Method and device for accurately and quickly obtaining multi-core metal cluster electronic structure and computer readable storage medium

Abstract

The invention discloses a method and device for accurately and rapidly obtaining a multi-core metal cluster electronic structure and a computer readable storage medium. The method comprises the following steps: S1, preparing a. Pdb file containing a metalloenzyme structure, simulating a metalloenzyme system by utilizing Amber software, and generating a. Prmtop topological file containing topological information of the metalloenzyme system; s2, inputting the. Prmtop topological file into Turbo software, selecting an atom sequence number containing the multi-core metal cluster, setting the weight of the full-high spin of the multi-core metal cluster, and carrying out Turbo single-point calculation to obtain alpha and beta track files in a full-high spin state; and S3, inputting an atom sequence number of the multi-core metal cluster into a flip module of the Turbo software, specifying an alpha track sequence number needing to be overturned and overturning the alpha track sequence number into a beta track to obtain an initial guess alpha and beta track file in a low-spin state, and performing Turbo single-point calculation again to obtain a correct electronic structure. According to the method, the calculation efficiency is improved, the consumption of calculation resources is reduced, and the research on the electronic structure of the multi-core metal cluster is more efficient and accurate.

Description

Technical Field

[0001] The present invention belongs to the technical field of computational chemistry simulation, and particularly relates to a method, an apparatus, and a computer-readable storage medium for accurately and rapidly obtaining the electronic structure of multinuclear metal clusters. Background Art

[0002] The catalytic reactions of enzymes usually require the participation of metals, especially transition metals such as 3d metal elements like iron, copper, and manganese. Iron-sulfur clusters (Fe-S clusters), as a common type of metal-sulfur cluster, are widely present in biological catalytic reactions and play an important role particularly in redox reactions, electron transfer, and catalytic reactions. The catalytic activity of these metal clusters is closely related to their electronic structure, and the electronic structure of metal clusters often has a high degree of complexity and dynamic changes. Determining the accurate electronic structure of multinuclear iron-sulfur clusters helps to study the electron distribution problem and further understand the reaction mechanism.

[0003] In the study of the electronic structure of multinuclear metal clusters, quantum chemical calculations have become a key tool. By calculating the molecular orbitals and electron state distributions, the electronic structure, bonding characteristics, and reaction mechanism of metal clusters can be revealed. However, the calculation of the electronic structure of metal clusters is particularly challenging because it not only involves complex interactions between multiple metal centers but is also affected by the electron spin states. Especially in transition metal clusters, since the metal centers usually have incompletely filled d orbitals, the electrons within the cluster can exist in different spin states, resulting in the diversity of electronic structures and reactivities. The optimization of spin states is crucial for correctly describing the electronic structure of metal clusters. Different spin states lead to energy differences and directly affect the catalytic activity, stability, and performance of metal clusters in chemical reactions. For example, in some catalytic processes, the low spin state may be more stable, while in other reactions, the high spin state may be more active. Therefore, researchers usually need to perform fine conversions and optimizations between high spin states and low spin states to obtain the accurate electronic structure. Currently, there are mainly two traditional methods for finding the electronic states of multinuclear metals: 1. directly setting the required spin multiplicity; 2. first obtaining the molecular orbitals of the metal in the fully high spin state and then obtaining the low spin electronic structure by flipping the orbitals. These two traditional methods often require repeated adjustment of the spin configuration of the molecular orbitals, resulting in long calculation times and low efficiency. In addition, traditional methods usually require the use of orbital visualization software to identify the shape of each orbital and the metal atoms to which they belong, and the calculation results are often incorrect or unsatisfactory. Summary of the Invention

[0004] In view of the problems existing in the existing calculation process of the electronic structure of multinuclear metal cluster systems, such as strong randomness, long time-consuming in the process of finding the electronic structure, often incorrect or unsatisfactory calculation results, and long calculation time, the purpose of the present invention is to provide a method, device and computer-readable storage medium for accurately and quickly obtaining the electronic structure of multinuclear metal clusters. Based on the flip module in Turbomole, the present invention can efficiently optimize the electronic structure of multinuclear metal clusters. By applying the flip module, the spins of unpaired electrons in the metal cluster can be quickly reversed, its spin state can be optimized, and an accurate electronic structure can be quickly obtained. This method not only improves the calculation efficiency, but also reduces the consumption of calculation resources, making the research on the electronic structure of multinuclear metal clusters more efficient and accurate.

[0005] To achieve the above object, the present invention adopts the following technical solutions:

[0006] In the first aspect, the present invention provides a method for accurately and quickly obtaining the electronic structure of multinuclear metal clusters, including the following steps:

[0007] S1. Prepare a.pdb file containing the structure of the metalloenzyme, and use Amber software to simulate the metalloenzyme system to generate a.prmtop topology file containing the topological information of the metalloenzyme system;

[0008] S2. Input the.prmtop topology file into Turbomole software, select the atomic numbers of the atoms containing the multinuclear metal cluster in the metalloenzyme and set the multiplicity of the full high-spin of the multinuclear metal cluster. After Turbomole single-point calculation, obtain the alpha and beta orbital files (alpha and beta files) of the metalloenzyme system in the full high-spin state;

[0009] S3. Input the atomic numbers of the multinuclear metal cluster into the flip module of Turbomole software, specify the alpha orbital numbers to be flipped and flip them to beta orbitals to obtain the initial guess alpha and beta orbital files in the low-spin state;

[0010] Input the initial guess alpha and beta orbital files in the low-spin state into Turbomole single-point calculation again to obtain the correct electronic structure of the multinuclear metal cluster.

[0011] As a widely used quantum chemistry calculation software, Turbomole provides a variety of efficient calculation modules for the electronic structure research of molecular systems. Turbomole has powerful SCF (self-consistent field) calculation capabilities and orbital optimization functions, and can handle large-scale systems and complex electronic structures. The flip module, as a special function in Turbomole, can be used to adjust the spin state of the system by reversing the spin configuration in the orbitals. This module effectively converts the spin state by exchanging the spin directions of the unpaired electrons in the metal cluster, and accelerates the optimization process of the electronic structure. Compared with traditional spin optimization methods, the flip module achieves a rapid adjustment of the spin state in a simple and direct way, reducing the computational complexity and time consumption. Especially in the research of multinuclear metal clusters, the flip module can effectively convert between different spin states, helping researchers quickly obtain the accurate electronic structure of multinuclear metal clusters. Based on the above concept, the present invention provides a method for accurately and quickly calculating the electronic structure of multinuclear metal clusters based on the flip module in Turbomole. By inputting the spin multiplicity of the fully high-spin state of the system, an initial guess of the electronic structure is obtained, and then the flip module is used to identify the occupied orbitals belonging to each metal and then perform orbital flipping, finally obtaining the required correct electronic structure. The present invention does not require the use of visualization software to identify the shape of each orbital and the metal atoms to which they belong, and the calculation process is fast and the results are more accurate.

[0012] In one embodiment of the present invention, in step S1, the preparation of the.pdb file containing the metal enzyme structure is to download the.pdb file containing the metal enzyme structure from the protein structure database according to the UniProt ID or name of the target protein.

[0013] In one embodiment of the present invention, in step S1, the topological information of the metal enzyme system includes the positions of all atoms, bond connection relationships, charges, force field parameters, solvent models, and periodic boundary conditions. The Amber software is a widely used molecular simulation software that can generate a topological file (.prmtop file) suitable for Turbomole calculations. This file contains necessary parameter information such as the atomic positions, bond connection information, and charges in the system, and is the basis for subsequent quantum chemistry calculations.

[0014] In one embodiment of the present invention, in step S2, the Turbomole is an efficient quantum chemistry calculation software package suitable for processing large-scale molecular systems, especially in metal enzyme systems, and can perform high-precision single-point calculations and electronic structure analyses.

[0015] In an embodiment of the present invention, in step S2, in the step of selecting the atomic numbers of the multi-nuclear metal clusters in the metalloenzyme, the.xyz file generated by a single point can be opened to query the atomic numbers of the metals. Taking the electronic structure of the multi-nuclear metal cluster as the [Fe4S4] in the SAM radical enzyme + cluster low-spin electronic structure as an example, the atomic numbers are selected as 50 - 53.

[0016] In an embodiment of the present invention, in step S2, in the step of setting the multiplicity of the fully high-spin of the multi-nuclear metal cluster, first determine the valence state and the number of single electrons of each metal, and then determine the total number of single electrons coupled by all metals in the fully high-spin state. Taking the electronic structure of the multi-nuclear metal cluster as the [Fe4S4]+ cluster low-spin electronic structure in the SAM radical enzyme as an example, the multiplicity of the fully high-spin of the multi-nuclear metal cluster is set to 18. Further, the [Fe4S4]+ cluster includes the following 1) and 2): 1) 3 divalent irons, each iron has 4 single electrons in the fully high-spin state; 2) one trivalent iron, this iron has 5 single electrons in the fully high-spin state; all four irons couple out 17 single electrons with the same spin in the fully high-spin state, and by default, they are 17 alpha electrons in the same direction.

[0017] In an embodiment of the present invention, in step S3, the specified alpha orbital numbers to be flipped are all the alpha orbital number information of the specified metal displayed under the flip module. Taking the electronic structure of the multi-nuclear metal cluster as the [Fe4S4] in the SAM radical enzyme + cluster low-spin electronic structure as an example, the specified alpha orbital numbers to be flipped are the four alpha electron orbitals on two divalent Fe atoms, including the orbital numbers 94, 98, 102, 104 of the Fe atom numbered 50 and the orbital numbers 115, 116, 117, and 121 of the Fe atom numbered 51. Specifically, in the flip module of Turbomole, the orbital flipping can be performed through command line operations. The specific operation process is as follows: Enter the define command and press Enter. After entering the flip module, enter the atomic number of the metal atom and the orbital number to be flipped, and the system will automatically execute the orbital flipping operation.

[0018] It can be understood that after the single point calculation in step S3, it is necessary to check the spin information of the atomic numbers of the multi-nuclear metal cluster to confirm whether it conforms to the expected spin state. If the result conforms to the expectation, the calculation of the electronic structure is completed.

[0019] In the embodiments of the present invention, in some complex metalloenzyme systems, multiple metal atoms are included. For example, the nitrogenase may contain a cluster structure with eight iron atoms. In this case, the orbital flipping operation can be carried out step by step. For example, the eight divalent irons in the inactive nitrogenase are finally coupled to a fully low-spin S = 0 state. Under the condition of obtaining an electronic structure with a fully high-spin S = 32 / 2, the iron atoms in the nitrogenase can be processed one by one or in groups to ensure that the spin state of each metal atom meets the expectation. For flipping the orbit one by one, the orbit on Fe1 can be flipped first to obtain an electronic structure with a medium spin S = 24 / 2, and then on this basis, the orbit on Fe2 can be flipped to obtain an electronic structure with S = 16 / 2. Then, flipping Fe3 as described above to obtain an electronic structure with S = 8 / 2, and finally flipping Fe4 to obtain the final fully low-spin S = 0. For flipping the orbits in groups, for example, Fe1 and Fe2 are grouped together and flipped into β electrons first to obtain an electronic structure with a medium spin S = 16 / 2. On this basis, the α orbits on another group of irons Fe3 and Fe4 are flipped again to obtain the final fully low-spin S = 0.

[0020] In a second aspect, the present invention provides a method for confirming the electronic structure of a metalloenzyme, including the method for accurately and rapidly obtaining the electronic structure of a multinuclear metal cluster described in any one of the above.

[0021] In a third aspect, the present invention provides a device for accurately and rapidly obtaining the electronic structure of a multinuclear metal cluster, including:

[0022] A metalloenzyme simulation unit for simulating a metalloenzyme system using Amber software for a.pdb file containing the structure of a metalloenzyme to generate a.prmtop topology file containing the topological information of the metalloenzyme system;

[0023] A unit for obtaining α and β orbital files in the fully high-spin state, which inputs the.prmtop topology file into Turbomole software, selects the atomic numbers of the atoms containing the multinuclear metal cluster in the metalloenzyme and sets the multiplicity of the fully high-spin of the multinuclear metal cluster, and obtains the α and β orbital files of the metalloenzyme system in the fully high-spin state through Turbomole single-point calculation;

[0024] A unit for obtaining the electronic structure of the multinuclear metal cluster, which inputs the atomic numbers of the multinuclear metal cluster into the flip module of Turbomole software, specifies the serial numbers of the α orbits to be flipped and flips them into β orbits to obtain the initial guess α and β orbital files in the low-spin state, and performs Turbomole single-point calculation on the initial guess α and β orbital files in the low-spin state again to obtain the correct electronic structure of the multinuclear metal cluster.

[0025] Fourthly, the present invention provides a computer-readable storage medium, on which computer program instructions are stored. When the computer program instructions are executed by a processor, they are used to implement the steps corresponding to the method for accurately and rapidly obtaining the electronic structure of a multinuclear metal cluster described in any one of the above.

[0026] The present invention has the following beneficial effects:

[0027] The present invention optimizes the method for calculating the electronic structure of a multinuclear metal cluster by quickly adjusting the spin state through the flip module. Compared with the traditional method, the present invention greatly improves the calculation efficiency. Especially when dealing with metal clusters containing multiple metal atoms and having complex spin states, it can significantly shorten the calculation time and reduce the consumption of calculation resources. Through this method, researchers can more efficiently obtain the electronic structure of multinuclear metal clusters, providing strong theoretical support for the mechanism research of metal cluster catalytic reactions and the design of new materials. Description of the Drawings

[0028] Figure 1 It is a schematic flowchart of the method for accurately and rapidly obtaining the electronic structure of a multinuclear metal cluster according to the present invention.

[0029] Figure 2 It is a schematic diagram of the spin flip from the high-spin electronic structure with S = 17 / 2 to the low electronic structure with S = 1 / 2.

[0030] Figure 3 It is a schematic diagram of the valence electron orbitals on Fe1 and Fe2 in Comparative Example 1. Detailed Embodiments

[0031] In the following description, specific details such as specific system structures and technologies are presented for the purpose of illustration rather than limitation, so as to thoroughly understand the embodiments of the present application. However, those skilled in the art should clearly understand that the present application can also be implemented in other embodiments without these specific details. In other cases, detailed descriptions of well-known systems, devices, circuits, and methods are omitted to avoid unnecessary details from interfering with the description of the present application.

[0032] It should be understood that the terms used herein are for the purpose of describing specific exemplary embodiments only and are not intended to be limiting. Unless the context clearly dictates otherwise, the singular forms "a", "an", and "the" as used herein may also include the plural forms. The terms "comprising", "including", "containing", and "having" are inclusive and thus specify the presence of the stated features, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, and / or combinations thereof. The method steps, processes, and operations described herein are not to be construed as necessarily requiring them to be performed in the particular order described or illustrated, unless the order of performance is explicitly stated. It should also be understood that additional or alternative steps may be used.

[0033] The present invention will be further described in detail below in conjunction with specific embodiments. The embodiments given are only for clarifying the present invention and not for limiting the scope of the present invention. The following embodiments can be used as a guide for those of ordinary skill in the art to make further improvements and do not constitute any limitation to the present invention in any way.

[0034] The methods used in the following embodiments, unless otherwise specified, are all conventional methods, carried out according to the techniques or conditions described in the literature in this field or according to the product instructions. The materials, reagents, etc. used in the following embodiments, unless otherwise specified, can all be obtained from commercial sources.

[0035] Example 1

[0036] Taking the [Fe4S4] cluster in the SAM radical enzyme as an example below, a calculation method for quickly and accurately obtaining the low-spin electronic structure of [Fe4S4] using the flip module in Turbomole described in the present invention. + cluster.

[0037] (1) First, download the structure of the SAM radical enzyme Dph2 and save it as a 6BXL.pdb file. Subsequently, use the Amber software to simulate the Dph2 enzyme system to generate a corresponding 6BXL.prmtop topology file. The 6BXL.prmtop file contains important topological information such as the positions of all atoms, bond connection relationships, and charges in the metalloenzyme system and can be recognized and used by the Turbomole software;

[0038] (2) Input the 6BXL.prmtop topology file generated in step (1) into the Turbomole software. Select the atomic numbers 50 - 53 of the atoms containing the [Fe4S4] + cluster in the metalloenzyme and set the Fe of the metal cluster to a multiplicity of 18 in the fully high-spin state. Here, [Fe4S4] +The cluster contains three divalent iron atoms (each with 4 unpaired electrons in the fully high-spin state), one trivalent iron atom (with 5 unpaired electrons in the fully high-spin state). When all four iron atoms are in the fully high-spin state, 17 unpaired electrons with the same spin are coupled out, which are here assumed to be 17 alpha electrons with the same direction. Using Turbomole single-point calculation, the alpha and beta orbital files (alpha and beta files) of the system in the fully high-spin state are obtained. Check the spin information on iron atoms numbered 50 - 53 in the fully high-spin state (Table 1).

[0039] Table 1 Spin distribution values on Fe numbered 50 - 53 in the cluster obtained from single-point calculation in Example 1 for [Fe4S4] in the fully high-spin state + Spin distribution values on Fe numbered 50 - 53 in the cluster

[0040] Fe1 (No. 50) Fe2 (No. 51) Fe3 (No. 52) Fe4 (No. 53) 3.7659 3.7028 3.7742 3.7036

[0041] (3) Use the flip module in Turbomole to perform orbital flipping. In the Turbomole command line, enter the command define and press Enter successively until entering the flip module. Then, enter the serial numbers 50 - 53 of the metal atoms in the metal cluster. The alpha and beta orbital serial numbers on each iron atom are shown in the flip module, as shown in Table 2.

[0042] Table 2 Alpha and beta orbital serial numbers occupied by valence electrons on Fe numbered 50 - 53 and the occupancy ratio of d orbitals shown in the flip module in Example 1

[0043]

[0044] Here, to obtain the low-electron structure with S = 1 / 2 from the high-spin electron structure with S = 17 / 2 ( Figure 2 ), and to ensure the fully high-spin state of each iron atom, four alpha electron orbitals on two divalent Fe atoms need to be flipped to beta orbitals, that is, 8 alpha orbitals need to be flipped. If the spins on iron atoms numbered 50 and 51 are flipped, query the alpha orbital serial numbers in Table 2. For iron atom numbered 50, the orbital serial numbers to be flipped are 94, 98, 102, 104. For iron atom numbered 51, the orbital serial numbers to be flipped are 115, 116, 117, 121. Enter these 8 orbital serial numbers, and the system will automatically flip these orbitals to beta orbitals to obtain the initial guess alpha and beta orbital files in the low-spin state. Perform single-point calculation again to update the electronic structure of the metal cluster;

[0045] (4) After completing the single-point calculation in step (3), check the spin information on iron atoms numbered 50 - 53 in the low-spin state (S = 1 / 2) (Table 3) to confirm whether it conforms to the expected low-spin state. The result conforms to the expectation, and the calculation of the electronic structure is completed.

[0046] Table 3 Spin distribution values on Fe atoms numbered 50 - 53 of the S = 1 / 2 spin [Fe4S4] cluster obtained by single-point calculation in Example 1 + Spin distribution values on Fe atoms numbered 50 - 53 of the

[0047] Fe1 (No. 50) Fe2 (No. 51) Fe3 (No. 52) Fe4 (No. 53) -3.5409 -3.5433 3.7708 3.6624

[0048] Comparative Example 1

[0049] When using the traditional method to flip the single electron on the Fe atom, the method is as follows:

[0050] (1) and (2) are the same as in Example 1.

[0051] (3) Similar to Example 1, convert the alpha electrons on the iron atoms numbered 50 (Fe1) and 51 (Fe2) into beta electrons. Open the molecular orbitals with orbital visualization software and find the alpha orbital numbers belonging to Fe1 and Fe2. As Figure 3 shown, the eight orbitals 179, 190, 200, 202, 203, 204, 205 have electron distributions on Fe1 or Fe2. However, it should be noted that these electrons will delocalize to the surrounding iron, resulting in inaccurate identification of which iron atom the orbitals belong to.

[0052] (4) After flipping the 179, 190, 200, 202, 203, 204, 205 orbitals to beta orbitals, perform a single-point calculation again to update the electronic structure of the metal cluster;

[0053] (5) After completing the single-point calculation in step (4), check the spin information on the iron atoms numbered 50 - 53 in the low-spin (S = 1 / 2) state. As can be seen from Table 4, Fe1 and Fe3 are in medium spin, that is, the traditional method of visualizing and identifying orbitals cannot accurately determine the orbital subordination problem, and thus it is impossible to conveniently, quickly, and accurately obtain the correct electronic structure.

[0054] Table 4 Spin distribution values on Fe atoms numbered 50 - 53 of the S = 1 / 2 spin [Fe4S4] cluster obtained by single-point calculation in Comparative Example 1 + Spin distribution values on Fe atoms numbered 50 - 53 of the

[0055] Fe1 (No. 50) Fe2 (No. 51) Fe3 (No. 52) Fe4 (No. 53) -2.1339 -3.5433 2.3500 3.7632

[0056] Comparing Example 1 and Comparative Example 1, it can be seen that the electronic structure calculated by the method of the present invention does not require visual identification of orbitals compared with the traditional method, and the method of the present invention is convenient, fast, and highly accurate, with obvious advantages.

[0057] Example 2

[0058] This example provides a device for accurately and quickly obtaining the electronic structure of a multi-core metal cluster, including:

[0059] A metal enzyme simulation unit for simulating a metal enzyme system of a.pdb file containing a metal enzyme structure using Amber software to generate a.prmtop topology file containing the topology information of the metal enzyme system;

[0060] A unit for obtaining α and β orbital files in the fully high-spin state, which is used to input the.prmtop topology file into Turbomole software, select the atomic numbers containing the polynuclear metal cluster in the metal enzyme and set the multiplicity of the fully high-spin of the polynuclear metal cluster, and through Turbomole single-point calculation, obtain the α and β orbital files of the metal enzyme system in the fully high-spin state;

[0061] A unit for obtaining the electronic structure of the polynuclear metal cluster, which is used to input the atomic numbers of the polynuclear metal cluster in the flip module of Turbomole software, specify the α orbital numbers to be flipped and flip them to β orbitals to obtain the initial guess α and β orbital files in the low-spin state, and perform Turbomole single-point calculation on the initial guess α and β orbital files in the low-spin state again to obtain the correct electronic structure of the polynuclear metal cluster.

[0062] The system provided in this embodiment is used to execute the above method embodiments. For the specific process and detailed content, please refer to the above embodiments and will not be elaborated here.

[0063] The device provided in this embodiment can be a software unit, a hardware unit, or a unit combining software and hardware built into an existing terminal device, can also be integrated into the terminal device as an independent pendant, or can exist as an independent terminal device.

[0064] Those skilled in the art can clearly understand that for the convenience and conciseness of description, only the above division of each functional unit and module is used as an example. In practical applications, the above functions can be allocated to different functional units and modules according to needs, that is, the internal structure of the device is divided into different functional units or modules to complete all or part of the functions described above. Each functional unit and module in the embodiment can be integrated in a processing unit, can also exist physically independently for each unit, or two or more units can be integrated in one unit. The above integrated units can be implemented in the form of hardware or in the form of software functional units. In addition, the specific names of each functional unit and module are only for the convenience of mutual distinction and do not limit the protection scope of this application. The specific working process of the units and modules in the above system can refer to the corresponding process in the foregoing method embodiments and will not be elaborated here.

[0065] Embodiment 3

[0066] This embodiment provides a computer program product corresponding to the method for accurately and quickly obtaining the electronic structure of a multinuclear metal cluster provided in Embodiment 1. The computer program product may include a computer-readable storage medium having thereon computer-readable program instructions for executing the method for accurately and quickly obtaining the electronic structure of a multinuclear metal cluster described in Embodiment 1.

[0067] A computer-readable storage medium may be a tangible device that retains and stores instructions for use by an instruction execution device. A computer-readable storage medium may be, for example, but not limited to, an electrical storage device, a magnetic storage device, an optical storage device, an electromagnetic storage device, a semiconductor storage device, or any combination of the foregoing.

[0068] For a computer-readable storage medium provided in the foregoing embodiment, its implementation principle and technical effects are similar to those of the foregoing method embodiment, and will not be elaborated herein.

[0069] The present invention is described with reference to the flowcharts and / or block diagrams of methods, apparatuses (systems), and computer program products according to embodiments of the present application. It should be understood that each process and / or block in the flowcharts and / or block diagrams, and the combination of processes and / or blocks in the flowcharts and / or block diagrams, can be implemented by computer program instructions. These computer program instructions can be provided to the processor of a general-purpose computer, a special-purpose computer, an embedded processor, or other programmable data processing devices to generate a machine, such that the instructions executed by the processor of the computer or other programmable data processing devices generate a device for implementing the functions specified in Figure 1 one process or multiple processes and / or blocks Figure 1 one block or multiple blocks.

[0070] These computer program instructions can also be stored in a computer-readable memory that can direct a computer or other programmable data processing device to work in a specific manner, such that the instructions stored in the computer-readable memory generate a manufactured article including an instruction device that implements the functions specified in Figure 1 one process or multiple processes and / or blocks Figure 1 one block or multiple blocks.

[0071] These computer program instructions can also be loaded onto a computer or other programmable data processing device, such that a series of operation steps are performed on the computer or other programmable device to generate a computer-implemented process, so that the instructions executed on the computer or other programmable device provide steps for implementing the functions specified in Figure 1 one process or multiple processes and / or blocks Figure 1 one block or multiple blocks.

[0072] Although the present invention has been disclosed above in preferred embodiments, it is not intended to limit the present invention. Anyone skilled in this technology can make various modifications and alterations without departing from the spirit and scope of the present invention. Therefore, the protection scope of the present invention should be defined by the claims.

Claims

1. A method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster, characterized in that: The steps include: S1. Prepare a .pdb file containing the metal enzyme structure, simulate the metal enzyme system using Amber software, and generate a .prmtop topology file containing the topological information of the metal enzyme system; S2, inputting the .prmtop topology file into Turbomole software, selecting the atomic number of the polynuclear metal cluster in the metalloenzyme and setting the multiplicity of the full high spin of the polynuclear metal cluster, and obtaining the α and β orbital files of the metalloenzyme system in the full high spin state through Turbomole single point calculation; S3, inputting the atomic number of the polynuclear metal cluster in the flip module of Turbomole software, specifying the number of the α orbital to be flipped and flipping it to the β orbital, and obtaining the initial guessed α and β orbital files in the low spin state; The initially guessed α and β orbital files of the low spin state are again subjected to Turbomole single point calculation to obtain the correct electronic structure of the multi-nuclear metal cluster.

2. The method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to claim 1, characterized in that: The topological information of the metal enzyme system includes the positions of all atoms, bond connections, charges, force field parameters, solvent models and periodic boundary conditions.

3. The method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to any one of claims 1 to 2, characterized in that: The electronic structure of the multi-nuclear metal cluster is [Fe4S4] in the SAM free radical enzyme + Cluster low-spin electronic structure.

4. The method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to claim 3, characterized in that: The atomic number of the multi-nuclear metal cluster is selected to be 50-53.

5. The method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to any one of claims 3 to 4, characterized in that: The multiplicity of the full high spin of the polynuclear metal cluster is set to 18.

6. The method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to claim 5, characterized in that: The [Fe4S4] + The cluster includes the following 1) and 2): 1) 3 divalent irons, each with 4 single electrons at full high spin; 2) one trivalent iron, with 5 single electrons at full high spin; all four irons are at full high spin and couple out 17 single electrons with the same spin, which are 17 alpha electrons in the same direction by default.

7. The method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to any one of claims 3 to 6, characterized in that: The alpha orbital numbers that need to be flipped are four alpha electron orbitals on two divalent Fe atoms, including orbital numbers 94, 98, 102, 104 of Fe atom No. 50 and orbital numbers 115, 116, 117 and 121 of Fe atom No.

51.

8. A method for confirming the electronic structure of a metal enzyme, characterized in that: The invention comprises the method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to any one of claims 1 to 7.

9. A device for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster, characterized in that: include: The metal enzyme simulation unit is used to simulate the metal enzyme system using the Amber software for the .pdb file containing the metal enzyme structure, and generate a .prmtop topology file containing the topological information of the metal enzyme system; A unit for acquiring α and β orbital files in a fully high spin state, for inputting the .prmtop topology file into Turbomole software, selecting the atomic number of the polynuclear metal cluster in the metal enzyme and setting the multiplicity of the fully high spin of the polynuclear metal cluster, and obtaining the α and β orbital files of the metal enzyme system in a fully high spin state through Turbomole single point calculation; The electronic structure acquisition unit of the multi-nuclear metal cluster is used to input the atomic number of the multi-nuclear metal cluster in the flip module of the Turbomole software, specify the α orbital number to be flipped and flip it to the β orbital, obtain the initial guess α and β orbital files in the low-spin state, and perform Turbomole single-point calculation on the initial guess α and β orbital files in the low-spin state again to obtain the correct electronic structure of the multi-nuclear metal cluster.

10. A computer-readable storage medium having computer program instructions stored thereon, characterized in that: When the computer program instructions are executed by a processor, they are used to implement the steps corresponding to the method for accurately and quickly obtaining the electronic structure of a multi-nuclear metal cluster according to any one of claims 1 to 7.

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