Host Cage Research Articles

Matching of Host-Guest Symmetry/Orientation and Molecular Dynamics in Two Double Perovskite-Like Azido Coordination Polymers.

Two new double perovskite-like azido coordination polymers with trimethylammonium as the guest cation, namely, (Me3NH)2[CrNa(N3)6] and (Me3NH)2[CrK(N3)6], have been prepared. The molecular dynamics for both compounds are investigated and are clearly uncovered by the first-principles molecular dynamics simulation and the significant dielectric relaxation. Structural analyses of these compounds in combination with their analogue (Me3NH)[Mn(N3)3] reveal that the guest trimethylammonium has flexible structural adaptability, especially with a variety of disordered distributions, to match the different symmetries of varied metal-azido frameworks. Interestingly, the replacement of the divalent metal ion by mixed monovalent/trivalent metal ions can change the symmetry, shape, and charge distribution of the host cage unit; thus it may influence and regulate the arrangement of the guest inclusion and its molecular dynamics as well as the structural phase transition.

"Pyrene Box" Cages for the Confinement of Biogenic Amines.

The complete structure of non-crystalline compounds can be determined by confining them in crystalline structures. The reduced motional degrees of freedom of encapsulated guests can be obtained through their anchoring to the host cages, which results in the reduction of a significant amount of disorder. The "pyrene box" cages that easily crystallize from aqueous solutions are recommended to achieve complete structure elucidation of compounds of biological interest. In this study, the "pyrene box" cages have been used for the in situ encapsulation of biogenic amines: histamine, dopamine, and serotonin. NMR spectroscopy illustrates that these systems are stable in aqueous solution. The X-ray single-crystal structure analysis reveals that the pyrene box/biogenic amine systems are stabilized through combined interactions, strongly contributing to in situ fixation and accurate determination of their crystal structures.

Effects of the CO₂ Guest Molecule on the sI Clathrate Hydrate Structure.

This paper analyzes the structural, energetic and mechanical properties of carbon dioxide hydrate clathrates calculated using finite cluster and periodic ab initio density-functional theory methodologies. Intermolecular interactions are described by the exchange-hole dipole moment method. The stability, gas saturation energetics, guest–host interactions, cage deformations, vibrational frequencies, and equation of state parameters for the low-pressure sI cubic phase of the CO2@H2O clathrate hydrate are presented. Our results reveal that: (i) the gas saturation process energetically favors complete filling; (ii) carbon dioxide molecules prefer to occupy the larger of the two cages in the sI structure; (iii) blue shifts occur in both the symmetric and antisymmetric stretching frequencies of CO2 upon encapsulation; and (iv) free rotation of guest molecules is restricted to a plane parallel to the hexagonal faces of the large cages. In addition, we calculate the librational frequency of the hindered rotation of the guest molecule in the plane perpendicular to the hexagonal faces. Our calculated spectroscopic data can be used as signatures for the detection of clathrate hydrates in planetary environments.

Spin-Spin Coupling in Nitrogen Atom Encapsulated C60, C59N, and Their Respective Dimers.

Density functional theoretical calculations were performed to study the stability and magnetic properties of nitrogen-encapsulated C60, C59N, and their respective dimers at B3LYP/6-311G* and B3LYP-GD2/6-311G* levels of theory. For the most stable spin state of each of the above complexes, spin density transfer and spin-spin coupling between different components are investigated. The nature of bonding between the guest and the host is analyzed based on the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap and the respective molecular orbital diagrams. The analysis of spin density showed that the encapsulated nitrogen retained its atomic state in N@C60 and N@C59N. Depending on the multiplicity of N@C59N, the unpaired electrons of the encapsulated nitrogen are coupled with those of the cage anti-ferromagnetically or ferromagnetically. The present study also showed that the complex (N@C60)2 can exist in two isoenergetic spin states, namely, (7)[(N@C60)2] and (1)[(N@C60)2]. In the former, the encapsulated nitrogens are ferromagnetically coupled, whereas they are coupled anti-ferromagnetically in the latter. A similar coupling between the guest species occurs in the nitrogen analogues (7)[(N@C59N)2] and (1)[(N@C59N)2]. The stabilization energy of the endohedral nitrogen complexes indicated that the interaction between the guest and the host cage is purely noncovalent.

Modifying the Flexibility of Water Cages by Co-Including Acidic Species within Clathrate Hydrate

Clathrate hydrates are crystalline materials made of water molecules forming host cages within which guest molecules are located. The hydrogen bond network ensuring the stability of the host substructure includes ionic defects, having an impact on the physicochemical properties of the systems. In this paper, a new way of introducing these ionic defects is proposed. Type II clathrate hydrates mixing tetrahydrofuran (THF) and perchloric acid guest molecules are synthesized and investigated by means of calorimetric, X-ray diffraction, and Raman scattering measurements together with a computational structure relaxation in the density functional theory approximation. The formation of the mixed clathrate hydrate with perchlorate anion included in the large cage of the cationic host-substructure of the THF type II clathrate hydrate requires the cooling of a (1-α) THF·αHClO4·17H2O solution with α less than 0.125. Above this inherent limitation, a multiphasic regime is observed in the formation of clathrate hydrate (mixture of type I and type II). The substitution of a THF molecule per perchlorate anion allows the modification of the melting of the type II clathrate hydrate, by preserving the clathrate structure. Shrinkage of the type II unit cell is measured together with a softening of the host lattice mode. In the harmonic approximation, the observation of both phenomena is counterintuitive and outline existing competition between anharmonicity of the cage energy landscape and ionic host–guest interaction. This study reveals the key role played by acidic defects existing in the host substructure on the physicochemical properties of clathrate hydrate.

Endohedral and exohedral metalloborospherenes: M@B40 (M=Ca, Sr) and M&B40 (M=Be, Mg).

The recent discovery of the all-boron fullerenes or borospherenes, D(2d) B40(-/0), paves the way for borospherene chemistry. Here we report a density functional theory study on the viability of metalloborospherenes: endohedral M@B40 (M=Ca, Sr) and exohedral M&B40 (M=Be, Mg). Extensive global structural searches indicate that Ca@B40 (1, C(2v), (1)A1) and Sr@B40 (3, D(2d), (1)A1) possess almost perfect endohedral borospherene structures with a metal atom at the center, while Be&B40 (5, C(s), (1)A') and Mg&B40 (7, C(s), (1)A') favor exohedral borospherene geometries with a η(7)-M atom face-capping a heptagon on the waist. Metalloborospherenes provide indirect evidence for the robustness of the borospherene structural motif. The metalloborospherenes are characterized as charge-transfer complexes (M(2+)B40(2-)), where an alkaline earth metal atom donates two electrons to the B40 cage. The high stability of endohedral Ca@B40 (1) and Sr@B40 (3) is due to the match in size between the host cage and the dopant. Bonding analyses indicate that all 122 valence electrons in the systems are delocalized as σ or π bonds, being distributed evenly on the cage surface, akin to the D(2d) B40 borospherene.

Endohedral and Exohedral Metalloborospherenes: M@B40 (M=Ca, Sr) and M&B40 (M=Be, Mg)

AbstractThe recent discovery of the all‐boron fullerenes or borospherenes, D2d B40−/0, paves the way for borospherene chemistry. Here we report a density functional theory study on the viability of metalloborospherenes: endohedral M@B40 (M=Ca, Sr) and exohedral M&B40 (M=Be, Mg). Extensive global structural searches indicate that Ca@B40 (1, C2v, 1A1) and Sr@B40 (3, D2d, 1A1) possess almost perfect endohedral borospherene structures with a metal atom at the center, while Be&B40 (5, Cs, 1A′) and Mg&B40 (7, Cs, 1A′) favor exohedral borospherene geometries with a η7‐M atom face‐capping a heptagon on the waist. Metalloborospherenes provide indirect evidence for the robustness of the borospherene structural motif. The metalloborospherenes are characterized as charge‐transfer complexes (M2+B402−), where an alkaline earth metal atom donates two electrons to the B40 cage. The high stability of endohedral Ca@B40 (1) and Sr@B40 (3) is due to the match in size between the host cage and the dopant. Bonding analyses indicate that all 122 valence electrons in the systems are delocalized as σ or π bonds, being distributed evenly on the cage surface, akin to the D2d B40 borospherene.

The HD molecule in small and medium cages of clathrate hydrates: quantum dynamics studied by neutron scattering measurements and computation.

We report inelastic neutron scattering (INS) measurements on molecular hydrogen deuteride (HD) trapped in binary cubic (sII) and hexagonal (sH) clathrate hydrates, performed at low temperature using two different neutron spectrometers in order to probe both energy and momentum transfer. The INS spectra of binary clathrate samples exhibit a rich structure containing sharp bands arising from both the rotational transitions and the rattling modes of the guest molecule. For the clathrates with sII structure, there is a very good agreement with the rigorous fully quantum simulations which account for the subtle effects of the anisotropy, angular and radial, of the host cage on the HD microscopic dynamics. The sH clathrate sample presents a much greater challenge, due to the uncertainties regarding the crystal structure, which is known only for similar crystals with different promoter, but nor for HD (or H2) plus methyl tert-butyl ether (MTBE-d12).

Systematic studies on anharmonicity of rattling phonons in type-I clathrates by low-temperature heat capacity measurements

A systematic study on the anharmonicity of phonons is made for single-crystal type-I clathrates: n-type Ba8Ga16Ge30 (n-BGG), p-type Ba8Ga16Ge30 (p-BGG), n-type Sr8Ga16Ge30 (n-SGG), n-type K8Ga16Sn30 (n-KGSn), and n-type Ba8Ga16Sn30 (n-BGSn), based on their heat capacity C-p at low temperatures (T) down to 360 mK. The low-T linear terms (obs)gamma T of C-p, including the tunneling term of the atoms accommodated in the host cages (gamma T-ph = alpha T) and the Sommerfeld itinerant-electron term (gamma T-e), are successfully separated through careful measurements of single crystals with various carrier concentrations. The values of the minimum density of anharmonic potentials are deduced from a to be 0.12 +/- 0.24 for n-KGSn, 0.47 +/- 0.24 for n-BGG, 1.9 +/- 0.8 for p-BGG, 6.0 +/- 0.9 for n-SGG, and 10.9 +/- 0.7 for n-BGSn in units of x 10(15) cm(-3). The effective mass (m*/ m(0)) is determined from gamma(e) to be 1.01 +/- 0.25 for n-BGG, 1.20 +/- 0.19 for p-BGG, 1.68 +/- 0.24 for n-SGG, 1.86 +/- 0.54 for n-KGSn, and 2.05 +/- 0.48 for n-BGSn in units of free electron mass m(0), and the electron-phonon interaction strength can be evaluated from these values. It is shown that both the thermal conductivity (kappa) and the electron-phonon interaction strength (lambda) agree well with the a parameters deduced from C-p. The differences in kappa known between n- and p-BGGs are ascribed to the influence of defects at the crystallographic 6c sites, which are clearly indicated by magnetic susceptibility measurements. This is very different from the situation in the other clathrates.

A quantum chemistry study of natural gas hydrates

The structure and properties of natural gas hydrates containing hydrocarbons, CO₂, and N₂ molecules were studied by using computational quantum chemistry methods via the density functional theory approach. All host cages involved in I, II, and H types structures where filled with hydrocarbons up to pentanes, CO₂ and N₂ molecules, depending on their size, and the structures of these host-guest systems optimized. Structural properties, vibrational spectra, and density of states were analyzed together with results from atoms-in-a-molecule and natural bond orbitals methods. The inclusion of dispersion terms in the used functional plays a vital role for obtaining reliable information, and thus, B97D functional was shown to be useful for these systems. Results showed remarkable interaction energies, not strongly affected by the type of host cage, with molecules tending to be placed at the center of the cavities when host cages and guest molecules cavities are of similar size, but with molecules approaching hexagonal faces for larger cages. Vibrational properties show remarkable features in certain regions, with shiftings rising from host-guest interactions, and useful patterns in the terahertz region rising from water surface vibrations strongly coupled with guest molecules. Likewise, calculations on crystal systems for the I and H types were carried out using a pseudopotential approach combined with Grimme's method to take account of dispersion.

Multidoping of Si Cages: High Spin States beyond the Single-Dopant Septet Limit

Density-functional theory based global geometry optimization is employed to systematically scrutinize the possibility of multi-doping of hydrogenated Si clusters in order to achieve high spin states beyond the septet limit of a single-atom dopant. While our unbiased configurational search reveals that the previously suggested Si18H12 double hexagonal prism structure is generally too small to accommodate two dopants in magnetized state, the larger Si24H24 cage turns out to be suitable for such applications. For dimer dopants M2+ = Cr2+, Mn2+ and CrMn+, the structural integrity of the host cage is conserved in the ground-state structure of corresponding M2+@Si24H24 aggregates, as is the unusually high spin state of the guest dopant, which in case of Cr2+ already exceeds the single-atom dopant septet limit by almost a factor of two. Moreover, the possibility of further increasing the cluster spin moment by encapsulating an even larger number of dopants into a suitably sized hydrogenated Si cage is illustrated for the example of a (CrMn+)2@Si28H28 aggregate with a total number of 18 unpaired electrons. These results strongly suggest multi-doping of Si clusters as a viable route to novel cluster-based materials for magneto-optic applications.

Hydronium dynamics in the perchloric acid clathrate hydrate

Clathrate hydrates are nanoporous crystalline materials made of a network of hydrogen-bonded water molecules (forming host cages) stabilized by the presence of foreign (generally hydrophobic) guest molecules. The encapsulation of strong acids such as perchloric acid (with an acid to water ratio of 5.5) leads to an ionic clathrate structure formed with perchlorate anions within cationic cages. The excess protons, at the origin of the large protonic conductivity of the compound, are delocalized over the cage sub-structure through a Grotthus mechanism. Such ionic crystal constitutes a good model system for investigating the spatial and time characteristics of the elementary steps of the proton conduction. In this paper, the dynamics of hydronium ions are investigated by means of incoherent quasi-elastic neutron scattering (QENS) experiments performed by tuning the observation time to the timescale of the probed dynamical process met in the perchloric acid clathrate hydrate at 220 K. Thanks to the specific versatility of time-of-flight spectrometer, two elementary processes have been identified for modeling the hydronium ion dynamics: hydronium reorientations coupled to intermolecular proton transfer. The hydronium ions undergo reorientations with a characteristic time of 42 ± 8 ps while the proton transfer within the hydrogen bond between hydronium ion and neighboring water molecule occurs with a characteristic time of 1.4 ± 0.3 ps. A previous high-resolution QENS investigation has shown that water molecules surrounding the hydronium ions undergo reorientations with a characteristic time of 0.7 ± 0.1 ns at 220 K. Such experimental results outline the key role played by the relaxation of the water molecules surrounding the hydronium ions prior to any proton transfer.

Neutron Scattering Measurements and Computation of the Quantum Dynamics of Hydrogen Molecules Trapped in the Small and Large Cages of Clathrate Hydrates

We report inelastic neutron scattering (INS) measurements on molecular hydrogen trapped in simple (D2O) and binary (D2O plus perdeuterated tetrahydrofuran) clathrate hydrates, performed at a low temperature using two different neutron spectrometers to probe both energy and momentum transfer. The INS spectra of binary clathrate samples exhibit a rich structure containing sharp bands arising from both the rotational transitions and the rattling modes of the guest H2 molecule. They agree well with the rigorous fully quantum simulations, which account for the subtle effects of the anisotropy, angular and radial, of the host cage on the H2 microscopic dynamics and the resulting spectra. The simple clathrate samples present a much greater challenge, due to the multiple H2 occupancy of the large cages, which makes the quantum calculations an extremely difficult task. In addition, we discuss in detail various physical aspects of the experimental and simulated INS spectra, such as their temperature dependence, the effects of the cage geometry, and the different features associated with the ortho-hydrogen and para-hydrogen species.

Shape-, Size-, and Functional Group-Selective Binding of Small Organic Guests in a Paramagnetic Coordination Cage

The host-guest chemistry of the octanuclear cubic coordination cage [Co(8)L(12)](16+) (where L is a bridging ligand containing two chelating pyrazolyl-pyridine units connected to a central naphthalene-1,5-diyl spacer via methylene "hinges") has been investigated in detail by (1)H NMR spectroscopy. The cage encloses a cavity of volume of ca. 400 Å(3), which is accessible through 4 Å diameter portals in the centers of the cube faces. The paramagnetism of the cage eliminates overlap of NMR signals by dispersing them over a range of ca. 200 ppm, making changes of specific signals easy to observe, and also results in large complexation-induced shifts of bound guests. The cage, in CD(3)CN solution, acts as a remarkably size- and shape-selective host for small organic guests such as coumarin (K = 78 M(-1)) and other bicyclic molecules of comparable size and shape such as isoquinoline-N-oxide (K = 2100 M(-1)). Binding arises from two independent recognition elements, which have been separately quantified. These are (i) a polar component arising from interaction of the H-bond accepting O atom of the guest with a convergent group of CH protons inside the cavity that lie close to a fac tris-chelate metal center and are therefore in a region of high electrostatic potential; and (ii) an additional component arising from the second aromatic ring (aromatic/van der Waals interactions with the interior surface of the cage and/or solvophobic interactions). The strength of the first component varies linearly with the H-bond-accepting ability of the guest; the second component is fixed at approximately 10 kJ mol(-1). We have also used (1)H-(1)H exchange spectroscopy (EXSY) experiments to analyze semiquantitatively two distinct dynamic processes, viz. movement of the guest into and out of the cavity and tumbling of the guest inside the host cavity. Depending on the size of the guest and the position of substituents, the rates of these processes can vary substantially, and the rates of processes that afford observable cross-peaks in EXSY spectra (e.g., between free and bound guest in some cases; between different conformers of a specific host·guest complex in others) can be narrowed down to a specific time window. Overall, the paramagnetism of the host cage has allowed an exceptionally detailed analysis of the kinetics and thermodynamics of its host-guest behavior.

Phononic filter effect of rattling phonons in the thermoelectric clathrate Ba8Ge40+xNi6−x

One of the key requirements for good thermoelectric materials is a low lattice thermal conductivity. Here we present a combined neutron scattering and theoretical investigation of the lattice dynamics in the type I clathrate system Ba-Ge-Ni, which fulfills this requirement. We observe a strong hybridization between phonons of the Ba guest atoms and acoustic phonons of the Ge-Ni host structure over a wide region of the Brillouin zone which is in contrast with the frequently adopted picture of isolated Ba atoms in Ge-Ni host cages. It occurs without a strong decrease of the acoustic phonon lifetime which contradicts the usual assumption of strong anharmonic phonon--phonon scattering processes. Within the framework of ab-intio density functional theory calculations we interpret these hybridizations as a series of an ti-crossings which act as a low pass filter, preventing the propagation of acoustic phonons. To highlight the effect of such a phononic low pass filter on the thermal transport, we compute the contribution of acoustic phonons to the thermal conductivity of Ba$_8$Ge$_{40}$Ni$_{6}$ and compare it to those of pure Ge and a Ge$_{46}$ empty-cage model system.

Energy landscape of clathrate hydrates

Clathrate hydrates are nanoporous crystalline materials made of a network of hydrogen-bonded water molecules (forming host cages) that is stabilized by the presence of foreign (generally hydrophobic) guest molecules. The natural existence of large quantities of hydrocarbon hydrates in deep oceans and permafrost is certainly at the origin of numerous applications in the broad areas of energy and environmental sciences and technologies (e.g. gas storage). At a fundamental level, their nanostructuration confers on these materials specific properties (e.g. their “glass-like” thermal conductivity) for which the host-guest interactions play a key role. These interactions occur on broad timescale and thus require the use of multi-technique approach in which neutron scattering brings unvaluable information. This work reviews the dynamical properties of clathrate hydrates, ranging from intramolecular vibrations to Brownian relaxations; it illustrates the contribution of neutron scattering in the understanding of the underlying factors governing chemical-physics properties specific to these nanoporous systems.

ENDOR Evidence of Electron–H2Interaction in a Fulleride Embedding H2

An endofulleropyrrolidine, with H2 as a guest, has been reduced to a paramagnetic endofulleride radical anion. The magnetic interaction between the electron delocalized on the fullerene cage and the guest H2 has been probed by pulsed ENDOR. The experimental hyperfine couplings between the electron and the H2 guest were measured, and their values agree very well with DFT calculations. This agreement provides clear evidence of magnetic communication between the electron density of the fullerene host cage and H2 guest. The ortho-H2/para-H2 interconversion is revealed by temperature-dependent ENDOR measurements at low temperature. The conversion of the paramagnetic ortho-H2 to the diamagnetic para-H2 causes the ENDOR signal to decrease as the temperature is lowered due to the spin catalysis by the paramagnetic fullerene cage of the radical anion fulleride.

Inclusion of Cl− or Br− anions within host framework formed by second-sphere interactions

In this study, we have deliberately utilized the second-sphere coordination approach into the construction of supramolecular inclusion solids Cl ⊂ [H2L1]·[InCl4] (Crystal I) and Br ⊂ [H2L1]·[TeBr6] (Crystal II). The chloride or bromine anions can be encapsulated inside the host assemblies formed by the diamine molecule (4,6-dimethyl-1,3-phenylene) bis(N,N-dibenzylmethane) (L1) and the metal complexes ([InCl4]− and [TeBr6]2−) via second-sphere interactions. The inclusion complexes have been structurally characterized by X-ray crystallography, indicating that weak C–H···Cl and C–H···Br hydrogen bonding synthons play a significant role in the construction of host framework. 2-D networks are formed in both complexes by the interconnection of 1-D networks through the multiple weak hydrogen bonding interactions with [InCl4]− or [TeBr6]2−. The guest Cl− or Br− anions are encapsulated inside the host cages through N–H···Cl hydrogen bonds. The inclusion selectively was studied for the two host assemblies.

Unusual Photoreaction of Triquinacene within Self‐Assembled Hosts

Triquinacene is a concave tricyclic hydrocarbon with diverse photoreactivity. In the cavity of an electron-accepting molecular host, triquinacene was specifically photooxidized at the peripheral allylic position into an alcohol, 1-hydroxytriquinacene, via guest-to-host electron transfer. The unusual reactivity stems from the extremely electron-deficient triazine panel ligand of the host cage, which allows the cage to function as a good electron acceptor. Thus, self-assembled coordination cages can serve not only as molecular-sized reaction vessels but also function electronically as redox media. Dissolved molecular oxygen is indispensable for the photoreaction and immediately traps a photogenerated radical.

Ab initio Derivation of Correlated Superatom Model for Potassium Loaded Zeolite A

We derive an effective low-energy Hamiltonian for potassium loaded zeolite A, a unique ferromagnet from non-magnetic elements. We perform ab initio density functional calculations and construct maximally localized Wannier functions for low-energy states made from potassium s electrons. The resulting Wannier orbitals, spreading widely in the alminosilicate cage, are found to be the superatomic s and p orbitals in the confining potential formed by the host cage. We then make a tight-binding model for these superatomic orbitals and introduce interaction parameters such as the Hubbard U . After mean-field calculations for the effective model, we find that ab initio spin density functional results are well reproduced by choosing appropriate sets of the interaction parameters. The interaction parameters turn out to be as large as the band width, ∼0.5 eV, indicating the importance of electron correlation, and that the present system is an interesting analog of correlated multi-orbital transition metal oxides.