Potentials of mean force with ab initio mixed Hamiltonian models of solvation

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.; Arcia, Edgar E.

doi:10.1016/s0166-1280(03)00297-5

Cited by 10 publications

(11 citation statements)

References 75 publications

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“…Therefore, in an alternative approach the entire or at least parts of the solvent are treated with a lower level of theory than the solute, for example, by molecular mechanics. [24,25,[27][28][29] Within these methods, known as QM/MM, the solvent-solvent and solute-solvent interactions are mostly given by a sum of electrostatic and van der Waals contributions. While the van der Waals interactions are often evaluated by Lennard-Jones-type potential functions, [27,28,30] an appropriate handling of the electrostatic interactions between solute and solvent, which couples the quantum-mechanically treated solute with the molecular-mechanically treated solvent, is important.…”

Section: Solvationmentioning

confidence: 99%

Water Formation on Pt and Pt‐based Alloys: A Theoretical Description of a Catalytic Reaction

2006

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In the past, the modeling of catalytic processes was limited by the size and complexity of the systems involved. However, the enormous progress in both computer power and theoretical methods has made computational modeling a valuable tool in increasing our knowledge of catalytic reactions on the atomic scale. While complex reactions can be studied by dividing the overall reaction into a series of steps calculable by quantum mechanics, the combination with methods appropriate for larger time and length scales enables the gap between these regimes to be bridged. This provides a more realistic modeling of the experimental system and allows important environmental effects such as solvation to be taken into account. In this Minireview we describe some of the main theoretical methodologies that are used to study catalytic properties and reactions on surfaces. Using these methods, we study the seemingly simple reaction of water formation out of hydrogen and oxygen on Pt and Pt/Ni alloy catalysts. To provide a more realistic description we also discuss the interesting effects determined by hydrating the system or using alloy nanoparticles rather than extended surfaces.

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Section: Solvationmentioning

confidence: 99%

Water Formation on Pt and Pt‐based Alloys: A Theoretical Description of a Catalytic Reaction

2006

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“….i (i) denotes the ensemble average of the difference in total QM/MM energies E i and E j of the system with solute in the i and j configurations respectively, and with the solvent molecules in configurations originating from a Monte Carlo random walk based on the energy of solute in the i configuration. We adopted the double perturbation approach of Dupuis et al 15 In this approach an intermediate MM/MM level of theory is used for the random walk, with the solute subsystem treated at the MM level of theory, with the same Lennard-Jones parameters as those used in the QM/MM model 16 and with atomic partial charges extracted from a fit to the electrostatic potential of the solute in the gas phase (CHELPG (charges from electrostatic potentials using a grid-based method) charges). 17 In the present work, for each solute configuration i, 20 000 000 solvent configurations were generated at the MM/MM level of theory, at constant temperature T = 298 K and constant volume (NVT ensemble).…”

Section: Methodsmentioning

confidence: 99%

Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

Ohisa

Yamataka

Dupuis

et al. 2008

Phys. Chem. Chem. Phys.

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Two-dimensional free-energy surfaces are calculated for alkyl chloride/chloride exchange/inversion reactions: Cl(-)+RCl (R=Me and t-Bu) surrounded by one hundred H(2)O molecules as a model of solvent. The methodology of free-energy calculation by perturbation theory based on a mixed-Hamiltonian model (QM/MM) combined with Monte Carlo sampling of the solvent configurations was used to obtain the changes in solvation free energy. We devised a special procedure to analyze the two-dimensional free-energy surfaces to gain unique insight into the differences in the reaction mechanisms between the two systems. The inversion reaction path for R=t-Bu on the free-energy surface is found to proceed in an asynchronous way within a concerted framework via the ion-pair region. This is in contrast to the R=Me system that proceeds as a typical S(N)2 reaction.

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“….i ðiÞ denotes the ensemble average of the difference in total QM/MM energies of gly-1W (in structures i and j) with the solvent molecules in configurations originating from a Monte Carlo random walk around gly-1W in structure i in a solvation sphere with a radius of 9.32 ¡ (Figure 1B), in which the water density is 1 g cm ¹3 . To sample the solvent configurations, we adopted the double perturbation approach of Dupuis et al 18 In this approach, an intermediate MM/MM level of theory is used for the random walk, with the gly-1W subsystem treated at the MM level of theory, using the same LennardJones parameters as in the QM/ MM model and with atomic partial charges extracted from a fit to the electrostatic potential of the solute in the gas phase (CHELPG charges). 19 In the present work, for each gly-1W structure i along the selected IRC points, 20000000 solvent configurations were generated at the MM/MM level of theory, at a constant temperature T = 298 K and constant volume (NVT ensemble), of which 2000 configurations were selected randomly to be used for QM/ MM calculations.…”

Section: þ=Kt Gi ðIþ ð2þmentioning

confidence: 99%

Ab Initio QM/MM-MC Study on Hydrogen Transfer of Glycine Tautomerization in Aqueous Solution: Helmholtz Energy Changes along Water-mediated and Direct Processes

Miyamoto

Aida

2013

Chemistry Letters

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Helmholtz free-energy changes in aqueous solution along two paths of glycine tautomerization were investigated by using an ab initio QM/MM-MC method with the thermodynamic perturbation theory. Glycine and one water molecule were treated at the quantum mechanics (QM) level of MP2/6-31G(d); these were surrounded by 100 water molecules at the molecular mechanics (MM) level of TIP3P. AIM (atoms-in-molecules) analysis showed that the transfer of two hydrogen atoms occurs simultaneously along the water-mediated path. The free-energy barrier height of this path in aqueous solution was higher than that of the direct path.Glycine is the smallest amino acid; it exists as the neutral (N) form in the gas phase, and as the zwitterionic (Z) form in the aqueous and crystalline states. Although the tautomerization of glycine between the N and Z forms has been studied extensively, the process of hydrogen transfer in glycine tautomerization is not yet understood completely.17 For micro-hydrated glycine complexes with two to five water molecules, it was shown that the energy barrier for hydrogen transfer via the direct path was lower than those for water-mediated paths. 7 The ab initio QM/MM-FEG method was applied to glycine tautomerization via direct hydrogen transfer surrounded by MM water molecules, 4 where QM energy calculations were performed at the theoretical level of MP2/ 6-31+G(d), with the glycine structural parameters optimized at the HF/6-31+G(d) level, and it was demonstrated that the computational free-energy difference between the N and Z forms compared well with experimentally observed values. On the other hand, a ReaxFF (reactive force field) MD simulation was applied to glycine tautomerization (direct as well as mediated by one or two water molecules), and it was suggested that the hydrogen transfer of glycine was mediated by a single water molecule in the aqueous environment.5 Thus, the hydrogen-transfer path in glycine tautomerization is still controversial.In this letter, we aim to present the probable route starting from the same complex in aqueous solution: one route is a singlewater-mediated hydrogen-transfer path, and the other is a direct hydrogen-transfer path. To this end, we treat a complex of glycine with one water molecule, gly-1W, at the QM level (ab initio molecular orbital (MO) method with MP2/6-31G(d)). The Helmholtz free-energy differences along the tautomerization routes are calculated on the basis of thermodynamic perturbation theory with Monte Carlo (MC) sampling of 100 MM water molecules surrounding the QM complex. Furthermore, we decompose the processes of single and double hydrogen transfers to neutral, transition state (TS), and zwitterionic regions on the basis of the AIM analysis, and we show that it is not a "proton" but a "hydrogen atom" that is transferred. First, the ab initio MO method was employed for the complex gly-1W in the gas phase. We obtained the stationary structures of intra-and intermolecular hydrogen-transfer reactions by using the MP2/6-31G(d) level of theory. Since it...

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Potentials of mean force with ab initio mixed Hamiltonian models of solvation

Cited by 10 publications

References 75 publications

Water Formation on Pt and Pt‐based Alloys: A Theoretical Description of a Catalytic Reaction

Water Formation on Pt and Pt‐based Alloys: A Theoretical Description of a Catalytic Reaction

Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

Ab Initio QM/MM-MC Study on Hydrogen Transfer of Glycine Tautomerization in Aqueous Solution: Helmholtz Energy Changes along Water-mediated and Direct Processes

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