Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

Structure, Dynamics, and Hydration Free Energy of Carbon Dioxide in Aqueous Solution: A Quantum Mechanical/Molecular Mechanics Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) Simulation Study

The solvation of carbon dioxide in solution represents a key step for the capture and fixation CO₂ in nature, which may be further influenced by the formation of (bi)carbonate species and/or the formation of CO₂ clusters in solution. The latter processes are strongly dependent on the exact environment of the liquid state (e.g., pH value, solvated ions, etc.) and may interfere with the experimental determination of structural, dynamical, and thermodynamic properties. In this work a hybrid quantum mechanical/molecular mechanical (QM/MM) simulation approach at correlated ab initio level of theory resolution-of-identity second-order Møller-Plesset Perturbation Theory (RI-MP2) has been applied in the framework of thermodynamic integration (TI) to study structure, dynamics, and the hydration free energy of a single carbon dioxide molecule in aqueous solution. A detailed analysis of the individual QM/MM potential energy contributions demonstrate that the overall potential remains highly consistent over the entire sampling phase and that no artificial contributions are influencing the determination of the hydration free energy. The latter value of 0.01 ± 0.92 kcal/mol was found in very good agreement with the values of 0.06 and 0.24 kcal/mol obtained via quasi-chemical theory and experimental measurements, respectively. In order to obtain detailed information about the C- and O _C-water interaction, conically restricted regions with respect to the main axis of the CO₂ molecule have been employed in structural analysis. The presented data not only provide detailed information about the hydration properties of CO₂ but act as a critical validation of the simulation technique, which will be beneficial in the study of nonaqueous solvents such as pure and aqueous NH₃ solutions, which have been suggested as potential candidates to capture CO₂ from anthropogenic sources.

Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li+ Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations

A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δ_s G_M⁺,wat^◦ of the Li⁺ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χ_wat^◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol^-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol^-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li⁺ are also compared to those for Na⁺ and K⁺ from a previous study in terms of relative hydration free energies ΔΔ_s G_M⁺,wat^◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔ_s G_M⁺,wat^• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li⁺ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput.2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of "water-in-water" model system.

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a crucial step toward an accurate polarizable model for modeling and simulations of biological macromolecules. Toward this goal we have undertaken a hierarchical approach in which force field parameter optimization is initially performed for small molecules for which experimental data exists that serve as building blocks of macromolecular systems. Small molecules representative of the ionic moieties of biological macromolecules include the cationic ammonium and methyl substituted ammonium derivatives, imidazolium, guanidinium and methylguanidinium, and the anionic acetate, phenolate, and alkanethiolates. In the present work, parameters for molecular ions in the context of the Drude polarizable force field are optimized and compared to results from the nonpolarizable additive CHARMM general force field (CGenFF). Electrostatic and Lennard-Jones parameters for the model compounds are developed in the context of the polarizable SWM4-NDP water model, with emphasis on assuring that the hydration free energies are consistent with previously reported parameters for atomic ions. The final parameters are shown to be in good agreement with the selected quantum mechanical (QM) and experimental target data. Analysis of the structure of water around the ions reveals substantial differences between the Drude and additive force fields indicating the important role of polarization in dictating the molecular details of aqueous solvation. The presented parameters represent the foundation for the charged functionalities in future generations of the Drude polarizable force field for biological macromolecules as well as for drug-like molecules.

Square planar or octahedral after all? The indistinct solvation of platinum(ii)

The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.