Theoretical simulations

Task 5 – Thermodynamics and molecular modeling

Task leader Virginie Marry
Participants PhENIx JHU/GL


Structural and thermodynamic parameters for adsorption and reactivity of biomolecules toward mineral surfaces will be calculated by molecular simulation. The results will be compared with the spectroscopic data and used to help interpreting the experiments. The calculated parameters, as adsorption constants will be used to optimize macroscopic surface complexation models. Then these models will allow a better description of surface speciation as a function of environmental conditions.

Description of work

  1. Selection of crystallographic surfaces and biomolecules for the simulations with pH dependent charges. Choice of force-fields.
  2. Classical molecular dynamics (MD) for the mechanisms of approach of the biomolecule toward surface in presence of water.
  3. Choice of the relevant collective variables for the exploration of the free energy landscape of adsorption process, with the help of quantum DFT results obtained in vacuum and configurations obtained from MD. Free energy landscape determination from metadynamics simulations (coll. R.Vuilleumier, ENS Paris). Calculation of adsorption constants.
  4. Comparison between calculated and measured spectroscopic data (Infrared and Raman).
  5. Determination of structural parameters from equilibrium configurations for thermodynamic models.
  6. Calculation of surface acido-basic sites pKa: influence of the presence of an already adsorbed biomolecule on the point of zero charge and on possible co-adsorption of another molecule.
  7. Application of surface complexation theory to develop models of surface speciation as a function of pH, ionic strength, surface loading, temperature and pressure.
  8. Integration of surface speciation from surface complexation models with spectroscopic data and molecular models
  9. Development of predictive models for biomolecule adsorption on a wide variety of minerals

Role of participants

V. Marry: Molecular dynamics
P. Bacle: Molecular dynamics
D. Sverjensky: Surface complexation models

Risks and contingency plan

The main risk is bound to limited computing time for time-consuming calculations. Metadynamics in particular requires the choice of a priori collective variables that could be wrong or incomplete in a first attempt. This technique may be assisted by coupling quantum DFT with classical DFT. This would allow to implicitly account for the solvent without making the calculations too heavy (coll. M. Levesque & D. Borgis, ENS Paris).
Surface complexation modeling is greatly facilitated by the availability of experimental adsorption data measured over as wide a range of environmental conditions as possible. For example, a wide pH range is extremely valuable, but this may not be feasible for some minerals with a limited range of stability. Under these circumstances, surface attachment modes suggested by the molecular modeling could be vital to constraining the surface complexation models.

Deliverables / Milestones

D5.1 – thermodynamic parameters for the adsorption
D5.2 – equilibrium configurations of adsorbed biomolecules
D5.3 – updated thermodynamic database
M5.1 – generation of initial configurations for metadynamics (m6)
M5.2 – free energy landscape determination (m18)
M5.3 – Surface complexation models of experimental adsorption data (m24)
M5.4 – Calculation of pKa (m30)
M5.5 – Integration of molecular modeling with macroscopic modeling and spectroscopic data (m36)