Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes ob served upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives 3-4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.

Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution

Frederico Alves Lima, Paul Beaud, Majed Chergui, Amal El Nahhas, Thomas James Penfold, Van Thai Pham, Ivano Tavernelli, Renske Marjan van der Veen

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L-1,L-3 edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I-/I-0(H2O)(n=1-4) clusters. The L-1 edge sub-picosecond spectra point to the existence of a transient species that is not present at SO ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I-0(OH2) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 Ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.

2011

Characterization of the Dizinc Analogue of the Synthetic Diiron Protein DF1 Using ab Initio and Hybrid Quantum/Classical Molecular Dynamics Simulations

Ursula Röthlisberger

The structural and dynamical properties of the four a-helix bundle Due Ferri 1, which is a generic mimic of diiron proteins, have been explored using d. functional theory (DFT) based and hybrid quantum/classical mol. dynamics (QM/MM) simulations. Four quantum mech. (QM) representations of the active site have been employed in order to systematically assess the role of first and second shell interactions: (a) a 66-atom fragment of the active site comprising only first shell ligands, (b and c) two systems (78 and 86 atoms) contg. different second shell hydrogen bonds, and (d) a 98-atom model including both the first and second shell residues. Two QM/MM partitioning schemes have been explored in order to explicitly consider the role of the whole protein environment: (a) a 54-QM-atom model in which only the first shell ligands are described at the DFT level, while the rest of the protein environment is taken into account at the MM level and (b) a 68-QM-atom model in which the first shell ligands plus a second shell hydrogen bond network is considered at the DFT level. All of the calcns. confirm the highly flexible nature of the carboxylate-bridged binuclear motif and demonstrate the importance of the whole protein environment in stabilizing the hydrogen bond networks that surround the active site. The present QM/MM approach allows for the identification of key factors governing the stability/reactivity of the active site and thus provides unique insights that can be exploited for the future tailoring of new highly selective biomimetic enzymic compds. [on SciFinder (R)]

2003

Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: Gas phase, linear solvent response, and non-linear response contributions

Jeremy Samuel Arey, Jennifer Guerard, Marianne Seijo, Peter Rudolf Tentscher

First principles simulations were used to predict aqueous one-electron oxidation potentials (E-ox) and associated half-cell reorganization energies (lambda(aq)) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted E-ox and lambda(aq) values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate E-ox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (Delta VIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (Delta NVEA(aq)). The simulated Delta VIEaq and Delta NVEA(aq) are found to contribute the principal sources of uncertainty in computational estimates of E-ox and lambda(aq). Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

Royal Soc Chemistry2015

Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: Gas phase, linear solvent response, and non-linear response contributions

Jeremy Samuel Arey, Jennifer Guerard, Marianne Seijo, Peter Rudolf Tentscher

Royal Soc Chemistry2015