Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

Accurately predicting receptor–ligand binding free energies is one of the holy grails of computational chemistry with many applications in chemistry and biology. Many successes have been reported, but issues relating to sampling and force field accuracy remain significant issues affecting our ability to reliably calculate binding free energies. In order to explore these issues in more detail we have examined a series of small host–guest complexes from the SAMPL6 blind challenge, namely octa-acids (OAs)–guest complexes and Curcurbit[8]uril (CB8)–guest complexes. Specifically, potential of mean force studies using umbrella sampling combined with the weighted histogram method were carried out on both systems with both known and unknown binding affinities. We find that using standard force fields and straightforward simulation protocols we are able to obtain satisfactory results, but that simply scaling our results allows us to significantly improve our predictive ability for the unknown test sets: the overall RMSD of the binding free energy versus experiment is reduced from 5.59 to 2.36 kcal/mol; for the CB8 test system, the RMSD goes from 8.04 to 3.51 kcal/mol, while for the OAs test system, the RSMD goes from 2.89 to 0.95 kcal/mol. The scaling approach was inspired by studies on structurally related known benchmark sets: by simply scaling, the RMSD was reduced from 6.23 to 1.19 kcal/mol and from 2.96 to 0.62 kcal/mol for the CB8 benchmark system and the OA benchmark system, respectively. We find this scaling procedure to correct absolute binding affinities to be highly effective especially when working across a “congeneric” series with similar charge states. It is less successful when applied to mixed ligands with varied charges and chemical characteristics, but improvement is still realized in the present case. This approach suggests that there are large systematic errors in absolute binding free energy calculations that can be straightforwardly accounted for using a scaling procedure. Random errors are still an issue, but near chemical accuracy can be obtained using the present strategy in select cases.     

Synthesis and host–guest complexation,photophysical and electrochemical studies on novel thiophenophanes

Synthesis of thiophene-based cyclophanes called thiophenophanes is described. The photophysical and electrochemical properties of thiophenophanes synthesised reveal that they show permanent fluorescence-sensing property, and the cyclic voltammogram reflects the ease with which the electron on the sulphur atom can be removed. Complexation studies of the thiophenophanes with TCNQ reveal the formation of 1:1 complex.     

Electrochemistry and electrochemiluminescence for the host–guest system laponite–tris(2,2′-bipyridyl)ruthenium(II)

The cationic luminescence probe, tris(2,2′-bipyridyl)ruthenium(II) complex ([Ru(bpy)₃]²⁺), was incorporated into laponite-modified glassy carbon electrode (GCE) via two strategies, namely, the adsorption and intercalation methods. These two incorporation methods resulted in different microenvironment for the immobilized [Ru(bpy)₃]²⁺ within laponite as well as the different host–guest and guest–guest interactions. Herein, cyclic voltammetry and electrochemiluminescence (ECL) were innovatively performed to monitor the interactions. Tripropylamine (TPA) was used as coreactant in the electrochemical and ECL system.     

Infrared Spectroscopic and Gravimetric Studies on the Dicyclopentylaminemetal(II) Tetracyanonickellate(II) Host–Aromatic Guest Systems

The host complexes M(Cyclopentylamine)₂Ni(CN)₄ (M=Co or Cd) havebeen prepared in powder form. The spectral data suggest that the structures of thesecompounds are similar to those of the Hofmann-dma-type hosts. The absorptionand the liberation processes of the aromatic guests (benzene, toluene, 1,2-, 1,3-,1,4-dichlorobenzene, 1,4-dibromobenzene o-, m-, p-xylene, naphthalene)in these hosts have been examined at room temperature by gravimetric and spectroscopicmeasurements. The desorption of the benzene guest against time has been measured. Thehost structures do not change on inclusion and liberation of the guests. The host compoundshave been suggested as sorbents for isomeric separations.     

Self-assembled (pseudo)rotaxane and polyrotaxane through host–guest chemistry based on the cucurbituril family

Cucurbit[n]uril and its derivatives, a new family of macrocyclic hosts comprising n glycoluril units, have gained much attention for their exceptional application in many fields. In this review, we introduced the cucurbituril family and the development of its derivatives, which can be used in the molecular recognition and self-assembled materials such as pseudorotaxane, polyrotaxane. Moreover, cucurbituril provides the possibility to design stimulus–response devices and imitate the life secret at molecule level, such as the molecular devices controlled by pH, photochemistry, thermal and so on.     

Host–guest interactions between dapsone and β-cyclodextrin (Part II): thermal analysis, spectroscopic characterization, and solubility studies

The complex of dapsone with β-cyclodextrin was prepared by the co-precipitation/freeze–drying method. The physical–chemical characteristics of the complex were investigated by different methods and compared with those of the physical mixture and of the isolated compounds. The methods used were infrared spectroscopy, X-ray diffractometry and differential scanning calorimetry. The stability constant was calculated from phase solubility diagram (Higuchi–Connors) and fluorescence spectroscopy. The stoichiometry of the complex was confirmed by Job’s plot. Fluorescence measurements at different temperatures provided the thermodynamic parameters of the complexation. The infrared spectrum showed the disappearance of the SO₂ asymmetric stretching band of the drug at 1275?cm^?1 after complexation. The amorphization of the samples, as revealed by the X-ray diffraction patterns, was an indirect proof of the inclusion complex. The thermal analysis showed that the curves of the physical mixture are combination of the curves of both constituents (dapsone and β-cyclodextrin) while the absence of the melting peak of the drug in the DSC curve of the complex suggests the inclusion of the drug molecule in the host cavity as a 1:1 complex as indicated by Job’s plot. There was a linear increase in its solubility with the increase of the cyclodextrin concentration and the complex was classified as an A_L-type. The value of the stability constant was 3,998?L?mol^?1 calculated by the Higuchi–Connors diagram and around 18,100?L?mol^?1 from the fluorescence method indicating a strong interaction between the host and the guest. Complex formation was a spontaneous and enthalpy directed process.     

Metallacrowns of copper(II) and aminohydroxamates: Thermodynamics of self assembly and host–guest equilibria

Metallacrowns (MCs) of copper(II) and aminohydroxamic acids have been extensively studied during the past few decades. Although their discovery dates back more than twenty years, systematic studies on the thermodynamics of self assembly of MCs and of their capability to act as guests for anions and cations are quite recent. This review focuses on the solution studies of these metallamacrocycles and, in particular, the following aspects are discussed: (i) the thermodynamics of self-assembly of 12-MC-4 complexes; (ii) the thermodynamics of self-assembly and core metal substitution of 15-MC-5 species; (iii) the thermodynamics of host–guest equilibria between 15-MC-5 complexes and anions.The overall thermodynamic parameters for the formation of a wide number of 12-MC-4 species of α-, β- and γ-aminohydroxamates are discussed together with the most relevant structural, spectroscopic and reactivity features reported in the literature for copper(II) metallacrowns. These data provide a thermodynamic quantitation of the “metallacrowns structural paradigm”, and show the possibility to devise new MCs with desired stabilities in different medium conditions through an appropriate choice of metal coordinating moieties and ligand dimensions. The thermodynamics of self-assembly of 15-MC-5 is discussed for Ca²⁺ and Ln³⁺ as core metals, and the overall formation constants are used to evaluate the copious literature data regarding the stability of these species in solution. The relative stability of 15-MC-5 complexes of different Ln³⁺ ions is also discussed, showing the extraordinary capability of these complexes to discriminate different Ln³⁺ ions on the basis of their dimensions. Finally, the thermodynamics of host–guest equilibria of 15-MC-5 complexes as receptors for carboxylates is presented: the binding affinities of different carboxylates for the 15-MC-5 species with Ln³⁺ as the core metal are discussed on the basis of guests hydrophobicity, dimension and basicity, and in terms of core metal Lewis acidity.     

Artificial light-harvesting systems fabricated by supramolecular host–guest interactions

Artificial light-harvesting systems(LHSs) have drawn increasing research interest in recent times due to the energy crisis worldwide. Concurrently, macrocycle-based host–guest interactions have played an important role in the development of supramolecular chemistry. In recent years, studies towards artificial LHSs driven by macrocycle-based host–guest interactions are gradually being disclosed. In this mini-review, we briefly introduce the burgeoning progress of artificial LHSs driven by host–guest interactions. We believe that an increasing number of reports of artificial LHSs driven by host–guest interactions will appear in the near future and will provide a viable alternative for the future production of renewable energy.     

Infrared and Mössbauer spectroscopic studies on N,N′ ethylenebis (salicylideneiminato) SnIVhal2

The configurations of the complexes hal₂Sn Salen (hal = Cl, Br) were investigated by infrared and Mössbauer spectroscopic studies. Single ν(Snhal₂) vibrational modes were observed to occur, which would suggest linear geometries of the Sn^IVhal₂ moieties, although bent configurations were not excluded. The computed quadrupole splittings essentially agreed with calculated values for regular and slightly distorted trans-hal₂ octahedral species.     

A family of metallocyclodextrins: synthesis,absorption and luminescence characteristic studies based on host–guest recognition

A family of metallocyclodextrins bearing one, two, three or six β-cyclodextrin binding sites on their ligands have been synthesised, and their structures were confirmed by ¹H NMR, ¹³C NMR, MALDI-TOF MS, UV–vis spectroscopy and elemental analysis. Comparative investigation of the luminescent properties of these metallocyclodextrins found that 6CD-Ru showed the strongest fluorescence intensity. The fluorescence quantum yield results show that 6CD-Ru exhibits the highest emission efficiency, as we expected. To gain insight into the binding properties of the most promising metallocyclodextrin 6CD-Ru, two guest compounds 4-dimethylaminoazobenzene-4′-carboxylic acid (Dab) and methylene blue (MB) were used as analytes. 6CD-Ru exhibited remarkable emission quenching compared with the reference compound CD-Ru. Furthermore, calculated binding constants demonstrated that 6CD-Ru has enhanced binding capacity due to the presence of multiple β-cyclodextrin binding sites. These prominent characteristics of 6CD-Ru suggest that it may be used to detect the two guests Dab and MB, and their analogues, with greater sensitivity, and the relevant research with these metallocyclodextrins is in progress in our group.     

Solid-state NMR studies of host–guest chemistry in metal-organic frameworks

Metal-organic frameworks (MOFs) are an emerging class of porous materials with potential applications in a wide variety of fields. The knowledge about the detailed interactions between MOFs and guest molecules is critical for the understanding of their structure-property relationships at working conditions. In this review, recent advances for solid-state NMR studies of host–guest chemistry of MOFs in the application fields of gaseous adsorption, chemical separation, drug delivery, chemical sensor, and heterogeneous catalysis were briefly introduced. The adsorption property and dynamic behavior of adsorbed gases confined inside the MOFs channels were elucidated from variable-temperature (VT) solid-state NMR. Moreover, the detailed mechanism of gas-phase and liquid-phase adsorptive separations on MOFs adsorbents was uncovered on the basis of solid-state NMR measurements. Multi-nuclear ¹H, ¹³C, ¹⁵N, and ³¹P MAS NMR was utilized to explore the interactions between drug molecules and MOFs at the atomic scale to monitor the controlled release process of drugs. Furthermore, the investigation of the interactions between guest molecules and MOFs in the application areas of chemical sensor, toxic chemicals removal, and catalysis using solid-state NMR was briefly discussed as well.     

Physicochemical characterization and molecular modeling study of host–guest systems of aripiprazole and functionalized cyclodextrins

Journal of Thermal Analysis and Calorimetry - Aripiprazole (ARP), an innovative atypical antipsychotic drug, exhibits very low aqueous solubility, affecting its dissolution and absorption and high...     

Transition metal atoms grafted on the nanodiamonds surface: Identification and guest–host spin–spin interactions

This survey describes recent achievements in creating a new type of materials – nanodiamonds grafted with atoms of transition metals. Structural features of some selected chelate complexes studied by density functional theory, their scope and limitations as well as possible applications are discussed. Using the example of copper ions, their location relative to subsurface defects of detonation diamond is investigated by the method of electron paramagnetic resonance (EPR).     

Infrared spectroscopic and DFT investigations of the vanadate–tellurate glasses structures

Vanadate–tellurate vitreous systems with composition (1 ? x)TeO₂·xV₂O₅ where x = 0.3 and 0.4 have been prepared by the conventional melt-quench method. The structural aspects have been investigated using FTIR spectroscopy and the density functional theory (DFT) calculations.The present study provides the interesting information concerning devitrification behavior of the vanadate–tellurate vitreous system which occur Te₂V₂O₉ crystalline phase. The structure of the heat-treated glasses was found to consist mainly of rings containing [TeO₃], [TeO₄], [VO₄] and some [VO₅] structural units.     

A hybrid hydrogel based on clay nanoplatelets and host–guest inclusion complexes

In this work,a monomer with double bond was introduced to the surface of clay nanosheets via inclusion complexation between cyclodextrin(CD)host and azobenzene(Azo)guest,as well as electrostatic interaction between clay nanoplatelets and cations of azobenzene derivatives.The obtained suprastructure acts as a supramolecular cross-linker in its copolymerization with macromonomer PEG resulting in a hybrid supramolecular hydrogel.Only viscous liquid was obtained in the absence of clay nanoplatelets,revealing the supramolecular cross-linker played an important role in the hydrogel formation.Such hybrid supramolecular hydrogel exhibited good stability and shear thinning property.     

Thermodynamic studies on the systems M–Te–O (M = Nd,Sm)

The standard Gibbs energies of formation of Nd₂TeO₆ and M₆TeO₁₂ (where M = Nd, Sm) were determined from vapour pressure measurements. The vapour pressure of TeO₂(g) was measured by employing thermogravimetry-based transpiration technique. The temperature dependence of the vapour pressure of TeO₂(g) over the mixtures Nd₂TeO₆+Nd₆TeO₁₂, generated by the incongruent vapourisation reaction, 3Nd₂TeO₆(s) → Nd₆TeO₁₂(s)+2TeO₂(g)+O₂(g), was measured in the temperature range 1,408–1,495 K. Similarly, the vapour pressure of TeO₂(g) over the mixtures M₆TeO₁₂+M₂O₃ (where M = Nd, Sm), generated by the incongruent vapourisation reaction, M₆TeO₁₂(s) → 3M₂O₃(s)+TeO₂(g)+½O₂(g), was measured in the temperature range 1,703–1,773 and 1,633–1,753 K for Nd₆TeO₁₂(s) and Sm₆TeO₁₂(s), respectively. Enthalpy increments of M₂TeO₆(s) (where M = Nd, Sm) were determined by inverse drop calorimetric method in the temperature range 573–1,273 K. The thermodynamic functions, viz., heat capacity, entropy and free energy functions, were derived from the measured values of enthalpy increments. A mean value of ?2,426.2 ± 0.6 and ?2,417.9 ± 1.1 kJ mol^?1 was obtained for $ \Updelta_{\text{f} } H_{298}^{\text{o}} $ (Nd₂TeO₆, s) and $ \Updelta_{\text{f}} H_{298}^{\text{o}} $ (Sm₂TeO₆, s), respectively, by combining the value of $ \Updelta_{\text{f}} G^{\text{o}} $ (Nd₂TeO₆, s) and $ \Updelta_{\text{f}} G^{\text{o}} $ (Sm₂TeO₆, s) derived from vapour pressure data and the free energy functions derived from the drop calorimetric data.     

Theoretical studies on the spectroscopic properties and the substituent effects of pyridyl triazole Os(Ⅱ) complexes

To explore the spectroscopic properties of pyridyl triazole Os(Ⅱ) complexes and how the substituent effects affect the spectroscopic properties of [Os(ptz)2L2] (L=PH3; ptzH=(2-pyridyl)-1,2,4-triazole) (1), [Os(bptz)2L2] (bptzH=3-tert-butyl-5-(2-pyridyl)-1,2,4-triazole) (2), [Os(fptz)2L2] (fptzH=3- (trifluoreomethyl)- 5-(2-pyridyl)-1,2,4-triazole) (3), and [Os(fbtz)2L2] (fbtzH=3-(trifluoreomethyl)-5-(4-tert-butyl- 2-pyridyl)-1,2, 4-triazole) (4), the density functional theory (DFT) method at the B3LYP level ...     

DNA-binding and photocleavage studies of metallofluorescein–porphyrin complexes of zinc(II) and copper(II)

The DNA-binding behaviors of the fluorescein?Cporphyrinatozinc(II) complex Zn(Fl-PPTPP) (Fl-PPTPP?=?5-(4-fluoresceinpropyloxy)phenyl-10,15,20-triphenylporphyrin) and fluorescein?Cporphyrinatocopper(II) complex Cu(Fl-PPTPP) with calf thymus DNA (CT-DNA) were investigated by UV?CVis absorption titrations, fluorescence spectra, viscosity measurements, thermal denaturation and circular dichroism. The results suggest that both complexes interact with CT-DNA by intercalation. In addition, their photocleavage reactions with pBR322 supercoiled plasmid DNA were investigated. Both complexes exhibit significant DNA cleavage activity, and singlet oxygen may play an important role in these reactions.     

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments.