Chiral recognition of neutral guests by chiral naphthotubes with a bis-thiourea endo-functionalized cavity

Developing chiral receptors with an endo-functionalized cavity for chiral recognition is of great significance in the field of molecular recognition. This study presents two pairs of chiral naphthotubes containing a bis-thiourea endo-functionalized cavity. Each chiral naphthotube has two homochiral centers which were fixed adjacent to the thiourea groups, causing the skeleton and thiourea groups to twist enantiomerically through chiral transfer. These chiral naphthotubes are highly effective at enantiomerically recognizing various neutral chiral molecules with an enantioselectivity up to 17.0. Furthermore, the mechanism of the chiral recognition has been revealed to be originated from differences in multiple non-covalent interactions. Various factors, such as the shape of cavities, substituents of guests, flexibility of host and binding modes are demonstrated to contribute to creating differences in the non-covalent interactions. Additionally, the driving force behind enantioselectivity is mainly attributed to enthalpic differences, and enthalpy -entropy compensation has also been observed to influence enantioselectivity.

1.For the chiral guests used for the chiral recognition, one pair of enantiomers instead of only one enantiomer (such as R-2, S-4a, and so on) will be more meaningful.
2. Compared with chiral guest 1, chiral guest 5b showed significant enhanced complexation ability and much highly enantioselective recognition.A reasonable explanation can be provided.
3. The absorption and emission changes of the naphthotubes in the presence of the chiral guests will be very helpful for mechanism investigation of the chiral recognition.
4. For the new chiral molecules, their optical rotations are suggested to be provided.

Reviewer #2 (Remarks to the Author):
This paper discusses the synthesis and binding properties of tube-like chiral hosts, which are able to enantiomerically discriminate in the binding of a series of chiral guest molecules.In terms of association constant value, enantioselectivities up to a factor of 17 are found.Some of the host-guest complexes are characterized by means of their solid state X-ray structures, in which it is clear that the host-guest binding is governed by multipoint interactions and differences in binding geometry.The binding mechanisms and the origins of the enantioselectivity are further discussed on the basis of spectroscopic measurements and DFT molecular modeling calculations.
The results in this paper are interesting and will appeal to the general supramolecular chemistry community.As the authors state, it is indeed far from straightforward to achieve decent enantioselective host-guest binding in artificial systems.The authors have succeeded in designing a series of tube-like hosts that fulfill this desire, and have successfully applied the biologically-inspired concept of multipoint binding interactions to a synthetic system.
Still, the newly designed receptors are elegantly simple, while at the same time they are able to bind significantly different types of guests.The new compounds have been characterized satisfactorily and the technical quality of the physical measurements is high.
The precise binding mechanisms have been investigated in great detail and are convincing.
It is my opinion that this work may become suitable for publication in this journal after the following comments have been addressed: 1.In the introduction, the authors mention previous research that reported other hosts that can achieve enantioselective binding.In the current work, a enantioselectivity factor of 17 is found, and it would be very informative if the authors would put this result in perspective to enantioselectivity factors found by the earlier reported systems (perhaps in the conclusion section).1, the paragraph about the preferences of the hosts for homochiral or heterochiral guest binding (lines 113-117) is somewhat confusing, in particular in terms of specification of the mentioned hosts that select heterochiral guests.For example, guest S-4a indeed preferentially binds in a heterochiral fashion to host RR-CT1, but in a homochiral fashion to the isomeric host SS-CT2.

When looking at the association constant values in Table
Same for guest R-4c.And guest S-4b binds with heterochiral preference to host RR-CT2, but homochiral to its isomer SS-CT1.A somewhat more exact description of the specific hostguest combinations would be desired here.
3. The statement in lines 147-151 in which the success or failure of crystallization of a hostguest complex is directly related to host-guest binding selectivity is much too strong (or even invalid), since crystallization may depend on many more factors than just host-guest binding strength.I thus suggest removal of this sentence.6.The thermodynamic parameters as shown in Table S2 confuse me, as it seems that each of the diastereomeric host-guest complex pairs always have the same delta-G, deltaH and deltaS values.Should the numbers not represent the calculated *differences* in energy/enthalpy/entropy values between the diastereomeric partners, i.e. "delta-delta" values?

Reviewer #3 (Remarks to the Author):
Wang and co-workers reported the synthesis of two pairs of chiral naphthotubes via endofunctionalization strategy and their chiral recognition performance towards bioactive cyclic dipeptides.The mechanism of the chiral recognition was studied through various tests, as well as DFT calculations, and is attributed to multiple noncovalent interactions, shape matching, orientation, and enthalpy-entropy compensation.This work is interesting and the topic is important, yet, the overly rich influence factors still make the confuse to the design of host receptors for chiral recognition of bioactive molecules.Considering that the authors mainly analyzes the recognition behavior of substrate 5, it is suggested to further combine the chiral recognition mechanism of other substrates, especially substrate 4, to get more clear image about the main influencing factors.Therefore, I recommend reconsidering the manuscript after major revisions.The following issues also need revisions.
1.As shown in Fig. 5, there is a difference in the CD spectrum before and after the guest visit, then similar to the 1H NMR spectrum, the CD spectrum should be provided for the titration experiment(J.Am.Chem.Soc.2019, 141, 16382−16387).

2.The 1H,1H-COSY NMR of different chiral conformational guest molecules coexisting with
the host receptor should be added to the discussion to more clearly elucidate the differences in interactions.
3.In Fig. 4, is these weak interactions such as hydrogen bond, N-H•••π or N-H•••π exist in the crystals will maintain when they dissolved in the solvents?Or greatly weakened?How about the effect of solvents on chiral recognition?In addition, I noticed that the squeeze in PLATON are used to eliminate the distribution of solvent molecules, however, the influence from solvent molecules is considered in the discussion of the host-guest interactions in the crystals.Thus, I strongly suggest to determine the solvent molecules in these crystals without squeeze.4.Fig.5b, the color of R-5a@S,S-CT2 seems not match the label.Please check.
5.Fig.S67, the authors claims the peaks shift from 7.77 to 7.90 ppm with the concentration increasing, however, with the concentration increasing, the peaks at about 7.7 located at the right also enhanced, Why?Is these peaks shift to the right?Meanwhile, the spectra of 0.11 sample seems different from others.
6.For X-ray crystallography, i)the GOOF, R1 and wR2 value of S,S-5c@S,S-CT2 are too high.
ii)The authors response all the Alert B is "The crystal has too weak diffraction to obtain high resolution data".I suggest that the authors put more effort into crystallographic testing to improve the quality of diffraction, for example by using MetalJet (Ga Kα) or synchrotron radiation to obtain high quality data.
iii)In this manuscript, only the molecular structure unit diagrams are shown, and the stacking and interactions between molecules and molecules should also be represented by the stacking diagram.

Reviewer #1 (Remarks to the Author):
This work by Yang et al. describes two pairs of chiral naphthotubes containing a bis-thiourea endofunctionalized cavity, which showed highly enantiomerically selective recognition towards various neutral chiral molecules, particularly bioactive cyclic dipeptides, with an enantiomeric selectivity up to 17.0.Moreover, the mechanism of the chiral recognition has been revealed, which might be attributed to slight differences of multiple noncovalent interactions, as well as the orientation of binding and enthalpy-entropy compensation.Publication of the results is suggested after revisions noted as below.
Response: Thank you very much for the kind recommendation and the valuable suggestions!We have changed the manuscript accordingly.
1.For the chiral guests used for the chiral recognition, one pair of enantiomers instead of only one enantiomer (such as R-2, S-4a, and so on) will be more meaningful.
Response: Thanks for your helpful suggestions and we totally agree with you!However, only one enantiomer is commercially available for some chiral guests, especially for cyclic dipeptides (CDPs) guests, which are usually composed of L-amino acids (Trends. Mol. Med. 2014, 20, 551).We exactly have considered synthesizing these compounds ourselves, but it would require much synthetic effort (Bull. Chem. Soc Jpn. 1983, 56, 568) for us, which is, however, not our focus in this research.
In fact, there are two methods for determining the enantioselectivities between a pair of enantiomeric guests and/or hosts.The first method involves utilizing one chiral host that binds to two enantiomeric guests, resulting in different association constants.The second method involves using two enantiomers of hosts, each with different association constants with the same chiral guest.
The selectivity obtained from both methods should agree with each other quantitatively and qualitatively.Previous reports from our group and others have also verified the reliability of the two methods (CCS Chem. 2020, 2, 440;Angew. Chem. Int. Ed. 2022, 61, e202202527).
We obtained two pairs of enantiomers of hosts (including syn-and anti-configuration) through chiral synthesis.This allows us to determine the chiral selectivity by the second method, and the feasibility of this approach also has been verified by using chiral guests with two enantiomeric forms, such as the chiral guests 1 and 3.
2. Compared with chiral guest 1, chiral guest 5b showed significant enhanced complexation ability and much highly enantioselective recognition.A reasonable explanation can be provided.
Response: Regarding the chiral guest S,S-5b, the amide bond, or peptide bond, is a more suitable hydrogen bond donor and acceptor due to the delocalized electron (Finkelstein, A. V., Ptitsyn, O. B., Lecture 2. In Protein Physics (Second Edition), Academic Press: Amsterdam, 2016; pp 17-25).More important, through the single crystal structure of the S,S-5b@R,R-CT2, it could be observed that NH-π interactions also play an important role in the host-guest binding.These factors ultimately contribute to the significant enhancement of complexation ability and higher enantioselectivity.
Accordingly, we have included corresponding explanations in the revised manuscript.
3. The absorption and emission changes of the naphthotubes in the presence of the chiral guests will be very helpful for mechanism investigation of the chiral recognition.

Reviewer #2 (Remarks to the Author):
This paper discusses the synthesis and binding properties of tube-like chiral hosts, which are able to enantiomerically discriminate in the binding of a series of chiral guest molecules.In terms of association constant value, enantioselectivities up to a factor of 17 are found.Some of the host-guest complexes are characterized by means of their solid state X-ray structures, in which it is clear that the host-guest binding is governed by multipoint interactions and differences in binding geometry.
The binding mechanisms and the origins of the enantioselectivity are further discussed on the basis of spectroscopic measurements and DFT molecular modeling calculations.
The results in this paper are interesting and will appeal to the general supramolecular chemistry community.As the authors state, it is indeed far from straightforward to achieve decent enantioselective host-guest binding in artificial systems.The authors have succeeded in designing a series of tube-like hosts that fulfill this desire, and have successfully applied the biologicallyinspired concept of multipoint binding interactions to a synthetic system.Still, the newly designed receptors are elegantly simple, while at the same time they are able to bind significantly different types of guests.The new compounds have been characterized satisfactorily and the technical quality of the physical measurements is high.The precise binding mechanisms have been investigated in 4. Line 162: it is not clear what protons 5 and 5' are, where are they located in the molecules?5. Lines 190 and 194: while the general readership of the journal might be aware of what DFT is, abbreviations like PCM and IGM are certainly not common knowledge and should be explained in much more detail.

Response:
Thanks for your helpful suggestion.The spectra of absorption and emission changes of the naphthotubes in the presence of the chiral guests have been included in supporting information ( Figs.S97-S102 and Figs.S111-S112) 4. For the new chiral molecules, their optical rotations are suggested to be provided.Response: Thank you for the helpful suggestion.The optical rotations of six new chiral molecules have been obtained and provided in supporting information.Specific rotation (R,R-6: [α] c, 0.002, DCE), S,S-CT1: [α] 25 D = -136.7 (c, 0.002, DCE), S,S-CT2: [α] 25 D = -10.0(c, 0.002, DCE).