Sample-forming material for x-ray structure analysis and method for determining molecular structure of organic compound using the same

Abstract

To provide a new forming material for forming a sample for X-ray structure analysis of an organic compound.SOLUTION: The sample-forming material for X-ray structure analysis of the present disclosure is a sample-forming material for fixing an organic compound in a regularly aligned state and subjecting the organic compound to X-ray structure analysis, and includes the following cyclodextrin molecular assembly. A cyclodextrin molecular assembly having a structure in which two molecules of cyclodextrin face each other on the secondary hydroxyl group side and associate with each other through a coordinate bond between the secondary hydroxyl group and a metal ion to form a cyclodextrin dimer, and a plurality of the cyclodextrin dimers are regularly aligned three dimensionally, and SELECTED DRAWING: None

Description

[Technical Field]

[0001] The present disclosure relates to a novel material for forming a specimen for X-ray structural analysis, and a method for determining the molecular structure of an organic compound using the material for forming a specimen for X-ray structural analysis. [Background technology]

[0002] As a method for determining the molecular structure of an organic compound, single crystal X-ray structural analysis, that is, a method in which a single crystal of an organic compound is subjected to X-ray structural analysis, is known. This method is very useful because it allows accurate determination of the molecular structure of an organic compound if a high-quality single crystal can be produced.

[0003] However, when the amount of organic compound is small, it is difficult to obtain a sufficient amount of single crystals, making it very difficult to determine the molecular structure by this method. Also, there are organic compounds that are difficult to crystallize, and the above method cannot be used to determine the molecular structure of such organic compounds.

[0004] Therefore, the crystalline sponge method was developed, which allows the molecular structure of organic compounds to be determined by X-ray structural analysis without going through the crystallization process. The crystalline sponge method uses a porous metal complex crystal (i.e., a metal complex crystal with regularly aligned pores) as a material for forming a sample for X-ray structural analysis (the so-called host), and impregnates and fixes the organic compound, whose molecular structure is to be determined, as guest molecules into the pores of the metal complex crystal together with a solvent, thereby regularly aligning the organic compound, which can then be used as a sample for X-ray structural analysis to determine its molecular structure.

[0005] Patent Document 1 discloses a microporous metal complex crystal obtained by coordinating zinc ions or cobalt ions with 2,4,6-tris(4-pyridyl)-1,3,5-triazine (TPT). However, the problem with this microporous metal complex crystal is that it lacks chirality, making it difficult to determine the absolute configuration of chiral guest molecules.

[0006] Non-Patent Document 1 discloses that the absolute configuration of a chiral guest can be determined by using microporous metal complex crystals [Co(S-man)2(bpy)3] and [Co(R-man)2(bpy)3] containing optically active mandelic acid (S-man or R-man), a 4,4'-bipyridine ligand (bpy), and cobalt ions. However, the internal volume of the pores of the microporous metal complex crystals is too small, so the guest molecules that can be included are limited, resulting in low versatility. [Prior art documents] [Patent documents]

[0007] [Patent Document 1] International Publication No. 2014 / 038220 [Non-patent literature]

[0008] [Non-Patent Document 1] Structural Insight into Guest Binding Sites in a Porous Homochiral Metal-Organic Material, J. Am. Chem. Soc. 2015, 137, 12045-12049. Summary of the Invention [Problem to be solved by the invention]

[0009] Therefore, an object of the present disclosure is to provide a novel forming material for forming samples for X-ray structural analysis of organic compounds. Another object of the present disclosure is to provide a novel material that is a forming material for forming samples for X-ray structural analysis of organic compounds, that enables molecular structural analysis of a wide range of organic compounds, and that can reliably identify the absolute configuration of chiral organic compounds. Another object of the present disclosure is to provide a method for determining the molecular structure of an organic compound using the material. [Means for solving the problem]

[0010] As a result of extensive research into solving the above problems, the present inventors have discovered the following. 1. CDs molecular assemblies, which are one type of metal complex crystal obtained by coordinating cyclic compounds, cyclodextrins (hereinafter sometimes referred to as "CDs"), to metal ions, have a structure in which CDs dimers are regularly aligned in three dimensions. Organic compounds can be encapsulated in the pores that penetrate the center of the CDs dimers or in the pores present between adjacent CDs dimers. When an organic compound is encapsulated in the pores and subjected to X-ray diffraction, the molecular structure of the organic compound can be easily determined. 2. The pores that penetrate the center of the CDs dimer are hydrophobic environments, allowing the inclusion of hydrophobic guest molecules. 3. The pores between adjacent CDs dimers are hydrophilic and can encapsulate hydrophilic guest molecules. 4. The volume of the pores can be easily adjusted by adjusting the number of glucose units constituting the CDs, making them suitable for a wide range of molecular weights of guest molecules. 5. Because CDs have chirality, if a chiral guest molecule is enclosed in the pore, the absolute configuration of the guest molecule can be reliably identified. The present disclosure has been completed based on these findings.

[0011] That is, the present disclosure provides a sample formation material for immobilizing organic compounds in a regularly aligned state for X-ray structural analysis, the sample formation material for X-ray structural analysis comprising the following cyclodextrin molecular assembly: Cyclodextrin molecular assembly: Two cyclodextrin molecules face each other with their secondary hydroxyl groups facing each other and associate through coordinate bonds between the secondary hydroxyl groups and metal ions to form a cyclodextrin dimer, with multiple cyclodextrin dimers arranged in a three-dimensional regular pattern.

[0012] The present disclosure also provides the material for forming a specimen for X-ray structural analysis, wherein the metal ion is a lithium ion or a sodium ion.

[0013] The present disclosure also provides the material for forming a specimen for X-ray structural analysis, wherein the organic compound is an organic compound having a functional group that interacts with a hydroxyl group.

[0014] The present disclosure also provides the material for forming a sample for X-ray structural analysis, wherein the organic compound is an organic compound having a functional group selected from a substituted or unsubstituted amino group, a carboxyl group, an active methylene group, a nitrile group, a ketone group, an aldehyde group, an ester group, an ether group, an amide group, a hydroxyl group, a halogen group, and a sulfonamide group.

[0015] The present disclosure also provides the sample-forming material for X-ray structural analysis, which is a sample-forming material for determining the absolute configuration of a chiral organic compound by X-ray structural analysis.

[0016] The present disclosure also provides a method for determining the molecular structure of an organic compound (X), comprising the following steps 1 and 2: Step 1: The organic compound (X) is impregnated into the material for forming a sample for X-ray structural analysis and fixed therein. Step 2: Irradiating the sample-forming material for X-ray structural analysis, on which the organic compound (X) is fixed, with X-rays, and analyzing the resulting diffraction data to determine the molecular structure of the organic compound (X). [Effects of the Invention]

[0017] The material for forming a sample for X-ray structural analysis according to the present disclosure includes a CDs molecular assembly in which CDs dimers are regularly aligned in three dimensions. The CDs dimer has a structure in which two CDs molecules face each other with their secondary hydroxyl groups facing each other and are associated by coordinate bonds between the secondary hydroxyl groups and metal ions. CDs molecular assemblies have pores penetrating the center of the CDs dimer and pores present between adjacent CDs dimers, and the volume of these pores is larger than that of the metal complex crystals described in Non-Patent Document 1. Furthermore, the pore volume can be further increased by increasing the number of glucose units constituting the CDs. Furthermore, increasing the number of glucose units improves the flexibility of CDs, thereby acquiring the versatility to change the shape of the pores in accordance with the structure of the guest molecules encapsulated within the pores. This allows for the inclusion of a wider range of guest molecules.

[0018] By using the X-ray structural analysis specimen-forming material, even if the amount of an organic compound is too small to form a single crystal or if the compound cannot be formed into a single crystal, the molecular structure of the organic compound can be determined by regularly arranging the organic compound in the pores of the X-ray structural analysis specimen-forming material and then subjecting the organic compound to X-ray structural analysis. If the organic compound has chirality, the absolute configuration can also be reliably identified. Therefore, the material for forming a specimen for X-ray structural analysis is extremely useful as a means for determining the molecular structure of organic compounds (especially organic compounds having chirality). [Brief explanation of the drawings]

[0019] [Figure 1] This is a schematic diagram of CDs. [Figure 2] Schematic diagram of a CDs dimer. [Figure 3] This is a schematic diagram of the CDs molecular assembly viewed from a direction perpendicular to the length of the pore. [Figure 4] This is a schematic diagram of the CDs molecular assembly viewed from a direction parallel to the length of the pore. [Figure 5] FIG. 1 is a schematic diagram showing the crystal structure of the CDs molecular assembly obtained in Example 1. [Figure 6] FIG. 2 is a schematic diagram showing the crystal structure of the sample for structural analysis obtained in Example 2. [Figure 7] FIG. 2 is a schematic diagram showing the interaction between the hydroxyl groups of CDs and the hydroxyl group of (-) menthol in the sample for structural analysis obtained in Example 2. DETAILED DESCRIPTION OF THE INVENTION

[0020] [Sample preparation materials for X-ray structural analysis] The sample formation material for X-ray structural analysis disclosed herein (hereinafter sometimes referred to as "sample formation material") is a material for forming a sample for subjecting an organic compound to X-ray structural analysis, and is used to fix the organic compound in a regularly aligned state.

[0021] The sample-forming material contains at least the following cyclodextrin molecular aggregate (CDs molecular aggregate). The sample-forming material may contain other components, but the proportion of the following CDs molecular aggregate in the total amount of the sample-forming material is, for example, 50% by weight or more, preferably 60% by weight or more, more preferably 70% by weight or more, even more preferably 80% by weight or more, particularly preferably 90% by weight or more, most preferably 95% by weight or more, and especially preferably 99% by weight or more. The sample-forming material may be substantially free of components other than the following CDs molecular aggregate.

[0022] (Cyclodextrin molecular aggregate) A cyclodextrin molecular assembly (CDs molecular assembly) is a metal complex crystal (preferably a microporous metal complex crystal) in which two CDs molecules face each other with their secondary hydroxyl groups facing each other and associate with a metal ion via a coordinate bond to form a CDs dimer, and multiple CDs dimers are regularly aligned in a three-dimensional array.

[0023] CDs are compounds with a cyclic structure in which D-glucose units are linked by α-1,4 glycosidic bonds.

[0024] As shown in Figure 1, CDs (1) is a compound with a bottomless bucket-like structure, which has a first opening (10) consisting of a primary hydroxyl group of D-glucose and a second opening (20) consisting of a secondary hydroxyl group of D-glucose that is wider than the first opening.

[0025] As shown in Figure 2, two CDs (1) molecules face each other with their secondary hydroxyl groups, i.e., the second opening (20), and associate through coordinate bonds between the secondary hydroxyl groups and metal ions to form a CDs dimer (2). The CDs dimer (2) is a hollow tubular structure with a pore (30) along its axis.

[0026] The CDs dimers (2) are then regularly aligned three-dimensionally to form a CDs molecular assembly (3). As shown in Figures 3 and 4, the CDs molecular assembly (3) is preferably a tubular complex (or a tubular metal complex crystal) in which a plurality of hollow tubular CDs dimers are aligned with the same axis to form a series of pores (30). This allows guest molecules to easily penetrate into the CDs dimers, and organic compounds serving as guest molecules can be more reliably included inside the CDs dimers.

[0027] The number of glucose units constituting CDs (more specifically, the number of D-glucose-derived constituent units constituting CDs) is, for example, 5 or more, preferably 6 or more, particularly preferably 7 or more, and most preferably 8 or more. The upper limit of this number is, for example, 20, preferably 15, particularly preferably 10. Increasing the number of glucose units constituting CDs increases the pore volume, while decreasing the number of glucose units constituting CDs decreases the pore volume. Furthermore, by changing the number of glucose units constituting CDs, CDs molecular assemblies can encapsulate organic compounds with a wide range of molecular weights.

[0028] Specific examples of CDs include α-cyclodextrin having 6 glucose units, β-cyclodextrin having 7 glucose units, and γ-cyclodextrin having 8 glucose units.

[0029] CDs may have a substituent. More specifically, one or more of the hydroxyl groups contained in CDs may be substituted with an alkoxy group (e.g., C 1-5 It may be substituted with an alkoxy group, an amino group, a carboxy group, a thiol group, or the like.

[0030] The metal ion is not particularly limited as long as it can form a coordinate bond with CDs to form the CDs molecular assembly. Examples of the metal ion include alkali metal ions such as lithium ions and sodium ions. Among them, sodium ions are preferred because they allow for easy control of the arrangement of CDs and are inexpensive and readily available.

[0031] The content ratio of CDs to metal ions in the CDs molecular assembly [CDs / metal ions; molar ratio] is, for example, 20 / 80 to 5 / 95, preferably 16 / 84 to 7 / 93, and particularly preferably 13 / 87 to 10 / 90.

[0032] The CDs molecular assembly has a structure in which CDs are associated with the metal ions through coordinate bonds. The CDs molecular assembly contains, in addition to CDs, a ligand (e.g., F - , Cl - , Br - , I - , SCN - , NO3 - , ClO4 - , BF4 - , SbF4 - , PF6 - , AsF6 - , CH3COO - The amount of CDs in the total amount of ligands coordinated to the metal ions is, for example, 50% by weight or more, preferably 60% by weight or more, more preferably 70% by weight or more, even more preferably 80% by weight or more, and particularly preferably 90% by weight or more. It is most preferable that substantially only CDs are coordinated to the metal ions.

[0033] The CDs molecular assembly is a three-dimensional network structure formed by regularly aligned CDs dimers, in which the pores present inside the CDs dimers have a hydrophobic environment and the pores present between adjacent CDs dimers have a hydrophilic environment. Therefore, the pores present inside the CDs dimers can encapsulate hydrophobic organic compounds as guests, and the pores present between adjacent CDs dimers can encapsulate hydrophilic organic compounds as guests.

[0034] The pores are preferably arranged in a three-dimensional order without disorder to the extent that they can be confirmed by X-ray structural analysis, and each pore preferably has a uniform shape and size to the extent that they can be confirmed by X-ray structural analysis.

[0035] When the number of glucose units constituting the CDs in the CDs molecular assembly is increased (for example, when the number of glucose units is increased to 8 or more), the CDs acquire flexibility and have the ability to change the shape of the pores depending on the shape of the guest to be incorporated into the pores, thereby enabling a wider range of guests to be encapsulated in the pores.

[0036] The pores present inside the CDs dimers of the CDs molecular assembly preferably have a volume large enough to encapsulate one to several (for example, 1 to 6) organic compounds as guests.

[0037] The molecular weight of the organic compound serving as the guest is, for example, 50 or more, preferably 100 or more, particularly preferably 150 or more, most preferably 300 or more, and particularly preferably 500 or more. The upper limit of the molecular weight of the organic compound is, for example, 1000, preferably 800, and particularly preferably 600.

[0038] The diameter of the pores present inside the CDs dimers of the CDs molecular assembly varies depending on the number of glucose units constituting the CDs, but is, for example, 2 to 15 Å. The lower limit of the diameter is preferably 4 Å, particularly preferably 5 Å, most preferably 6 Å, and particularly preferably 7 Å, from the viewpoint of facilitating the inclusion of organic compounds. The upper limit of the diameter is preferably 12 Å, more preferably 10 Å, particularly preferably 9 Å, and most preferably 8 Å, from the viewpoint of increasing the toughness of the three-dimensional network structure.

[0039] The diameter of the pore inside the CDs dimer is determined by observing the crystal plane that is closest to perpendicular to the length direction of the pore (i.e., the direction in which the pore extends) from above, and is determined by single crystal X-ray structural analysis.

[0040] The CDs molecular assembly can firmly fix the organic compound as a guest within the pores by hydrogen bonding between the hydroxyl groups contained in the D-glucose constituting the CDs and the organic compound.

[0041] [Method for producing CDs molecular assemblies] The CDs molecular assembly can be produced, for example, by reacting cyclodextrin with a salt of a metal ion and a counter ion (metal salt) in the presence of a solvent.

[0042] Examples of the metal ions include alkali metal ions such as lithium ions and sodium ions.

[0043] Examples of the counter ion include F - , Cl - , Br - , I - , SCN - , NO3 - , ClO4 - , BF4 - , SbF4 - , PF6 - , AsF6 - , CH3COO - Examples of anions include:

[0044] The amount of the metal salt used is, for example, 3 to 15 mol, preferably 5 to 12 mol, and particularly preferably 6 to 10 mol, per mol of cyclodextrin.

[0045] Examples of presolvents include water; benzene derivatives such as benzene, toluene, xylene, ethylbenzene, trifluoromethylbenzene (or trifluorotoluene), chlorobenzene, anisole, benzonitrile, nitrobenzene, and ethyl benzoate, in which the benzene ring may be substituted with a halogen atom, an alkyl group, a haloalkyl group, an alkoxy group, a cyano group, a nitro group, a substituted oxycarbonyl group, or the like; aliphatic hydrocarbons such as hexane, heptane, and octane; alicyclic hydrocarbons such as cyclohexane; haloalkanes such as carbon tetrachloride, chloroform, dichloromethane, and 1,2-dichloroethane; ketones such as acetone and methyl ethyl ketone; esters such as methyl acetate, ethyl acetate, isopropyl acetate, and butyl acetate; amides such as N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMA), and N-methylpyrrolidone; nitriles such as acetonitrile and propionitrile; linear or cyclic ethers such as diethyl ether, dibutyl ether, dimethoxyethane, dioxane, and tetrahydrofuran; and organic acids such as acetic acid. These may be used alone or in combination of two or more.

[0046] Of these, water is preferred as the presolvent.

[0047] The amount of the presolvent used is, for example, 5 to 50 times the total weight of the cyclodextrin and the metal salt.

[0048] The reaction temperature is, for example, 1 to 50° C., preferably 1 to 30° C. If the reaction temperature is too high, it tends to be difficult to obtain a tubular complex (or tubular metal complex crystal).

[0049] The reaction time is, for example, 48 to 480 hours.

[0050] The reaction atmosphere is not particularly limited as long as it does not inhibit the reaction, and may be, for example, an air atmosphere, a nitrogen atmosphere, an argon atmosphere, or the like.

[0051] After the reaction is completed, the resulting reaction product can be separated and purified by common methods such as recrystallization, precipitation, washing, and filtration.

[0052] [Method for determining the molecular structure of organic compound (X)] The method for determining the molecular structure of the organic compound (X) includes the following steps 1 and 2: Step 1: The sample-forming material (or the CDs molecular assembly) is impregnated with an organic compound (X) to immobilize it. Step 2: Irradiating the sample-forming material (or the CDs molecular assembly) to which the organic compound (X) is fixed with X-rays, and analyzing the resulting diffraction data to determine the molecular structure of the organic compound (X).

[0053] The organic compound (X) is a so-called guest molecule, and is, for example, a compound having a functional group that interacts with a hydroxyl group of the sample-forming material (or the CDs molecular assembly) via, for example, a hydrogen bond.

[0054] Examples of the functional group that interacts with a hydroxyl group include a substituted or unsubstituted amino group (e.g., C 1-5 Examples of the amino group include an alkyl-substituted amino group, ...

[0055] The molecular weight of the organic compound (X) is, for example, 50 or more, preferably 100 or more, particularly preferably 150 or more, most preferably 300 or more, and particularly preferably 500 or more. The upper limit of the molecular weight of the organic compound (X) is, for example, 1000, preferably 800, and particularly preferably 600.

[0056] The organic compound (X) is preferably a hydrophobic compound. The logP (octanol / water partition coefficient) value of the organic compound (X) is, for example, −5 to 7. In terms of improving the determination rate of the molecular structure, the lower limit of the logP is preferably −3, particularly preferably −1, most preferably 1, and particularly preferably 2, and the upper limit of the logP is preferably 6, particularly preferably 5.

[0057] The logP value of the organic compound (X) can be determined using commercially available software (for example, the software "EPI suite" jointly developed by the US EPA (The Estimations Programs Interface for Windows) and Syracuse).

[0058] (Process 1) Step 1 is a step of permeating an organic compound (X) into a sample-forming material containing the CDs molecular assembly, thereby capturing and immobilizing the organic compound (X) in the pores of the CDs molecular assembly.

[0059] As the CDs molecular assembly, it is preferable to select and use one having excellent transparency and a clear external shape (e.g., needle-like, block-like, flake-like, etc.) from among the CDs molecular assemblies obtained by the above-mentioned method for producing a CDs molecular assembly, in terms of improving the determination rate of the molecular structure.

[0060] The size of the CDs molecular aggregate, for example, when the CDs molecular aggregate has a needle-like or block-like shape, may be 10 μm or more, preferably 10 to 500 μm, and particularly preferably 10 to 200 μm. If the CDs molecular aggregate is too small, the measurement time tends to be long, whereas if the CDs molecular aggregate is too large, it becomes difficult to sufficiently penetrate the organic compound (X), and the determination rate of the molecular structure tends to decrease.

[0061] The amount of the CDs molecular assembly used is, for example, 0.1 to 50 mg (preferably 0.5 to 15 mg, particularly preferably 1 to 3 mg).

[0062] The method for infiltrating the organic compound (X) into the CDs molecular assembly and immobilizing the organic compound (X) in the pores of the CDs molecular assembly can be appropriately selected depending on the state (solid or liquid) of the organic compound (X). When the organic compound (X) is a solid, for example, the sample-forming material is placed in a container such as a test tube, and a solution of the organic compound (X) dissolved in an inert solvent is added thereto, followed by allowing the mixture to stand at −20 to 100° C. for 0.25 to 24 hours. When the organic compound (X) is a liquid, for example, the sample-forming material is placed in a container such as a test tube, and the organic compound (X) is added thereto, followed by standing at −20 to 100° C. for 0.25 to 24 hours.

[0063] When the organic compound (X) is a solid, the solution may be concentrated after the standing. By performing the concentration treatment, the immobilization rate of the organic compound (X) in the pores tends to be increased, and the determination rate of the molecular structure tends to be improved.

[0064] Examples of the inert solvent include ketones such as acetone and methyl ethyl ketone; alcohols such as methanol, ethanol, and isopropyl alcohol; chain or cyclic ethers such as tetrahydrofuran (THF), dimethoxyethane, and dioxane; aliphatic hydrocarbons such as hexane, heptane, and octane; and alicyclic hydrocarbons such as cyclohexane. These may be used alone or in combination of two or more.

[0065] When the organic compound (X) is a solid, the concentration of the organic compound (X) in a solution obtained by dissolving the organic compound (X) in an inert solvent is, for example, 0.001 to 50 μg / μL, preferably 0.01 to 10 μg / μL, and more preferably 0.1 to 5 μg / μL.

[0066] Since the CDs molecular assembly has hydroxyl groups, when an organic compound (X) having a functional group that interacts with hydroxyl groups is permeated into a sample-forming material containing the CDs molecular assembly, the organic compound (X) is taken into the pores of the CDs molecular assembly and firmly fixed by hydrogen bonds.

[0067] Through this step, a sample for X-ray structural analysis is obtained in which the organic compound (X) is fixed in the pores of the CDs molecular assembly.

[0068] (Process 2) Step 2 is a step of irradiating the sample for X-ray structural analysis obtained in the previous step with X-rays, and analyzing the resulting diffraction data to determine the molecular structure of the organic compound (X).

[0069] According to the method for determining the molecular structure of organic compound (X), even if the amount of organic compound (X) obtained is too small to obtain a single crystal, or even if organic compound (X) is a compound that cannot be crystallized into a single crystal, the molecular structure can be easily determined by X-ray structural analysis without undergoing a crystallization process.

[0070] Furthermore, according to the method for determining the molecular structure of organic compound (X), a chiral CDs molecular assembly is used as a sample forming material. Therefore, when organic compound (X) has chirality, the absolute configuration can be reliably identified by a relative method.

[0071] According to the method for determining the molecular structure of organic compound (X), the structures of trace impurities in pharmaceuticals, substances that cause odors or smells (e.g., fragrances), food additives, trace components in plants and animals, etc. can be easily determined.

[0072] The above-described configurations and combinations thereof of the present disclosure are merely examples, and additions, omissions, substitutions, and modifications of the configurations are possible as appropriate without departing from the spirit of the present disclosure. Furthermore, each aspect disclosed in this specification can be combined with any other feature disclosed in this specification. Furthermore, the present disclosure is not limited by the embodiments. [Example]

[0073] The present disclosure will be explained in more detail below using examples, but the present disclosure is not limited to these examples.

[0074] Single crystal X-ray structural analysis was carried out using the following automatic single crystal X-ray diffractometer. Single crystal automatic X-ray diffraction equipment: "XtaLABSynergy Custom", manufactured by Rigaku Corporation Radiation source: Cu-Kα radiation (wavelength 0.83Å) Output: 50mA, 24kV

[0075] Example 1 (Production of CDs molecular assembly) γ-Cyclodextrin (130 mg, 0.1 mmol), NaOH (48 mg, 0.8 mmol), and water (2 mL) were placed in a vial, the vial was tightly capped, and the mixture was stirred at 25° C. for 5 minutes. Thereafter, the contents of the vial were filtered through a syringe filter (pore size: 0.45 μm), and the obtained filtrate was placed in a glass test tube (1 cm×5 cm). The glass test tube containing the filtrate was placed in a 50 mL vial containing ultra-dehydrated methanol (5 mL), and the glass test tube was sealed and allowed to stand at room temperature in a dark room for 14 days. The crystals precipitated in the glass test tube were collected and washed with methanol, yielding transparent block-shaped single crystal particles (CDs molecular aggregates 1) with a side length of 50 to 200 μm. The crystal structure of the obtained CDs molecular assembly 1 was confirmed by single-crystal X-ray structural analysis. A schematic diagram of CDs molecular assembly 1 is shown in Figure 5. Single crystal X-ray structural analysis confirmed that CDs molecular assembly 1 is a tubular metal complex crystal with a three-dimensional network structure. The diameter of the pores present in CDs molecular assembly 1 was 7.5 Å.

[0076] Example 2 (Immobilization of (-) menthol on CDs molecular assembly) One single crystal particle of CDs molecular assembly 1 in a methanol solution obtained in Example 1 was added to a microvial. Then, as much methanol as possible was removed using a pipette. Next, 15 μL of an acetone solution (1 μg / μL) of (-)menthol (logP value: 3.19) was added, and the microvial was then capped with a septum cap pierced with a syringe needle and allowed to stand at room temperature for two days to volatilize the acetone. Thereafter, the CDs molecular assembly 1 was taken out and used as a sample 1 for structural analysis.

[0077] The obtained structural analysis sample 1 was mounted on an X-ray structural analyzer and subjected to crystal structure analysis. A schematic diagram of structural analysis sample 1 is shown in Figure 6, and the interaction between the hydroxyl group at the 6-position of cyclodextrin contained in sample formation material 1 and the hydroxyl group of (-)menthol is shown in Figure 7. By the crystal structure analysis, it was possible to observe that one molecule of (-) menthol was fixed in one pore of the structural analysis sample 1 (or CDs molecular assembly 1) whose absolute configuration was known, and it was confirmed that the absolute configuration of the guest could be determined by the relative method.

[0078] In summary, the configuration of the present disclosure and its variations are noted below. [1] A sample formation material for X-ray structural analysis, which is used to fix organic compounds in a regularly aligned state and provide them for X-ray structural analysis, and which comprises the following cyclodextrin molecular aggregates: Cyclodextrin molecular assembly: Two cyclodextrin molecules face each other with their secondary hydroxyl groups facing each other and associate through coordinate bonds between the secondary hydroxyl groups and metal ions to form a cyclodextrin dimer, with multiple cyclodextrin dimers arranged in a three-dimensional regular pattern. [2] The material for forming a specimen for X-ray structural analysis according to [1], wherein the metal ion is a lithium ion or a sodium ion. [3] The material for forming a specimen for X-ray structural analysis according to [1] or [2], wherein the organic compound is an organic compound having a functional group that interacts with a hydroxyl group. [4] The material for forming a sample for X-ray structural analysis according to any one of [1] to [3], wherein the organic compound is an organic compound having a functional group selected from a substituted or unsubstituted amino group, a carboxyl group, an active methylene group, a nitrile group, a ketone group, an aldehyde group, an ester group, an ether group, an amide group, a hydroxyl group, a halogen group, and a sulfonamide group. [5] The sample-forming material for X-ray structural analysis according to any one of [1] to [4], wherein the sample-forming material for X-ray structural analysis is a sample-forming material for determining the absolute configuration of an organic compound having chirality by X-ray structural analysis. [6] A method for determining the molecular structure of an organic compound (X), comprising the following steps 1 and 2: Step 1: An organic compound (X) is impregnated into the material for forming a sample for X-ray structural analysis according to any one of [1] to [5] and fixed therein. Step 2: Irradiating the sample-forming material for X-ray structural analysis, on which the organic compound (X) is fixed, with X-rays, and analyzing the resulting diffraction data to determine the molecular structure of the organic compound (X). [Explanation of symbols]

[0079] 1 CD 2 CDs dimer 3 CDs molecular assembly 10. The first opening consists of the primary hydroxyl group of D-glucose 20. A second opening consisting of the secondary hydroxyl group of D-glucose 30 pores

Claims

1. A sample-forming material for X-ray structural analysis, which is used to fix organic compounds in a regularly aligned state and to provide them for X-ray structural analysis, comprises the following cyclodextrin molecular aggregate. Cyclodextrin molecular assembly: Two cyclodextrin molecules face each other with their secondary hydroxyl groups facing each other and associate through coordinate bonds between the secondary hydroxyl groups and metal ions to form a cyclodextrin dimer, with multiple cyclodextrin dimers arranged in a three-dimensional regular pattern.

2. 2. The material for forming a specimen for X-ray structural analysis according to claim 1, wherein the metal ions are lithium ions or sodium ions.

3. 3. The material for forming a specimen for X-ray structural analysis according to claim 1, wherein the organic compound is an organic compound having a functional group that interacts with a hydroxyl group.

4. 3. The material for forming a specimen for X-ray structural analysis according to claim 1, wherein the organic compound is an organic compound having a functional group selected from a substituted or unsubstituted amino group, a carboxyl group, an active methylene group, a nitrile group, a ketone group, an aldehyde group, an ester group, an ether group, an amide group, a hydroxyl group, a halogen group, and a sulfonamide group.

5. 3. The material for forming a sample for X-ray structural analysis according to claim 1, wherein the material for forming a sample for X-ray structural analysis is a material for forming a sample for determining the absolute configuration of an organic compound having chirality by X-ray structural analysis.

6. A method for determining the molecular structure of an organic compound (X), comprising the following steps 1 and 2: Step 1: The organic compound (X) is impregnated into the material for forming a sample for X-ray structural analysis according to claim 1 or 2 and fixed therein. Step 2: Irradiating the material for forming a sample for X-ray structural analysis, on which the organic compound (X) is fixed, with X-rays, and analyzing the obtained diffraction data to determine the molecular structure of the organic compound (X).

Images