Structure and Dynamics of the Flexible Triple Helix of Water inside VPI-5 Molecular Sieves

Hydrogen-bonded structures and low temperature transitions of the confined water in subnano channels

The interfacial and confined water have long been attractive objects due to their crucial roles in biological, geological processes, etc. In this paper, we investigate the hydrogen-bonded structures of water and their low temperature transitions in the subnano channels of AlPO4-11 for the first time on the basis of infrared spectroscopy. The number of the adsorbed water molecules is estimated to be 8.45 per channel in one unit cell by thermogravimetric analysis. It is found that the confined water molecules are involved in saturated and unsaturated coordination with different hydrogen bond strengths at ambient temperature. The former refers to ice-like four-coordinated water and the latter includes liquid-like structures, Al-coordinated and relatively free water molecules. Unique coordination between water molecules and framework Al sites is responsible for the ice-like structures in the channels above the ice melting point. The appearance of liquid-like structures is closely related to the strong channel confinement, which does not allow the formation of extensive tetrahedral hydrogen-bonded configuration. As temperature decreases, a structural transformation of confined water happens in the channels of AlPO4-11. Isolated small water oligomers and two new components with stronger hydrogen bonds, such as low-density amorphous ice-like structures and a kind of low-density liquid-like structures are preferred. Our results provide important insights into the structural organizations and thermal-dynamic behaviors of confined water in extreme narrow channels.

Revisiting the Structure of Calcined and Hydrated AlPO-11 with DFT-Based Molecular Dynamics Simulations*

Published crystal structures of the AEL‐type aluminophosphate AlPO‐11 in its calcined form (space group Ima2 ) show some peculiar features, such as unusually short Al−O and P−O bonds and near‐linear Al−O−P angles. Although experimental evidence for the presence of dynamic disorder was presented, the nature of the associated distortions remained unresolved. In this study, ab initio molecular dynamics (AIMD) calculations in the framework of density functional theory (DFT) were employed to study the dynamic behaviour of this zeotype. At 100 K, static local distortions that break the Ima2 symmetry are present in the time‐averaged structures computed from the AIMD trajectories. At 300 and 500 K, the time‐averaged structures approach Ima2 symmetry. Although shortened Al−O and P−O bonds and near‐linear Al−O−P angles were found in the average structures, an analysis of radial and angular distribution functions confirmed their absence in the instantaneous structures. This deviation is due to a precession‐like motion of some oxygen atoms around the Al−P connection line, which moves their time‐averaged positions closer to this line. In hydrated AlPO‐11, some of the water molecules are coordinated to framework Al atoms, leading to an octahedral coordination of 1/5 of the Al sites. DFT optimisations and AIMD simulations on partially hydrated models delivered evidence for a preferential adsorption at the Al1 site. No dynamic disorder was observed for the hydrated form.

Proton Acidity and Proton Mobility in ECR-40, a Silicoaluminophosphate that Violates Löwenstein's Rule

The silicoaluminophosphate zeotype ECR-40 contains linkages of AlO4 tetrahedra via a common oxygen atom, thereby violating the famous "Löwenstein's rule". In this work, a combination of static density functional theory (DFT) calculations and DFT-based ab-initio molecular dynamics (AIMD) simulations were employed to study the acidity and mobility of protons associated with such unusual linkages. It was found that the Al-O-Al linkages are preferentially protonated, as deprotonation causes a local accumulation of negative charge. The protons at these linkages possess a somewhat lower Brønsted acidity than those at Si-O-Al links. AIMD simulations for fully hydrated ECR-40 predicted a partial deprotonation of the Al-O-Al linkages, whereas Si-O-Al linkages were fully deprotonated. Frequently, a coordination of water molecules to framework Al atoms was observed in the vicinity of the Al-O-Al links. Hence, these linkages appear prone to break upon dehydration, potentially explaining why Löwenstein's rule is mostly obeyed in materials formed in aqueous media.

Water in zeolite L and its MOF mimic

Confinement of molecules in one dimensional arrays of channel-shaped cavities has led to technologically interesting materials. However, the interactions governing the supramolecular aggregates still remain obscure, even for the most common guest molecule: water. Herein, we use computational chemistry methods (#compchem) to study the water organization inside two different channel-type environments: zeolite L – a widely used matrix for inclusion of dye molecules, and ZLMOF – the closest metal-organic-framework mimic of zeolite L. In ZLMOF, the methyl groups of the ligands protrude inside the channels, creating nearly isolated nanocavities. These cavities host well-separated ring-shaped clusters of water molecules, dominated mainly by water-water hydrogen bonds. ZLMOF provides arrays of “isolated supramolecule” environments, which might be exploited for the individual confinement of small species with interesting optical or catalytic properties. In contrast, the one dimensional channels of zeolite L contain a continuous supramolecular structure, governed by the water interactions with potassium cations and by water-water hydrogen bonds. Water imparts a significant energetic stabilization to both materials, which increases with the water content in ZLMOF and follows the opposite trend in zeolite L. The water network in zeolite L contains an intriguing hypercoordinated structure, where a water molecule is surrounded by five strong hydrogen bonds. Such a structure, here described for the first time in zeolites, can be considered as a water pre-dissociation complex and might explain the experimentally detected high proton activity in zeolite L nanochannels.

First-Principles Study of AlPO₄-H3, a Hydrated Aluminophosphate Zeotype Containing Two Different Types of Adsorbed Water Molecules

Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two “types” of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type small-pore aluminophosphate AlPO₄-H3 contains both types of H₂O molecules. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO₄-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO₄-C, leading to the identification of a few “fingerprint” modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO₄-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.

A high pressure Raman study on confined individual iodine molecules as molecular probes of structural collapse in the AlPO4-5 framework

The mechanical stability of porous zeolitic materials has long been an important issue due to their advanced applications in many fields. Here, we choose to study the pressure induced structural modifications on the AlPO₄-5 (AFI) framework. We find that the Raman characteristics of the confined iodine molecules in the AFI channels, with a low filling density, show discontinuities at around 3 and 10 GPa, which can be attributed to the implications of framework changes. Subsequent theoretical simulations on the AFI framework demonstrate that both a tilting mechanism along the c axis and a rotating mechanism in the ab plane of the tetrahedrons contribute to the structural deformation, and the AFI framework is collapsible at 4 and 10 GPa, which confirms those values found in the Raman studies. In this nanoconfinement system of I@AFI, the host and guest depend on and interact with each other mutually. No supporting effect on the AFI framework is found for the confined individual iodine molecules with such a low filling density, but they can be regarded as molecular probes to reflect the structural collapse of AFI. Thus, we provide a novel way to detect the structural deformation of porous materials under high pressure.

Supramolecular Organization in Confined Nanospaces

Empty spaces are abhorred by nature, which immediately rushes in to fill the void. Humans have learnt pretty well how to make ordered empty nanocontainers, and to get useful products out of them. When such an order is imparted to molecules, new properties may appear, often yielding advanced applications. This review illustrates how the organized void space inherently present in various materials: zeolites, clathrates, mesoporous silica/organosilica, and metal organic frameworks (MOF), for example, can be exploited to create confined, organized, and self-assembled supramolecular structures of low dimensionality. Features of the confining matrices relevant to organization are presented with special focus on molecular-level aspects. Selected examples of confined supramolecular assemblies - from small molecules to quantum dots or luminescent species - are aimed to show the complexity and potential of this approach. Natural confinement (minerals) and hyperconfinement (high pressure) provide further opportunities to understand and master the atomistic-level interactions governing supramolecular organization under nanospace restrictions.

Irreversible Conversion of a Water-Ethanol Solution into an Organized Two-Dimensional Network of Alternating Supramolecular Units in a Hydrophobic Zeolite under Pressure

Turning disorder into organization is a key issue in science. By making use of X-ray powder diffraction and modeling studies, we show herein that high pressures in combination with the shape and space constraints of the hydrophobic all-silica zeolite ferrierite separate an ethanol-water liquid mixture into ethanol dimer wires and water tetramer squares. The confined supramolecular blocks alternate in a binary two-dimensional (2D) architecture that remains stable upon complete pressure release. These results support the combined use of high pressures and porous networks as a viable strategy for driving the organization of molecules or nano-objects towards complex, pre-defined patterns relevant for the realization of novel functional nanocomposites.

Interaction of water with (silico)aluminophosphate zeotypes: a comparative investigation using dispersion-corrected DFT

The adsorption of water in six structurally different aluminophosphates and their silicoaluminophosphate analogues is investigated using dispersion-corrected density-functional theory calculations. In addition to predicting the interaction energies, the structural changes of the materials upon water adsorption are assessed.

Molecular dynamics methods for modeling complex interactions in biomaterials

The molecular dynamics method is a powerful computer simulation technique which provides access to the detailed time evolution (trajectory) of a system in specified conditions, such as a particular temperature or pressure. The full trajectory of the system can be analyzed using statistical mechanics tools to obtain thermodynamical quantities and dynamical properties; the mechanism of chemical reactions and other time-dependent processes, such as diffusion, can also be revealed in high detail. When applied to model extended and complex system such as biomaterials, MD simulations represent an invaluable tool to discover structure-activity relationships and rationalize biomedical applications.

Computational study for water sorption in AlPO(4)-5 and AlPO(4)-11 molecular sieves

The unusual water adsorption behavior in aluminophosphate molecular sieves AlPO(4)-5 and AlPO(4)-11 was studied using canonical Monte Carlo and periodic density functional theory (DFT) calculation. The number of adsorbed water molecules per cavity ranging from 1 to 12 were located inside the molecular sieves by canonical Monte Carlo simulation methods using a "compass" forcefield. The DFT calculations were done for optimizing each structure with and without adsorbed water molecules employing generalized gradient approximation with the Perdew-Burke-Ernzerhof exchange-correction functional. Both classical and quantum mechanical calculations have exhibited hydrogen bonding between adsorbed water molecules inside the main 12-membered ring. The Al-O-P angles were observed to decrease after adsorbing water molecules in geometry optimized AlPO(4)-5 and AlPO(4)-11 molecular sieves. DFT calculations illustrate that the initial loading of water in the large cavity is due to the mild acidity in the framework but the isobaric increase in loading is due to the abundant hydrogen bonding between adsorbed water at higher water loading.

Modeling the water-bioglass interface by ab initio molecular dynamics simulations

The hydration of the surface of a highly bioactive silicate glass was modeled using ab initio (Car-Parrinello) molecular dynamics (CPMD) simulations, focusing on the structural and chemical modifications taking place at the glass-water interface immediately after contact and on the way in which they can affect the bioactivity of these materials. The adsorption of a water dimer and trimer on the dry surface was studied first, followed by the extended interface between the glass and liquid water. The CPMD trajectories provide atomistic insight into the initial stages relevant to the biological activity of these materials: following contact of the glass with an aqueous (physiological) medium, the initial enrichment of the surface region in Na+ cations establishes dominant Na+-water interactions at the surface, which allow water molecules to penetrate into the open glass network and start its partial dissolution. The model of a Na/H-exchanged interface shows that Ca2+-water interactions are mainly established after the dominant fraction of Na is leached into the solution. Another critical role of modifier cations was highlighted: they provide the Lewis acidity necessary to neutralize OH(-) produced by water dissociation and protonation of nonbridging oxygen (NBO) surface sites. The CPMD simulations also highlighted an alternative, proton-hopping mechanism by which the same process can take place in the liquid water film. The main features of the bioactive glass surface immediately after contact with an aqueous medium, as emerged from the simulations, are (a) silanol groups formed by either water dissociation at undercoordinated Si sites or direct protonation of NBOs, (b) OH(-) groups generally stabilized by modifier cations and coupled with the protonated NBOs, and (c) small rings, relatively stable and unopened even after exposure to liquid water. The possible role and effect of these sites in the bioactive process are discussed.

On the role of Ti(IV) as a Lewis acid in the chemistry of titanium zeolites: Formation, structure, reactivity, and aging of Ti-peroxo oxidizing intermediates. A first principles study

The ethylene epoxidation cycle in a H2O2/H2O-loaded Ti zeolite has been simulated by a Car-Parrinello approach. Results indicate a process where the zeolitic framework is the active oxygen mediator. The dissociative chemisorption of H2O2 leads, via a transient Ti-hydroperoxo species, to H2O and a Ti-peroxo zeolite intermediate. Transfer of active oxygen to ethylene follows, giving the epoxide and recovering the catalyst. A thorough theoretical characterization indicates that the active oxidizing species is an asymmetric eta2-Ti-peroxo, absorbing in the visible range. The lability of the intermediate is found related to eta2 <--> eta1 interconversions of the Ti-peroxo structure. The interconversions, triggered by water molecules, could account for the experimentally found reduced catalytic activity in aged TS-1 catalysts. The results provide a microscopic picture of the reactivity and dehydration/aging processes of the catalyst fully consistent with experiments and highlight the fundamental role of the Lewis acid character of Ti in the formation, reactivity, and degradation of the active oxidizing species.

Molecular simulation studies of water physisorption in zeolites

We report a series of Grand Canonical Monte Carlo simulations of water adsorption in NaY and NaX faujasite, as well as in silicalite-1. Computed adsorption isotherms and heats of adsorption were in good agreement with the available experiments. The existence of cyclic water hexamers in NaX located in the 12-ring windows, recently disclosed by neutron diffraction experiments (Hunger et al., J. Phys. Chem. B, 2006, 110, 342-353) was reproduced in our simulations. Interestingly enough, such cyclic hexamer clusters were also observed in the case of NaY, in which no stabilizing cation is present in the 12-ring window. We also report cation redistribution upon water adsorption for sodium faujasite with varying cation contents (Si ratio Al ratio in the range 1.53-3). A simple and transferable forcefield was used, that enabled to reproduce the different aspects of water physisorption in stable zeolites. The high pressure water condensation in hydrophobic silicalite-1 was reproduced without any parameter readjustment. The method and forcefield used here should be useful for engineering oriented applications such as the prediction of multi-component mixture adsorptive separations in various stable zeolites. It allows to address the issue of the effect of the small amounts of water that are almost inevitably present in zeolite-based separation processes.

Modeling the Concentration Dependence of the Methanol Self-Diffusivity in Faujasite Systems: Comparison with the Liquid Phase

Molecular dynamics simulations were performed to understand further the concentration dependence of the self-diffusion of methanol in the faujasite zeolite systems. The evolution of the self-diffusivity was investigated as a function of coverage for DAY and NaY systems to study the effect of both the pore confinement and the presence of the extraframework cations within the supercage. It was found that the self-diffusivity decreases with loading for DAY, whereas for NaY it passes through a maximum at intermediate coverage, in agreement with pulse-field gradient NMR and quasi elastic neutron scattering data reported in similar systems. The activation energies of the methanol diffusion corresponding to a combination of both intra- and intercage motions were evaluated as a function of the coverage. The simulated trends are interpreted on the basis of the predominant interactions which take place in both systems. Finally, the preferential arrangement of the adsorbate molecules are provided and compared with those simulated in the liquid phase. For the fully loaded materials, it was seen that the methanol molecules form a one-dimensional hydrogen-bonded chain along the channels in DAY whereas only dimers are present in NaY.

First-principles molecular dynamics investigation of the D-amino acid oxidative half-reaction catalyzed by the flavoenzyme D-amino acid oxidase

Large-scale Car-Parrinello molecular dynamics simulations of D-alanine oxidation catalyzed by the flavoenzyme D-amino acid oxidase have been carried out. A model of the enzyme active site was built by starting from the enzyme X-ray structure, and by testing different subsystems comprising different sets of aminoacyl residues. In this process, the stability of the enzyme-substrate complex was taken as a measure of the accuracy of the model. The activated transfer of the amino acid alpha-hydrogen from the substrate to the flavin N5 position was then induced by constraining a suitable transfer reaction coordinate, and the free energy profile of the reaction was calculated. The evolution of electronic and structural properties of both enzyme-bound substrate and flavin cofactor along the reaction path is consistent with a hydride-transfer mechanism. The calculated free energy barrier for this process (13 kcal/mol) is in excellent agreement with the activation energy value derived from the experimentally determined rate constant for the corresponding enzyme-catalyzed reaction. The electronic distribution of the reduced flavin shows that the transferred electrons tend to be centered near the C4a position rather than delocalized over the flavin pyrimidine ring. This feature is mechanistically relevant in that such an electronic distribution may promote the subsequent enzyme-catalyzed reduction of molecular oxygen to yield hydrogen peroxide via a postulated flavin 4a-peroxide intermediate. These results also show that a first-principles molecular dynamics approach is suitable to study the mechanism of complex enzymatic processes, provided that a smaller, yet reliable, subsystem of the enzyme can be identified, and special computational techniques are employed to enhance the sampling of the reactive event.