Encapsulated Water Molecules Research Articles

Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics.

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn(2+) aqua complex, as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate, H2O + CO2 → H(+) + HCO3(-). On the basis of potential-of-mean-force (PMF) calculations, stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (ΔG = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile, proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (ΔΔG = 1.4 kcal/mol), suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast, the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity, due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme, providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.

Solvent dynamics in a reverse micellar water-pool: a spectroscopic investigation of DDAB–cyclohexane–water systems

We have measured the hydrogen bonded structure and sub-ns relaxation dynamics of water molecules encapsulated in the DDAB-cyclohexane (Cy)-water reverse micellar (RM) water-pool dependent on water concentration (w(0) = [water]/[DDAB]) and temperatures. The interfacial film of DDAB-Cy undergoes significant alteration upon addition of water as the microscopic phase changes from cylindrical aggregates to discrete droplets which is in contrast to the conventional RM systems. FTIR spectroscopy in mid-infrared (MIR) and far-infrared (FIR) regions suggests the encapsulated water molecules to undergo a transition with increasing w(0) towards a bulk-like behavior. Time resolved fluorescence spectroscopy using Coumarin-500 as the fluorophore reveals a decrease in solvation time constant with increasing w(0) as well as with increasing temperature, a behavior consistent with conventional RM systems. The temperature dependent relaxation dynamics is found to follow an Arrhenius type behavior with a value for E(act) in the range of 2.5-3 kcal mol(-1) for all the studied systems. Our results show that phase modification has a marginal effect on the relaxation dynamics.

Release of High-Energy Water as an Essential Driving Force for the High-Affinity Binding of Cucurbit[n]urils

Molecular dynamics simulations and isothermal titration calorimetry (ITC) experiments with neutral guests illustrate that the release of high-energy water from the cavity of cucurbit[n]uril (CBn) macrocycles is a major determinant for guest binding in aqueous solutions. The energy of the individual encapsulated water molecules decreases with increasing cavity size, because larger cavities allow for the formation of more stable H-bonded networks. Conversely, the total energy of internal water increases with the cavity size because the absolute number of water molecules increases. For CB7, which has emerged as an ultrahigh affinity binder, these counteracting effects result in a maximum energy gain through a complete removal of water molecules from the cavity. A new design criterion for aqueous synthetic receptors has therefore emerged, which is the optimization of the size of cavities and binding pockets with respect to the energy and number of residing water molecules.

Water Encapsulation in a Polyoxapolyaza Macrobicyclic Compound

A new heteroditopic macrobicyclic compound (t(2)pN(5)O(3)) containing two separate polyoxa and polyaza compartments was synthesized in good yield through a [1 + 1] "tripod-tripod coupling" strategy. The X-ray crystal structure of H(3)t(2)pN(5)O(3)(3+) revealed the presence of one encapsulated water molecule accepting two hydrogen bonds from two protonated secondary amines and donating a hydrogen bond to one amino group. The acid-base behavior of the compound was studied by potentiometry at 298.2 K in aqueous solution and at ionic strength 0.10 M in KCl. The results revealed unusual protonation behavior, namely a surprisingly low fourth protonation constant contrary to what was expected for the compound. (1)H NMR and DOSY experiments, as well as molecular modeling studies, showed that the water encapsulation and the conformation observed in the solid state are retained in solution. The strong binding of the encapsulated water molecule, reinforced by the cooperative occurrence of a trifurcated hydrogen bond at the polyether compartment of the macrobicycle, account for the very low log K(4)(H) value obtained.

Water molecule encapsulated in carbon nanotube model systems: effect of confinement and curvature

Water present in the nanoscale confined medium like the hydrophobic interior of the carbon nanotubes (CNT) is known to extol unique properties that depart largely from their behavior in the bulk form. Considering suitable model systems that structurally resemble single unit of the CNT, we demonstrate that two unique parameters namely the local nanoscale curvature and the confinement length are of cardinal importance in governing the structural and electronic properties of water molecule present inside CNT in a general manner. Water molecule encapsulated between the model systems that offer both the above two effects exhibits dramatic trend in the interaction energy with respect to the variation of these parameters. In relation to the curvature of the model system, we propose three different regimes where water molecule experiences a distinct trend in the stabilization energy. Similarly, a confinement distance of 6 A also marks as a borderline for the distinct manifestations in the stabilization energy of the water molecule. These two parameters also play a key role in governing the significant variations in the structural parameters, Mulliken charges, and red and blue shift in the O–H vibrational frequencies of the encapsulated water molecule. There seems to be interplay between curvature and confinement in deciding the electronic properties of water in the nanoscale confinement.

Molecular dynamics of β-CD in water/co-solvent mixtures

Molecular dynamics (MD) simulations on β-cyclodextrin (β-CD) in water, ethanol (EtOH), methanol (MeOH) and mixtures of these solvents have been carried out at 300 K over a time period of 15 ns using the AMBER force field. The hydrated X-ray crystallographic structure has four water molecules inside the cavity, defined by a more precise boundary for the β-CD cavity. From the simulations, 2–4 encapsulated water molecules are most probably found. In an ethanol co-solvent system, the β-CD cavity is occupied with one ethanol molecule located in two discrete sites: below and above the O4(n) plane, which is in agreement with experimental results. In all systems, the average values of tilt angles of the obtained structures are higher than the tilt angles of the X-ray structures. The investigations of the alcohol orientations in co-solvent mixtures reveal the hydrophobic environment of the cavity and the hydrophilic atmosphere at both rims of β-CD.

Designed synthesis, structure, and 3-D topology of a supramolecular dimer and inorganic–organic cocrystal

Synthesis and structure of a supramolecular dimer and inorganic–organic cocrystal of composition [{CuIIL1⊂(H2O)}2(C8H6O4)] (1) are described (H2L1= N,N′-ethylenebis(3-ethoxysalicylaldimine); C8H6O4 = terephthalic acid). Crystal engineering has been utilized for the designed synthesis of the title compound. Compound 1 crystallizes in a triclinic system with P 1 space group. The structure consists of terephthalic acid and two symmetry related inclusion products [CuIIL1⊂(H2O)], in which the water molecule is encapsulated in the O4 compartment by forming bifurcated hydrogen bonds involving two hydrogen of water and phenolate and ethoxy oxygens of the compartmental ligand. Hydrogen bonding between encapsulated water molecules and terephthalic acid forms the supramolecular dimer. The title compound is an example of an inorganic–organic cocrystal as well. Weak interactions, such as semicoordination of phenoxo oxygen of one unit to the metal center of a symmetry related unit and C–H ··· O, and O–H ··· O hydrogen bonds result in generation of an overall 3-D topology in the title compound. The 3-D topology can be understood as interlinking of two different 2-D sheets.

Hierarchic Nanostructure for Auto‐Modulation of Material Release: Mesoporous Nanocompartment Films

AbstractThe preparation of mesoporous nanocompartment films composed of both hollow silica capsules and silica particles by using layer‐by‐layer (LbL) adsorption is described. The resultant nanocompartment films exhibit stepwise release of encapsulated water molecules without application of external stimuli. The hollow hierarchic pore structure of the silica capsules, including their internal void and mesoporous walls, is a key factor for the regulation and stepwise release of water, and is probably caused by the non‐equilibrated concurrent evaporation of material from the mesopore and capillary penetration into the mesopores. The number of release steps and rate of release can be tuned by variation of several parameters including water content, ambient temperature, layer multiplicity, and co‐adduct particle size. Application of the mesoporous nanocompartment films for the release of substances, including therapeutic agents and fragrances, indicates that the stepwise material release can be applied for a wide range of liquid substances. The films should lead to a novel material release system useful even for biomedical applications capable of controlled and sustained delivery of drug molecules.

First-Principles Study of Water Chains Encapsulated in Single-Walled Carbon Nanotube

Water molecules confined inside a single-walled (6, 6) carbon nanotube were investigated using density functional theory. In this narrow-sized carbon nanotube (of about 0.8 nm in diameter), the encapsulated water molecules form chain-like configurations via hydrogen bonding. As compared to the water chains in vacuum, the intramolecular charge transfer in the encapsulated water chain is enhanced and the dipole moment is reduced due to the screening effect of the carbon nanotube. The tube-molecule interaction characterized by the coupling energy is about 0.28 eV per water molecule by local density approximation and 0.1 eV by general gradient approximation; the latter one is close to the results by empirical potentials. Weak coupling between the molecular orbitals of the encapsulated water molecules and the delocalized pi electrons from the carbon nanotube was observed, implying that the tube-water interaction is not a simple effect of geometry confinement. Vibrational analysis revealed some unique hydrogen-bond modes for the water chains as well as red shift of the O-H stretching modes for the encapsulated water molecules with regard to the vacuum frequencies due to the tube-water interaction.

Water Clusters Confined in Nonpolar Cavities by Ab Initio Calculations

Encapsulation of (H2O)n clusters (n = 1−22) in fullerene cages of different diameters (0.73−1.41 nm) has been investigated using gradient-corrected density functional theory. A linear relationship between cavity volume and maximum number of the encapsulated water molecules has been obtained. The interaction between water molecules and the fullerene wall was identified as physisorption with an adsorption energy of about 1.1 kcal/mol per molecule. The equilibrium configurations of small confined water clusters (n < 12) roughly resemble those of gas-phase clusters, whereas larger water clusters tend to adopt cage-like configurations when they are encapsulated in fullerene cages of sufficiently large diameter (i.e., >1.4 nm). The dipole moments of water clusters in the confined phase are smaller than those in the gas phase due to the screening effect of the outer fullerene cage. These results might shed some light on the behavior of water clusters confined in the nonpolar cavities of biological interests.

Tuning the thermodynamic stability of oxothiomolybdenum wheels: crystal structures, studies in solution and DFT calculations

The complexes [Mo12O12S12(OH)12(Muco)]2- (Muco2- = muconate, C6H4O4(2-)) and [Mo12,O12S12(OH)12(TMT)]2 (TMT2- = tetramethylterephthalate, C12H12O4(2-)) have been obtained from the condensation of the [Mo2O2S2]2+ building block in the presence of Muco2- and TMT2-, respectively. Both compounds were structurally characterized, revealing host-guest architectures with one or two encapsulated water molecules. 1H NMR spectra in DMSO and D2O showed that both complexes had an average symmetry higher than that in the solid state, due to changes in the distribution of encapsulated water molecules. The relative stabilities in water of the seven complexes encapsulating various di- or tricarboxylate guests, either rigid or non-rigid, have been determined. The stability scale obtained for the dianionic complexes is interpreted in relation with the rigidity or flexibility of the guests. A DFT study demonstrates that additional stabilization arises from the presence of inner hydrogen bonds involving 1, 2 or 3 water molecules, which even permit the extension of the H-bonds network to the first solvation sphere of the anion. DFT calculations were carried out on all investigated complexes as isolated or solvated anions and provide the sequence of the bond energies between the host and the guests, which is compared to the experimental data.

Structure and Dynamics of β-Cyclodextrin in Aqueous Solution at the Density-Functional Tight Binding Level

Structure and dynamics of beta-cyclodextrin (beta-CyD), a prototype host for inclusion compounds of biological interest, is investigated by means of density-functional based tight-binding molecular dynamics (MD) simulations. The computational protocol is benchmarked against available experimental data and first-principles calculations. Solvent-solute interactions, including the diffusion into and dwell time of the solvent in the cavity of beta-CyD, are studied with a hybrid QM/MM method. Comparison of MD simulations of beta-CyD in the gas phase and in water shows that the solvent reduces the flexibility of the structure framework, while the terminal hydroxyl groups become more flexible and are embedded in a network of hydrogen bonds. Our 160 ps MD simulations, provide enough sampling to discuss the dynamics of the water inside the cavity. The dwell time of the encapsulated water molecule has a wide distribution with a peak at 70 fs. Surprisingly, despite only the 17% difference between the "top" and "bottom" opening area of the beta-CyD cone, 64% of the water molecules enter the cavity through the slightly bigger "bottom" aperture.