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Helicity and Topological Chirality in HydrogenBonded Supermolecules Characterized by Advanced Graph Set Analysis and Solid-State VCD Spectroscopy Toshiyuki Sasaki, Mikiji Miyata, and Hisako Sato Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.8b00599 • Publication Date (Web): 26 Jun 2018 Downloaded from http://pubs.acs.org on June 28, 2018

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Crystal Growth & Design

Helicity and Topological Chirality in HydrogenBonded Supermolecules Characterized by Advanced Graph Set Analysis and Solid-State VCD Spectroscopy Toshiyuki Sasaki,*,†,# Mikiji Miyata, ‡ Hisako Sato*,† †

Department of Chemistry, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577,

Japan ‡

The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki,

Osaka 567-0047, Japan.

ABSTRACT. The applicability of advanced graph set analysis and solid-state vibrational circular dichroism (SD-VCD) spectroscopy to the characterization of supramolecular chirality has been demonstrated. Recrystallization of R-(+)-1-phenylethylammonium 1-naphthoate affords two polymorphic crystals: one is composed of hydrogen-bonded (HB) twofold helices with helicity while the other contains HB clusters with topological chirality. Handedness and origins of the chirality were crystallographically characterized by advanced graph set analysis. SD-VCD

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measurements were then recorded for these polymorphic crystals using the VCD spectrometer, PRESTO-S-2007 which we developed. Unique VCD spectra were observed because of the difference in features of the chiral supramolecular structures. Enhancement of VCD signals depending on dimensionality of the supermolecules is especially noteworthy. Generality of twofold helices, demonstrated by statistics from the Cambridge Structural Database, and geometical characteristics and theoretical simplicity of the HB clusters, because of their finite number of components connected by closed-hydrogen bonding networks, let them become reasonable representative examples for chiral supermolecules.

INTRODUCTION Supermolecules, or molecular assemblies by non-covalent bonds, are fascinating research targets because of their sophisticated functions, which overwhelming their component single molecules, in accordance with their structural varieties.1–7 Chirality is one of the most fundamental and important structure-dependent properties of supermolecules. Unsurprisingly, supermolecules having structural flexibilities could generate a greater variety of chirality than single molecules.8– 14

On the other hand, the complexity of supramolecular structures makes it difficult to evaluate

their chirality: not only handedness but also origins of chirality. We have been working on characterization of supramolecular chirality by developing advanced graph set analysis15 and solid-state vibrational circular dichroism (SD-VCD) spectroscopy.16–22 The graph set analysis is well established method to understand hydrogen-bonding networks by classifying them into patterns.23–25 Because of robustness, complementarity, and anisotropic nature of hydrogen bonds, the graph set analysis has made great contributions to


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prediction/design of molecular crystal by combination with another concepts such as supramolecular synthon.26 From the viewpoint of chirality, however, the graph set analysis excludes parts of symmetry information as a result of simplification based on undirected graph. The advanced graph set analysis has been developed to characterize chirality by introducing symmetry information to the graph set analysis. With respect to VCD spectroscopy, it has been mainly used to evaluate chiral single molecules or a few molecular assemblies in solution states.27–35 Precise information about conformations as well as absolute configurations of target molecules is obtainable by combining VCD with simulations based on density functional theory (DFT).36,37 For evaluation of supramolecular chirality, it is reasonable to conduct SD-VCD measurements because chiral supermolecules become steady and exhibit clear chirality in solid-state.16–22,38–42 Herein we demonstrate precise characterization of chiral supramolecular structures based on Xray crystallographic study using the advanced graph set analysis and the SD-VCD measurements in combination with linear dichroism (LD) spectra by PRESTO-S-2007 which we developed. Origins of supramolecular chirality and structure-dependent characteristic VCD spectra were successfully clarified by focusing on two types of representative chiral supramolecular structures as model cases. One is twofold helicity.43,44 It is a particularly important and fundamental chirality in crystals as demonstrated by statistics of the Cambridge Crystallographic Data Centre. It should be noted that a twofold helix is achiral and chiral according to “mathematical“43 and “chemical/material“ crystallography,45–52 respectively (Fig. 1a). In matematical crystallography, the twofold helix is the symmetry operation: a rotation of 180° around a line followed by a translation parallel to that


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line. Because of the 180° rotation, the twofold helix has no directionality and is achiral (Fig. 1a(i)). On the other hand, the twofold helix is a helical structure constructed by components with anisotropic shapes in the chemical/material crystallography. Directionality, or handedness, of the twofold helix is definable according to orientations of the components with respect to the helical axis (Fig. 1a(ii)).

Figure 1. (a) Twofold helicity in (i) mathematical and (ii) chemical/material crystallography. (b) Topological chirality of a cubic network. Chirality of (i) faces and (ii) cubes, originating from priority orders of vertices and faces, respectively. The numbers 1 to 3 and 1’ to 3’ denote priority order of the faces and that of the mirror imaged faces, respectively.


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The other is topological chirality of supramolecular clusters which have cubic hydrogen bonding networks (Fig. 1b).53 The supramolecular cluster could be a representative model of chiral supermolecules because of the following two reasons. Firstly, it is comprised of a finite number of molecules, and is thus relatively easy to handle theoretically. To date, VCD spectra of chiral supermolecules have been simulated based on chiral structures of the component single molecules or a fragment of the supermolecule, except in cases where special theoretical techniques have been used.54,55 Alternatively, simulated VCD spectra of supramolecular clusters can be obtained using the entire assembly of component molecules. Secondly, supramolecular clusters have topologically diverse hydrogen bonding networks which strongly reflect key characteristics of supermolecules: variety and flexibility. For example, faces have chirality when their components have a priority order (Fig. 1b(i)). Furthermore, cubic networks also have chirality, which is clarified after defining a priority order of their component faces (Fig. 1b(ii)). RESULTS AND DISCUSSION Crystallographic studies. Crystals composed of chiral supermolecules were prepared from the salt R-(+)-1-phenylethylammonium 1-naphthoate, RPh-1NA (Scheme 1). The salt was recrystallized from ethanol/toluene or chloroform/hexane mixed solutions to afford single crystals for X-ray analysis. From the crystallographic studies on RPh-1NA, two polymorphs were identified: a crystal composed of hydrogen-bonded (HB) supramolecular twofold helices, named RPh-1NA-H, and a crystal composed of HB supramolecular clusters, named RPh-1NA-C. Their crystallographic parameters and crystal structures are summarized in Supporting Information Table S1 and Figure 2, respectively.


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Scheme 1. The chemical structure of the organic salt: R-1-(+)-phenylethylammonium 1naphthoate, RPh-1NA, and structures of its two types of chiral supramolecular structures.

Figure 2. The crystal structures of RPh-1NA-H: (a) a hydrogen-bonded supramolecular twofold helix, (b) a molecular packing diagram viewed down the b axis, and RPh-1NA-C: (c) a hydrogen-bonded supramolecular cluster and (d) a molecular packing diagram viewed down the a axis.

The crystal structures of RPh-1NA-H and RPh-1NA-C belong to Sohncke space groups C2 and P1, respectively, forming chiral crystals. In the crystal structure of RPh-1NA-H, HB twofold helices exist along the b axis. The N···O distances for the N-H···O hydrogen bonds are 2.73,


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2.76, and 2.79 Å. The helical pitch is 6.34 Å. HB twofold helices stack along the a and c axes with twofold rotation and twofold helical manners, respectively. With respect to the crystal structure of RPh-1NA-C, the HB supramolecular clusters comprise twelve hydrogen bonds with N···O distances in the range 2.71–2.95 Å. The HB supramolecular clusters stack along the a, b, and c axes and are related by translation symmetry only.

Supramolecular helicity of the HB twofold helix. Firstly, chirality of the HB supramolecular twofold helix in the crystal RPh-1NA-H was evaluated from the viewpoint of the chemical/material crystallography (Fig. 3). The HB supramolecular twofold helix is repetition of a ring-type hydrogen bonding network, or a “face”, which is composed of ten atoms, including three hydrogen bond acceptors and four hydrogen bond donors. According to the graph set analysis,15 the face is denoted as R34(10) (Fig. 3a). Furthermore, carboxylate anions in the face have two types of oxygen atoms: oxygen α (Oα) and oxygen β (Oβ), which are doubly and singly hydrogen bonded, respectively. The positive direction of carboxylate anions was defined as Oα to Oβ. The directionality of the face is based on the positive direction of the component carboxylate anion, both of which oxygen atoms are included in the face. Consequently, the face and its mirror-imaged one in the HB supramolecular twofold helix are described as R34(10Re) and R34(10Si), respectively, according to the advanced graph set analysis.15 The symbols “Re” and “Si” denote clockwise and counterclockwise directions, respectively. Chirality of the face and the mirror-imaged one was then defined as right-handed (supR) and left-handed (supS), respectively, based on their directionality as is observable in the projection given as Figure 3a. The superscript “sup” is attached to R and S symbols to distinguish supramolecular chirality from molecular chirality.56–59 The HB supramolecular twofold helix in the crystal structure of RPh-


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1NA-H is composed of repetition of the supR face, and thus it is defined as a right-handed helix, sup

P (Fig. 3b). In the same way, the mirror-imaged one is defined as a left-handed helix,

sup

M.

The superscript “sup” is attached to P and M symbols to distinguish supramolecular helicity from molecular helicity.56–59 The supramolecular helicity is also definable according to the supramolecular-tilt-chirality method by focusing on hydrogen bonds which are in front of the twofold helical axis.47–49 The hydrogen bonds tilt to the right and left, and the supramolecular helicity is denoted as supP, and supM, respectively.

Figure 3. (a) The right-handed (Real,

sup

R) and mirror-imaged left-handed (Mirror,

sup

S) ring-

type hydrogen bonding networks with the descriptions R34(10Re) and R34(10Si), respectively, according to the advanced graph set analysis.15 (b) The right-handed (Real, imaged left-handed (Mirror,

sup

sup

P) and mirror-

M) hydrogen-bonded supramolecular twofold helices in the

crystal structure of RPh-1NA-H. Substituents are omitted for clarity.

Supramolecular topological chirality of the HB cluster. The HB supramolecular cluster in RPh-1NA-C has a closed cubic hydrogen bonding network (Fig. 4a,b), which is similar to the hydrogen bonding networks of water octamers with topological chirality.60 The cubic hydrogen bonding network has C2 symmetry and is composed of six ring-type hydrogen bonding networks, or faces, with and without chirality (Fig. 4c). As with the faces of the HB supramolecular twofold helix, each of the six faces: face-1, face-2, face-3, face-4, face-5, and face-6, is denoted as R44(12m), R44(12Si), R34(10Re), R34(10Re), R24(8m), and R44(12m), respectively, according to


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the advanced graph set analysis.15 The symbol “m” denotes mirror symmetry. The chirality of the HB supramolecular cluster is dependent on the arrangement of these six chiral or achiral faces. When face-1 to 3 are arranged clockwise around an ammonium cation, the HB supramolecular cluster is defined as right-handed (supR) (Fig. 4d). For comparison, its mirror-imaged left-handed cubic hydrogen bonding network (supS) is also shown.

Figure 4. (a) The cubic hydrogen bonding network of a supramolecular cluster in RPh-1NA-C. (b) Schematic representation of the cubic hydrogen bonding network: mirror (left) and real ones (right). (c) Six ring-type hydrogen bonding networks, or faces, which compose the cubic hydrogen bonding network. The face-1, -5, -6, and -2, -3, -4 are achiral and chiral, respectively. Each of the faces is characterized by the advanced graph set analysis.15 (d) Right- (Real,

sup

R)

and left-handedness (Mirror, supS) of the cubic hydrogen bonding networks of the supramolecular cluster. The numbers 1 to 3 and 1’ to 3’ denote face numbers in the figure (c) and their mirrorimaged faces, respectively.

It has been well known that the chirality of supermolecules is flexible and variable or switchable depending on surrounding environments even when they are constructed of one-


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handed chiral single molecules.15–17,61,62 Therefore, chirality characterization by focusing on the arrangement of components instead of their chirality is important to handle chiral supermolecules reasonably. Vibrational spectroscopy of the chiral supermolecules. Infrared (IR) and VCD spectra of the RPh-1NA-H, RPh-1NA-C, and their enantiomeric organic crystals: SPh-1NA-H, and SPh1NA-C, were then measured by KBr method to evaluate their supramolecular chirality spectroscopically in the solid-state (Fig. 5). By measuring LD and VCD spectra several times after rotating or reversing the KBr pellets (Figs. 5a and 5b bottom), it was confirmed that the effects of LD on the VCD spectra were negligible. It is possible to make the VCD spectra of enantiomers completely symmetric by spectra correction based on subtraction of average values of enantiomeric spectra. However, the spectra correction could cause problems, e.g. mixing up false and real signals, especially in the case of SD-VCD because of the difficulty in forming ideal KBr pellets. Therefore, the VCD spectra, which look not mirror-imaged because of non ideal KBr pellets, were evaluated without any correction. The IR spectra show slight differences while the VCD spectra were considerably different, reflecting differences in supramolecular structure and chirality. The enantiomeric pairs: RPh-1NA-H/SPh-1NA-H and RPh-1NA-C/SPh1NA-C, showed mirror-imaged Cotton effects, especially in the 1500–1600 cm-1 (RG1), and 1300–1400 cm-1 (RG2) regions. The VCD signals were then assigned to molecular vibrations based on simulations calculated by DFT (Figs. 5c and 5d).63,64 The partial and complete supramolecular structures of the HB twofold helix and cluster, respectively, were extracted from the crystal structures for the calculation. The supermolecules were then modified to reduce calculation cost by substituting the naphthyl groups to methyl groups (Supporting Information Fig. S1). Difference in wavenumber between the measured and simulated IR/VCD spectra is


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attributable to their calculation condition, especially the use of simplified model structures rather than whole crystal structures. Unsurprinsingly, IR/VCD signals of RPh/SPh-1NA-H and RPh/SPh-1NA-C observed in the same frequency regions were assigned to the same types of vibrational modes. The signals in the RG1 (Nos. 1–6 and 1–5 in the spectra of RPh-1NA-H and RPh-1NA-C, respectively) are attributable to stretching and bending vibrations of C=O and N–H, respectively. The signals in the RG2 (Nos. 7–12 and 6, 7 in the spectra of RPh-1NA-H and RPh1NA-C, respectively) originate from stretching vibrations of C–C of carboxylic groups and their α-carbons and bending vibrations of C–H of α-carbon of amines, reflecting molecular chirality strongly. It could be said that the signals in RG1 and RG2 mainly originate from suramolecular and molecular chirality, respectively. In addition, R/SPh-1NA-H show larger VCD signals in RG1 than those in RG2 while R/SPh-1NA-C has the opposite trend. These results indicate an important fact that VCD signals are much more enhanced by the formation of higher order supermolecules. A similar observation has been described for proteins.65 These results clearly demonstrate that SD-VCD spectroscopy is applicable to the characterization not only of supramolecular helicity but also other types of supramolecular chirality, namely topological chirality of HB supramolecular clusters in the present case.


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Figure 5. Measured VCD (top), IR (middle), and LD (bottom) spectra of (a) RPh- and SPh1NA-H and (b) RPh- and SPh-1NA-C crystals. Simulated VCD (top) and IR (bottom) spectra of hydrogen-bonded supramolecular structures in (c) RPh-1NA-H and (d) RPh-1NA-C crystals.

CONCLUSION The applicability of the advanced graph set analysis and solid-state vibrational circular dichroism (SD-VCD) spectroscopy for the evaluation of unique supramolecular chirality has been demonstrated. Two types of chiral supermolecules: a hydrogen-bonded (HB) twofold helix and a HB cluster, were confirmed in the two polymorphic crystals obtained from R-(+)-1phenylethylammonium 1-naphthoate (RPh-1NA). Their supramolecular chirality, helicity and


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topological chirality including their origins were successfully detected and characterized by Xray crystallography using the advanced graph set analysis and SD-VCD spectroscopy in combination with simulations by density functional theory. With respect to the VCD spectra, they show a clear dependence on supramolecular structures. In particular, it was experimentally confirmed that VCD signals are enhanced by the formation of supermolecules with high dimensionality. These results suggest the future applicability of VCD spectroscopy to structure predictions of chiral supermolecules in both solution and solid-state. ASSOCIATED CONTENT Supporting Information. The following files are available free of charge. The experimental details, the crystallographic parameters, and model structures for IR/VCD simulations of the crystals RPh-1NA-H and RPh-1NA-C (PDF) The Crystallographic Information Files: CCDC 1822565 and 1822566 (CIF). They are also obtained free of charge from The Cambridge Crystallographic Data Centre. AUTHOR INFORMATION Corresponding Author *(T.S.) E-mail: [email protected]; tel. +81 45 787 2184 Present Addresses #

Department of Materials System Science, Yokohama City University, 22-2 Seto, Kanazawa-ku,

Yokohama, Kanagawa 236-0027, Japan. Author Contributions


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The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. All authors contributed equally. Notes Any additional relevant notes should be placed here. ACKNOWLEDGMENT This work was financially supported by a JSPS KAKENHI Grant-in-Aid for JSPS Research Fellow (Number 15J00237 to T.S.), and JSPS MEXT KAKENHI Grants-in-Aid for Exploratory Research (Number JP26620068 to H.S.) and Innovative Areas (Number JP16H00840 to H.S.). The authors thank Mr. Tsubasa Uesugi for IR, VCD, and LD measurements. The computations were performed using the Research Center for Computational Science, Okazaki, Japan. REFERENCES (1) Lehn, J.-M. Supramolecular Chemistry: Concepts and Perspectives; Wiley-VCH: Weinheim, Germany, 1995. (2) Verbiest, T.; Elshocht, S. V.; Kauranen, M.; Hellemans, L.; Snauwaert, J.; Nuckolls, C.; Katz, T. J.; Persoons, A. Strong Enhancement of Nonlinear Optical Properties Through Supramolecular Chirality. Science, 1998, 282, 913. (3) Fiedler, D.; Leung, D. H.; Bergman, R. G.; Raymond, K. N. Selective Molecular Recognition, C−H Bond Activation, and Catalysis in Nanoscale Reaction Vessels. Acc. Chem. Res. 2005, 38, 351. (4) Imai, Y.; Takeshita, M.; Sato, T.; Kuroda, R. Successive Optical Resolution of Two Compounds by One Enantiopure Compound. CrystEngComm 2006, 1070.


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For Table of Contents Use Only Helicity and Topological Chirality in Hydrogen-Bonded Supermolecules Characterized by Advanced Graph Set Analysis and Solid-State VCD Spectroscopy Authors: Toshiyuki Sasaki,* Mikiji Miyata, Hisako Sato*

Two types of chiral hydrogen-bonded supramolecular structures: a twofold helix with helicity and a cluster with topological chirality, were confirmed in polymophic crystals. The origins of their unique supramolecular chirality were clarified by advanced graph set analysis crystallographically. At the same time, solid-state vibrational circular dichroism spectroscopy successfully characterized their supramolecular structure-dependent chirality.


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Helicity and Topological Chirality in Hydrogen ... - ACS Publications

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