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.

Carbon dioxide adsorption isotherms have been computed for the metal−organic framework (MOF) Fe 2 (dobdc), where dobdc 4− = 2,5-dioxido-1,4-benzenedicarboxylate. A force field derived from quantum mechanical calculations has been used to model adsorption isotherms within a MOF. Restricted open-shell Møller−Plesset second-order perturbation theory (ROMP2) calculations have been performed to obtain interaction energy curves between a CO 2 molecule and a cluster model of Fe 2 (dobdc). The force field parameters have been optimized to best reproduced these curves and used in Monte Carlo simulations to obtain CO 2 adsorption isotherms. The experimental loading of CO 2 adsorbed within Fe 2 (dobdc) was reproduced quite accurately. This parametrization scheme could easily be utilized to predict isotherms of various guests inside this and other similar MOFs not yet synthesized.

The structure of the sodiated peptide GGGGGGGG-Na ϩ or G 8 -Na ϩ 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 ϩ 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 ϩ at room temperature. (J Am Soc Mass Spectrom 2010, 21, 728 -738) © 2010 American Society for Mass Spectrometry T he biological importance of sodium in performing or facilitating essential biological processes, such as neurotransmission, osmotic balance, and cellular metabolism is well documented [1][2][3]. Mass spectrometric methods have been used extensively to provide insight into peptide sequences [4,5] starting from sodium-cationized species, however with considerable debate as to the structure of the parent species and the fragmentation mechanisms [6 -8]. In this context, sodiated oligoglycines have been used in the last decade as a valuable testing ground for new experimental developments designed to obtain refined energetic and/or structural data. These include ion mobility measurements for global shape information [9,10], H/D exchange extent and kinetics for isomeric/ conformational content [11], the kinetic [12, 13] and the threshold collision induced decomposition [14] methods for thermochemical measurements, as well as infrared multiple photon dissociation (IRMPD) spectroscopy [15] for identification of functional groups and their interactions. All these studies have been complemented by extensive molecular modeling as required for translating experimental data into properties of specific molecular structures.Oligoglycines owe their value as model peptides to their relative simplicity. While the number of residues is an obvious source of conformational complexity, the absence of side chains limits the number of factors shaping their structures and energies. On the one hand, the main components of sodium-molecule interactions are electrostatic and polarization, favoring m...

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.

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.

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 β 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.

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.

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 β-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.