The Fast Multipole Method and Point Dipole Moment Polarizable Force Fields

We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of FMM combined with state-of-the-art chemical models in molecular dynamical systems.Comment: 11 pages, 8 figures, accepted by J. Chem. Phy

Simulated solvation of organic ions II: Study of linear alkylated

International audienceWe investigated the solvation of carboxylate ions from formate to hexanoate, in droplets of 50 to 1000 water molecules and neat water, by computations using standard molecular dynamics and sophisticated polarizable models. The carboxylate ions from methanoate to hexanoate show strong propensity for the air/water interface in small droplets. Only the ions larger than propanoate retain propensity for the interface in larger droplets, where their enthalpic stabilization by ion/water dispersion is reduced there by 3 kcal mol–1 per CH2 group. This is compensated by entropy effects over +3.3 cal mol–1 K–1 per CH2 group. On the surface, the anionic headgroups are strongly oriented toward the aqueous core, while the hydrophobic alkyl chains are repelled into air and lose their structure-making effects. These results reproduce the structure-making effects of alkyl groups in solution, and suggest that the hydrocarbon chains of ionic headgroups and alkyl substituents solvate independently. Extrapolation to bulk solution using standard extrapolation schemes yields absolute carboxylate solvation energies. The results for formate and acetate yield a proton solvation enthalpy of about 270 kcal mol–1, close to the experiment-based value. The largest carboxylate ions yield a value smaller by about 10 kcal mol–1, which requires studies in much larger droplets

Benchmark binding energies of ammonium and alkyl-ammonium ions interacting with water. Are ammonium–water hydrogen bonds strong?

International audienceAlkyl-ammonium ion/water interactions are investigated using high level quantum computations, yielding thermodynamics data in good agreement with gas-phase experiments. Alkylation and hydration lead to weaken the NH O hydrogen bonds. Upon complete hydration by four water molecules, their main features are close to those of the OH O bond in the isolated water dimer. Energy decomposition analyses indicate that hydration of alkyl-ammonium ions are mainly due to electrostatic/polarization effects, as for hard monoatomic cations, but with a larger effect of dispersion

Chitosan polysaccharides from a polarizable multiscale approach

International audienceWe report simulations of chitosan polysaccharides in the aqueous phase, at infinite dilute conditions and zero ionic strength. Those simulations are performed by means of a polarizable multiscale modeling scheme that relies on a polarizable all atom force field to model solutes and on a polarizable solvent coarse grained approach. Force field parameters are assigned only from quantum chemistry ab initio data. We simulate chitosan monomer units, dimers and 50-long chains. Regarding the 50-long chains we simulate three sets of ten randomly built chain replica at three different pH conditions (corresponding to different chain protonation states, the chain degree of deacetylation is 85%). Our simulations show the persistence length of 50-long chitosan chains at strong acidic conditions (pH <5) to be 24 ± 2 nm (at weak/negligible ionic strength conditions), and to be 1 order of magnitude shorter at usual pH conditions. Our simulation data support the most recent simulation and experimental studies devoted to chitosan polysaccharides in the aqueous phase

Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid waters

International audienceIn this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3478999

Hybrid polarizable simulations of a conventional hydrophobic polyelectrolyte. Toward a theoretical tool for green science innovation

International audienceHybrid modeling approaches based on all-atom force fields to handle a solute and coarse grained models to account for the solvent are promising numerical tools that can be used to understand the properties of large and multi components solutions and thus to speed up the development of new industrial products that obey the standard of green and sustainable chemistry. Here w