Ammonia Solvation vs Aqueous Solvation of Samarium Diiodide. A Theoretical and Experimental Approach to Understanding Bond Activation Upon Coordination to Sm(II).

Coordination-induced desolvation or ligand displacement by cosolvents and additives is a key feature responsible for the reactivity of Sm(II)-based reagent systems. High-affinity proton donor cosolvents such as water and glycols also demonstrate coordination-induced bond weakening of the O-H bond, facilitating reduction of a broad range of substrates. In the present work, the coordination of ammonia to SmI2 was examined using Born-Oppenheimer molecular dynamics simulations and mechanistic studies, and the SmI2-ammonia system is compared to the SmI2-water system. The coordination number and reactivity of the SmI2-ammonia solvent system were found to be similar to those of SmI2-water but exhibited an order of magnitude greater rate of arene reduction by SmI2-ammonia than by SmI2-water at the same concentrations of cosolvent. In addition, upon coordination of ammonia to SmI2, the Sm(II)-ammonia solvate demonstrates one of the largest degrees of N-H bond weakening reported in the literature compared to known low-valent transition metal ammonia complexes.

Proton donor effects on the reactivity of SmI2. Experimental and theoretical studies on methanol solvation vs. aqueous solvation.

Proton donors are important components of many reactions mediated by samarium diiodide (SmI2). The addition of water to SmI2 creates a reagent system that enables the reduction of challenging substrates through proton-coupled electron-transfer (PCET). Simple alcohols such as methanol are often used successfully in reductions with SmI2 but often have reduced reactivity. The basis for the change in reactivity of SmI2-H2O and SmI2-MeOH is not apparent given the modest differences between water and methanol. A combination of Born-Oppenheimer molecular dynamics simulations and mechanistic experiments were performed to examine the differences between the reductants formed in situ for the SmI2-H2O and SmI2-MeOH systems. This work demonstrates that reduced coordination of MeOH to Sm(ii) results in a complex that reduces arenes through a sequential electron proton transfer at low concentrations and that this process is significantly slower than reduction by SmI2-H2O.

Solving the CH_{4}

Several types of experiments showed the existence of negative methane ions CH_{4}^{-} over a period of 50 years but the nature of this elusive species remains unknown. A benchmark study has shown that the experimentally observed species cannot be described by the attachment of an electron in the doublet ground state of CH_{4}^{-}. Here we find CH_{4}^{-} as being a metastable species in its lowest quartet spin state, a CH_{2}^{-}:H_{2} exciplex with three open shells lying ca. 10 eV above the methane singlet ground state but slightly below the dissociation fragments. The formation of charged high-spin exciplexes is a novel mechanism to explain small molecular anions with implications in a plethora of basic and applied research fields.

Tracing source and mobility of arsenic and trace elements in a hydrosystem impacted by past mining activities (Morelos state, Mexico).

The Sierra Huautla (Morelos State, Mexico) is a biological reserve with historical mines of Ag and Pb. In this area, waters used by inhabitants are contaminated by arsenic (As). An integrated environmental survey was realized both in waters and sediments to better constrain the source and the mobility of As and other trace elements. Two areas of interest were selected: (1) the Nexpa River ecosystem to determine the local geochemical background, and (2) the Huautla area, affected by past mining activities. This study allowed the definition of the local geochemical baseline in sediments or in waters, demonstrated uncontaminated by TE in the Nexpa area, except for As in the dissolved phase or for Cd in Suspended Particulate Matters (SPM). In the Huautla area, TE contents in water were higher than the World Health Organization (WHO) limits for Al, As and Mn in unfiltered waters, and only for As in the dissolved phase. Speciation analyses revealed arsenic to be present only as the toxic-inorganic arsenate species, As(+V). In SPM, Ag, As, Cd and Zn concentrations were higher than Sediment Quality Guidelines (SQG). The different geochemical indice (EF: 5, PLI: 3, EF: Igeo: 5-3) demonstrated that SPM were significantly contaminated and consistute an health risk for Huautla inhabitants exposed to As-contaminated waters and TE-rich SPM. The combination of mineralogy, chemistry, C and S stable isotopes with thermodynamic modeling indicate dissolutions of minerals from local geological formations, sorption-desorption phenomena from clays and oxy-hydroxides, and the weathering responsible for the transport of the TE-rich SPM (1.8 wt% for 17% of the total TE concentration). Moreover, the past mining activity would be a source of the contamination only for As in waters from flooded mines.

Experimental and Theoretical Studies on the Aqueous Solvation and Reactivity of SmCl2 and Comparison with SmBr2 and SmI2.

Water addition to Sm(II) has been shown to increase reactivity for both SmI2 and SmBr2. Previous work in our groups has demonstrated that this increase in reactivity can be attributed to coordination induced bond weakening enabling substrate reduction through proton-coupled electron transfer. The present work examines the interaction of water with samarium dichloride (SmCl2) and illustrates the importance of the Sm-X interaction and bond distance upon water addition critical for the reactivity of the reagent system. Born-Oppenheimer molecular dynamics simulations identify substantial variations among the reductants created in solution upon water addition to SmI2, SmBr2, and SmCl2 with the latter showing the least halide dissociation. This results in a lower water coordination number for SmCl2, creating a more powerful reducing system. As previously shown with the other SmX2-water systems, coordination-induced bond-weakening of the O-H bond of water bound to Sm(II) results in significant bond weakening. In the case of SmCl2, the bond weakening is estimated to be in the range of 83 to 88.5 kcal/mol.

Experimental and Theoretical Studies on the Implications of Halide-Dependent Aqueous Solvation of Sm(II).

The addition of water to samarium(II) has been demonstrated to have a significant impact on the reduction of organic substrates, with the majority of research dedicated to the most widely used reagent, samarium diiodide (SmI2). The work presented herein focuses on the reducing capabilities of samarium dibromide (SmBr2) and demonstrates how the modest change in halide ligand results in observable mechanistic differences between the SmBr2-water and the SmI2-water systems that have considerable implications in terms of reactivity between the two reagents. Quantum chemical results from Born-Oppenheimer molecular dynamics simulations show significant differences between SmI2-water and SmBr2-water, with the latter displaying less dissociation of the halide, which results in a lower coordination number for water. Experimental results are consistent with computational results and demonstrate that the coordination sphere of SmBr2 is saturated at lower concentrations of water. In addition, coordination-induced bond-weakening of the O-H bond is demonstrably different for water bound to SmBr2, leading to an estimated O-H bond-weakening of at least 83 kcal/mol, nearly 10 kcal/mol larger than the bond-weakening observed in SmI2-H2O. Experimental results also demonstrate that the use of alcohols in place of water with SmBr2 leads to substrate reduction, albeit several orders of magnitude slower than for SmBr2-water. The difference in rates resulting from the change in proton donor is attributed to a rate-limiting proton-coupled electron transfer in SmBr2-water and a sequential electron transfer then proton transfer in SmBr2-alcohol systems, where electron transfer is rate-limiting.

Hydration of CH3HgOH and CH3HgCl compared to HgCl2, HgClOH, and Hg(OH)2: A DFT microsolvation cluster approach.

We address the aqueous microsolvation of the CH3HgCl and CH3HgOH molecules using a stepwise hydration scheme including up to 33 water molecules and compare our results with the previously studied HgCl2, HgClOH, and Hg(OH)2 complexes. Optimized geometries and Gibbs free energies were obtained at the B3PW91/aug-RECP(Hg)-6-31G(d,p) level. At least 33 water molecules were required to build the first solvation shell around both methylmercury compounds. Optimized geometries were found having favorable interactions of water molecules with Hg, Cl, and the OH moiety. Born-Oppenheimer molecular dynamics simulations were performed on the largest CH3HgX(X = Cl, OH)-(H2O)33 clusters at the same level of theory. Born-Oppenheimer molecular dynamics simulations at T = 300 K (ca. 0.62 kcal/mol) revealed the presence of configurations with hydrogen-bonded networks that include the OH moiety in CH3HgOH and exclude both the Hg and Cl in CH3HgCl, favoring a clathrate-type structure around the methyl moiety. The comparison to the microsolvated HgClOH, Hg(OH)2, and HgCl2 molecules showed that, in all cases, the water molecules easily move away from Cl, thus supporting the idea that HgCl2 behaves as a non-polar solute. The theoretical (LIII edge) X-ray absorption near edge structure spectra are obtained and found in good agreement with experimental data, especially for the CH3HgCl species.

A Four-Site Molecular Model for Simulations of Liquid Methanol and Water-Methanol Mixtures: MeOH-4P.

In this work, we present a new four-site potential for methanol, MeOH-4P, fitted to reproduce the dielectric constant ε, the surface tension γ s, and the liquid density ρ of the pure liquid at T = 298.15 K and p = 1 bar. The partial charges on each site were taken from the OPLS/2016 model with the only difference of putting the negative charge on the fourth site ( M) instead of on the O atom, as done in four-site water models. The original Lennard-Jones (LJ) parameters of OPLS/2016 for the methyl moiety (Me) were modified for the fitting of ρ and γ s, whereas the parameters of the TIP4P-FB water model were used for the O atom without change. Taking into account the energetic cost of the enhanced dipole relative to the isolated molecule, the results from simulations with this model showed good agreement with experiments for ρ, α p, κ T, C p, and Δ H v- l. Also, the temperature dependence of γ s and ε is satisfactory in the interval between 260 and 360 K, and the critical point description is similar to that of OPLS/2016. It is shown that orientational correlations, described by the Kirkwood factor G k, play a prominent role in the appropriate description of dielectric constants in existing models; unfortunately, the enhancement of the dipole moment produced a low diffusion coefficient DMeOH; thus, a compromise was required between a good reproduction of ε and an acceptable DMeOH. The use of a fourth site resulted in a significant improvement for water-methanol mixtures described with TIP4P-FB and MeOH-4P, respectively, but required the modification of the LJ geometric combination rule to allow a good description of the methanol molar-fraction dependence of ρ, ε, and methanol (water) diffusion coefficients DMeOH ( DH2O) and excess volume of mixing Δ Vmix in the entire range of composition. The resulting free energy of hydration Δ Ghyd shows excellent agreement with experiments in the interval between 280 and 360 K.

A Theoretical Study of the Hydration of Methane, from the Aqueous Solution to the sI Hydrate-Liquid Water-Gas Coexistence.

Monte Carlo and molecular dynamics simulations were done with three recent water models TIP4P/2005 (Transferable Intermolecular Potential with 4 Points/2005), TIP4P/Ice (Transferable Intermolecular Potential with 4 Points/ Ice) and TIP4Q (Transferable Intermolecular Potential with 4 charges) combined with two models for methane: an all-atom one OPLS-AA (Optimal Parametrization for the Liquid State) and a united-atom one (UA); a correction for the C-O interaction was applied to the latter and used in a third set of simulations. The models were validated by comparison to experimental values of the free energy of hydration at 280, 300, 330 and 370 K, all under a pressure of 1 bar, and to the experimental radial distribution functions at 277, 283 and 291 K, under a pressure of 145 bar. Regardless of the combination rules used for σC,O, good agreement was found, except when the correction to the UA model was applied. Thus, further simulations of the sI hydrate were performed with the united-atom model to compare the thermal expansivity to the experiment. A final set of simulations was done with the UA methane model and the three water models, to study the sI hydrate-liquid water-gas coexistence at 80, 230 and 400 bar. The melting temperatures were compared to the experimental values. The results show the need to perform simulations with various different models to attain a reliable and robust molecular image of the systems of interest.

Direct Coexistence Methods to Determine the Solubility of Salts in Water from Numerical Simulations. Test Case NaCl.

The solubility of NaCl, an equilibrium between a saturated solution of ions and a solid with a crystalline structure, was obtained from molecular dynamics simulations using the SPC/E and TIP4P-Ew water models. Four initial setups on supersaturated systems were tested on sodium chloride (NaCl) solutions to determine the equilibrium conditions and computational performance: (1) an ionic solution confined between two crystal plates of periodic NaCl, (2) a solution with all the ions initially distributed randomly, (3) a nanocrystal immersed in pure water, and (4) a nanocrystal immersed in an ionic solution. In some cases, the equilibration of the system can take several microseconds. The results from this work showed that the solubility of NaCl was the same, within simulation error, for the four setups, and in agreement with previously reported values from simulations with the setup (1). The system of a nanocrystal immersed in supersaturated solution was found to equilibrate faster than others. In agreement with laser-Doppler droplet measurements, at equilibrium with the solution the crystals in all the setups had a slight positive charge.

A non-polarizable model of water that yields the dielectric constant and the density anomalies of the liquid: TIP4Q.

A four-site rigid water model is presented, whose parameters are fitted to reproduce the experimental static dielectric constant at 298 K, the maximum density of liquid water and the equation of state at low pressures. The model has a positive charge on each of the three atomic nuclei and a negative charge located at the bisector of the HOH bending angle. This charge distribution allows increasing the molecular dipole moment relative to four-site models with only three charges and improves the liquid dielectric constant at different temperatures. Several other properties of the liquid and of ice Ih resulting from numerical simulations with the model are in good agreement with experimental values over a wide range of temperatures and pressures. Moreover, the model yields the minimum density of supercooled water at 190 K and the minimum thermal compressibility at 310 K, close to the experimental values. A discussion is presented on the structural changes of liquid water in the supercooled region where the derivative of density with respect to temperature is a maximum.

Dynamics and structure of Ln(III)-aqua ions: a comparative molecular dynamics study using ab initio based flexible and polarizable model potentials.

Aqueous solutions of a light (Nd3+), a middle (Gd3+), and a heavy (Yb3+) lanthanide ion were studied using ab initio based flexible and polarizable analytical potentials in classical molecular dynamics simulations to describe their thermodynamic, structural, and dynamic features. To avoid the spurious demise of O-H bonds, it was necessary to reparametrize an existing water model, which resulted in an improved description of pure water. The good agreement of the results from the simulations with the experimental hydration enthalpies, the Ln(III)-water radial distribution functions, and the water-exchange rates validated the potentials, though the r(Ln-Ow) distances were 6% longer than the experimentally determined values. A nona-coordinated state was found for Nd3+ in 95% of the simulation, with a tricapped trigonal prism (TCTP) geometry; the corresponding water-exchange mechanism was found to be of dissociative interchange (Id) character through a short-lived octa-coordinated transition state in a square antiprism (SQA) geometry. An octa-coordinated state in SQA geometry was found for Yb3+ in 99% of the simulation, and the observed exchange events exhibited characteristics of an interchange (I) mechanism. For Gd3+ an equilibrium was observed between 8-fold SQA and 9-fold TCTP coordinated states that was maintained by the frequent exchange of a water molecule from the first hydration shell with the bulk, thus producing significant deviations from the ideal geometries, and a fast exchange rate. Though strong water-water interactions prevented a full alignment of the dipoles to the ion's electric field, the screening was found large enough as to limit its range to 5 A; water molecules further apart from the ion were found to have the same dipole as the molecules in the bulk, and a random orientation. The interplay among the water-ion and the water-water interactions determined the different coordination numbers and the different dynamics of the water exchange in the first hydration shell for each ion.

Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation.

Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.

A molecular dynamics calculations of hole transfer rates in DNA strands.

A computational model, which includes both tunneling and thermal hopping mechanisms, has been applied to study the charge transfer in DNA (GC)n and (AT)n strands. The calculations revealed the crucial role played by the A or G NH2-group vibrations in the hole transfer in both types of strands. Charge-transfer rates in the two strands have been determined based on the molecular dynamics calculations. They are in good agreement with the available experimental data. The modeling approach used here may be employed in the theoretical study of the charge transfer in natural and artificial DNA strands containing AT and GC pairs.

Ion hydration in nanopores and the molecular basis of selectivity.

Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2.5 A. The reason for the selectivity in the first region is that the potassium ion allows for a greater distortion of its hydration shell and can therefore maintain a better coordination, and the reason for the reverse selectivity in the second region is that the smaller ions retain their hydration shells in these pores. This is relevant to the molecular basis of ion selective channels, and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes.

Water liquid-vapor equilibria predicted by refined ab initio derived potentials.

Coexistence properties for water near the critical point using several ab initio models were calculated using grand canonical Monte Carlo simulations with multiple histogram reweighting techniques. These models, that have proved to yield a good reproduction of the water properties at ambient conditions, perform rather well, improving the performance of a previous ab initio model. It is also shown that bulk geometry and dipole values, predicted by the simulation, can be used and a good approximation obtained with a polarizable rigid water model but not when polarization is excluded.

Water models based on a single potential energy surface and different molecular degrees of freedom.

Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernandez-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors--nonadditivity, polarizability, and intramolecular flexibility--are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force field improves by the quality of the molecular calculations, all levels of modeling can be improved.

Minimalist molecular model for nanopore selectivity.

Using a simple model it is shown that the cost of constraining a hydrated potassium ion inside a narrow nanopore is smaller than the cost of constraining the smaller hydrated sodium ion. The former allows for a greater distortion of its hydration shell and can therefore maintain a better coordination. We propose that in this way the larger ion can go through narrow pores more easily. This is relevant to the molecular basis of ion selective nanopores and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes, from biological to synthetic.

An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model.

The method of flexible constraints was implemented in a Monte Carlo code to perform numerical simulations of liquid water and ice Ih in the constant number of molecules, volume, and temperature and constant pressure, instead of volume ensembles, using the polarizable and flexible mobile charge densities in harmonic oscillators (MCDHO) model. The structural and energetic results for the liquid at T=298 K and rho=997 kg m(-3) were in good agreement with those obtained from molecular dynamics. The density obtained at P=1 atm with flexible constraints, rho=1008 kg m(-3), was slightly lower than with the classical sampling of the intramolecular vibrations, rho=1010 kg m(-3). The comparison of the structures and energies found for water hexamers and for ice Ih with six standard empirical models to those obtained with MCDHO, show this latter to perform better in describing water far from ambient conditions: the MCDHO minimum lattice energy, density, and lattice constants were in good agreement with experiment. The average angle HOH of the water molecule in ice was predicted to be slightly larger than in the liquid, yet 1.2% smaller than the experimental value.