2011, 7, 1990-1997
Molecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865–9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocyclic ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/H148D.
Vallverdu, G.; Demachy, I.; Mérola, F.; Pasquier, H.; Ridard, J. & Lévy, B. Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations Proteins: Structure, Function and Bioformatics, 2010, 78, 1040-1054
The present article presents a theoretical study of the dynamics of the chromophore of the Green Fluorescent Protein in its excited state on a long time scale (a few ten nanoseconds) in order to help the interpretation of time resolved experiments. The starting hypothesis is that the quenching of fluorescence is related to the internal motion of the chromophore, usually called ‘φ torsion’. In fact, that motion is hindered by the protein and cannot be studied by standard molecular dynamics. Therefore we have developed a different approach involving three steps.
First the potential of mean force (PMF) along the considered torsion is obtained by biased molecular dynamics (umbrella sampling). Then, a long time scale, single particle Brownian dynamics is performed using that PMF and an appropriate diffusion constant. Finally we determine the nth passage time (NPT) distribution functions at geometries or regions where nonradiative ground state recovery may occur. The NPT distributions generalize the more usual ’mean first passage time’ and allow determining different quantities like fluorescence decay profiles, mean fluorescence lifetime, quantum yield etc.
These quantities are used here in a qualitative discussion of the fluorescence decay in Green Fluorescent Protein.
Vallverdu, G.; Demachy, I.; Ridard, J. & Lévy, B. Using biased molecular dynamics and Brownian dynamics in the study of fluorescent proteins Journal of Molecular Structure: THEOCHEM, 2009, 898, 73-81
We have studied the fluorescence decays of the purified enhanced cyan fluorescent protein (ECFP, with chromophore sequence Thr-Trp-Gly) and of its variant carrying the single H148D mutation characteristic of the brighter form Cerulean. Both proteins exhibit highly complex fluorescence decays showing strong temperature and pH dependences. At neutral pH, the H148D mutation leads (i) to a general increase in all fluorescence lifetimes and (ii) to the disappearance of a subpopulation, estimated to be more than 25% of the total ECFP molecules, characterized by a quenched and red-shifted fluorescence. The fluorescence lifetime distributions of ECFP and its H148D mutant remain otherwise very similar, indicating a high degree of structural and dynamic similarity of the two proteins in their major form. From thermodynamic analysis, we conclude that the multiexponential decay of ECFP cannot be simply ascribed, as is generally admitted, to the slow conformational exchange characterized by NMR and X-ray crystallographic studies [Seifert, M. H., et al. (2002) J. Am. Chem. Soc. 124, 7932−7942; Bae, J. H., et al. (2003) J. Mol. Biol. 328, 1071−1081]. Parallel measurements in living cells show that these fluorescence properties in neutral solution are very similar to those of cytosolic ECFP.
Villoing, A.; Ridhoir, M.; Cinquin, B.; Erard, M.; Alvarez, L.; Vallverdu, G.; Pernot, P.; Grailhe, R.; Mérola, F. & Pasquier, H. Complex fluorescence of the cyan fluorescent protein: Comparisons with the H148D variant and consequences for quantitative cell imaging Biochemistry, 2008, 47, 12483-12492
The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A’ and B’ of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A’ and B’ are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the β barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A‘. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A‘ and B‘ exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.
Demachy, I.; Ridard, J.; Laguitton-Pasquier, H.; Durnerin, E.; Vallverdu, G.; Archirel, P. & Lévy, B. Cyan fluorescent protein: Molecular dynamics, simulations, and electronic absorption spectrum Journal of Physical Chemistry B, 2005, 109, 24121-24133