PREPARATION METHOD OF CRYSTAL STRUCTURE ANALYSIS SAMPLE FOR STRUCTURAL ANALYSIS USING CRYSTAL SPONGE METHOD

Abstract

An object of the present invention is to provide a method of preparing a sample for crystallographic analysis used for structure determination based on the crystalline sponge method. The present invention provides a method of preparing a sample for crystallographic analysis used for structure determination based on the crystalline sponge method, the method including the steps: (A) forming an ionic pair of a target compound of analysis with a counterionic compound, and (B) soaking the ionic pair of the compounds into a crystalline sponge, wherein the target compound of analysis is a basic compound or an acidic compound.

Claims

1. A method of preparing a sample for crystallographic analysis used for structure determination based on the crystalline sponge method, the method comprising the steps: (A) forming an ionic pair of a target compound of analysis with a counterionic compound, and (B) soaking the ionic pair of the compounds into a crystalline sponge, wherein the target compound of analysis is a basic compound or an acidic compound.

2. The method according to claim 1, wherein the target compound of analysis is a basic compound, and wherein the basic compound forms an ionic pair with an acidic compound in the step (A).

3. The method according to claim 1, wherein the target compound of analysis is an acidic compound, and wherein the acidic compound forms an ionic pair with a basic compound in the step (A).

4. The method according to any one of claim 1, wherein the step (A) and the step (B) are performed sequentially or simultaneously.

5. A method of determining the structure of a target compound of analysis, the method comprising the steps of: performing the preparation method according to any one of claim 1 to prepare a sample for crystallographic analysis; and performing structural analysis of the prepared sample for crystallographic analysis.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0016] FIG. 1 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of (1R,2R)-2-(cyclopropylamino)cyclohexanol, a target compound of analysis, based on the CS method.

[0017] FIG. 2 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of methanesulfonic acid, a target compound of analysis, based on the CS method.

[0018] FIG. 3 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of trifluoroacetic acid, a target compound of analysis, based on the CS method.

[0019] FIG. 4 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between (1R,2R)-2-(cyclopropylamino) cyclohexanol as a target compound of analysis and methanesulfonic acid as a counterionic compound.

[0020] FIG. 5 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 4.

[0021] FIG. 6 shows a result (in the asymmetric unit solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between (1R,2R)-2-(cyclopropylamino) cyclohexanol as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0022] FIG. 7 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 6.

[0023] FIG. 8 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between 2-phenylethylamine as a target compound of analysis and trifluoromethanesulfonic acid as counterionic compound.

[0024] FIG. 9 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 8.

[0025] FIG. 10 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between 2-phenylethylamine as a target compound of analysis and trifluoroacetic acid as a counterionic compound.

[0026] FIG. 11 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 10.

[0027] FIG. 12 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between rac-trans-2-(phenethylamino)cyclopentan-1-ol as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0028] FIG. 13 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 12.

[0029] FIG. 14 shows a result (chromatogram) from analyzing rac-trans-2(phenethylamino)cyclopentan-1-ol by HPLC.

[0030] FIG. 15 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between a compound corresponding to Peak 1 in FIG. 14 as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0031] FIG. 16 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 15.

[0032] FIG. 17 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between a compound corresponding to Peak 2 in FIG. 14 as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0033] FIG. 18 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 17.

[0034] FIG. 19 shows a result (chromatogram) from analyzing rac-trans-2-(phenethylamino)cycloheptan-1-ol by HPLC.

[0035] FIG. 20 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between a compound corresponding to Peak 3 in FIG. 19 as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0036] FIG. 21 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 20.

[0037] FIG. 22 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between a compound corresponding to Peak 4 in FIG. 19 as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0038] FIG. 23 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 22.

[0039] FIG. 24 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of N,N-dimethylcyclohexylamine, a target compound of analysis, based on the CS method.

[0040] FIG. 25 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between N,N-dimethylcyclohexylamine as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0041] FIG. 26 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 25.

[0042] FIG. 27 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between 1,1,3,3-tetramethylguanidine as a target compound of analysis and trilluoromethanesulfonic acid as a counterionic compound.

[0043] FIG. 28 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 27.

[0044] FIG. 29 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between 1,3-diphenylguanidine as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0045] FIG. 30 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 29.

[0046] FIG. 31 shows a result (in the asymmetric unit; solvent molecules are omitted) from crystallographic analysis of a sample for crystallography based on the CS method, wherein the sample is prepared by formation of an ionic pair between diazabicycloundecene as a target compound of analysis and trifluoromethanesulfonic acid as a counterionic compound.

[0047] FIG. 32 shows an enlarged view of a part of the crystal structure enclosed by a dotted line in FIG. 31.

DETAIL DESCRIPTION OF THE INVENTION

[0048] The present invention is a method for preparing a sample for crystallography used for structural analysis of a target compound of analysis. The method of the invention comprises a step (A) of forming an ionic pair of a target compound of analysis with a counterionic compound, and a step (B) of soaking the ionic pair of the compounds into a crystalline sponge.

[0049] In the step (A) of the method according to the invention, the target compound of analysis is allowed to form an ionic pair with a counterionic compound. In this respect, the “ionic pair” refers to a combination of two oppositely charged compounds, such as a combination of a cationic compound and an anionic compound. Moreover, the “counterionic compound” refers to a compound with an opposite charge to the target compound of analysis.

[0050] In the method of the invention, the target compound of analysis can be either a basic compound or an acidic compound. Preferably, the target compound of analysis is an organic compound.

[0051] The basic compound is a compound with one or more functional groups that individually act as a proton (H.sup.+) acceptor, preferably a compound with lone pair electrons. The basic compound to be analyzed is not specifically limited but includes nitrogen-containing compounds (for example, nitrogen-containing aromatic compounds, nitrogen-containing aliphatic compounds, and the like), such as primary amines, secondary amines, tertiary amines, guanidine, amidine, pyridine, and pyrrole,

[0052] The acidic compound is a compound with one or more functional groups that individually act as a proton (H.sup.+) donor, preferably a compound capable of releasing a proton (H.sup.+). The acidic compound to be analyzed is not specifically limited but includes, for example, acidic compounds such as carboxylic acids, sulfonic acids, and organic phosphoric acids.

[0053] The target compound of analysis is preferably a compound which is not amenable to structural analysis based on the crystalline sponge method because of the influence of reactivity of the compound (for example, destruction of a crystalline sponge) or the influence of molecular structure or molecular size of the compound (for example, incompatible interaction with the framework of a crystalline sponge). For example, many basic compounds are nucleophilic compounds and can be analyzed by the method of the invention. Additionally, the target compound of analysis by the method of the invention can be a compound that interacts with the framework of a crystalline sponge so weakly that the compound is not regularly held in pores, or on the contrary, so strongly that the compound is only allowed to move in a limited space near the entrance of pores and is unevenly distributed inside the pores, which causes a difficulty in analysis of the compound, among basic and acidic compounds.

[0054] In the method of the invention, a target compound of analysis can be paired with an acidic compound in the step (A) for ionic pair formation when the target compound of analysis is a basic compound. Any acidic compound can be selected as the compound that forms an ionic pair with the target compound of analysis, and the acidic compound can be selected such that the ionic pair formed between the compounds is small enough in size to pass through the pores of a crystalline sponge standard pore size: 10Å×10Å). Moreover, the acidic compound can also be selected considering the interaction (for example, π-πbond, CH-πbond, hydrogen bond, halogen -πbond, or the like) with a polymer metal complex used in the framework structure of a crystalline sponge.

[0055] In the method of the invention, a target compound of analysis can be paired with a basic compound in the step (A) for ionic pair formation when the target compound of analysis is an acidic compound. Any basic compound can be selected as the compound that forms an ionic pair with the target compound of analysis, and the basic compound can be selected such that the ionic pair formed between the compounds is small enough in size to pass through the pores of a crystalline sponge (standard pore size: 10Å×10Å). Moreover, the basic compound can also be selected considering the interaction (for example, π-πbond, CH-πbond, hydrogen bond, halogen-πbond, or the like) with a polymer metal complex used in the framework structure of a crystalline sponge.

[0056] In cases where the target compound of analysis in the method of the invention is a compound with functional groups that individually act as either a proton (H.sup.+) acceptor or a proton (H.sup.+) donor in the molecule, an ionic pair may be formed by adding a counterionic compound that reacts with either of the functional groups or by adding counterionic compounds that react with both the functional groups. Moreover, in cases where the target compound of analysis contains multiple functional groups that individually act as a proton (H.sup.+) acceptor or multiple functional groups that individually act as a proton (H.sup.+) donor, a counterionic compound that reacts with only some of the functional groups or counterionic compounds that react with all the functional groups may be added.

[0057] An ionic pair can be formed by mixing a target compound of analysis and a counterionic compound in a solvent that can dissolve both the compounds. The solvent is not specifically limited as long as both the compounds can be dissolved and mixed in the solvent, and examples of the solvent include aliphatic hydrocarbons (for example, n-hexane, pentane, heptane, octane, nonane, decane, cyclopentane, cyclohexane, and the like), aromatic hydrocarbons (for example, benzene, toluene, xylene, and the like), halogenated hydrocarbons (for example, chloroform, dichloromethane, chloromethane, dichloroethane, chloroethane, and the like), ethers (for example, diethyl ether, dimethyl ether, methyl tert-butyl ether, tetrahydrofuran, and the like), esters (for example, methyl acetate, ethyl acetate, methyl formate, ethyl formate, and the like), ketones (for example, acetone, methyl ethyl ketone, pentanone, and the like), alcohols (for example, methanol, ethanol, propanol, butanol, pentanol, hexanol, and the like), nitriles (for example, acetonitrile, and the like), amides (for example, dimethylformamide, dimethylacetamide, and the like), dimethyl sulfoxide or water, and a combination of the above solvents in any blending ratio. In cases where the step (A) and the step (B) are performed sequentially or simultaneously as described below, the solvent can be selected considering the step of soaking in a crystalline sponge (Step B). In other words, when a solvent is selected for formation of an ionic pair with a target compound of analysis, it is desirable to consider the potential of the solvent to damage or dissolve a crystalline sponge depending on the combination of the type of the crystalline sponge used and the composition of the solvent in which the crystalline sponge is soaked because such damage to or dissolution of a crystalline sponge may compromise the function of the crystalline sponge in the crystalline sponge method.

[0058] For the mixing between a target compound of analysis and a counterionic compound, the target compound of analysis and the counterionic compound can be added to a solvent to yield arbitrary concentrations, provided that the concentrations are enough to allow formation of an ionic pair. However, it is preferable that both the compounds are added to a solvent to yield equimolar concentrations. Moreover, the ionic pair formation may be simultaneous with the soaking in a crystalline sponge in the step (B) described below. In other words, the step (A) and the step (B) can be performed simultaneously by separately dissolving the target compound of analysis and the counterionic compound in a solvent and adding the resulting solutions sequentially or simultaneously to a crystalline sponge.

[0059] In the step (B), the target compound of analysis in the ionic pair formed in the step (A) is soaked into a crystalline sponge to prepare a sample for crystallography. In this respect, the crystalline sponge is a single crystal material with three-dimensionally regular porous structures and can he made, for example, from metal-organic frameworks (MOF:), covalent organic frameworks (COF's), inorganic compounds, such as zeolites, or the like. However, the source of the single crystal material is not limited, provided that a compound is incorporated as a guest into pores of the single crystal material. An example of the crystalline sponge composed of a metal-organic framework is a polymer metal complex with a three-dimensional network structure, which is composed of a ligand with two or more coordination sites and a metal ion as a coordination center. The “three-dimensional network structure” as used herein refers to a network structure composed of repeating structural units, extending in three dimensions, each unit formed by a ligand ligand with two or more coordination sites or any of other monodentate ligands) and a metal ion bound thereto.

[0060] A single crystal metal-organic framework that can be used as a crystalline sponge is described in the following literature: for example, Nature 2013, 495, 461-466; Chem. Commun. 2015, 51. 11252-11255; Science 2016, 353, 808-811; Chem. Commun. 2016, 52, 7013-7015; Chem. Asian J. 2017, 12, 208-211; J. Am Chem, Soc. 2017, 139, 11341-11344; and JP 5969616 B. A[(ZnX.sub.2).sub.3(tpt).sub.2(solvent).sub.a].sub.n-type crystalline sponge (wherein X represents a halogen atom such as chlorine, bromine, iodine, or fluorine, and “tpt” represents 2,4,6-tri(4-pyridyl)-1,3,5-triazine, and “solvent” represents a solvent confined in pores and other structures, and “a” represents a number of not less than 0, and “n”represents a positive integer; the same applies below) described, for example, in Nature 2013, 495, 461-466 and Chem. Commun. 2015, 51, 11252-11255 is preferred, and a [(ZnCl.sub.2).sub.3(tpt).sub.2.Math.(solvent).sub.a].sub.n-type crystalline sponge is more preferred, in consideration of convenience for single crystal preparation.

[0061] For the production of a sample for crystallography, the method for soaking the target compound of analysis, a member of the formed ionic pair, into a crystalline sponge for incorporation of the target compound as a guest into pores is not specifically limited, as long as the method allows the target compound to be incorporated as a guest into pores. For example, the target compound of analysis can be incorporated as a guest into pores by a method described in the following literature: for example, IUCrj 2016, 3, 139-151; Chem. Fur. J. 2017, 23, 15035-15040; CrystEngComm, 2017, 19, 4528-4534; Org. Lett. 2018, 20, 3536-3540; Science 2016, 353, 808-811; and Chem. Commun. 2015. 51, 11252-11255. For example, the target compound of analysis can be incorporated into cavities in the three-dimensional network structure of a crystalline sponge by soaking the compound into the crystalline sponge at a temperature of 0 to 120° C for a period of 0.5 hours to 14 days.

[0062] Another aspect of the present invention provides a method of determining the structure of a target compound of analysis, wherein the method comprises a step of performing structural analysis of a sample for crystallography obtained by performing the method of the invention for preparation of a sample for crystallography. Any technique selected from X-ray diffraction, neutron diffraction, and electron diffraction may be used for the structural analysis of the sample for crystallography. Additionally, the measurement data, or the structure of the target compound of analysis, can be analyzed by a known method, such as a method described in WO 2014/038220 or in IUCrJ 2016, 3, 139-151.

[0063] Advantageously, the method of the invention allows for the structural analysis of a target compound of analysis even if the compound is not amenable to crystallographic analysis based on the crystalline sponge method due to the properties of the compound in the unmodified state. In addition, it is another advantage that the method of the invention allows for simultaneous performance of the ionic pair formation and the soaking in a crystalline sponge, which enables quick analysis by a simple procedure.

EXAMPLES

[0064] The present invention will he specifically described in more detail by examples below, but the present invention is not limited to those examples.

(Crystalline Sponge)

[0065] A [(ZnCl.sub.2).sub.3(tpt).sub.2.Math.(n-hexane).sub.a].sub.n-type crystalline sponge prepared according to the method described in Non-Patent Document 1 was used in the examples.

(Single Crystal X-Ray Structural Analysis)

[0066] In the examples, single crystal X-ray structural analysis was performed using a single crystal X-ray diffractometer Synergy-R (Rigaku Corporation). The data was acquired using a radiation source of Cu Kα (λ=1.5418 Å) at a measurement temperature of 100 K. The diffraction data was analyzed according to the method described in Non-Patent Document 1.

Example 1: X-Ray Structural Analysis Based on the Crystalline Sponge Method (1)

[0067] In Example 1. the crystalline sponge method was evaluated for applicability to crystallographic analysis of basic and acidic compounds.

(1) Target Compounds of Analysis

[0068] Target compounds of analysis in Example I are as shown in Table 1.

TABLE-US-00001 TABLE 1 Target compounds of analysis Comparative Basic (1R,2R)-2-(cyclopropylamino)cyclohexanol Example 1 compounds (*) Comparative (1R,2R)-2-(cyclopropylamino)cyclohexanol Example 2 (*) Comparative 2-phenylethylamine (Tokyo Chemical Example 3 Industry Co., Ltd.) Comparative rac-trans-2-(phenethylamino)cyclopentan- Example 4 1-ol (**) Comparative Acidic trifluoromethanesulfonic acid (Tokyo Example 5 compounds Chemical Industry Co., Ltd.) Comparative methanesulfonic acid (Tokyo Chemical Example 6 Industry Co., Ltd.) Comparative trifluoroacetic acid (Tokyo Chemical Example 7 Industry Co., Ltd.) (*) produced by a known method (Bull. Chem. Soc. Jpn. 2018, 91, 678-683). (**) produced by a known method (WO 2015/194508).

(2) Experimental Procedure

A. Comparative Examples 1 and 3 to 5

[0069] In Comparative Examples 1 and 3 to 5, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial, A target compound of analysis was dissolved in dimethoxyethane to a concentration of 1 mg/mL, and 5 μL of the resulting solution (equivalent to 5 μg of the target compound of analysis) was added to the above vial containing the crystalline sponge. The vial was capped and sealed and then incubated at 50° C. for 1 day. One day later, the crystalline sponge was recovered from the solution, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

B. Comparative Example 2

[0070] In Comparative Example 2, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL, V-bottom vial. A target compound of analysis was dissolved in dimethoxyethane to a concentration of 1 mg/mL, and 1 μL of the resulting solution (equivalent to 1 μg of the target compound of analysis) was added to the above vial containing the crystalline sponge. The vial was capped and sealed, and the cap was pierced with an injection needle, and the vial was incubated at 4° C. for 5 days to gently evaporate the solvent. Five days later, the crystalline sponge was recovered from the vial, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

C. Comparative Example 6

[0071] In Comparative Example 6, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-ml V-bottom vial. A target compound of analysis was dissolved in dimethoxyethane to a concentration of 1 mg/mL, and 5 μL of the resulting solution (equivalent to 5 μg of the target compound of analysis) was added to the above vial containing the crystalline sponge. The vial was capped and sealed and then incubated. at 50° C. for 2 days. Two days later, the crystalline sponge was recovered from the solution, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

D. Comparative Example 7

[0072] In Comparative Example 7, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial. A target compound of analysis was dissolved in dimethoxyethane to a concentration of 1 mg/mL, and 5 μL of the resulting solution (equivalent to 5 μg of the target compound of analysis) was added to the above vial containing the crystalline sponge. The vial was capped and sealed, and the cap was pierced with an injection needle, and the vial was incubated at 50° C. for 1 day to gently evaporate the solvent. One day later, the crystalline sponge was recovered from the vial, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

(3) Results

[0073] The results from the X-ray crystallographic analysis of the target compounds analyzed in Comparative Examples 1, 6, and 7 were as shown in FIGS. 1, 2, and 3, respectively, which indicated failure in observing the crystal structures of the target compounds of analysis. In Comparative Examples 1 and 7, degradation products from the framework of the crystalline sponge were observed to be incorporated as a guest, as shown in a region enclosed by a dotted line in FIGS. 1 and 3. In Comparative Example 6, only the framework of the crystalline sponge was observed as seen in FIG. 2, which suggest that the target compound of analysis was not held in pores of the crystalline sponge. Additionally, the results from the X-ray crystallographic analysis of the target compounds analyzed in Comparative Example 2 (the temperature and time conditions employed in Comparative Example 1 for soaking in a crystalline sponge were changed to milder conditions as described in Non-Patent Document 1) and Comparative Examples 3 and 4 were similar to that in Comparative Example 1, which indicated failure in observing the crystal structures of the target compounds of analysis (data not shown). In Comparative Example 5, the crystalline sponge was found to be dissolved in the solution one day after incubation and not to exist as a crystal, and the crystalline sponge was thus not subjected to the X-ray analysis. Without being bound by the following theory, it was understood that these resulted from destruction of the crystalline sponge-constituting framework due to the reactivity (nucleophilicity, coordinating property, and the like) of the basic or acidic compounds as targets of analysis or from incompatible interaction between the target compounds of analysis and the crystalline sponge.

[0074] In Non-Patent Document 1, the [(ZnCl.sub.2).sub.3(tpt).sub.2.Math.(n-hexane).sub.a].sub.n-type crystalline sponge is described to be suitable for analysis of nitrogen-containing compounds, but the results of Comparative Examples 1 to 4 indicated that there are practically many examples of basic compounds that are not amenable to crystallographic analysis based on the crystalline sponge method due to the reactivity (nucleophilicity coordinating property, and the like) of the target compounds of analysis. Additionally, the results of Comparative Examples 5 to 7 indicated that there are examples of acidic compounds that are not amenable to crystallographic analysis based on the crystalline sponge method due to the reactivity of the compounds, and furthermore that there are examples of acidic compounds that are amenable to crystallographic analysis due to the incompatible interaction with a crystalline sponge:

Example 2: X-Ray Structural Analysis of a Compound in an Ionic Pair (2)

[0075] In Example 2, the crystalline sponge method was evaluated for applicability to crystallographic analysis of target compounds of analysis, following ionic pair formation with counterionic compounds.

(1) Ionic pairs

[0076] Target compounds of analysis and counterionic compounds for ionic pair formation in Example 2 are as shown in Table 2.

TABLE-US-00002 TABLE 2 Ionic pairs Crystal structure Target compound of analysis Counterion Crystallographic Crystal (enlarged (basic compound) (acidic compound) data structure view) Practical (1R,2R)-2-(cyclopropylamino)cyclohexanol methanesulfonic acid Table 3 FIG. 4 FIG. 5 Example 1 1 mg/mL [the concentration at the time of 0.5 mg/mL [the concentration mixing and dissolving] at the time of mixing and 5 μg [the amount at the time of soaking in dissolving] crystalline sponge] 2.5 μg [the amount at the time of soaking in crystalline sponge] Practical (1R,2R)-2-(cyclopropylamino)cyclohexanol trifluoromethanesulfonic acid Table 4 FIG. 6 FIG. 7 Example 2 1 mg/mL [the concentration at the time of 1 mg/mL [the concentration at mixing and dissolving] the time of mixing and 5 μg [the amount at the time of soaking in dissolving] crystalline sponge] 5 μg [the amount at the time of soaking in crystalline sponge] Practical 2-phenylethylamine trifluoromethanesulfonic acid Table 5 FIG. 8 FIG. 9 Example 3 1 mg/mL [the concentration at the time of 1.3 mg/mL [the concentration mixing and dissolving] at the time of mixing and 5 μg [the amount at the time of soaking in dissolving] crystalline sponge] 6.5 μg [the amount at the time of soaking in crystalline sponge] Practical 2-phenylethylamine trifluoroacetic acid Table 6 FIG. 10 FIG. 11 Example 4 1 mg/mL [the concentration at the time of 1 mg/mL [the concentration at mixing and dissolving] the time of mixing and 5 μg [the amount at the time of soaking in dissolving] crystalline sponge] 5 μg [the amount at the time of soaking in crystalline sponge] Practical rac-trans-2-(phenethylamino)cyclopentan- trifluoromethanesulfonic acid Table 7 FIG. 12 FIG. 13 Example 5 1-ol 0.7 mg/mL [the concentration 1 mg/mL [the concentration at the time of at the time of mixing and mixing and dissolving] dissolving] 5 μg [the amount at the time of soaking in 3.5 μg [the amount at the time crystalline sponge] of soaking in crystalline sponge]

(2) Experimental Procedure

A. Practical Examples 1, 2, and 5

[0077] in Practical Examples 1, 2, and 5, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial. A target compound of analysis and a counterion were both mixed and dissolved in dimethoxyethane to yield the concentrations shown in Table 2, and 5 μL of the resulting solution was added to the above vial containing the crystalline sponge. The vial was capped and sealed and then incubated at 50° C. for 2 days. Two days later, the crystalline sponge was recovered from the solution, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

B. Practical Examples 3 and 4

[0078] In Practical Examples 3 and 4, one granule of the crystalline sponge and n-hexane (45 μL ) were added together to a 1.2-mL V-bottom vial. A target compound of analysis and a counterion were both mixed and dissolved in dimethoxyethane to yield the concentrations shown in Table 2, and 5 μL of the resulting solution was added to the above vial containing the crystalline sponge. The vial was capped and sealed, and the cap was pierced with an injection needle, and the vial was incubated at 50° C. for 1 day to gently evaporate the solvent. One day later, the crystalline sponge was recovered from the vial, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

(3) Results

[0079] The crystallographic data and X-ray crystal structure (in the asymmetric unit) of each of the practical examples were as shown in Tables 3 to 7 and in FIGS. 4, 6, 8, 10, and 12 (enlarged views of the crystal structures are shown in FIGS. 5, 7, 9, 11, and 13), respectively. in any of the practical examples, the crystal structures of a basic compound added as a target compound of analysis and of an acidic compound added as a counterion were observed. The basic compounds and the acidic compounds were understood to stay in proximity to each other as ionic pairs and to be incorporated as ionic pairs into pores of the crystalline sponge. It is suggested that the framework of the crystalline sponge was prevented from degradation by masking the reactivity of the basic compounds, or alternatively by masking the reactivity of the acidic compounds, and this allowed for crystallographic observation of the target compounds of analysis.

TABLE-US-00003 TABLE 3 Crystallographic Data (Practical Example 1) Crystal system Monoclinic a (Å) 32.9394(2) b (Å) 14.4644(1) c (Å) 31.3590(2) β (°) 101.055(1) V (Å.sup.3) 14663.70(17) Z 4 Space group C2 Rint 0.0228 R.sub.1 0.0617 wR.sub.2 0.1923 GoF 1.089 Flack parameter (Parsons) 0.088(6)

TABLE-US-00004 TABLE 4 Crystallographic Data (Practical Example 2) Crystal system Monoclinic a (Å) 33.14256(13) b (Å) 14.49914(4) c (Å) 30.99391(10) β (°) 100.8389(4) V (Å.sup.3) 14628.06(9) Z 4 Space group C2 Rint 0.0201 R.sub.1 0.0610 wR.sub.2 0.1879 GoF 1.102 Flack parameter (Parsons) 0.037(4)

TABLE-US-00005 TABLE 5 Crystallographic Data (Practical Example 3) Crystal system Monoclinic a (Å) 32.6800(2) b (Å) 14.4136(1) c (Å) 31.4683(2) β (°) 101.258(1) V (Å.sup.3) 14537.50(17) Z 8 Space group C2/c Rint 0.0169 R.sub.1 0.0710 wR.sub.2 0.2377 GoF 1.078

TABLE-US-00006 TABLE 6 Crystallographic Data (Practical Example 4) Crystal system Monoclinic a (Å) 32.8055(4) b (Å) 14.3860(1) c (Å) 32.7018(4) β (°) 103.215(1) V (Å.sup.3) 15024.6(3) Z 8 Space group C2/c Rint 0.0263 R.sub.1 0.1026 wR.sub.2 0.3353 GoF 1.082

TABLE-US-00007 TABLE 7 Crystallographic Data (Practical Example 5) Crystal system Monoclinic a (Å) 32.8449(2) b (Å) 14.4015(1) c (Å) 31.8571(2) β (°) 101.926(1) V (Å.sup.3) 14743.65(17) Z 8 Space group C2/c Rint 0.0196 R.sub.1 0.0730 wR.sub.2 0.2422 GoF 1.071

Example 3: Structure Determination of Enantiomers [Optical Resolution of Enantiomers (Practical Example 6) and Structural Analysis of Enantiomer (Practical Examples 7 and 8)]

[0080] In Example 3, the crystalline sponge method was evaluated for applicability to crystallographic analysis of enantiomers of a target compound of analysis, following ionic pair formation shown in Table 9.

(1) Method

A. Optical Resolution

[0081] Rac-trans-2-(phenethylamino)cyclopentan-1-ol was optically resolved into a pair of enantiomers under the conditions shown in Table 8.

TABLE-US-00008 TABLE 8 HPLC conditions Column CHIRALPAK AD-H (4.6 mm × 250 mm, particle size: 5 μm) Column temperature 35° C. Mobile phase n-hexane/isopropanol/diethylamine 95/5/0.1 (v/v/v) Flow rate 1.2 mL/min Detection UV 254 nm Injection volume 10 μL Sample 20 mg/mL concentration Analysis time 12 minutes

B. Structure Determination

[0082] One granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial. A compound corresponding to the early peak (Peak 1) in FIG. 14 and trifluoromethanesulfonic acid were both mixed and dissolved in dimethoxyethane to concentrations of 1 mg/mt. and 0.7 mg/mL, respectively, and 5 μL , of the resulting solution (equivalent to 5 μg of the compound of Peak 1 and 3.5 μg of trifluoromethanesulfonic acid) was added to the above vial containing the crystalline sponge. The vial was capped and sealed and then incubated at 50° C. for 2 days. Two days later, the crystalline sponge was recovered from the solution, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer. A compound corresponding to the later peak (Peak 2) in FIG. 14 was analyzed under the same conditions as those for the compound of Peak 1

TABLE-US-00009 TABLE 9 Ionic pairs Crystal structure Taget compound of analysis Counterionic compound Crystallographic Crystal (enlarged (basic compound) (acidic compound) data structure view) Practical Compound of Peak 1 trifluoromethanesulfonic Table 10 FIG. 15 FIG. 16 Example 7 acid Practical Compound of Peak 2 trifluoromethanesulfonic Table 11 FIG. 17 FIG. 18 Example 8 acid

(2) Result

[0083] The result of the optical resolution was as shown in the chromatogram of FIG. 14.

[0084] The crystallographic data and X-ray crystal structures (in the asymmetric unit) of the compounds of Peak 1 and Peak 2 were as shown in Tables 10 and 11 and in FIGS. 15 and 17 (enlarged views of the crystal structures are shown in FIGS. 16 and 18), respectively. The crystal structures of both the compounds were observed. The target compounds of analysis and trifluorotnethanesulfonic acid as a counterion to the compounds were understood to stay in proximity to each other as ionic pairs and to be incorporated as ionic pairs into pores of the crystalline sponge. It is suggested that the framework of the crystalline sponge was prevented from degradation by masking the reactivity of the basic compound, or alternatively by masking the reactivity of the acidic compound, and this allowed for crystallographic observation of the target compound of analysis.

[0085] From the analysis result, the compounds of Peak 1 and Peak 2 were determined to have the structures of (1S,2)-2-(phenethylamino)cyclopentan-1-ol and (1R,2R)-2-(phenethylamino)cyclopentan-1-ol, respectively.

TABLE-US-00010 TABLE 10 Crystallographic Data (compound of Peak 1) Crystal system Monoclinic a (Å) 32.88483(10) b (Å) 14.39898(3) c (Å) 31.69071(9) β (°) 101.7528(3) V (Å.sup.3) 14691.22(7) Z 4 Space group C2 Rint 0.0226 R.sub.1 0.0571 wR.sub.2 0.1879 GoF 1.077 Flack parameter (Parsons) 0.099(4)

TABLE-US-00011 TABLE 11 Crystallographic Data (compound of Peak 2) Crystal system Monoclinic a (Å) 32.86021(9) b (Å) 14.40160(3) c (Å) 31.69286(8) β (°) 101.7291(2) V (Å.sup.3) 14685.15(6) Z 4 Space group C2 Rint 0.0215 R.sub.1 0.0549 wR.sub.2 0.1787 GoF 1.072 Flack parameter (Parsons) 0.092(4)

Example 4: Structure Determination of Enantiomers [Optical Resolution of Enantiomers (Practical Example 9) and Structural Analysis of Enantiomer (Practical Examples 10 and 11)]

[0086] In Example 4, the crystalline sponge method was evaluated for applicability to crystallographic analysis of enantiomers of a target compound of analysis, following ionic pair formation shown in Table 12

(1) Method

A. Optical Resolution

[0087] Rac-trans-2-(pheriethylamino)cyclobeptan-1-ol produced by a known method (WO 2015/194508) was optically resolved into a pair of enantiomers under the conditions in Table 8 for Example 3,

B. Structure Determination

[0088] One granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-hottom vial. A compound corresponding to the early peak (Peak 3) in FIG. 19 and trifluoromethanesulfonic acid were both mixed and dissolved in dimethoxyethane to concentrations of 1 mg/mL, and 0.7 mg/mL, respectively, and 5 μL of the resulting solution (equivalent to 5 μg of the compound of Peak 3 and 3.5 μg of trifluoromethanesulfonic acid) was added to the above vial containing the crystalline sponge. The vial was capped and sealed and then incubated at 50° C. for 2 days. Two days later, the crystalline sponge was recovered from the solution, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer. A compound corresponding to the later peak (Peak 4) in FIG. 19 was analyzed under the same conditions as those for the compound of Peak 3.

TABLE-US-00012 TABLE 12 Ionic pairs Crystal structure Target compound of analysis Counterion Crystallographic Crystal (enlarged (basic compound) (acidic compound) data structure view) Practical Compound of Peak 3 trifluoromethanesulfonic Table 13 FIG. 20 FIG. 21 Example 10 acid Practical Compound of Peak 4 trifluoromethanesulfonic Table 14 FIG. 22 FIG. 23 Example 11 acid

(2) Result

[0089] The result of the optical resolution was as shown in the chromatogram of FIG. 19.

[0090] The crystallographic data and X-ray crystal structures (in the asymmetric unit) of the compounds of Peak 3 and Peak 4 were as shown in Tables 13 and 14 and in FIGS. 20 and 22 (enlarged views of the crystal structures are shown in FIGS. 21 and 23), respectively. The crystal structures of both the compounds were observed. The target compounds of analysis and trifluoromethanesulfonic acid were understood to stay in proximity to each other as ionic pairs and to be incorporated as ionic pairs into pores of the crystalline sponge. It is suggested that the framework of the crystalline sponge was prevented from degradation by masking the reactivity of the basic compound, or alternatively by masking the reactivity of the acidic compound, and this allowed for crystallographic observation of the target compound of analysis.

[0091] From the analysis result, the compounds of Peak 3 and Peak 4 were determined to have the structures of (1, 2S)-2-(phenethylamino)cycloheptan-1-ol and (1R,2R)-2-(phenethylamin cycloheptan-1-ol, respectively.

TABLE-US-00013 TABLE 13 Crystallographic Data (compound of Peak 3) Crystal system Monoclinic a (Å) 32.65890(11) b (Å) 14.43287(4) c (Å) 31.47521(12) β (°) 101.4063(3) V (Å.sup.3) 14543.18(9) Z 4 Space group C2 Rint 0.0175 R.sub.1 0.0652 wR.sub.2 0.2114 GoF 1.055 Flack parameter (Parsons) 0.055(4)

TABLE-US-00014 TABLE 14 Crystallographic Data (compound of Peak 4) Crystal system Monoclinic a (Å) 32.62130(11) b (Å) 14.43883(4) c (Å) 31.51628(11) β (°) 101.4006(3) V (Å.sup.3) 14551.69(8) Z 4 Space group C2 Rint 0.0167 R.sub.1 0.0610 wR.sub.2 0.1943 GoF 1.060 Flack parameter (Parsons) 0.049(5)

Example 5: X-Ray Structural Analysis Based on the Crystalline Sponge Method (2)

[0092] Example 5, the crystalline sponge method was evaluated for applicability to crystallographic analysis of basic compounds.

(1) Target Compounds of Analysis

[0093] Target compounds of analysis in Example 5 are as shown in Table 15.

TABLE-US-00015 TABLE 15 Target compounds of analysis Comparative Basic N,N-dimethylcyclohexylamine (Tokyo Example 8 compounds Chemical Industry Co., Ltd.) Comparative 1,1,3,3-tetramethylguanidine (Tokyo Example 9 Chemical Industry Co., Ltd.) Comparative 1,3-diphenylguanidine (Tokyo Chemical Example 10 Industry Co., Ltd.) Comparative diazabicycloundecene (Tokyo Chemical Example 11 Industry Co., Ltd.)

(2) Experimental Procedure

[0094] In Comparative Examples 8 to 11, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial. A target compound of analysis was dissolved in dimethoxyethane to a concentration of 1 mg/mL and 5 μL of the resulting solution (equivalent to 5 μg of the target compound of analysis) was added to the above vial containing the crystalline sponge. The vial was capped and sealed, and the cap was pierced with an injection needle, and the vial was incubated at 50° C. for I day to gently evaporate the solvent. One day later, the crystalline sponge was recovered from the vial, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

(3) Results

[0095] The result from the X-ray crystallographic analysis of the target compound analyzed in Comparative Example 8 was as shown in FIG. 24, which indicated failure in observing the crystal structure of the target compound of analysis. In Comparative Example 8, degradation products from the framework of the crystalline sponge were observed to be incorporated as a guest, as shown in a region enclosed by a dotted line in FIG. 24. In Comparative Examples 9, 10, and 11, the crystalline sponge was damaged and the crystallinity was completely lost, and diffraction data was thus not obtained. Without being bound by the following theory, it was understood that these resulted from destruction of the crystalline sponge-constituting framework due to the reactivity (nucleophilicity, coordinating property, and the like) of the basic compounds as targets of analysis. Additionally, the results indicated that, for example, tertiary amines (Comparative Example 8), guanidines (Comparative Examples 9 and 10), and amidines (Practical Example 11) may not he amenable to structural analysis due to the potential to cause significant damage to crystalline sponges in spite of the relatively low nucleophilicity of the compounds.

Example 6: X-Ray Structural Analysis of a Compound in an Ionic Pair (2)

[0096] In Example 6, the crystalline sponge method was evaluated for applicability to crystallographic analysis of target compounds of analysis, following ionic pair formation with counterionic compounds.

(1) Ionic pairs

[0097] Target compounds of analysis and counterioni c compounds for ionic pair formation in Example 6 are as shown in Table 16.

TABLE-US-00016 TABLE 16 Ionic pairs Crystal structure Target compound of analysis Counterionic compound Crystallographic Crystal (enlarged (basic compound) (acidic compound) data structure view) Practical N,N-dimethylcyclohexylamine trifluoromethanesulfonic acid Table 17 FIG. 25 FIG. 26 Example 12 1 mg/mL [the concentration at the 1.2 mg/mL [the concentration time of mixing and dissolving] at the time of mixing and 5 μg [the amount at the time of dissolving] soaking in crystalline sponge] 6 μg [the amount at the time of soaking in crystalline sponge] Practical 1,1,3,3-tetramethylguanidine trifluoromethanesulfonic acid Table 18 FIG. 27 FIG. 28 Example 13 1 mg/mL [the concentration at the 1.4 mg/mL [the concentration time of mixing and dissolving] at the time of mixing and 5 μg [the amount at the time of dissolving] soaking in crystalline sponge] 7 μg [the amount at the time of soaking in crystalline sponge] Practical 1,3-diphenylguanidine trifluoromethanesulfonic acid Table 19 FIG. 29 FIG. 30 Example 14 1 mg/mL [the concentration at the 0.8 mg/mL [the concentration time of mixing and dissolving] at the time of mixing and 5 μg [the amount at the time of dissolving] soaking in crystalline sponge] 4 μg [the amount at the time of soaking in crystalline sponge] Practical diazabicycloundecene trifluoromethanesulfonic acid Table 20 FIG. 31 FIG. 32 Example 15 1 mg/mL [the concentration at the 1 mg/mL [the concentration time of mixing and dissolving] at the time of mixing and 5 μg [the amount at the time of dissolving] soaking in crystalline sponge] 5 μg [the amount at the time of soaking in crystalline sponge]

(2) Experimental Procedure

A. Practical Examples 12 and 15

[0098] In Practical Examples 12 and 15, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial. A target compound of analysis and a counterion were both mixed and dissolved in dimethoxyethane to yield the concentrations shown in Table 16. and 5 μL of the resulting solution was added to the above vial containing the crystalline sponge. The vial was capped and sealed, and the cap was pierced with an injection needle, and the vial was incubated at 50° C for 1 day to gently evaporate the solvent, One day later, the crystalline sponge was recovered from the vial, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractotneter.

B. Practical Examples 13 and 14

[0099] In Practical Examples 13 and 14, one granule of the crystalline sponge and n-hexane (45 μL) were added together to a 1.2-mL V-bottom vial. A target compound of analysis and a counterion were both mixed and dissolved in ditnethoxyethane to yield the concentrations shown in Table 16, and 5 μL, of the resulting solution was added to the above vial containing the crystalline sponge. The vial was capped and sealed and then incubated at 50° C. for 3 days (Practical Example 13) or for 4 days (Practical Example 14). Subsequently, the crystalline sponge was recovered from the solution, coated with an inert oil layer, and then analyzed with a single crystal X-ray diffractometer.

(3) Results

[0100] The crystallographic data and X-ray crystal structure (in the asymmetric unit) of each of the practical examples were as shown in Tables 17 to 20 and in FIGS. 25, 27, 29, and 31 (enlarged views of the crystal structures are shown in FIGS. 26, 28, 30, 32), respectively. In any of the practical examples, the crystal structures of a basic compound added as a target compound of analysis and of an acidic compound added as a counterion. were observed. The basic compounds and the acidic compounds were understood to stay in proximity to each other as ionic pairs and to he incorporated as ionic pairs into pores of the crystalline sponge. It is suggested that the framework of the crystalline sponge was prevented from degradation by masking the reactivity of the basic compounds, and this allowed for crystallographic observation of the target compounds of analysis.

TABLE-US-00017 TABLE 17 Crystallographic Data (Practical Example 12) Crystal system Monoclinic a (Å) 30.0720(5) b (Å) 14.64415(18) c (Å) 33.1881(4) β (°) 100.2173(14) V (Å.sup.3) 14383.6(3) Z 4 Space group P2.sub.1/n Rint 0.0301 R.sub.1 0.1212 wR.sub.2 0.3621 GoF 1.105

TABLE-US-00018 TABLE 18 Crystallographic Data (Practical Example 13) Crystal system Monoclinic a (Å) 34.3570(5) b (Å) 14.4761(2) c (Å) 30.3158(4) β (°) 102.809(1) V (Å.sup.3) 14702.5(4) Z 8 Space group C2/c Rint 0.0219 R.sub.1 0.0979 wR.sub.2 0.2993 GoF 1.030

TABLE-US-00019 TABLE 19 Crystallographic Data (Practical Example 14) Crystal system Monoclinic a (Å) 33.2049(5) b (Å) 14.4213(2) c (Å) 30.9613(6) β (°) 101.095(2) V (Å.sup.3) 14549.0(4) Z 8 Space group C2/c Rint 0.0215 R.sub.1 0.0856 wR.sub.2 0.2600 GoF 1.113

TABLE-US-00020 TABLE 20 Crystallographic Data (Practical Example 15) Crystal system Monoclinic a (Å) 32.2091(3) b (Å) 14.5751(2) c (Å) 30.9842(4) β (°) 100.263(1) V (Å.sup.3) 145312.8(3) Z 8 Space group C2/c Rint 0.0308 R.sub.1 0.0913 wR.sub.2 0.2960 GoF 1.106