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Biomimetic Recognition of Organic Drug Molecules in Water by Amide Naphthotubes

2020; Chinese Chemical Society; Volume: 3; Issue: 4 Linguagem: Inglês

10.31635/ccschem.020.202000288

2096-5745

Yan‐Long Ma, Mao Quan, Xiulian Lin, Qian Cheng, Huan Yao, Xiran Yang, Ming‐Shuang Li, Wei‐Er Liu, Linming Bai, Ruibing Wang, Wei Jiang,

Malaria Research and Control

Open AccessCCS ChemistryRESEARCH ARTICLE1 Apr 2021Biomimetic Recognition of Organic Drug Molecules in Water by Amide Naphthotubes Yan-Long Ma, Mao Quan, Xiu-Lian Lin, Qian Cheng, Huan Yao, Xi-Ran Yang, Ming-Shuang Li, Wei-Er Liu, Lin-Ming Bai, Ruibing Wang and Wei Jiang Yan-Long Ma State Key Laboratory of Quality Research in Chinese Medicines, and the Institute of Chinese Medical Science, University of Macau, Avenida da Universidade, Taipa, Macau 999078 Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Mao Quan Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Xiu-Lian Lin Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Qian Cheng State Key Laboratory of Quality Research in Chinese Medicines, and the Institute of Chinese Medical Science, University of Macau, Avenida da Universidade, Taipa, Macau 999078 , Huan Yao Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Xi-Ran Yang Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Ming-Shuang Li Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Wei-Er Liu Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Lin-Ming Bai Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 , Ruibing Wang *Corresponding authors: E-mail Address: [email protected] E-mail Address: [email protected] State Key Laboratory of Quality Research in Chinese Medicines, and the Institute of Chinese Medical Science, University of Macau, Avenida da Universidade, Taipa, Macau 999078 and Wei Jiang *Corresponding authors: E-mail Address: [email protected] E-mail Address: [email protected] Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055 https://doi.org/10.31635/ccschem.020.202000288 SectionsSupplemental MaterialAboutAbstractPDF ToolsAdd to favoritesTrack Citations ShareFacebookTwitterLinked InEmail Molecular recognition in water is the basis of numerous biological functions. The key for efficient and selective recognition of an organic drug molecule is to bind both its polar and nonpolar groups. This is achieved by bioreceptors for which specific noncovalent interactions are efficiently used in a hydrophobic pocket. In contrast, most synthetic receptors cannot efficiently bind the neutral, polar groups of drug molecules and, thus, often exhibit poor binding selectivity and affinity. In this research, we report a systematic study on the binding behaviors of three types of macrocyclic hosts (amide naphthotubes, cucurbit[7]uril, and β-cyclodextrin) to 18 model compounds and 13 drug molecules. Our results show that the high desolvation penalty of polar groups of guests is the reason for the relatively low binding affinity of cucurbit[7]uril and β-cyclodextrin. However, amide naphthotubes with a biomimetic cavity bind efficiently and selectively to organic guests through hydrophobic effects and hydrogen bonding. Drug molecules with multiple polar groups can be better accommodated by these naphthotubes. The anti-configured naphthotube show good biocompatibility according to preliminary cell experiments and is capable of enhancing the water solubility of two poorly soluble drug molecules. Therefore, they may have practical applications in pharmaceutical sciences. Download figure Download PowerPoint Introduction Selective and efficient recognition of organic molecules in water is the basis of life and is responsible for numerous biological processes, including signal transduction, membrane transportation, cell recognition, and drug–receptor binding.1 The substrates of bioreceptors, for example, drug molecules, usually contain both polar and nonpolar groups. The polar groups contain rich information but are highly solvated in water. Specific interactions of a receptor with these polar groups are the key to compensating their desolvation penalty and selectively binding the substrate in water. However, it is well known that specific noncovalent interactions, such as hydrogen bonding, are significantly attenuated in the polar environment of water.2–5 Bioreceptors cleverly circumvent this problem by positioning all binding sites inside the low-dielectric environment of a hydrophobic pocket. Consequently, specific noncovalent interactions can be effectively used even in water together with the hydrophobic effect. High binding affinity and selectivity can be achieved for bioreceptors to organic substrates. For example, teriflunomide (Tf) is a potent inhibitor (Ka = 5.6 × 106 M–1) to dihydroorotate dehydrogenase (DHODH), and they bind to each other through multiple hydrogen bonds inside a hydrophobic cavity (Figure 1a, left).6,7 Figure 1 | Cartoon representations of the molecular recognition of organic molecules in water (a) by a biomimetic cavity or (b) by a hydrophobic cavity. Download figure Download PowerPoint A biomimetic receptor, capable of binding an organic molecule through interacting with both its polar and nonpolar groups (Figure 1a, right), not only serves as a good model system to better understand the mechanism of biomolecular recognition but also provides tools for analytical sciences, pharmaceutical sciences, and chemical biology.8 However, the majority of water-soluble synthetic receptors9–31 have no functional groups inside a hydrophobic cavity. For an organic molecule with both polar and nonpolar groups, these receptors either fully encapsulate the guest within the hydrophobic cavity (Figure 1b, left) or only bind to the nonpolar group by exposing the polar groups to the bulk water (Figure 1b, right). For the first case, the dehydration penalty of the polar groups is not well compensated; in the second case, the polar groups are not involved in the binding. Therefore, the receptors with only a hydrophobic cavity often show poor binding affinity and selectivity to organic molecules.32 Recently, several biomimetic receptors with polar binding sites in their hydrophobic pockets have been reported.33–42 These receptors have been demonstrated to recognize saccharides,33,34 pyridine oxides, and lactams,35,36 as well as squaraine and croconaine dyes.37,38,39 The polar groups of these guests are well complemented by the hydrogen bonding sites of the receptors inside the hydrophobic cavity. Even extremely high binding affinities were achieved. However, this kind of biomimetic receptor is still very rare43; the scope of the organic guests is limited, and no drug molecules were studied; in addition, the effect of polar groups on the binding affinities has not been well analyzed. Very recently, we reported a pair of biomimetic macrocyclic receptors with hydrogen-bonding donors inside their deep hydrophobic cavities.44–47 These naphthotubes (NT; Figure 2a) are able to bind highly hydrophilic molecules in water by combining the hydrophobic effect with hydrogen bonding shielded inside the hydrophobic cavity.48 The guest molecules include solvent molecules,45,48 heterocycles,48 polyethylene glycols,49 epoxides,50,51 phosphate esters,52 and environmental contaminants.45,53 Most of these guests are small, hydrophilic molecules. Although these amide naphthotubes were also shown to bind several organic molecules with both polar (acetal,48 epoxide,50,51 or phosphate ester52) and nonpolar groups, these kinds of organic guests are very limited, and the effect of polar groups on the binding affinities was not revealed. No drug molecules were studied. In this research, we report a systematic study on the binding of a series of model organic molecules and drug molecules with the biomimetic naphthotubes (NT-syn and NT-anti) and the receptors cucurbit[7]uril (CB[7]) and β-cyclodextrin (β-CD) (Figure 2a). Their binding behaviors were then compared. The effects of polar groups on the binding affinities were revealed for these three types of receptors by considering the different hydration energies of guest molecules in water. It was demonstrated that the naphthotubes can efficiently bind drug molecules and improve the water solubility of two poorly soluble drugs. The present research may further the understanding of biomolecular recognition and pave the way for the application of these naphthotubes in pharmaceutical science as excipients or drug delivery vehicles. Figure 2 | Chemical structures and models of three types of macrocyclic receptors, 18 neutral organic guests, and 13 drug molecules. Download figure Download PowerPoint Experimental/Computational Methods β-Cyclodextrin, cucurbit[7]uril, and all the guest molecules involved in this research were commercially available and used without further purification unless otherwise noted. Solvents were either employed as purchased or dried prior to use by standard laboratory procedures. 1H, 2D NMR spectra were recorded on a Bruker Avance-400 or 500 NMR spectrometer. All chemical shifts are reported in ppm with residual solvents or sodium methyl sulfonate as the internal standard. Fluorescence and UV–vis spectra were obtained on a Shimadzu RF-5301 pc spectrometer and UV–vis spectrophotometer (UV-2600), respectively. Isothermal titration calorimetry (ITC) experiments were carried out in deionized water (or 50 mM PBS buffer, pH = 7.4) at 25 °C on a Malvern VP-ITC instrument. Further details on the titration experiments and the fitting equations can be found in the Supporting Information. The synthesis of amide naphthotubes (NT-syn and NT-anti) has been reported earlier.45,47,49 Quantum chemistry calculations were performed using a Gaussian 09 package.54 All the structures of the hosts and complexes have been optimized employing density functional theory (DFT) with dispersion corrected method (wB97XD)55 in combination with 6-31G* basis set including the SMD water model.56,57 Minima were characterized by the absence of imaginary frequencies. Results and Discussion Determination of binding constants and thermodynamic parameters With respect to the hosts, CB[7] and β-CD were used in comparison with naphthotubes NT-syn and NT-anti (with the new configurational assignment47). CB[7] and β-CD are the best binders to neutral organic guests in their families.9–16 These two macrocycles are commercially available and have been extensively studied with regard to their drug binding behavior. Structurally, it is not completely accurate to say that CB[7] and β-CD have no functional groups. However, these functional groups (carbonyl or hydroxyl groups) are located at the portals of their cavities. Therefore, the interactions with a guest by these functional groups of CB[7] or β-CD are not completely shielded from bulk water. This situation is different from that of naphthotubes and bioreceptors, for which specific noncovalent interactions between guests and hosts are shielded inside a hydrophobic cavity. Therefore, CB[7] and β-CD are included here as representative receptors without functional groups in a hydrophobic cavity. Most organic drug molecules contain both polar and nonpolar groups. In particular, 18 neutral organic molecules (Figure 2b) were selected as representative model compounds: the phenyl group, which is one of the most popular structural elements in bioactive compounds,58 was used as a typical nonpolar group; different functional groups were attached to the phenyl group and used as polar groups. The polar groups include methoxyl, methylthio, cyano, methylamino, dimethylamino, nitro, ester, amide, ketone, oxazole, thiazole, pyrimidine, and so on. In addition, 13 drug molecules (Figure 2c) were studied to further reveal the differences of the three types of macrocycles. These drug molecules contain one or two of the 18 model compounds as their structural backbones. 1H NMR experiments ( Supporting Information Figures S1–S72) were performed on all of the host–guest pairs at a 1∶1 ratio. The 1H NMR peak shifts of the complexed host and guest relative to the free host and guest are used to evaluate whether the binding occurs or not. Most of the binding constants and thermodynamic parameters were determined by ITC experiments ( Supporting Information Figures S73–S90). For the ones that could not be determined by ITC experiments, 1H NMR titrations or UV–vis titrations were performed ( Supporting Information Figures S91–S112). Most of the binding studies were performed in water. However, guests 7, 8, and 14– 18 contain a basic group (for their pKas, see Supporting Information Table S1), and CB[7] is known to up-shift the pKa of its guest and can bind the protonated state of guests even in basic conditions.59 Therefore, the binding studies of CB[7] to these seven guests were performed in 50 mM PBS buffer (pH = 7.4) to maintain the neutral forms of the guests. The high salt content in PBS buffer may decrease these binding affinities. All experiments were performed in triplicate unless otherwise noted and the averaged values and standard errors are reported. Some of the binding parameters of CB[7] and β-CD were taken from the literature.60–62 The binding constants of NT-syn and NT-anti to benzene or toluene have been determined with the ammonium salts48 but were redetermined here with the sodium salts of the hosts to keep consistency. The current binding constants are slightly larger than the ones with the ammonium salts. The binding constants and binding free energies are reported in Table 1, and the other binding thermodynamic parameters can be found in Supporting Informtion Table S2. Table 1 | Binding Constants (Ka, M−1) and ΔG° (kJ mol−1) of the Hosts with Guests and Drugs were Determined by ITC, UV–Vis, and NMR Titrations at 25 °C, as well as the Hydration Free Energy (ΔG°hyd, kJ mol−1) of Guests Guests ΔG°hyda NT-syn NT-anti CB[7] β-CD Ka ΔG° Ka ΔG° Ka ΔG° Ka ΔG° 1 −3.7 930 ± 30 −16.9 ± 0.1 (1.6 ± 0.1) × 103 −18.3 ± 0.2 (9.5 ± 0.5) × 105 −34.1 ± 0.1 194b −13.1c 2 −3.4 (1.3 ± 0.1) × 104 −23.5 ± 0.1 (1.8 ± 0.1) × 104 −24.2 ± 0.1 (8.6 ± 0.3) × 105 −33.9 ± 0.1 214b −13.3c 3 −15.2 (5.2 ± 0.1) × 103 −21.2 ± 0.1 (1.7 ± 0.1) × 104 −24.2 ± 0.1 (7.7 ± 0.2) × 104 −27.9 ± 0.1 170b −12.7c 4 −17.6 (2.3 ± 0.2) × 103 −19.2 ± 0.2 (1.3 ± 0.1) × 104 −23.5 ± 0.1 (1.1 ± 0.1) × 105 −28.7 ± 0.1 279b −14.0c 5 −10.7 (1.1 ± 0.1) × 104 −22.9 ± 0.3 (1.7 ± 0.1) × 104 −24.1 ± 0.2 (2.6 ± 0.3) × 104 −25.0 ± 0.4 209b −13.2c 6 −12.5 (2.1 ± 0.1) × 104 −24.7 ± 0.1 (8.9 ± 0.4) × 104 −28.2 ± 0.1 (5.1 ± 0.1) × 104 −26.9 ± 0.1 458 ± 28e −15.2c 7 −19.0 (3.1 ± 0.1) × 104 −25.7 ± 0.1 (3.8 ± 0.1) × 104 −26.1 ± 0.1 (3.3 ± 0.1) × 103d −20.1 ± 0.1 131b −12.1c 8 −14.3 (1.6 ± 0.1) × 103 −18.5 ± 0.7 (1.4 ± 0.1) × 104 −23.7 ± 0.1 (2.8 ± 0.1) × 103d −19.7 ± 0.1 252b −13.7c 9 −19.3 (2.9 ± 0.2) × 103 −19.7 ± 0.2 (2.2 ± 0.1) × 104 −24.8 ± 0.1 (1.3 ± 0.1) × 104 −23.5 ± 0.1 188b −13.0c 10 −16.2 (7.6 ± 0.1) × 103 −22.1 ± 0.1 (5.9 ± 0.1) × 104 −27.2 ± 0.1 (1.1 ± 0.1) × 103 −17.4 ± 0.4 317b −14.3c 11 —h (1.8 ± 0.1) × 104 −24.2 ± 0.1 (3.9 ± 0.1) × 104 −26.2 ± 0.1 (4.1 ± 0.2) × 103 −20.6 ± 0.1 152 ± 11e −12.5c 12 —h 940 ± 10 −17.0 ± 0.1 (5.9 ± 0.2) × 103 −21.5 ± 0.1 (4.1 ± 0.1) × 103 −20.6 ± 0.1 36 ± 11e −8.9c 13 —h (1.2 ± 0.1) × 103 −17.5 ± 0.1 (3.1 ± 0.1) × 103 −19.9 ± 0.1 (4.9 ± 0.1) × 104 −26.7 ± 0.1 157b −12.5c 14 —h (7.4 ± 0.1) × 103 −22.1 ± 0.1 (6.3 ± 0.2) × 104 −27.4 ± 0.1 —d,e,g 466 ± 28e −15.2c 15 —h (3.2 ± 0.1) × 104 −25.7 ± 0.1 (8.4 ± 1.1) × 104 −28.1 ± 0.3 26d,e,f −8.1c 406 ± 43e −14.9c 16 —h (8.4 ± 0.1) × 104 −28.1 ± 0.1 (3.1 ± 0.1) × 105 −31.3 ± 0.1 38d,e,f −9.0c 393 ± 25e −14.8c 17 —h (1.0 ± 0.1) × 105 −28.5 ± 0.2 (3.9 ± 0.3) × 105 −31.9 ± 0.2 368d,f −14.6 357 ± 44e −14.6c 18 —h (7.7 ± 0.1) × 104 −27.9 ± 0.1 (7.0 ± 0.1) × 105 −33.4 ± 0.1 —d,e,g 339 ± 36e −14.4c Cp 664 ± 30e −16.1c (1.3 ± 0.1) × 104 −23.4 ± 0.1 (4.8 ± 0.1) × 103 −21.0 ± 0.1 303 ± 10e −14.2c Ch (1.3 ± 0.1) × 104 −23.6 ± 0.1 (3.2 ± 0.2) × 105 −31.3 ± 0.1 (1.9 ± 0.1) × 104 −24.5 ± 0.1 472 ± 23e −15.3c Lp (8.1 ± 0.1) × 103d −22.3 ± 0.1 (5.5 ± 0.1) × 104d −27.1 ± 0.1 (5.1 ± 0.1) × 104d −26.9 ± 0.1 536 ± 45d,e −15.6c Fb (7.7 ± 0.1) × 104 −27.9 ± 0.1 (3.1 ± 0.1) × 105 −31.3 ± 0.1 (1.6 ± 0.1) × 104 −24.0 ± 0.1 3913 ± 310e −20.5c Bz (1.1 ± 0.1) × 104d −23.0 ± 0.1 (1.0 ± 0.1) × 105d −28.6 ± 0.3 300j −14.1c 549k −15.6c Pc 475 ± 7d,e −15.3c (1.4 ± 0.1) × 104d,e −23.7c (3.3 ± 0.1) × 105 −31.4 ± 0.1 60 ± 17d,e −10.1c Tf (1.1 ± 0.2) × 104d,e −23.1c (1.8 ± 0.1) × 104d −24.2 ± 0.1 96 ± 17d,i −11.3c 2243 ± 28d,e −19.1c Ct (1.0 ± 0.1) × 104d −22.9 ± 0.1 (2.0 ± 0.1) × 105d −30.2 ± 0.1 (1.2 ± 0.1) × 106d −34.6 ± 0.1 5148 ± 20d,e −21.2c Fa 1010 ± 54e −17.1c (1.0 ± 0.1) × 104 −23.1 ± 0.1 605 ± 33d,i −15.9c 543 ± 31e −15.6c Bp 4466 ± 463e −20.8c (1.0 ± 0.1) × 105 −28.5 ± 0.1 694 ± 145i −16.2c 1470 ± 102e −18.1c Ef (3.4 ± 0.1) × 104 −25.9 ± 0.1 (1.5 ± 0.1) × 106 −35.2 ± 0.1 (2.3 ± 0.1) × 104 −24.9 ± 0.1 2932 ± 481e −19.8c aSee Table S3 in Supporting Information. bData were taken from the literature.56 cΔG° = −RTlnKa. dKa of these guests were determined in the PBS buffer (50 mM, pH = 7.4). eKa of these guests were determined by NMR titrations. fThese Ka values are too small and may be inaccurate. gKa are too small to be measured. hNo experimental data are available. iKa of these guests were determined by UV–vis titrations. jData (PBS buffer, pH = 7.4) were taken from the literature.57 kData were taken from the literature.58 All titration experiments were repeated three times unless otherwise noted, and standard deviations are reported. Comparative analysis among three types of macrocycles for the binding with the model compounds The binding free energies for guests 1– 18 in Table 1 are presented in the columns in Figure 3 for viewing clarity. Generally speaking, CB[7], NT-anti, and NT-syn are better receptors (Ka > 103 M–1) than β-CD (Ka < 500 M–1) for most of these guests. The exceptions are guests 14– 18 with heterocycles as the functional groups: the binding affinities of guests 15– 17 to CB[7] are comparable or weaker than those to β-CD; the binding between guests 14/ 18 and CB[7] is not even detectable. However, for guests 1– 5 and 13, CB[7] is the best receptor, and for other guests with a large polar group, NT-anti is generally a better receptor than CB[7] and β-CD. NT-syn shows a similar binding trend as NT-anti but is a slightly weaker binder than NT-anti. Figure 3 | Graphic representation of the binding free energies (ΔG°) of the four receptors to 18 neutral organic guests. Download figure Download PowerPoint Many of the binding constants of NT-syn, NT-anti, and CB[7] were determined by ITC experiments. Therefore, their thermodynamic parameters, including ΔH° and TΔS°, are available as well. The binding constants of β-CD were mainly determined by NMR titrations. Most of the binding constants are small, and no attempt was made to determine their thermodynamic parameters because large errors may exist. As shown in Figure 4, all the binding of NT-syn, NT-anti, and CB[7] is enthalpically driven. For CB[7], the enthalpic contribution is significant, but the entropic contribution is generally unfavorable for all guests except for guest 1. The binding enthalpy (ΔH°) and entropy (TΔS°) of CB[7] to 1 are –27.8 and 6.3 kJ/mol, respectively. The most significant thermodynamic parameters with CB[7] were observed for guest 8: ΔH° = –45.9 kJ/mol and TΔS° = –26.2 kJ/mol. Meanwhile, NT-syn and NT-anti have a small (either favorable or unfavorable) entropic contribution. For example, the most stable complex 18@NT-anti (Ka = 7.0×105 M–1) has ΔH° = –37.7 kJ/mol and TΔS° = –4.3 kJ/mol. Again, entropy–enthalpy compensation is followed loosely.48,63 Figure 4 | Thermodynamic data (ΔH° and TΔS°) for the binding of neutral guests with NT-syn (blank dots), NT-anti (red dots), or CB[7] (blue triangles). Download figure Download PowerPoint Effect of polar groups on the binding Although each of the guests 1– 18 has a nonpolar phenyl group, their binding affinities to the same receptor are rather different. Additionally, the three types of receptors show different responses to this series of guests. Benzene is a guest that lacks any functional groups, and all of the other guests can be obtained by substituting one hydrogen atom on benzene with one functional group. Therefore, the influence of polar groups on the binding affinities can be evaluated by comparing the guest binding affinities to that of benzene. To better analyze the effect of polar groups on the binding, the binding free energies of benzene (guest 1) are subtracted from those of guests 2– 18. This way of analysis is commonly used in biomolecular recognition.64 The resulting differential free energies of four receptors are presented in Figure 5 as a column graph for viewing clarity. Figure 5 | Graphic representation of the differential binding free energies (ΔΔG°) of the host–guest complexes with the complexes of benzene as the references. Download figure Download PowerPoint Toluene has one more hydrophobic methyl group relative to benzene. Surprisingly, this additional hydrophobic methyl group does not significantly change the binding affinity of toluene to CB[7] and β-CD, even though these two receptors prefer to bind more hydrophobic guests.9–16 Nevertheless, the binding constants of NT-syn and NT-anti to toluene (∼104 M–1) are about one order of magnitude larger than those to benzene (∼103 M–1). The increased binding affinity mainly originates from the enthalpic contribution (ΔΔH° = –6.4 and –5.5 kJ/mol, TΔΔS° = 0.4 and 0.2 kJ/mol for NT-syn and NT-anti, respectively). The different responses of the three types of macrocycles to the additional hydrophobic methyl group may be due to the different dimensions of their hydrophobic cavities (Figure 2a). The three types of macrocycles have similar cavity widths, but their lengths are different ( Supporting Information Figure S113). As reported in literature, the lengths of CB[7] and β-CD are ca. 9.1 and 7.9 Å, respectively.9–16 Therefore, the cavity of β-CD is able to completely encapsulate benzene (length: ∼7.4 Å), but is too short for toluene (length: ca. 9.5 Å). For CB[7], the length of the cavity is sufficient for toluene, but the converged, polar carbonyl groups may have unfavorable interaction or encounter steric hindrance with the methyl group of the guest. However, the cavities of NT-syn and NT-anti (∼12 Å), by considering the regions defined by the methylene groups of the four side chains, are long enough to fully encapsulate one toluene molecule and no unfavorable interactions exist. Further DFT calculations ( Supporting Information Figures S114–S117) with four receptors confirm this analysis. The polar groups of guests 3– 18 exert no obvious influence on the binding (ΔΔG° = –2.1 to 4.2 kJ/mol) of β-CD when compared with that of benzene. However, the polar groups provide generally positive contributions (–0.1 to –15.1 kJ/mol) to the binding with NT-syn and NT-anti. The difference between the binding free energies of 18@NT-anti and 1@NT-anti is the largest (–15 kJ/mol). Thermodynamically, the increased binding affinities for guests 3– 18 with one polar group are mainly from enthalpic gain (ΔΔH° = –6.4 to –31.5 kJ/mol and –5.5 to –29.2 kJ/mol for NT-anti and NT-syn, respectively). The entropic changes are generally unfavorable (TΔΔS° = –4.8 to –20.6 kJ/mol and –5.7 to –15.0 kJ/mol for NT-anti and NT-syn, respectively) in comparison to guest 1 (benzene). That is, the influence of the polar groups on the binding to the naphthotubes is through a favorable enthalpic effect, suggesting the existence of hydrogen bonds. In great contrast, all the polar groups of guests 3– 18 provide negative contributions to their binding to CB[7]. A difference as large as 26 kJ/mol was observed between the binding free energies of 15@CB[7] and 1@CB[7] with benzene ( 1) to be a significantly better guest. No binding was detected for guests 14 and 18 ( Supporting Information Figures S97 and S110, respectively). When compared to benzene ( 1), the unfavorable entropic contribution (TΔΔS° = –7.3 to –32.5 kJ/mol) is dominated for these guests bearing one polar group. The differential enthalpic change is favorable (ΔΔH° = –1.8 to –18.1 kJ/mol) for guests 3– 6, 8, and 15, but is unfavorable (ΔΔH° = 0.6 to 7.6 kJ/mol) for guests 7 and 9– 12. Therefore, the polar groups of guests 3– 18 decrease the binding to CB[7] mainly through an unfavorable entropic effect. This entropic effect presumably originates from the desolvation penalty of polar groups. Binding origin of organic molecules containing polar groups At first glance, it is surprising that the polar groups of guests 3– 18 have different effects on the binding affinities to the three types of macrocycles. Molecular recognition in water is complex and often does not depend on single parameters. Noncovalent interactions between host and guest and their interactions with water molecules should all be considered. In the following discussion, the following three aspects will be analyzed: solvation of organic guests in water; cavity features of NT, CB[7], and β-CD and the "high-energy" waters in the cavities; noncovalent interactions and complementarity between guest and host. Additional polar groups on the phenyl group unavoidably increase the solvation extent of the guest in water. As shown in Table 1 and Supporting Information Table S3, the hydration free energy of benzene ( 1) is only –3.7 kJ/mol, but the hydration free energies of guests 3– 10 with a polar group are generally lower than –10 kJ/mol. The hydration free energies of the other guests are not available and should be similar or even larger than those of guests 3– 10. The following three scenarios exist for the binding of these guests (Figure 1): (1) for a biomimetic receptor, which can interact with the polar groups, the desolvation penalty of the polar groups may be fully compensated by these additional interactions; (2) when a receptor only binds the nonpolar group of this organic guest, the polar groups will exert no obvious effect on the binding; (3) if the organic molecules are completely encapsulated within the cavity of a receptor, a weakened binding should be observed due to the high desolvation penalty of the polar groups. Cavity features of NT, CB[7], and β-CD and the numbers of their "high-energy" water molecules are different. The cavity widths of these three types of macrocycles are similar and can accommodate a benzene molecule, but the cavity lengths and functional groups inside the cavity or attached to the portals are different. As discussed earlier, the cavity length of NT (∼12 Å) is slightly longer than that of CB[7] (9.1 Å) and of β-CD (7.9 Å). This has been demonstrated with the binding of toluene (see aforementioned). In addition, hydrogen bonding donors exist in the hydrophobic cavities of NT and can interact with the hydrogen bonding acceptors of guests inside a relatively low-dielectric environment. The two portals of CB[7] are lined by 14 carbonyl groups, which are known to bind positively charged groups of guests through ion–dipole interactions.12–16 However, these carbonyl groups may have repulsive interactions with hydrogen bonding acceptors of guests when they are brought in proximity during binding. Hydrogen bonds may be formed between the carbonyl groups of CB[7] and the hydrogen bonding donors of some guests,14,65 but these hydrogen bonds are generally considered weak because they are located outside the hydrophobic cavity and experience a high dielectric environment.12–16 β-CD has a cavity with a similar structural arrangement to that of CB[7]. Hydroxyl groups are located at the two rims, and hydrogen bonds may form with guests but are only a minor contributor to the binding affinity.9–11 All three types of macrocycles contain "high-energy" water molecules, and the release of these molecules is one of th