Cucurbit[6]uril: A Possible Host for Noble Gas Atoms

Noble gas dative bonding with coinage metal carbene complexes: A theoretical study

The structure and stability of noble gas (Ng) bound [NHCM]+ complexes (M = Cu, Ag, and Au) were investigated using Quantum chemical calculations. Dissociation energies, enthalpy, and free energy changes were computed to comprehend the stability of these Ng-bonded complexes. The nature of interactions associated to the bonding between metal and noble gas atoms was studied through the computation of electron density-based descriptors. Detailed electronic structure study revealed electron donation from the noble gas atoms towards the metal center, resulting in the formation of dative bonds.

Hitting the Bull's Eye: Stable HeBeOH+ Complex

It is now known that the heavier noble gases (Ng=Ar-Rn) show some varying degrees of reactivity with a gradual increase in reactivity along Ar-Rn. However, because of their very small size and very high ionization potential, helium and neon are the hardest targets to crack. Although few neon complexes are isolated at very low temperatures, helium needs very extreme situations like very high pressure. Here, we find that protonated BeO, BeOH⁺ can bind helium and neon spontaneously at room temperature. Therefore, extreme conditions like very low temperature and/or high pressure will not be required for their experimental isolation. The Ng-Be bond strength is very high for their heavier homologs and the bond strength shows a gradual increase from He to Rn. Moreover, the Ng-Be attractive energy is almost exclusively originated from the orbital interaction which is composed of one Ng(s/p_σ )→BeOH⁺ σ-donation and two weaker Ng(p_π )→BeOH⁺ π-donations, except for helium. Helium uses its low-lying vacant 2p orbitals to accept π-electron density from BeOH⁺ . Previously, such electron-accepting ability of helium was used to explain a somewhat stronger helium bond than neon for neutral complexes. However, the present results indicate that such π-back donations are too weak in nature to decide any energetic trend between helium and neon.

Broad-Spectrum Extracellular Antiviral Properties of Cucurbit[n]urils

Viruses are microscopic pathogens capable of causing disease and are responsible for a range of human mortalities and morbidities worldwide. They can be rendered harmless or destroyed with a range of antiviral chemical compounds. Cucurbit[n]urils (CB[n]s) are a family of macrocycle chemical compounds existing as a range of homologues; due to their structure, they can bind to biological materials, acting as supramolecular "hosts" to "guests", such as amino acids. Due to the increasing need for a nontoxic antiviral compound, we investigated whether cucurbit[n]urils could act in an antiviral manner. We have found that certain cucurbit[n]uril homologues do indeed have an antiviral effect against a range of viruses, including herpes simplex virus 2 (HSV-2), respiratory syncytial virus (RSV) and SARS-CoV-2. In particular, we demonstrate that CB[7] is the active homologue of CB[n], having an antiviral effect against enveloped and nonenveloped species. High levels of efficacy were observed with 5 min contact times across different viruses. We also demonstrate that CB[7] acts with an extracellular virucidal mode of action via host-guest supramolecular interactions between viral surface proteins and the CB[n] cavity, rather than via cell internalization or a virustatic mechanism. This finding demonstrates that CB[7] acts as a supramolecular virucidal antiviral (a mechanism distinct from other current extracellular antivirals), demonstrating the potential of supramolecular interactions for future antiviral disinfectants.

In silico capture of noble gas atoms with a light atom molecule

Noble gas atoms (Ng = He, Ne, Ar, and Kr) can be captured in silico with a light atom molecule containing only C, H, Si, O, and B atoms. Extensive density functional theory (DFT) calculations on series of peri-substituted scaffolds indicate that confined spaces (voids) capable to energy efficiently encapsulate and bind Ng atoms are accessible by design of a tripodal peri-substituted ligand, namely, [(5-Ph₂B-xan-4-)₃Si]H (xan = xanthene) comprising (after hydride abstraction) four Lewis acidic sites within the cationic structure [(5-Ph₂B-xan-4-)₃Si]⁺. The host (ligand system) thereby provides an adoptive environment for the guest (Ng atom) to accommodate for its particular size. Whereas considerable chemical interactions are detectable between the ligand system and the heavier Ng atoms Kr and Ar in the host guest complex [(5-Ph₂B-xan-4-)₃Si·Ng]⁺, the lighter Ng atoms Ne and He are rather tolerated by the ligand system instead of being chemically bound to it, nicely highlighting the gradual onset of (weak) chemical bonding along the series He to Kr. A variety of real-space bonding indicators (RSBIs) derived from the calculated electron and pair densities provides valuable insight to the situation of an "isolated atom in a molecule" in case of He, uncovering its size and shape, whereas minute charge rearrangements caused by polarization of the outer electron shell of the larger Ng atoms results in formation of polarized interactions for Ar and Kr with non-negligible covalent bond contributions for Kr. The present study shows that noble gas atoms can be trapped by small light-atom molecules without the forceful conditions necessary using cage structures such as fullerenes, boranes and related compounds or by using super-electrophilic sites like [B₁₂(CN)₁₁]^- if the chelating effect of several Lewis acidic sites within one molecule is employed.

Solubility of Hydrophobes into Macrocyclic Hosts

The intrinsic nature of macrocyclic molecules to preferentially absorb a specific solute has been opening up supramolecular chemistry. Nevertheless, the determinant factor with molecular perspectives in promoting host-guest complexations remains inconclusive, due to the lack of rigorous thermodynamic examination on the guest solubility inside the host. Here, we quantify the solute-solvent energetic and entropic contributions between the end states and on the docking route during inclusion of noble gases in cucurbit[5]uril, cucurbit[6]uril, and α-cyclodextrin, using molecular dynamics simulations in combination with the potential distribution theorem. Results show that in all of the pairs examined both the solute-solvent energy and entropy favor the inclusion, while the former is rather dominant. The frequency of interior drying, which pertains to the entropic contribution, differs between the hosts and is controlled by the existence of lid water at portal and the flexibility of host framework. Moreover, the hosts exhibit various types of absorption manners, involving non-, single-, and double-free-energy barriers.

Atomic Clusters: Structure, Reactivity, Bonding, and Dynamics

Atomic clusters lie somewhere in between isolated atoms and extended solids with distinctly different reactivity patterns. They are known to be useful as catalysts facilitating several reactions of industrial importance. Various machine learning based techniques have been adopted in generating their global minimum energy structures. Bond-stretch isomerism, aromatic stabilization, Rener-Teller effect, improved superhalogen/superalkali properties, and electride characteristics are some of the hallmarks of these clusters. Different all-metal and nonmetal clusters exhibit a variety of aromatic characteristics. Some of these clusters are dynamically stable as exemplified through their fluxional behavior. Several of these cluster cavitands are found to be agents for effective confinement. The confined media cause drastic changes in bonding, reactivity, and other properties, for example, bonding between two noble gas atoms, and remarkable acceleration in the rate of a chemical reaction under confinement. They have potential to be good hydrogen storage materials and also to activate small molecules for various purposes. Many atomic clusters show exceptional opto-electronic, magnetic, and nonlinear optical properties. In this Review article, we intend to highlight all these aspects.

Possible effects of fluxionality of a cavitand on its catalytic activity through confinement

The discovery of fullerenes was a huge milestone in the scientific community, and with it came the urge to discover and analyze various small and large atomic and molecular clusters having a cavity. These cavitands of varied shapes and sizes have wide applications in the encapsulation of rare gas atoms to induce bond formation between them, storage of hydrogen and hydrocarbons to be used as alternative sources of fuel, catalyzation of otherwise slow reactions without using a catalyst, activation of small gas molecules, etc. Various cavitands like fullerenes, [ExBox]4+, cucurbit[n]urils, borospherenes, octa acid, etc. have been used for this purpose. Some clusters including cavitands exhibit fluxional behaviour. Systems in a confined environment often manifest interesting variations in their properties and behaviour, compared to their unconfined counterparts, facilitating the aforementioned applications. In this perspective article, we explore the possibility of making use of this extra degree of freedom, viz., the fluxionality, in changing the catalytic activity of the cavitand.

Comparison Between Electride Characteristics of Li3@B40 and Li3@C60

Density functional theory (DFT) based computation is performed on the endohedrally encapsulated Li3 cluster inside the B40 and C60 cages namely, Li3@B40 and Li3@C60. For both these systems, the Li-Li bond lengths are shorter than that in the free Li3 cluster. Due to confinement, the Li-Li vibrational frequencies increase in both the systems as compared to that in the free Li3 cluster. Thermodynamically, the formation of these two systems is spontaneous in nature as predicted by the negative values of Gibbs' free energy changes (ΔG). For both the systems one non-nuclear attractor (NNA) is present on the middle of the Li3 cluster which is predicted and confirmed by the electron density analysis. The NNA population and the percentage localization of electron density at the NNA of the Li3@C60 system are higher than that in the Li3@B40 system. At the NNA the values of the Laplacian of electron density are negative and an electron localization function basin is present at the center of the Li3 cluster for localized electrons. Both systems show large values of nonlinear optical properties (NLO). Both the Li3 encapsulated endohedral systems behave as electrides. Electrides have low work function and hence have a great potential in catalytic activity toward the activation of small molecules (such as CO2, N2). Even some electrides have greater catalytic activity than some well-studied metal-loaded catalysts. As the systems under study behave as electrides, they have the power to show catalytic activity and can be used in catalyzing the activation of small molecules.

Noble Gas Binding Ability of an Au(I) Cation Stabilized by a Frustrated Lewis Pair: A DFT Study

The noble gas (Ng) binding ability of a monocationic [(FLP)Au]⁺ species has been investigated by a computational study. Here, the monocationic [(FLP)Au]⁺ species is formed by coordination of Au(I) cation with the phosphorous (Lewis base) and the boron (Lewis acid) centers of a frustrated Lewis pair (FLP). The bonds involving Au and P, and Au and B atoms in [(FLP)Au]⁺ are partially covalent in nature as revealed by Wiberg bond index (WBI) values, electron density analysis and energy decomposition analysis (EDA). The zero point energy corrected bond dissociation energy (D₀), enthalpy and free energy changes are computed for the dissociation of Au-Ng bonds to assess the Ng binding ability of [(FLP)Au]⁺ species. The D₀ ranges from 6.0 to 13.3 kcal/mol, which increases from Ar to Rn. Moreover, the dissociation of Au-Ng bonds is endothermic as well as endergonic for Ng = Kr-Rn, whereas the same for Ng = Ar is endothermic but exergonic at room temperature. The partial covalent character of the bonds between Au and Ng atoms is demonstrated by their WBI values and electron density analysis. The Ng atoms get slight positive charges of 0.11–0.23 |e|, which indicates some amount of charge transfer takes place from it. EDA demonstrates that electrostatic and orbital interactions have equal contributions to stabilize the Ng-Au bonds in the [(FLP)AuNg]⁺ complex.

Effect of substitution on the bonding in He dimer confined within dodecahedrane: A computational study

The effect of substitution in the dodecahedrane (C₂₀ H₂₀ ) cage on bonding in the confined He dimer is analyzed. The HeHe distances inside the halogenated dodecahedrane C₂₀ X₂₀ (X = FBr) cages are found to be less than half of that in the free He dimer. Comparing the equilibrium structure of He₂ @C₂₀ H₂₀ with He₂ @C₂₀ X₂₀ at ωB97XD/def2-TZVPP level, it is found that the He-He distances are relatively larger in the latter cases indicating the influence of halogen groups on the interaction between the cage and the trapped He pair. The viability of the He₂ @C₂₀ X₂₀ complexes is reflected in the presence of a very high activation energy barrier against the thermochemically feasible dissociation process producing free He₂ and C₂₀ X₂₀ . Quantum theory of atoms in molecules (QTAIM) approach reveals a partial covalent interaction between He pair.

Confinement Effects of a Noble Gas Dimer Inside a Fullerene Cage: Can It Be Used as an Acceptor in a DSSC?

A detailed density functional theory investigation of He₂-encapsulated fullerene C₃₆ and C₄₀ has been presented here. When confinement takes place, He-He bond length shortens and a non-covalent type of interaction exists between two He atoms. Energy decomposition analysis shows that though an attractive interaction exists in free He₂, when it is confined inside the fullerenes, repulsive interaction is observed due to the presence of dominant repulsive energy term. Fullerene C₄₀, with greater size, makes the incorporation of He₂ much easier than C₃₆ as confirmed from the study of boundary crossing barrier. In addition, we have studied the possibility of using He₂-incorporated fullerene as acceptor material in dye-sensitized solar cell (DSSC). Based on the highest energy gap, He₂@C₄₀ and bare C₄₀ fullerenes are chosen for this purpose. Dye constructed with He₂@C₄₀ as an acceptor has the highest light-harvesting efficiency and correspondingly will possess the maximum short circuit current as compared to pure C₄₀ acceptor.

Toward crystalline porosity estimators for porous molecules

Our data-mining of crystalline molecular materials reveals the correlations between the molecular and crystalline porosity.

Intriguing structural, bonding and reactivity features in some beryllium containing complexes

We highlighted our contributions to Be chemistry which include bond-stretch isomerism in Be₃²⁻ species, Be complexes bound with noble gas, CO, and N₂, Be based nanorotors, and intriguing bonding situations in some Be complexes.

How Far Can One Push the Noble Gases Towards Bonding?: A Personal Account

Noble gases (Ngs) are the least reactive elements in the periodic table towards chemical bond formation when compared with other elements because of their completely filled valence electronic configuration. Very often, extreme conditions like low temperatures, high pressures and very reactive reagents are required for them to form meaningful chemical bonds with other elements. In this personal account, we summarize our works to date on Ng complexes where we attempted to theoretically predict viable Ng complexes having strong bonding to synthesize them under close to ambient conditions. Our works cover three different types of Ng complexes, viz., non-insertion of NgXY type, insertion of XNgY type and Ng encapsulated cage complexes where X and Y can represent any atom or group of atoms. While the first category of Ng complexes can be thermochemically stable at a certain temperature depending on the strength of the Ng-X bond, the latter two categories are kinetically stable, and therefore, their viability and the corresponding conditions depend on the size of the activation barrier associated with the release of Ng atom(s). Our major focus was devoted to understand the bonding situation in these complexes by employing the available state-of-the-art theoretic tools like natural bond orbital, electron density, and energy decomposition analyses in combination with the natural orbital for chemical valence theory. Intriguingly, these three types of complexes represent three different types of bonding scenarios. In NgXY, the strength of the donor-acceptor Ng→XY interaction depends on the polarizing power of binding the X center to draw the rather rigid electron density of Ng towards itself, and sometimes involvement of such orbitals becomes large enough, particularly for heavier Ng elements, to consider them as covalent bonds. On the other hand, in most of the XNgY cases, Ng forms an electron-shared covalent bond with X while interacting electrostatically with Y representing itself as [XNg]+Y-. Nevertheless, in some of the rare cases like NCNgNSi, both the C-Ng and Ng-N bonds can be represented as electron-shared covalent bonds. On the other hand, a cage host is an excellent moiety to examine the limits that can be pushed to attain bonding between two Ng atoms (even for He) at high pressure. The confinement effect by a small cage-like B12N12 can even induce some covalent interaction within two He atoms in the He2@B12N12 complex.

Noble-Noble Strong Union: Gold at Its Best to Make a Bond with a Noble Gas Atom

This Review presents the current status of the noble gas (Ng)‐noble metal chemistry, which began in 1977 with the detection of AuNe⁺ through mass spectroscopy and then grew from 2000 onwards; currently, the field is in a somewhat matured state. On one side, modern quantum chemistry is very effective in providing important insights into the structure, stability, and barrier for the decomposition of Ng compounds and, as a result, a plethora of viable Ng compounds have been predicted. On the other hand. experimental achievement also goes beyond microscopic detection and characterization through spectroscopic techniques and crystal structures at ambient temperature; for example, (AuXe₄)²⁺(Sb₂F₁₁⁻)₂ have also been obtained. The bonding between two noble elements of the periodic table can even reach the covalent limit. The relativistic effect makes gold a very special candidate to form a strong bond with Ng in comparison to copper and silver. Insertion compounds, which are metastable in nature, depending on their kinetic stability, display an even more fascinating bonding situation. The degree of covalency in Ng–M (M=noble metal) bonds of insertion compounds is far larger than that in non‐insertion compounds. In fact, in MNgCN (M=Cu, Ag, Au) molecules, the M−Ng and Ng−C bonds might be represented as classical 2c–2e σ bonds. Therefore, noble metals, particularly gold, provide the opportunity for experimental chemists to obtain sufficiently stable complexes with Ng at room temperature in order to characterize them by using experimental techniques and, with the intriguing bonding situation, to explore them with various computational tools from a theoretical perspective. This field is relatively young and, in the coming years, a lot of advancement is expected experimentally as well as theoretically.

A Noncovalent Binding Strategy to Capture Noble Gases, Hydrogen and Nitrogen

A molecular design strategy to develop receptor systems for the entrapment of noble gases, H₂ and N₂ is described using M06L-D3/6-311++G(d,p)//M06L/6-311++G(d,p) DFT method. These receptors made with two-, three-, four- and five-fluorinated benzene cores, linked with methelene units viz. R_I , R_II , R_III and R_IV as well as the corresponding non-fluorinated hydrocarbons viz. R_IH , R_IIH , R_IIIH and R_IVH show a steady and significant increase in binding energy (E_int ) with increase in the number of aromatic rings in the receptor. A stabilizing "cage effect" is observed in the cyclophane type receptors R_IV and R_IVH which is 26-48% of total E_int for all except the larger sized Kr, Xe and N₂ complexes. E_int of R_IV …He, R_IV …Ne, R_IV …Ar, R_IV …Kr, R_IV …H₂ and R_IV …N₂ is 4.89, 7.03, 6.49, 6.19, 8.57 and 8.17 kcal/mol, respectively which is 5- to9-fold higher than that of hexafluorobenzene. Similarly, compared to benzene, multiple fold increase in E_int is observed for R_IVH receptors with noble gases, H₂ and N₂ . Fluorination of the aromatic core has no significant impact on E_int (∼ ±0.5 kcal/mol) for most of the systems with a notable exception of the cage receptor R_IV for N₂ where fluorination improves E_int by 1.61 kcal/mol. The E_int of the cage receptors may be projected as one of the highest interaction energy ranges reported for noble gases, H₂ and N₂ for a neutral carbon framework. Synthesis of such systems is promising in the study of molecules in confined environment. © 2018 Wiley Periodicals, Inc.

Noble gas encapsulated B40 cage

The efficacy of B₄₀ borospherene to act as a host for noble gas atoms is explored via density functional theory based computations. Although the Ng@B₄₀ complexes are thermochemically unstable with respect to dissociation into free Ng and B₄₀, it does not rule out their viability as all the systems possess a high activation free energy barrier (84.7-206.3 kcal mol^-1). Therefore, once they are formed, it is hard to take out the Ng atom. Two Ng atoms can also be incorporated within B₄₀ for the lighter Ng atoms (He and Ne). In fact, the destabilization offered by the encapsulation of one and two He atoms and one Ne atom inside B₄₀ is significantly less than that in experimentally synthesized He@C₂₀H₂₀, highlighting their greater possibility for synthesis. Although Ar₂ and Kr₂ encapsulated B₄₀ systems are very much destabilized by the repulsive interaction between Ng₂ and B₄₀, an inspection of the bonding situation reveals that the confinement can even induce some degree of covalent interaction between two otherwise non-bonded Ng atoms. Ng atoms transfer electrons towards B₄₀ which is smaller for lighter Ng atoms and gradually increases along He to Rn. Even if the electrostatic interaction between Ng and B₄₀ is the most predominant term in these systems, the extent of the orbital interaction is also considerable. However, the very large Pauli repulsion counterbalances the attractive interaction, eventually turning the interaction repulsive in nature. Ng@B₄₀ also shows dynamical behaviour involving continuous exchange between hexagonal and heptagonal holes, similar to the host cage, as understood from the very little variation in the activation barrier because of the Ng encapsulation. Furthermore, sandwich complexes like [(η⁵-C₅Me₅)Fe(η⁶-B₄₀)]⁺ and [(η⁵-C₅Me₅)Fe(η⁷-B₄₀)]⁺ are noted to be viable with the latter being slightly more stable than the former. The encapsulation of Xe slightly improves the dissociation energy associated with the decomposition into Xe@B₄₀ and [Fe(η⁵-C₅Me₅)]⁺ compared to that in the bare one.

Tetracyclo(9-methyl-2,7-carbazole) as a promising nanohoop for gas trapping: a multiscale study

H₂S, CS₂, NO₂, Br₂, HF, and C₂H₆ are the ideal adsorbates within the TCC host from their respective congeners.

The role of non-covalent interaction for the adsorption of CO2 and hydrocarbons with per-hydroxylated pillar[6]arene: a computational study

A systematic study has been performed with DFT calculations for the physisorption of CO₂, CH₄, and n-butane gases by pillar[6]arene (PA[6]) in gas phase.

Endohedral gas adsorption by cucurbit[7]uril: a theoretical study

Cucurbit[7]uril adsorbs SO₂ selectively over other gas molecules such as C₂H₂, C₂H₄, C₂H₆, CH₄, F₂, Cl₂, NO₂, NO, CO₂, CO, H₂S, N₂, and H₂, because of the combined effects of electrostatic and dispersion interactions.

Surface modification induced enhanced CO2 sorption in cucurbit[6]uril, an organic porous material

Theoretical and experimental studies on CO₂ sorption of the organic macrocycle cucurbit[6]uril (CB[6]).

Noble gas bound beryllium chromate and beryllium hydrogen phosphate: a comparison with noble gas bound beryllium oxide

Two new beryllium based compounds, beryllium hydrogen phosphate and beryllium chromate are found to have remarkable noble gas binding ability, particularly for Ar–Rn atoms.

Comparative Study on the Noble-Gas Binding Ability of BeX Clusters (X = SO4, CO3, O)

Ab initio computations are carried out to assess the noble gas (Ng) binding capability of BeSO4 cluster. We have further compared the stability of NgBeSO4 with that of the recently detected NgBeCO3 cluster. The Ng-Be bond in NgBeCO3 is somewhat weaker than that in NgBeO cluster. In NgBeSO4, the Ng-Be bond is found to be stronger compared with not only the Ng-Be bond in NgBeCO3 but also that in NgBeO, except the He case. The Ar-Rn-bound BeSO4 analogues are viable even at room temperature. The Wiberg bond indices of Be-Ng bonds and the degree of electron transfer from Ng to Be are somewhat larger in NgBeSO4 than those in NgBeCO3 and NgBeO. Electron density and energy decomposition analyses are performed in search of the nature of interaction in the Be-Ng bond in NgBeSO4. The orbital energy term (ΔE(orb)) contributes the maximum (ca. 80-90%) to the total attraction energy. The Ar/Kr/Xe/Rn-Be bonds in NgBeSO4 could be of partial covalent type with a gradual increase in covalency along Ar to Rn.

On the stability of noble gas bound 1-tris(pyrazolyl)borate beryllium and magnesium complexes

1-Tris(pyrazolyl)borate beryllium and magnesium cationic complexes are found to bind Ar–Rn atoms quite effectively.

In silico studies on the origin of selective uptake of carbon dioxide with cucurbit[7]uril amorphous material

The efficient capture and storage of flue gases is of current interest due to environmental problems. The DFT calculation demonstrates the origin of the physisorption of flue gases (CO₂, N₂and CH₄) on amorphous solid cucurbit[7]uril.