Method for calculating valence states of metal atoms in metal organic framework material

Abstract

The invention discloses a method for calculating valence states of metal atoms in a metal organic framework material, which comprises the following steps of: firstly, acquiring. Cif files of original metal organic frameworks (MOFs) from a CSD database, carrying out bonding on the. Cif files by using an open-source xyz2mol program, outputting corresponding bonding information, and then deleting the metal atoms of the MOFs structure; calculating the RSD value of the non-metal framework according to the bonding information of all non-metal atoms, and calculating the total charge of the non-metal framework according to the relation between the RSD and the TSD of the elements; reversely deducing the oxidation state of the metal atoms by using the fact that the complete MOFs present charge balance; and finally, comparing the metal oxidation state numerical value with a numerical value provided by a CSD database, and evaluating the accuracy and feasibility of the method. According to the method, the metal center oxidation state value in the MOFs can be efficiently calculated, so that whether the MOFs meet the requirement of skeleton neutrality or not is judged.

Description

Technical Field

[0001] This invention relates to the fields of computational chemistry and nanocomposite materials, and specifically to a method for calculating the valence state of metal atoms in metal-organic framework materials. Background Technology

[0002] The oxidation state (OS) of the metal center in metal-organic frameworks (MOFs) directly affects its coordination ability and mechanism with organic ligands, thus determining the crystal structure and stability of MOFs. Different oxidation states of metal centers can lead to completely different framework topologies, and even affect the thermal stability and mechanical strength of the material. Furthermore, determining the metal oxidation state is essential for judging whether the overall MOF framework is neutral and for conducting theoretical calculations of metal clusters in MOFs. As of April 2023, the Cambridge Crystal Structure Database (CSD) contains crystallographic files (files with the .cif extension) of over 120,000 MOFs; however, for determining the oxidation state of metal atoms in a large number of MOFs, there is currently a lack of a universally applicable method for automatically determining the oxidation state of metal atoms in MOFs. Summary of the Invention

[0003] The purpose of this invention is to provide a method for calculating the valence state of metal atoms in metal-organic framework materials, which can more efficiently calculate the oxidation state of the metal center in MOFs.

[0004] To achieve the above objectives, the present invention provides a method for calculating the oxidation state of metal atoms in metal-organic framework materials, comprising the following steps:

[0005] S1. Obtain the original .cif files of MOFs from the CSD database;

[0006] S2. Use the xyz2mol program to perform batch bonding on the .cif file obtained in step S1, obtain the atom numbering information in the .cif file, obtain the type and number information of all atoms in the .cif file from the atom numbering information, and save and record it.

[0007] S3. Based on the atom numbering information obtained in step S2, delete all information related to metal atoms in the .cif file;

[0008] S4. Reacquire information from the .cif file processed in step S3. Acquire information including the bonding type, number of bonds, and type of bonded atom pairs of non-metallic atoms. Calculate the actual saturation values ​​of all non-metallic atoms in the .cif file after the metal atoms are missing based on the reacquired information.

[0009] S5. The total charge value of the non-metallic framework in MOFs after removing metal atoms can be obtained by using the difference between the actual saturation value and the theoretical saturation value of the non-metallic atoms; the absolute value of the total charge value of the non-metallic framework in MOFs is the total positive charge value of the missing metal atoms.

[0010] S6. Using the charge conservation formula: Oxidation state of metal atom × Number of metal atoms = Inverse of the total charge value of nonmetallic framework in MOFs lacking metal atoms, the oxidation state of metal atom in MOFs can be calculated.

[0011] Furthermore, in step S5, the theoretical saturation value of the non-metallic atoms is:

[0012] nonmetallic atoms Theoretical saturation value nonmetallic atoms Theoretical saturation value H 1 Ar 0 He 0 As 5 B 3 Se 6 C 4 Br 1，7 N 3 Kr 0 O 2 Te 6 F 1 I 1，7 Ne 0 Xe 0 Si 4 At 1 P 3，5 Rn 0 S 2，6 Og 0 Cl 1，7 .

[0013] Furthermore, in step S5, when the actual saturation values ​​of non-metallic atoms P, S, Cl, Br, and I are greater than 4, the corresponding theoretical saturation values ​​are 5, 6, 7, 7, and 7, respectively.

[0014] Furthermore, in step S4, when non-metallic atoms P, S, Si, and B directly bond with highly electronegative atoms O, F, Cl, Br, and I, the formal charges of P, S, Si, and B need to be reversed.

[0015] Preferably, in step S1, the original MOFs' .cif files are obtained by manual screening or computer-aided screening.

[0016] Preferably, in step S4, the bonding type is one of single bond, double bond, or triple bond.

[0017] Furthermore, the calculation results of the final oxidation state of the metal atoms in step S6 are evaluated to determine whether they are reasonable. If the calculation result is negative or not an integer, the calculation result is unreasonable. If the calculation result is a positive integer, it is further compared with the common oxidation states of metal elements. If they are consistent, the calculation result is determined to be reasonable. If they are inconsistent, the calculation result is determined to be unreasonable.

[0018] The xyz2mol program mentioned in this invention is a structure conversion tool designed to convert the atomic connection information (adjacency matrix) of a molecule into three-dimensional geometric structure and bond order information. By using atomic valence information and universal selection criteria, the program automatically generates the most energy-stable bond order matrix and uses a graph traversal algorithm to identify the structural features of the molecule, ultimately converting the generated SMILES string into three-dimensional coordinates. The xyz2mol program is efficient and accurate, and can be widely used in molecular structure modeling and isomer search.

[0019] The .cif (Crystallographic Information File) file mentioned in this invention is a standard file format used to record and transmit crystal structure data. This format was developed and maintained by the International Union of Crystallography (IUCr) and is primarily used to store crystal structure information resolved through experimental methods such as X-ray diffraction (XRD) and neutron diffraction.

[0020] This invention first obtains the original .cif files of MOFs from the CSD database, uses the open-source xyz2mol program to perform bonding on these .cif files, and outputs the corresponding bonding information. Then, the metal atoms in the MOF structures are removed. Based on the bonding information of all non-metal atoms, the Real Saturated Degree (RSD) of the non-metal framework is calculated. Based on the relationship between elemental RSD and Theoretical Saturated Degree (TSD), the total charge of the non-metal framework is calculated. Utilizing the fact that complete MOFs exhibit charge balance, the oxidation state of the metal atoms is deduced in reverse. Finally, the metal oxidation state values ​​calculated using this method are compared with those provided by the CSD database to evaluate the accuracy and feasibility of this method. By comparing the oxidation state data of metal centers given in the Cambridge Structure Database (CSD) (this invention uses 56,669 .cif structure files containing metal oxidation state information), the accuracy of the calculation results reaches 94.16%.

[0021] This invention is applicable not only to structures of various data types, but also to the objective evaluation of the rationality of metal oxidation state calculation results. This method is robust to crystallographic files with experimental uncertainties and can more efficiently calculate the oxidation state values ​​of the metal centers in MOFs, thereby determining whether the CIF structure of MOFs satisfies framework neutrality. Attached Figure Description

[0022] Figure 1 A flowchart for calculating the valence states of metal atoms in metal-organic framework materials;

[0023] Figure 2 A flowchart illustrating the method for calculating the valence states of metal atoms in metal-organic framework materials;

[0024] Figure 3 This is a special treatment for nonmetallic elements that have two theoretical saturation values;

[0025] Figure 4 This involves special treatment of the four elements P, S, Si, and B. Detailed Implementation

[0026] The present invention will be further described in detail below with reference to the accompanying drawings and embodiments.

[0027] Example 1

[0028] like Figure 1 As shown, a method for calculating the valence state of metal atoms in metal-organic framework materials, taking Cu-BTC (a name for MOFs, see the image below) as an example, includes the following steps:

[0029] S1. Obtain the original Cu-BTC structure .cif file from the CSD database;

[0030] S2. Use the xyz2mol program to perform batch bonding on the .cif files obtained in step S1, obtain the atom numbering information in the .cif files, extract the types and numbers of all atoms in the .cif files from the atom numbering information, and save and record it; the bonded data is as follows. Figure 2 As shown in box A, the Cu-BTC structure is composed of four elements: Cu, C, O, and H.

[0031] S3. Based on the atom numbering information obtained in step S2, delete all information related to metal atoms in the .cif file; that is, remove the metal element Cu from Cu-BTC (as follows). Figure 2 As shown in box B), after removing the metal, only 32 BTC ligands (O6C9H3) remain in Cu-BTC;

[0032] S4. Reacquire information from the .cif file processed in step S3. Acquire information including the bonding type, number of bonds, and type of bonded atom pairs of non-metallic atoms. Calculate the actual saturation values ​​of all non-metallic atoms in the .cif file after the metal atoms are missing based on the reacquired information.

[0033] Calculate the formal charge Q of each atom in the BTC ligand, and thus derive the Q of the BTC ligand (as follows). Figure 2 As shown in box C), the H atoms in the BTC ligand all belong to the same type (H①: directly connected to C atoms on the benzene ring by a single bond); the O atoms in the BTC ligand exist in two types (O②: connected to C atoms by a single bond; O③: connected to C atoms by a double bond); and the C atoms in the BTC ligand exist in three types (C④: directly bonded to two O atoms; C⑤: connected to H atoms on the benzene ring by a single bond; C⑥: directly bonded to three C atoms on the benzene ring). The actual saturation of H, O, and C in the ligand is statistically analyzed. In this embodiment, the RSD of C is 4, the RSD of H is 1, and the RSD of O is 1 or 2. The theoretical saturation TSD values ​​of C, H, and O are shown in the following list: {'C': 4, 'H': 1, 'O': 2};

[0034] S5. The total charge value of the non-metallic framework in MOFs after removing metal atoms can be obtained by using the difference between the actual saturation value and the theoretical saturation value of the non-metallic atoms. Since a complete and reasonable MOF framework must be electrically neutral, after removing the metal atoms, the MOF framework must carry a certain amount of negative charge (metal atoms are usually positively charged), and the absolute value of this value must be equal to the total positive charge value of the missing metal atoms.

[0035] The formal charges of C, H, and O atoms can be calculated using the formula (Formal Charge = RSD Value - TSD Value). Detailed calculations and results are provided below. Figure 2 As shown in box C. After solving for the Q of each atom in the BTC ligand, it can be deduced that the Q of the BTC ligand is -3. Cu-BTC contains a total of 32 BTC ligands. Further calculation shows that after removing the metallic element Cu, the total Q of the nonmetallic framework is -96.

[0036] S6. From the charge conservation formula: Oxidation state of metal atom × Number of metal atoms = Inverse value of total charge of nonmetallic framework in MOFs lacking metal atoms, we can deduce that the oxidation state of Cu atom in Cu-BTC structure is 2 (as follows). Figure 2 (as shown in box D).

[0037] The calculation results of the final metal atom oxidation state in step S6 are evaluated to determine whether they are reasonable. Since the calculation result 2 is a positive integer, which is consistent with the positive divalent oxidation state (+1 or +2) of Cu, the result calculated in this embodiment is determined to be reasonable.

[0038] It should be noted that since the final solution is for the oxidation state of the metal center in MOFs, the metal oxidation state is equal to the numerical value of the charge of the metal atom. The numerical value of the charge of all metal atoms is equal to the negative of the charge of the nonmetal framework. Therefore, in the actual operation of this method, we directly solve for the negative of the formal charge of the nonmetal atom (negative of the formal charge of the nonmetal atom = TSD value - RSD value). Then, we sum these values ​​and use the formula ∑(TSD-RSD) / n(metal) to derive the actual oxidation state of the metal atom.

[0039] To demonstrate the universality of this method, 100 MOFs were randomly selected from the CSD database according to the letters A to Z, and their metal oxidation state values ​​were calculated. Table 1 below shows the CSD names of these 100 MOFs, along with the metal element types and their oxidation state values ​​given by the CSD database. The metal oxidation state values ​​calculated by this method are compared with those given by the CSD database. The comparison results show that this method has a high accuracy rate in calculating the oxidation state of metal atoms in MOFs (the accuracy rate for calculating the valence state of the randomly selected 100 MOFs is 100%).

[0040] Table 1. Price State Comparison of 100 MOFs

[0041]

[0042]

[0043]

[0044] Example 2

[0045] like Figure 3 As shown, for elements with two theoretical saturations, when RSD ≥ 4, the larger TSD value is used for calculation. (Clo4 is an example.) - Taking ions as an example, other steps can be referred to Example 1, mainly focusing on the calculation of the formal charge of atoms. Since Cl atoms have two TSD values, 1 and 7, ... Figure 3 It can be known that in ClO4 - The RSD value of the Cl atom in the ion is 7, which is greater than 4. When calculating Q(Cl), the TSD value of Cl(Cl) = 7 needs to be used, so Q(Cl) = 0. Finally, Q(ClO4) = -1 is calculated. For the detailed solution process, please refer to [link / reference]. Figure 3 .

[0046] Example 3

[0047] like Figure 4 As shown, when nonmetallic atoms P, S, Si, and B directly bond with highly electronegative atoms such as O, F, Cl, Br, and I, the formal charges of P, S, Si, and B need to be reversed. Taking BF4 as an example... - Taking ions as an example, all other steps can be referred to Example 1, but when calculating the formal charge of B atoms, from Figure 4 It is known that the B atom is directly bonded to 4 F atoms, so Q(B) = -(RSD - TSD) = -1. Therefore, Q(BF4) is calculated. - ) = -1, for detailed solution process please refer to Figure 4 .

Claims

1. A method for calculating the valence state of metal atoms in metal-organic framework materials, characterized in that, Includes the following steps: S1. Obtain the original .cif files of MOFs from the CSD database; S2. Use the open-source xyz2mol program to perform batch bonding on the .cif files obtained in step S1, obtain the atom numbering information in the .cif files, extract the types and numbers of all atoms in the .cif files from the atom numbering information, and save and record them. S3. Based on the atom numbering information obtained in step S2, delete all information related to metal atoms in the .cif file; S4. Re-acquire information from the .cif file processed in step S3. The information acquired includes the bonding type, number of bonds, and type of bonded atom pairs of non-metallic atoms. Based on the information obtained again, the actual saturation values ​​of all non-metal atoms in the .cif file after the missing metal atoms are calculated; S5. The difference between the actual saturation value and the theoretical saturation value of non-metallic atoms can be used to obtain the total charge value of MOFs in the .cif file after removing metal atoms; the absolute value of the total charge value of MOFs is the total positive charge value of the missing metal atoms. S6. Calculate the valence state of metal atoms in MOFs using the charge conservation formula: valence state of metal atom × number of metal atoms = the negative of the total positive charge of missing metal atoms.

2. The method for calculating the valence state of metal atoms in a metal-organic framework material according to claim 1, characterized in that, In step S5, the theoretical saturation value of non-metallic atoms is:

3. A method for calculating the valence state of metal atoms in a metal-organic framework material according to claim 1 or 2, characterized in that, In step S5, when the actual saturation values ​​of non-metallic atoms P, S, Cl, Br, and I are greater than 4, the corresponding theoretical saturation values ​​are 5, 6, 7, 7, and 7, respectively.

4. A method for calculating the valence state of metal atoms in a metal-organic framework material according to claim 1 or 2, characterized in that, In step S4, when non-metallic atoms P, S, Si, and B directly bond with highly electronegative atoms O, F, Cl, Br, and I, the formal charges of P, S, Si, and B need to be reversed.

5. A method for calculating the valence state of metal atoms in a metal-organic framework material according to claim 1 or 2, characterized in that, In step S1, the original MOFs' .cif files are obtained by manual screening or computer-aided screening.

6. A method for calculating the valence state of metal atoms in a metal-organic framework material according to claim 1 or 2, characterized in that, In step S4, the bonding type is one of single bond, double bond, or triple bond.

7. A method for calculating the valence state of metal atoms in a metal-organic framework material according to claim 1 or 2, characterized in that, The final calculation result of the metal atom valence state in step S6 is evaluated to determine whether it is reasonable. If the calculation result is negative or not an integer, the calculation result is unreasonable. If the calculation result is a positive integer, it is further compared with the common valence states of metal elements. If they are consistent, the calculation result is considered reasonable. If they are inconsistent, the calculation result is considered unreasonable.

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