Host-guest Interaction Energy Research Articles

Crown Ether-Magnesium Ion Complexes: A Reliable Theoretical Estimation of Host-Guest Interaction and Binding Energies in a Solvent.

Metal ion detection is of a paramount importance for health monitoring. The host should properly accommodate the desired ion and be selective with respect to other potential guests, which makes devising ion sensors a demanding task. Recently (Phys. Chem. Chem. Phys. 2023, 25, 32656), we suggested a procedure for a computational design of crown ethers that can capture magnesium ions. In the present contribution we apply the same approach to search for Mg2+ trap with thiophene units, in accord with proposed hosts for Na+ and K+ ions (Adv. Funct. Mater., 2016, 26, 514). Additionally, we present a procedure based on the combination of Density Functional Theory based Molecular Dynamics and the Interacting Quantum Fragments methodology for determination of host-guest interaction and binding energies in a model with a large number of explicit solvent molecules. The presented strategy could be applied for identification of the right host for an arbitrary guest.

Improving the therapeutic window of anticancer agents by β-cyclodextrin encapsulation: Experimental and theoretical insights

3-Nitro-2H-chromene derivatives exhibit promising anticancer activities, but their clinical translation is hindered by poor aqueous solubility. Herein, we report a cyclodextrin complexation strategy to improve the solubility and therapeutic efficacy of 8-methoxy-2-(4-methoxy phenyl)-3-nitro-2H-chromene (MNC), a potent anticancer agent. Solid inclusion complexes of MNC: β-cyclodextrin (β-CD) were synthesized by co-precipitation and kneading methods, and comprehensively characterized using UV–vis, Fluorescence, Fourier Transform Infrared (FT-IR), Differential scanning calorimetry (DSC), X-ray diffraction (XRD), Scanning electron microscope (SEM), 1H NMR, and mass spectrometric techniques. A 1:1 host–guest stoichiometry was verified by phase solubility and UV–Vis spectroscopic studies. β-CD complexation remarkably enhanced the aqueous solubility of hydrophobic MNC. Cytotoxicity evaluation against different human cancer cell lines such as breast cancer (MCF-7, MDA-MB-231), lung cancer (A549), and liver cancer (HepG2) demonstrated superior anticancer activity of the co-precipitated MNC: β-CD complex compared to free MNC and the chemotherapeutic 5-fluorouracil. Although the host–guest interaction energy obtained from molecular docking was modest (−5.1 kcal/mol), it facilitated effective MNC encapsulation and delivery by β-CD. Density functional theory (DFT) calculations provided further insights into the inclusion phenomenon. This cyclodextrin complexation approach paves the way for developing an effective MNC formulation with improved bioavailability and anticancer therapeutic efficacy.

Elucidating protein-ligand binding kinetics based on returning probability theory.

The returning probability (RP) theory, a rigorous diffusion-influenced reaction theory, enables us to analyze the binding process systematically in terms of thermodynamics and kinetics using molecular dynamics (MD) simulations. Recently, the theory was extended to atomistically describe binding processes by adopting the host-guest interaction energy as the reaction coordinate. The binding rate constants can be estimated by computing the thermodynamic and kinetic properties of the reactive state existing in the binding processes. Here, we propose a methodology based on the RP theory in conjunction with the energy representation theory of solution, applicable to complex binding phenomena, such as protein-ligand binding. The derived scheme of calculating the equilibrium constant between the reactive and dissociate states, required in the RP theory, can be used for arbitrary types of reactive states. We apply the present method to the bindings of small fragment molecules [4-hydroxy-2-butanone (BUT) and methyl methylthiomethyl sulphoxide (DSS)] to FK506 binding protein (FKBP) in an aqueous solution. Estimated binding rate constants are consistent with those obtained from long-timescale MD simulations. Furthermore, by decomposing the rate constants to the thermodynamic and kinetic contributions, we clarify that the higher thermodynamic stability of the reactive state for DSS causes the faster binding kinetics compared with BUT.

Molecular Recognition of Aromatics in Spherical Nanocages.

In general, due to the lack of efficient specific molecular interactions, achieving host-guest molecular recognition inside large and neutral metal organic cages (MOCs) is challenging. Preferential molecular recognition of aromatics using the internal binding sites of interlocked icosahedral (i.e., spherical) M12L8MOCs within poly-[n]-catenane (1) is reported. The guest absorption has been monitored directly in the solid-state by consecutive single-crystal-to-single-crystal (SCSC) reactions in a gas-solid environment, using single-crystal X-ray diffraction (SC-XRD) experiments. The preferential guest uptake is corroborated by Density Functional Theory (DFT) calculations by determining the host-guest interaction energy (Ehost-guest) with the nitrobenzene (NB) >> p-xylene (p-xy) >> o-dichlorobenzene (o-DCB) trend (i.e., from 44 kcal/mol to 25 kcal/mol), assessing the XRD outcomes. Combining SC-XRD, DFT and solid-state 13C NMR, the exceptional stability of the M12L8 cages, together with the guest exchange/release properties are rationalized by the presence of mechanical bonds (efficient π-π interactions) and by the pyridine's rotor-like behaviour (with 3 kcal/mol rotational energy barrier). The structure-function properties of M12L8 makes 1 a potential candidate in the field of molecular sensors.

Evolution exploration and structure prediction of Keggin-type group IVB metal-oxo clusters

The fascinating chemical structure and broad application prospect of Keggin-type polyoxometalates (POMs) have attracted many chemists to explore and discover continuously. Unlike the traditional Keggin, larger metal atomic radius, higher metal coordinated numbers, lower metal valence states and other features allow the group IVB metal-based Keggin (IVB-Keggin) more space and unknown in terms of structure and performance. Herein, density functional theory (DFT) calculations were performed to explore the influences including cores, shells, caps, and terminal ligands, et al. on IVB-Keggin, and analyze the possibility of novel structure synthesis. From the perspective of multi-layer onion-like clusters, molecular energy level, host-guest interaction energy, surface charge and covalent bond polarity can be further adjusted to achieve the oriented design of functional IVB-Keggin. These insights are expected to provide theoretical support for experimental synthesis, opening a new perspective to understand the growth of Keggin.

Engineering Host–Guest Interactions in Organic Framework Materials for Drug Delivery

AbstractMetal‐organic frameworks (MOF) and covalent organic frameworks (COFs) are promising nanocarriers for targeted drug delivery. Noncovalent interactions between frameworks and drugs play a fundamental role in the therapeutic uptake and release of the latter. However, the scope of framework functionalizations and deliverable drugs remains underexplored. Using a multilevel approach combining molecular docking and density functional theory, we show for a range of drugs and frameworks that experimentally reported release metrics are in good agreement with the in silico computed host–guest interaction energies. Functional groups within the framework significantly impact the strength of these host–guest interactions, while a given framework can serve as an efficient delivery agent for drugs beyond the prototypical few. Our findings identify the interaction energy as a reliable and relatively easy to compute descriptor of organic framework materials for drug delivery, able to facilitate their high‐throughput screening and targeted design towards extended‐release times.

Coarse-grained modeling of zeolitic imidazolate framework-8 using MARTINI force fields.

In this contribution, the well-known MARTINI particle-based coarse graining approach is tested for its ability to model the ZIF-8 metal-organic framework. Its capability to describe structure, lattice parameters, thermal expansion, elastic constants and amorphization is evaluated. Additionally, the less coarsened models were evaluated for reproducing the swing effect and the host-guest interaction energies were analyzed. We find that MARTINI force fields successfully capture the structure of the Metal-Organic Framework (MOF) for different degrees of coarsening, with the exception of the MARTINI 2.0 models for the less coarse mapping. MARTINI 2.0 models predict more accurate values of C11 and C12, while MARTINI 3.0 has a tendency to underestimate them. Among the possibilities tested, the choice of bead flavors within a particular MARTINI version appears to have a less critical impact in the simulated properties of the empty framework. None of the coarse-grained (CG) models investigated were able to capture the amorphization nor the swing effect within the scope of MD simulations. A perspective on the importance of having a proper Lennard-Jones (LJ) parametrization for modeling guest-MOF and MOF-MOF interactions is highlighted.

Torsional Rotation in Ditopic Receptor Host and its Complex Formation with Resorcinol Guest: A Computational Study.

Noncovalent interactions due to the presence of heteroatoms in supramolecular compounds have gained a lot of attention. These different heteroatom-based supramolecular compounds have inspired us to examine the noncovalent interaction in the isolated host and host-guest complexes. In view of this, in the current manuscript, we investigated the stability and torsional energy barrier of different conformers of the ditopic receptor host 1,6-bis(2,6-bis(benzothiazol-2-yl) pyridine-4-yloxy) hexane (bbh). The conformer that is accompanied by intramolecular C-H⋯N and C-H⋯S interactions is relatively more stable than the others. Due to torsional angle rotation within the host, the C-H⋯N and C-H⋯S interactions get disrupted and exhibit different binding sites for capturing guest molecules. In addition, we have extended the investigation to understand the interaction energy and nature of interaction in host-guest (1 : 1 and 1 : 2) complexes formed between the host (bbh) and guest (resorcinol) by using different DFT functionals. Extended transition state-natural orbital chemical valence (ETS-NOCV) analysis of complexes revealed that the electrostatic interaction significantly contributes to the host-guest interaction energy. The noncovalent (NCI) analysis provides the existence of intermolecular hydrogen bonding and other weak interactions within the complexes.

Improved Estimates of Host-Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations.

Endohedral fullerenes have evinced much interest from the fundamental and applications points of view. However, given the nature of the weak interaction between the guest species and the host cage in these confined systems, the interaction energy values obtained using various theoretical methods, and different basis sets vary over a wide range. For example, the reported interaction energy for the HF@C60 system ranges from -2.5 kcal/mol to -14.9 kcal/mol. In the present manuscript, we report reliable interaction energy values for different endohedral fullerenes (He@C60 , Ne@C60 , Ar@C60 , Kr@C60 , H2 @C60 , HF@C60 , H2 O@C60 , NH3 @C60 , CH4 @C60 , Li+ @C60 , Na+ @C60 , and K+ @C60 ) obtained using the domain-based local pair natural orbital coupled-cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) method and the def2-TZVP basis set. We believe that these energy values could be considered as benchmark values, and the performance of other quantum chemical methods could be assessed accordingly. Local energy decomposition analysis within the DLPNO-CCSD(T) framework is used to estimate the electrostatic, exchange, and dispersion components of the interaction energy for some of the endohedral fullerenes.

Hosting AlCl3 on ternary metal oxide composites for catalytic oligomerization of 1-decene: Revealing the role of supports via performance evaluation and DFT calculation

Enhancing catalytic activity and stability of supported Lewis acid catalysts remain a particular challenge owing to the limited understanding and unsatisfactory tuning of the interplay between the active components and the supports. Herein, upon immobilizing AlCl3 on a series of ternary metal oxides including La2O3–Al2O3–SiO2, NiO–Al2O3–SiO2 and Ga2O3–Al2O3–SiO2, we clearly revealed the influence of the compositions and structures of the supports on the catalyst performances through experiments together with density functional theory (DFT) calculations. The catalytic performances of the supported samples were evaluated by oligomerization of 1-decene using both batch reactor and fixed-bed apparatus. The results suggest that the AlCl3 supported by NiO–Al2O3–SiO2 composites exhibits the highest catalytic activity and stability because of its positive pore structure and thereof the high loading of active species. Importantly, DFT calculations indicate that the variations of the host-guest interaction energy between the ternary oxide composites and AlCl3 are in good agreement with the experimental results. This study highlights the compositions and structures of the supports are crucial to the catalytic performances of Lewis acid catalysts, and provides fundamental guidance for design of high-performance supported catalysts.

Strength and Nature of Host-Guest Interactions in Metal-Organic Frameworks from a Quantum-Chemical Perspective.

Metal‐organic frameworks (MOFs) offer a convenient means for capturing, transporting, and releasing small molecules. Their rational design requires an in‐depth understanding of the underlying non‐covalent host‐guest interactions, and the ability to easily and rapidly pre‐screen candidate architectures in silico. In this work, we devised a recipe for computing the strength and analysing the nature of the host‐guest interactions in MOFs. By assessing a range of density functional theory methods across periodic and finite supramolecular cluster scale we find that appropriately constructed clusters readily reproduce the key interactions occurring in periodic models at a fraction of the computational cost. Host‐guest interaction energies can be reliably computed with dispersion‐corrected density functional theory methods; however, decoding their precise nature demands insights from energy decomposition schemes and quantum‐chemical tools for bonding analysis such as the quantum theory of atoms in molecules, the non‐covalent interactions index or the density overlap regions indicator.

Computational investigations of Bio-MOF membranes for uremic toxin separation

Developing new and efficient methods as an alternative to hemodialysis is important due to the challenges associated with poor efficiency of membranes and long dialysis sessions. Recently, metal organic frameworks (MOFs) have attracted interest in the membrane community due to their tunable physical and chemical properties. However, their potential in uremic toxin separations is still unknown and it is not practical to test each synthesized MOF for uremic toxin separations. The main objective of this study is to computationally assess membrane-based uremic toxin separation performances of 60 bio-compatible MOFs (bio-MOFs). Combining grand canonical Monte Carlo (GCMC) and equilibrium molecular dynamics (EMD) simulations, we predicted urea, creatinine, and water permeabilities of bio-MOFs and their membrane selectivities for urea/water and creatinine/water separations. Results showed that OREZES, a carboxylate-based MOF exhibited the highest membrane selectivity (347.94) for urea/water separation whereas BEPPIX, an amino-based MOF gave the highest creatinine/water selectivity (1.5 × 105) at infinite dilution and 310 K. Guest-guest and host–guest interaction energies for uremic toxins were also computed during EMD simulations and van der Waals interactions were found to be much stronger than the coulombic interactions. We finally examined the effect of MOF's flexibility on the predicted membrane performance and membrane selectivities of bio-MOFs for urea/water separation significantly enhanced when the structural flexibility was considered in simulations. Our results will be a guide for further studies to design novel bio-MOF membranes for uremic toxin separations.

Symmetry-Binding Correlations of Crown Ether Complexes with Li+ and Na.

The gas-phase structure of 18-crown-6 in the presence of Li+ and Na+ cations is highly flexible and generally distorted. Using density functional theory calculations, natural bond orbital analysis, and symmetry measures, we reveal the driving forces behind the structural and energy trends of 18-crown-6 and its phenyl substituents. We show that the structural deviation from C3-symmetry increases with the non-bonded interactions between the occupied spx orbitals of the crowns’ oxygen atoms and the unoccupied 2s orbital of the cation. These orbital interactions are strongly correlated with the overall host–guest interaction energy. Our approach highlights the role of non-bonded interactions and paves the way for deeper understanding of structure–reactivity relations of flexible host–guest systems.

Origin of High Selectivity of Dimethyl Ether Carbonylation in the 8-Membered Ring Channel of Mordenite Zeolite

The mechanisms of dimethyl ether (DME) carbonylation in the 8-membered ring (MR) and the 12-MR channels of H-mordenite (H-MOR) zeolite were separately investigated by quantum-chemical methods to unravel the origin of high selectivity of the methyl acetate product in the 8-MR channel. It is shown that not only the formation of surface methoxy species (SMS) but also its following carbonylation reaction are more energetically feasible in the 8-MR channel. Based on the kinetic analysis of the carbonylation reaction in the two channels, the effective rate constants were determined to reveal the reactivity difference. It was found that at 423 K, the effective rate constant in the 8-MR channel was ca. 13 magnitudes higher than that in the 12-MR channel, revealing the unique selectivity for acetyl intermediate formation in the 8-MR channel. The calculated host–guest interaction energies (Eint) provided evidence that the DME carbonylation reaction exclusively occurring in the 8-MR channel can be ascribed to the strong pore confinement. Among the different components of the Eint, the Pauli repulsive interaction (EPauli) is responsible for the SMS formation route, while the electrostatic (Ees) and orbital terms (Eoi) dictate the high selectivity of the carbonylation step in the 8-MR channel. These results suggested that the experimental observation of acetyl intermediate species solely in the 8-MR channel could be mainly ascribed to the difference of the Pauli repulsion, electrostatic interaction, and orbital interaction in the two channels. The theoretical results provide new insights into the DME carbonylation reaction mechanism over H-MOR zeolite.

Role of Guest Molecules in the Mechanical Properties of Clathrate Hydrates

Clathrate hydrates (CHs) are promising molecular structures for versatile applications such as gas capture and storage, cold storage, and gas separation. Understanding the mechanical responses is of importance for utilizing and predicting the stability of their formations, but remains very limited. Here, mechanical characteristics of CHs entrapping a variety of gas molecules are investigated by molecular dynamics (MD) simulations. All studied CHs are structurally stable host–host hydrogen (H)-bonds yet show distinct host–guest interaction energies under load-free conditions. Tension MD simulations reveal that the tensile strength and Young’s modulus of CHs depend not only on the size and shape of guest molecules but also on their polarity; however, all CHs undergo brittle fracture on either the (0 0 1) or (1 0 1) plane also relying on the type of guest molecules. Interestingly, elastic deformation of CHs causes a reduction in the number of H-bonds, yet stronger interaction of specific triatomic guest mole...

Hydrogen-tetrahydrofuran mixed hydrates: A computational study

The present work examines the host-guest interactions in H2-THF mixed hydrates in a fused dodeca-hexakaidecahedral cage at the molecular level. The host-guest interaction energies are analyzed to get insight on the occupancies of H2 and THF in different host cages. The maximum and optimum storage capacity of H2 in dodecahedral and hexakaidecahedral cages is determined. The studies show that THF in a hexakaidecahedral cage interacts with water molecules of the neighboring dodecahedral cage whereas H2 due to its smaller size does not interact with water molecules of a neighboring cage. The interaction energy and free energy associated with the encapsulation of guest species revealed that simultaneous encapsulation of H2 and THF in the large cavities of sII hydrates is feasible. Energy decomposition analysis indicates that electrostatic and dispersion interactions contribute significantly to the stability of the complexes. The occupancy of H2 in small and large cages of mixed hydrates are analyzed in terms of 1H and 13C chemical shifts.

Unveiling the relative stability and proton binding of non-classical Wells-Dawson isomers of [(NaF6)W18O54(OH)2]7- and [(SbO6)W18O54(OH)2]9-: a DFT study.

Density functional theory calculations combined with the energy and building-block decomposition analyses have been carried out to investigate the structures, stability orders, redox potentials and proton binding of the six Baker-Figgis isomers (α, β, γ, α*, β* and γ*) of [(SbO6)W18O54(OH)2]9- {H2SbW18} and [(NaF6)W18O54(OH)2]7- {H2NaW18} anions at the level of PBEsol-D3/TZP. Both bonding energy and Gibbs free energy analyses exhibit that the two non-classical Wells-Dawson (WD) species behave quite differently from each other. The pyroanimonate {H2SbW18}, with a stability order of γ* > β* > α > α* > β > γ, is a non-classical WD species, while the hexafluoride {H2NaW18} (α > β > γ > γ* > β* > α*) is a transition intermediate between classical and non-classical WD types, possessing both non-classical ([XW18O60(OH)2]n-, X = I, Te and W) and classical [Si2W18O62]8- properties. Energy decomposition analyses (EDA) reveal that spatial arrangement (Ehost), host-guest fragment interaction energy (FIE), and structural distortion energy (DE) are three key factors governing the relative stability of isomers; among these, DE is always dominant, while FIE and Ehost are subordinated but are still important. Building-block decomposition analyses (BDA) disclose that the octahedral {MO6} units of the equatorial belt, particularly the staggered belt, are always more distorted than those of the two polar caps inside each structure. The theoretical redox potentials demonstrate that the oxidizing power increases with a trend of α < β < γ and α* < β* < γ* for both species, and the first redox potential is closely related to the energy level of the LUMO of each anion. Evaluation of the proton inclusion energies suggests that {H2NaW18} can only embed two protons, while {H2SbW18} may encapsulate four; the number of embedded protons is controlled by both the charge of the heteroatom X and the volume of the tetrahedral {O4}/{OF3} cavity.

Quantifying Host–Guest Interaction Energies in Clathrates of Dianin’s Compound

The subtle intermolecular host–guest interaction energies have been quantified for 17 different clathrates of the Dianin’s compound. Energy framework analysis of the host structure reveals that, in addition to strong electrostatic forces due to H-bonding, the framework is stabilized by very strong dispersion interactions, resulting in a three-dimensional energy framework. Compared to the host framework, the host–guest interactions are rather weak, and the enclathration only perturbs the host energy framework. Larger guest molecules result in more attractive host–guest interactions, although the shape of the guest molecule is also found to be important. Easy rotation about the c-axis was found for the hexane guest molecule, while the rotation is hindered in the cases of CCl4, CCl3CN, and C(CH3)3CN. For the Dianin clathrates containing the C(CH3)3CN or the acetone guest species, attractive interaction energies between guest molecules in adjacent cavities suggest short-range ordering of the guest molecules. ...

Shedding Light on the Nature of Host–Guest Interactions in PAHs-ExBox4+ Complexes

Host–guest (HG) systems formed by polycyclic aromatic hydrocarbons and ExBox4+ are suitable models to gain a deeper understanding of π–π interactions, which are fundamental in supramolecular chemistry. The physical nature of HG interactions between ExBox4+ (1) and polycyclic aromatic hydrocarbons (PAHs) (2-12) is investigated at the light of the energy decomposition (EDA-NOCV), noncovalent interactions (NCI), and magnetic response analyses. The EDA-NOCV results show that the dispersion forces play a crucial role in the HG interactions in PAHs⊂ExBox4+ complexes. The HG interaction energies are dependent on both the size of the PAH employed and the number of π-electrons in the guest molecules. The parallel face-to-face arrangement between HG aromatic moieties is also fundamental to maximize the dispersion interaction and consequently for the attractive energy which leads to the inclusion complex formation.

In silico design of calixarene-based arsenic acid removal agents

Contamination of water resources with arsenic is a worldwide challenge with an important social impact. Development of adsorptive materials with high affinity and selectivity towards arsenic is an important and ongoing challenge. The aim of this work is to study calix[n]arenes with 4, 5, 6 and 8 rings, as well as COOH, C2H4OH, SO3H, t-Bu, PO3H2 and PO4H2, upper-rim functional groups through computational chemistry models as tailor-made sequestering agents using pentavalent arsenate species (H3AsO4, H2AsO4− and HAsO42−). Host–guest interaction energies (Eint) were determined using Density functional theory (DFT) calculations at the M06-2X/6-31G(d,p) level of theory carried out on host–guest adducts in order to find the most suitable candidates as extracting agents for these arsenate species. Hydrogen-bond donor groups such as SO3H, PO3H2 and the hypothetical calixarene with R = PO4H2 on the upper rim of calix[n]arenes are shown to be the most suitable functional groups for encapsulating these As(V) species under study.