The capture of CO2 from flue gas in coal, natural gas, and other fossil fuel burning power stations and storage of CO2 in depleted gas reservoirs in the form of the solid clathrate hydrate have been suggested as methods of carbon capture and storage. These methods have the benefit of only needing water as the CO2 capturing material. The flue gas contains impurities including SO2, CH4, N-2, and H2S which can interfere with the CO2 hydrate formation process. Some of these gases may also be found as residuals in depleted natural gas reservoirs. In this work, we use the molecular dynamics thermodynamic integration method to calculate the Gibbs free energy of the substitution reactions at conditions relevant to carbon capture (T = 200 K and 0.1 MPa and at 273 K and 1.0 MPa conditions), clathrate[CO2, p, T] + Y(fluid,p, T) clathrate[Y,p, T] + CO2(fluid,p, T) where Y is the impurity species in the flue. Knowledge of the Gibbs free energy for this reaction will allow us to determine whether the impurities need to be eliminated from the flue or can participate in the hydrate formation process as neutral species without affecting the stability of the desired CO2 clathrate hydrate. For the thermodynamic integration, we use the nonlinear mixing scheme. In addition to calculating the Delta G for the above reaction, the contributions of different terms in the intermolecular potential of the guest molecules to the Delta G will be determined. (C) 2011 Elsevier Ltd. All rights reserved.