Resolving local configurational contributions to X-ray and neutron radial distribution functions within solutions of concentrated electrolytes - a case study of concentrated NaOH.

Extreme conditions of complex materials often lead to a manifold of local environments that challenge characterization and require new advances at the intersection of modern experimental and theoretical techniques. In this contribution, highly caustic and viscous aqueous NaOD solutions were characterized with a combination of X-ray and neutron radial distribution function (RDF) analyses, molecular dynamics simulations and sub-ensemble analysis. While this system has been the topic of some study, the current work expands upon the state of knowledge regarding the extent to which water is perturbed within this chemically extreme solution. Further, we introduce analyses that goes beyond merely identifying the different local environments (ion solvation and coordination environments) that are present, but toward understanding their relative contributions to the ensemble solution RDF. This integrated approach yields unique insight into the experimental sensitivity of RDFs to changes in local geometries, the composition of solvation environments about ions, and the challenge of experimentally differentiating the ensemble of all superimposed local environments-a feature of increasing importance within the extreme condition of high ionic strength.

Coupled Multimodal Dynamics of Hydrogen-Containing Ion Networks in Water-Deficient, Sodium Hydroxide-Aluminate Solutions.

The (meta)stability of low water activity sodium hydroxide/aluminate (Na+OH-/Al(OH)4-) electrolytes dictates kinetics in the Bayer process for aluminum refining and high-level nuclear waste processing. We utilized quasi-elastic neutron scattering (QENS) and proton nuclear magnetic resonance spectroscopy (1H NMR) in extremely concentrated sodium aluminate solutions to investigate the picosecond (ps) to microsecond (ms) timescale motions of H-bearing species (Al(OH)4- monomers/clusters, OH- and H2O). In the QENS data, in contrast to typical liquids, no short-time translational diffusion was observed at 293 K, but two types of localized motions were found: (i) local backbone tumbling or a formation of large hydrated ion clusters on the order of 40-60 ps; and (ii) much slower, complex, and collective dynamics of the ensemble of H-bearing species on the order of 350-750 ps. Variable temperature, pulsed field gradient, diffusion-ordered 1H NMR was used to determine the ensemble translational motion along with relaxometry to calculate rotational correlation coefficients. The ensemble rotational correlation times were on the order of 184-300 ps from 1H NMR, which is consistent with the timescale of the QENS components. Complementary molecular dynamics simulation of NaOH solutions exhibit extensive ion networks potentially responsible for the observed dynamical coupling of water with the motion of large hydrated ion clusters. Understanding these collective motions will aid in predicting the behavior of complex solutions during aluminum production and during nuclear waste processing.

Are Zr6-based MOFs water stable? Linker hydrolysis vs. capillary-force-driven channel collapse.

Metal-organic frameworks (MOFs) built up from Zr6-based nodes and multi-topic carboxylate linkers have attracted attention due to their favourable thermal and chemical stability. However, the hydrolytic stability of some of these Zr6-based MOFs has recently been questioned. Herein we demonstrate that two Zr6-based frameworks, namely UiO-67 and NU-1000, are stable towards linker hydrolysis in H2O, but collapse during activation from H2O. Importantly, this framework collapse can be overcome by utilizing solvent-exchange to solvents exhibiting lower capillary forces such as acetone.

Empirical and theoretical insights into the structural features and host-guest chemistry of M8L4 tube architectures.

We demonstrate a general method for the construction of M8L4 tubular complexes via subcomponent self-assembly, starting from Cu(I) or Ag(I) precursors together with suitable elongated tetraamine and 2-formylpyridine subcomponents. The tubular architectures were often observed as equilibrium mixtures of diastereomers having two different point symmetries (D2d or D2 ⇄ D4) in solution. The equilibria between diastereomers were influenced through variation in ligand length, substituents, metal ion identity, counteranion, and temperature. In the presence of dicyanoaurate(I) and Au(I), the D4-symmetric hosts were able to bind linear Au(Au(CN)2)2(-) (with two different configurations) as the best-fitting guest. Substitution of dicyanoargentate(I) for dicyanoaurate(I) resulted in the formation of Ag(Au(CN)2)2(-) as the optimal guest through transmetalation. Density functional theory was employed to elucidate the host-guest chemistries of the tubes.

Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations.

Infrared spectra of biomolecules are obtained from molecular dynamics simulations at finite temperature using the AMOEBA force field. Diverse examples are presented such as N-methylacetamide and its derivatives and a helical peptide. The computed spectra from polarizable molecular dynamics are compared in each case to experimental ones at various temperatures. The role of high-level electrostatic treatment and explicit polarization, including parameters improvements, is highlighted for obtaining spectral sensitivity to the environment including hydrogen bonds and water molecules and a better understanding of the observed experimental bands.

Relationship between conformational dynamics and electron transfer in a desolvated peptide. Part I. Structures.

The structures, dynamics and energetics of the protonated, derivatized peptide DyeX-(Pro)(4)-Arg(+)-Trp, where "Dye" stands for the BODIPY analogue of tetramethylrhodamine and X is a (CH(2))(5) linker, have been investigated using a combination of modeling approaches in order to provide a numerical framework to the interpretation of fluorescence quenching data in the gas phase. Molecular dynamics (MD) calculations using the new generation AMOEBA force field were carried out using a representative set of conformations, at eight temperatures ranging from 150 to 500 K. Force field parameters were derived from ab initio calculations for the Dye. Strong electrostatic, polarization and dispersion interactions combine to shape this charged peptide. These effects arise in particular from the electric field generated by the charge of the protonated arginine and from several hydrogen bonds that can be established between the Dye linker and the terminal Trp. This conclusion is based on both the analysis of all structures generated in the MD simulations and on an energy decomposition analysis at classical and quantum mechanical levels. Structural analysis of the simulations at the different temperatures reveals that the relatively rigid polyproline segment allows for the Dye and Trp indole side chain to adopt stacking conformations favorable to electron transfer, yielding support to a model in which it is electron transfer from tryptophan to the dye that drives fluorescence quenching.

Relationship between conformational dynamics and electron transfer in a desolvated peptide. Part II. Temperature dependence.

Recent time-resolved lifetime measurements studied the quenching of the fluorescence emitted by a dye covalently bound to the desolvated peptide Dye-Pro(4)-Arg(+)-Trp. This peptide sequence was chosen for study since intramolecular interactions constrain all large-scale fluctuations except for those of the interacting dye and Trp side chain. It was shown that quenching occurred as a result of interaction between the excited dye and tryptophan side chain. These measurements exhibited a temperature dependence that suggested the quenching mechanism was related to electron transfer. This paper presents a comparison of the experimental quenching rate with the Marcus electron transfer model performed with molecular dynamics (MD) calculations. Taking advantage of the AMOEBA force field that explicitly includes polarizability ensures that the intramolecular electrostatic and polarization interactions in this desolvated peptide ion are treated realistically. MD calculations identify both large-scale fluctuations between conformations as well as small-scale fluctuations within a conformation that are shown to be correlated with torsional dynamics of the Trp side chain. Trajectories of the Dye-Trp distance identify the occurrence of close separations required for efficient electron transfer. The temperature dependence of the quenching rate closely follows the rate predicted by the Marcus electron transfer model within uncertainties resulting from statistical averages. Estimates of the energy parameters characterizing the Marcus model indicate the electronic coupling matrix element and the reaction free energy derived from the fits are consistent with published values for transfer in polyproline bridged peptides. These calculations help to provide a molecular basis for investigating conformational changes in desolvated biomolecular ions by fluorescence quenching measurements.

Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe(2.).

We extend the AMOEBA polarizable molecular mechanics force field to the Fe(2+) cation in its singlet, triplet, and quintet spin states. Required parameters are obtained either directly from first principles calculations or optimized so as to reproduce corresponding interaction energy components in a hexaaquo environment derived from quantum mechanical energy decomposition analyses. We assess the importance of the damping of point-dipole polarization at short distance as well as the influence of charge-transfer for metal-water interactions in hydrated Fe(2+); this analysis informs the selection of model systems employed for parametrization. We validate our final Fe(2+) model through comparison of molecular dynamics (MD) simulations to available experimental data for aqueous ferrous ion in its quintet electronic ground state.

Structure of sodiated polyglycines.

The intrinsic folding of peptides about a sodium ion has been investigated in detail by using infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD spectroscopy was carried out on sodiated polyglycines G(n)-Na(+) (n=2-8), in both the fingerprint and N-H/O-H stretching regions. Interplay between experimental and computational approaches (classical and quantum) enables us to decipher most structural details. The most stable structures of the small peptides up to G(6)-Na(+) maximize metal-peptide interactions with all peptidic C=O groups bound to sodium. In addition, direct interactions between peptide termini are possible for G(6)-Na(+) and larger polyglycines. The increased flexibility of larger peptides leads to more complex folding and internal peptide structuration through γ or ß turns. A structural transition is found to occur between G(6)-Na(+) and G(7)-Na(+), leading to a structure with sodium coordination that becomes tri-dimensional for the latter. This transition was confirmed by H/D exchange experiments on G(n)-Na(+) (n=3-8). The most favorable hydrogen-bonding pattern in G(8)-Na(+) involves direct interactions between the peptide termini and opens the way to salt-bridge formation; however, there is only good agreement between experimental and computational data over the entire spectral range for the charge solvation isomer.

Structures and IR spectra of the Gramicidin S peptide: pushing the quest for low-energy conformations.

An extensive molecular modeling study was carried out on the doubly protonated cyclic decapeptide Gramicidin S following several recent gas-phase experiments. Our computational strategy includes replica-exchange molecular dynamics simulations with the new generation force field AMOEBA for exploration and density functional calculations using several functionals for refinement of structures and computation of IR spectra. This procedure yields low-energy structures of which three are proposed to correspond to the three conformers detected in low-temperature IR experiments. The most stable structure has C(2) symmetry and four strong ß-sheet interactions between Orn and Val residues. Furthermore, all the other peptidic N-H bonds are involved in seven-membered C(7) motifs. The computed IR spectra of the three conformers are in good agreement with the experimental ones in the 1400-2000 cm(-1) range. In the 3000-3600 cm(-1) region, the computed spectrum is also in good agreement with experiment for the main conformer, and predictions are made of structure-specific signatures for the other two conformers. The accuracy of several density functionals is discussed in detail. These results point out that efficient potential energy surface explorations coupled to appropriate density functional theory (DFT) calculations are able to reveal the structures of molecules as large and flexible as decapeptides.

Structural, energetic and dynamical properties of sodiated oligoglycines: relevance of a polarizable force field.

Oligoglycine peptides (from two to ten residues) complexed to the sodium ion were studied by quantum chemical and molecular mechanics calculations to understand their structural and energetic properties. Modeling such systems required the use of a polarizable force field and AMOEBA, as developed by Ren and Ponder [J. Comput. Chem., 2002, 23, 1497], was chosen. Some electrostatic and torsional parameters were re-optimized using a rigorous procedure and validated against both geometric and energetic ab initio data in the gas phase. Molecular dynamics simulations were performed on seven sodiated octa-glycine (G(8)) structures. Structural transitions were generally observed (with the notable exception of the a-helix), leading to new structures that were further proved by ab initio calculations to be of low energies. The main result is that for G(8)-Na(+), there is a compromise between sodium peptide interactions and multiple hydrogen bonding. The accuracy achieved with AMOEBA demonstrates the potential of this force field for the realistic modeling of gaseous peptides.

Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling.

The structure of the sodiated peptide GGGGGGGG-Na(+) or G(8)-Na(+) was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G(8)-Na(+) is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G(8)-Na(+) at room temperature.