Hydration Structure and Water Exchange Reaction of Nickel(II) Ion: Classical and QM/MM Simulations

Nickel as a modifier of calcium oxalate: an in situ liquid cell TEM investigation of nucleation and growth

Despite extensive research on the nucleation and growth of calcium oxalate (CaOx) crystals, there are still several challenges and unknowns that remain. In particular, the role of trace metal elements in the promotion or inhibition of CaOx crystals is not well understood. In the present study, in situ graphene liquid cell transmission electron microscopy (in situ GLC TEM) was used to observe real-time, nanoscale transformations of CaOx crystals in the presence of nickel ions (Ni2+). The results showed that Ni2+ form Ni-water complexes, acting as a shape-directing species, generating a unique morphology and altering growth kinetics. Transient adsorption of Ni-water complexes resulted in a metastable phase formation of calcium oxalate trihydrate. Atomistic molecular dynamics simulations confirmed that Ni2+ acts as a weak inhibitor which slows down the CaOx crystallization, elucidating that Ni2+ impacts small-sized CaOx clusters by bringing more water into the clusters. This work highlighted the intricacies behind the effect of Ni2+ on CaOx biomineralization that were made possible to discern using in situ GLC TEM.

The structural basis of proton driven zinc transport by ZntB

Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc concentration have evolved. In Enterobacteriaceae, several membrane transporters are involved in zinc homeostasis and linked to virulence. ZntB has been proposed to play a role in the export of zinc, but the transport mechanism of ZntB is poorly understood and based only on experimental characterization of its distant homologue CorA magnesium channel. Here, we report the cryo-electron microscopy structure of full-length ZntB from Escherichia coli together with the results of isothermal titration calorimetry, and radio-ligand uptake and fluorescent transport assays on ZntB reconstituted into liposomes. Our results show that ZntB mediates Zn²⁺ uptake, stimulated by a pH gradient across the membrane, using a transport mechanism that does not resemble the one proposed for homologous CorA channels.

The bacterial zinc transporter ZntB is important for maintaining zinc homeostasis and is mechanistically not well understood. Here, the authors present the cryo-EM structure of ZntB at 4.2 Å resolution, perform transport assays and propose a model for its Zn²⁺ transport mechanism.

The low frequency motions of solvated Mn(ii) and Ni(ii) ions and their halide complexes

Concentration dependent THz/FIR absorption measurements allow determination of individual solvated ion resonances and their influence on the hydration water spectrum.

Force field development for actinyl ions via quantum mechanical calculations: an approach to account for many body solvation effects

Advances in computational algorithms and methodologies make it possible to use highly accurate quantum mechanical calculations to develop force fields (pair-wise additive intermolecular potentials) for condensed phase simulations. Despite these advances, this approach faces numerous hurdles for the case of actinyl ions, AcO2(n+) (high-oxidation-state actinide dioxo cations), mainly due to the complex electronic structure resulting from an interplay of s, p, d, and f valence orbitals. Traditional methods use a pair of molecules (“dimer”) to generate a potential energy surface (PES) for force field parametrization based on the assumption that many body polarization effects are negligible. We show that this is a poor approximation for aqueous phase uranyl ions and present an alternative approach for the development of actinyl ion force fields that includes important many body solvation effects. Force fields are developed for the UO2(2+) ion with the SPC/Fw, TIP3P, TIP4P, and TIP5P water models and are validated by carrying out detailed molecular simulations on the uranyl aqua ion, one of the most characterized actinide systems. It is shown that the force fields faithfully reproduce available experimental structural data and hydration free energies. Failure to account for solvation effects when generating PES leads to overbinding between UO2(2+) and water, resulting in incorrect hydration free energies and coordination numbers. A detailed analysis of arrangement of water molecules in the first and second solvation shell of UO2(2+) is presented. The use of a simple functional form involving the sum of Lennard-Jones + Coulomb potentials makes the new force field compatible with a large number of available molecular simulation engines and common force fields.

Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations

In many applications of multilevel/multiscale methods, an active zone must be modeled by a high-level electronic structure method, while a larger environmental zone can be safely modeled by a lower-level electronic structure method, molecular mechanics, or an analytic potential energy function. In some cases though, the active zone must be redefined as a function of simulation time. Examples include a reactive moiety diffusing through a liquid or solid, a dislocation propagating through a material, or solvent molecules in a second coordination sphere (which is environmental) exchanging with solvent molecules in an active first coordination shell. In this article, we present a procedure for combining the levels smoothly and efficiently in such systems in which atoms or groups of atoms move between high-level and low-level zones. The method dynamically partitions the system into the high-level and low-level zones and, unlike previous algorithms, removes all discontinuities in the potential energy and force whenever atoms or groups of atoms cross boundaries and change zones. The new adaptive partitioning (AP) method is compared to Rode's "hot spot" method and Morokuma's "ONIOM-XS" method that were designed for multilevel molecular dynamics (MD) simulations. MD simulations in the microcanonical ensemble show that the AP method conserves both total energy and momentum, while the ONIOM-XS method fails to conserve total energy and the hot spot method fails to conserve both total energy and momentum. Two versions of the AP method are presented, one scaling as O(2N) and one with linear scaling in N, where N is the number of groups in a buffer zone separating the active high-level zone from the environmental low-level zone. The AP method is also extended to systems with multiple high-level zones to allow, for example, the study of ions and counterions in solution using the multilevel approach.

Searching for Stable, Five-Coordinate Aquated Al(III) Species. Water Exchange Mechanism and Effect of pH

Density functional theory calculations have been performed for the water exchange mechanism of aquated Al(III). The effect of pH was considered by studying the exchange processes for [Al(H2O)6]3+ and its conjugated base, [Al(H2O)5OH]2+. Both complexes were found to exchange water in a dissociative way with activation energies (EA) of 15.9 and 10.2 kcal/mol, respectively. The influence of solvent molecules on the gas-phase cluster model was considered by the addition of up to four water molecules to the model system. The stabilizing effect of the solvent on the transition state decreases EA to 8.6 (hexa-aqua complex) and 7.6 (monohydroxo complex) kcal/mol, whereas EA for all hydroxo species is consistently significantly lower than those for the related aqua systems, which indicates a much faster water exchange rate. For the hydroxo complex, all calculated five-coordinate intermediates, nH2O.[Al(H2O)4(OH)]2+ (n = 1, 2, 3, 4, 5), are more stable than the corresponding six-coordinate reactants. Our results therefore suggest the presence of a stable five-coordinate species of aquated Al(III), namely, the [Al(H2O)4(OH)]2+ complex.

Water exchange dynamics of manganese(II), cobalt(II), and nickel(II) ions in aqueous solution

The first row transition metal ions Mn(2+), Co(2+), and Ni(2+) have been studied by classical umbrella sampling molecular dynamics simulations. The water exchange mechanisms, estimates of reaction rates, as well as structural changes during the activation process are discussed. Mn(2+) was found to react via an I(A) mechanism, whereas Co(2+) and Ni(2+) both proceed via I(D). Reaction rate constants are generally higher than those obtained by experiment but the simply constructed metal(II) ion-water potential reproduces the relative order quite well.

Detection of Second Hydration Shells in Ionic Solutions by XANES: Computed Spectra for Ni2+ in Water Based on Molecular Dynamics

A general procedure to compute X-ray absorption near-edge structure (XANES) spectra within multiple-scattering theory starting from molecular dynamics (MD) structural data has been developed and applied to the study of a Ni(2+) aqueous solution. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems using a proper description of the thermal and structural fluctuations. The XANES spectrum of Ni(2+) in aqueous solution has been calculated using the structural information obtained from the MD simulations without carrying out any minimization in the structural parameter space. A very good reproduction of the experimental data was obtained including the second-shell water molecules in the calculation, thus showing that the second hydration shell provides a detectable contribution to the XANES spectra of ionic solutions. The analysis including the first-shell cluster only permitted us to quantitatively determine the effect of disorder on the amplitude of the XANES spectra for molecular complexes. These results simultaneously confirm the reliability of the procedure and the structural results obtained from MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

On the role of the counter-ion in defining water structure and dynamics: order, structure and dynamics in hydrophilic and hydrophobic gadolinium salt complexes

The crystal structures of the hydrated salts of [Gd.DOTAM]3+ and its more hydrophobic derivative [Gd.]3+, bearing 4 alpha-phenylethyl groups, (both Gd and Yb salts) are reported and compared. The nature of the anion determines the degree of ordering in the lattice and the extent of hydration. These effects are correlated with the results of 17O and 1H NMR measurements of water exchange dynamics in solution. With [Gd.DOTAM]3+, structural ordering or the extent of hydration in the hydrated lattice follows the sequence Cl->Br->I- and this order also defines the water exchange rate in solution: 7.3, 19.5, 33.3x10(4) s-1 (298 K), respectively. For [Gd.]3+ salts, the measured relaxivity is determined purely by the outer sphere term and the water exchange rate at 298 K is very similar (typically 1x10(4) s-1) for chloride, bromide, iodide, acetate, triflate and nitrate salts, notwithstanding the different nature and extent of hydration found in the crystalline lattice.

Electronic relaxation dynamics of Ni2+-ion aqueous solution: Molecular-dynamics simulation

Electronic relaxation dynamics of Ni2+-ion aqueous solution is investigated using molecular-dynamics (MD) simulations with the model-effective Hamiltonian developed previously. The nonadiabatic transition rates from the first three excited states to the ground state are evaluated by the golden rule formula with the adiabatic MD simulations. The MD simulations with the fewest-switch surface-hopping method are also carried out to obtain a more detailed description of the electronic relaxation dynamics among the excited states. We found out that the transitions among the three excited states are very fast, in the order of 10 fs, while the transition between the excited and ground states is slow, about 800 ps. These findings are consistent with the time scales of energy dissipation detected by the transient lens experiment. In both simulations, we explore the effects of the quantum decoherence, where the decoherence functions are derived by the energy-gap dynamics with the displaced harmonic-oscillator model.

Ab Initio QM/MM Simulation of Ag+in 18.6% Aqueous Ammonia Solution: Structure and Dynamics Investigations

Structure and dynamics investigations of Ag(+) in 18.6% aqueous ammonia solution have been carried out by means of the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation method. The most important region, the first solvation shell, was treated by ab initio quantum mechanics at the Restricted Hartree-Fock (RHF) level using double-zeta plus polarization basis sets for ammonia and plus ECP for Ag(+). For the remaining region in the system, newly constructed three-body corrected potential functions were used. The average composition of the first solvation shell was found to be [Ag(NH(3))(2)(H(2)O)(2.8)](+). No ammonia exchange process was observed for the first solvation shell, whereas ligand exchange processes occurred with a very short mean residence time of 1.1 ps for the water ligands. No distinct second solvation shell was observed in this simulation.

The solvation structure of Pb(II) in dilute aqueous solution: An ab initio quantum mechanical/molecular mechanical molecular dynamics approach

Structural properties of the hydrated Pb(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical molecular dynamics simulations at Hartree-Fock quantum mechanical level. The first shell coordination number was found to be nine, and several other structural parameters such as angular distribution functions, radial distribution functions, and tilt- and theta-angle distributions allow the full characterization of the hydration structure of the Pb(II) ion.

Potential energy surfaces and dynamics of Ni[sup 2+] ion aqueous solution: Molecular dynamics simulation of the electronic absorption spectrum

We develop a model effective Hamiltonian for describing the electronic structures of first-row transition metals in aqueous solutions using a quasidegenerate perturbation theory. All the states consisting of 3d(n) electronic configurations are determined by diagonalizing a small effective Hamiltonian matrix, where various intermolecular interaction terms such as the electrostatic, polarization, exchange, charge transfer, and three-body interactions are effectively incorporated. This model Hamiltonian is applied to constructing the ground and triplet excited states potential energy functions of Ni(2+) in aqueous solution, based on the ab initio multiconfiguration quasidegenerate perturbation theory calculations. We perform molecular dynamics simulation calculations for the ground state of Ni(2+) aqueous solution to calculate the electronic absorption spectral shape as well as the ground state properties. Agreement between the simulation and experimental spectra is satisfactory, indicating that the present model can well describe the Ni(2+) excited state potential surfaces in aqueous solution.

New Insights into the Jahn-Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water

The CuII hydration shell structure has been studied by means of classical molecular dynamics (MD) simulations including three-body corrections and hybrid quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations at the Hartree-Fock level. The copper(II) ion is found to be six-fold coordinated and [Cu(H2O)6]2+ exhibits a distorted octahedral structure. The QM/MM MD approach reproduces correctly the experimentally observed Jahn-Teller effect but exhibits faster inversions (< 200 fs) and a more complex behaviour than expected from experimental data. The dynamic Jahn-Teller effect causes the high lability of [Cu(H2O)6]2+ with a ligand-exchange rate constant some orders or magnitude higher than its neighbouring ions NiII and ZnII. Nevertheless, no first-shell water exchange occurred during a 30-ps simulation. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and various angular distributions and the dynamical properties as librational and vibrational motions and reorientational times were evaluated, which lead to detailed information about the first hydration shell. Second-shell water-exchange processes could be observed within the simulation time scale and yielded a mean ligand residence time of approximelty 20 ps.

Many-body effects on structure and dynamics of aqueous ionic solutions

We performed several molecular dynamic studies of metal cations in aqueous solution. The alkali metal ion Li(+) and the first-row transition metal ion Mn(2+) have been chosen as model systems. Two different three-body corrections are proposed to mimic the crucial many-body effects of electrolyte solutions. The correction function, which includes attractive features of the three-body potential, performs considerably better than the purely repulsive interaction function. Structural and dynamic results show that this simple enhancement is able to satisfactorily reproduce experimental and higher-level results for the first hydration shell.

Structure and dynamics of metal ions in solution: QM/MM molecular dynamics simulations of Mn(2+) and V(2+)

Structural and dynamical properties of the transition metal ions V(2+) and Mn(2+) in aqueous solution, resulting from combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations have been compared. The necessity of polarization functions on the ligand's oxygen for a satisfactory description of such ions in aqueous solution is shown using V(2+) as test case. Radial distribution functions, coordination number distributions, and several angle distributions were pursued for a detailed structural comparison of the first hydration shells. Dynamical properties, such as the librational and vibrational motions of water molecules were evaluated by means of velocity autocorrelation functions. Approximative normal coordinate analyses were employed to calculate the rotational frequencies and vibrational motions around the three principal axes. The very low exchange rates for the first shell water exchanges only allow an investigation of the water exchange processes in the second shell, which take place within the picosecond range.