We carried out ab initio molecular dynamic simulations in order to determine the free energy surfaces of two selected reactions including solvents, namely a rearrangement of a ruthenium oxoester in water and a carbon dioxide addition to a palladium complex in carbon dioxide. For the latter reaction we also investigated the gas phase reaction in order to take solvent effects into account. We used two techniques to reconstruct the free energy surfaces: thermodynamic integration and metadynamics. Furthermore, we gave a reasonable error estimation of the computed free energy surface. We calculated a reaction barrier of ΔF = 59.5 ± 8.5 kJ mol−1 for the rearrangement of a ruthenium oxoester in water from thermodynamic integration. For the carbon dioxide addition to the palladium complex in carbon dioxide we found a ΔF = 44.9 ± 3.3 kJ mol−1 from metadynamics simulations with one collective variable. The investigation of the same reactions in the gas phase resulted in ΔF = 24.9 ± 6.7 kJ mol−1 from thermodynamic integration, in ΔF = 26.7 ± 2.3 kJ mol−1 from metadynamics simulations with one collective variable, and in ΔF = 27.1 ± 5.9 kJ mol−1 from metadynamics simulations with two collective variables

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- (1981). A greatly improved procedure for ruthenium tetraoxide catalyzed oxisations of organic-compounds.
- (2001). A package for molecular simulation and trajectory analysis.
- (2005). A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.
- (1984). A uniﬁed formulation of the constant temperature molecular dynamics methods.
- (2006). Accurate Coulomb-ﬁtting basis sets for H to Rn.
- (2006). Activation of Small Molecules;
- (2005). Assessing the accuracy of metadynamics.
- Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy.
- (2005). Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics.
- (1999). Calculation of bulk properties of liquids and supercritical ﬂuids from pure theory.
- (1985). Canonical dynamics: Equilibrium phase space distributions.
- (2010). Carbon Dioxide as Chemical Feedstock;
- (2003). Constrained reaction coordinate dynamics for systems with constraints.
- (1989). Constrained reaction coordinate dynamics for the simulation of rare events.
- (2005). Cooperative versus dispersion effects: What is more important in an associated liquid such as water?
- (2010). CP2k Developers Home Page. CP2k developers group under the terms of the GNU General Public License. Avaiable online: http://cp2k.berlios.de (accessed on
- (1986). Density-Functional approximation for the correlation energy of the inhomogenous electron gas.
- (1988). Density-functional exchange-energy approximation with correct asymptotic behavior.
- (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.
- (2003). Efﬁcient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.
- (1991). Energy-adjusted ab initio pseudopotentials for the 2nd-row and 3rd-row transition-elements Molecular test for Ag2,
- (2002). Escaping free-energy minima.
- (2007). Free energy ab initio metadynamics: A new tool for the theoretical study of organometallic reactivity? Example of the C–C and C–H reductive eliminations from platinum(IV) complexes. Organometeallics
- (2007). Free Energy Calculations Theorey and Applications in Chemistry and Biology;
- (1998). Free energy from constrained molecular dynamics.
- (1988). Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations.
- (2007). Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases.
- Matplotlib: A 2D graphics environment.
- (1992). Nose–Hoover chains: The canonical ensemble via continuous dynamics.
- (1953). Oxidations with ruthenium tetraoxide.
- (2010). Oxygen Exchange in Uranyl Hydroxide via Two “Nonclassical” Ions.
- (1994). Practical and rapid vicinal hydroxylation of alkenes by catalytic ruthenium tetraoxide.
- (2002). Quantum chemical calculation of vibrational spectra of large molecules—Raman and IR spectra for buckminsterfullerene.
- (2009). Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics.
- (1998). Relativistic separable dual-space Gaussian pseudopotentials from H to Rn.
- (1973). Self-consistent molecular Hartree-Fock-Slater calculations—I. The computational procedure.
- (2006). Semiempirical GGA-type density functional constructed with a long-range dispersion correction.
- (1996). Separable dual-space Gaussian pseudopotentials.
- (1979). Some approximations in applications of X-alpha theory.
- (2010). Statistical Mechanics: Theory and Molecular Simulations;
- (1994). Synthesis of the 1st carbon-dioxide coordinated palladium(0) complex,
- (1999). The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations.
- (2007). Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efﬁciently and accurately?
- Theoretical Investigation of Solvent Effects and Complex Systems: Toward the calculations of bioinorganic systems from ab initio molecular dynamics simulations and static quantum chemistry.
- (2007). Theory of complicated liquids.
- (2007). Towards a rational design of ruthenium CO2 hydrogenation catalysts by ab initio metadynamics.
- (2002). Understanding Molecular Simulation: From Algorithms to Applications;
- (2010). Understanding Selectivities
- (2008). Well-tempered metadynamics: A smoothly converging and tunable free-energy method.