A method, program, device and storage medium for automatically generating coordinates of a uranyl ion coordination structure for quantum chemistry calculation

Abstract

The application discloses a kind of uranium ion coordination structure coordinate automatic generation method, program, equipment and storage medium for quantum chemistry calculation, belong to radionuclide coordination structure modeling and chemical technology field.It is determined that the coordination site and its spatial distribution characteristics possibly participate in the coordination of uranium ion by automatically identifying the functional group of organic ligand molecule.The uranium ion is introduced into ligand molecule space, generates initial three-dimensional coordination structure model satisfying the linear structure constraint and coordination geometry requirement of uranium ion, and the model is checked and adjusted for geometric reason, to obtain the coordinate of uranium ion coordination structure that can be directly used for subsequent quantum chemistry calculation or structure analysis.The method reduces the dependence on experience of manual modeling steps, improves the automation degree and consistency of uranium ion coordination structure construction, and is suitable for uranium ion coordination system of different functional group types and various coordination modes.

Description

Technical Field

[0001] This invention relates to the field of radionuclide coordination structure modeling and computational chemistry, specifically to a method, program, device, and storage medium for automatically generating coordinates of uranyl ion coordination structures for quantum chemical calculations. Background Technology

[0002] Uranyl ion (UO2) 2+ As one of the most common actinide forms in the nuclear fuel cycle and radioactive waste treatment, the coordination structure characteristics of uranyl ions directly affect extraction and separation behavior, coordination stability, and related thermodynamic properties. Therefore, accurately constructing a coordination structure model between uranyl ions and organic ligands is an important foundation for conducting coordination mechanism research and performance prediction.

[0003] In existing studies, the initial configuration of uranyl ion coordination structures is typically constructed based on human experience, such as manually selecting coordinating atoms, setting coordination distances, and adjusting the spatial configuration. This approach not only relies on the professional experience of researchers but also suffers from low modeling efficiency, poor structural consistency, and difficulty in scaling up when dealing with a large number of different ligand molecules.

[0004] Especially in organic ligand systems containing multiple functional groups, the coordination ability of different functional groups to uranyl ions varies significantly. For example, carbonyl groups, amide oxygens, phosphoryl oxygens, and nitrogen atoms can all serve as potential coordination sites. If the types of functional groups and their spatial distribution in the ligands cannot be systematically identified and distinguished, it is often difficult to construct a reasonable uranyl ion coordination structure model.

[0005] Therefore, there is an urgent need for a method that can automatically identify the type of functional group in the ligand and construct the uranyl ion coordination structure accordingly, so as to improve the construction efficiency and structural rationality and meet the needs of large-scale structure generation and computational screening. Summary of the Invention

[0006] To address the technical problems of existing uranyl ion coordination structure modeling processes, such as reliance on manual experience, low modeling efficiency, and poor structural consistency, this invention provides an automatic generation method for uranyl ion coordination structure coordinates in quantum chemical calculations. This method automatically generates uranyl ion coordination structures based on the physicochemical parameters of uranyl ions and ligands through inference calculations, and features a high degree of automation in the modeling process, clear structure construction rules, and wide applicability.

[0007] This invention provides an automatic method for generating coordinates of uranyl ion coordination structures for quantum chemical calculations, comprising the following steps:

[0008] Step 1: Obtain the structural information of uranyl ion ligand molecules and identify and analyze the functional groups of the ligand molecules; screen the functional groups in the ligand molecules to obtain functional groups with potential coordination ability;

[0009] Step 2: Analyze the functional groups with potential coordination ability, determine the types of atoms in each functional group that can act as metal coordinating atoms and their spatial position information, and construct a coordination site information representation to characterize the coordination ability of ligands.

[0010] Step 3: Based on the coordination site information constructed in Step 2, an initial coordination structure is generated between the uranyl ion center and the ligand molecule;

[0011] Step 4: After obtaining the initial coordination configuration of uranyl ions and ligands, the configuration is geometrically adjusted to satisfy the distance constraints between non-bonded atoms and the angle constraints between adjacent coordinating atoms.

[0012] Step 5: Based on the adjusted initial coordination configuration, output the coordinates of the uranyl ion-ligand coordination structure.

[0013] Furthermore, before obtaining the structural information, the uranyl ion ligand molecular structure is first standardized; the ligand molecular structure information comes from the molecular formula, two-dimensional structural formula or three-dimensional initial configuration of the uranyl ion ligand molecule; the functional group identification and analysis of the ligand molecule includes functional group type, atomic composition characteristics, bond connection relationship and local geometric configuration.

[0014] Furthermore, the functional group screening is based on the functional group matching rules described by SMARTS.

[0015] Furthermore, the coordination site information includes information on the functional group category, the type of atom that can participate in coordination within the functional group, and the spatial position of the atom in the ligand molecule.

[0016] Furthermore, the axial uranium-oxygen bond length of the uranyl ion in the initial coordination structure It is 1.7~1.9 Å;

[0017]

[0018] in, The axial uranium-oxygen bond length under ligand-free or weakly ligand conditions; The modulation coefficient; Functional group coordination capacity factor;

[0019] In the initial coordination structure, the initial coordination distance between the coordinating atom and the uranium atom in the equatorial plane is... The range is 2.3~2.7 Å;

[0020]

[0021] in, The equatorial coordination distance under conditions of no ligand or weak ligand; The coordination shrinkage coefficient;

[0022]

[0023] in, For the first Coordination ability factor of functional groups of each ligand.

[0024] Furthermore, the geometric adjustment involves rigidly translating and rotating the entire ligand with the uranium atom U in the uranyl ion as the origin and the coordinating atom as the center.

[0025] Furthermore, the adjusted geometry satisfies the following conditions:

[0026] Non-bonded atom distance constraint: any two non-bonded atoms and Distance between Not less than the set threshold , It is 1.2~2 Å;

[0027] Angle constraint between adjacent coordinating atoms: Angle between adjacent coordinating atoms Not less than the set threshold , The angle is 60° to 90°. , and These are coordinating atoms.

[0028] The present invention also provides a computer device, including a memory, a processor, and a computer program stored in the memory, wherein the processor executes the computer program to implement the steps of the automatic generation method for uranyl ion coordination structure coordinates described above.

[0029] The present invention also provides a computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, implements the steps of the automatic generation method for uranyl ion coordination structure coordinates described in any of the preceding claims.

[0030] The present invention also provides a computer program product, including a computer program that, when executed by a processor, implements the steps of the automatic generation method for uranyl ion coordination structure coordinates described in any of the preceding claims.

[0031] The beneficial effects of this invention are as follows:

[0032] This invention introduces an automatic generation mechanism for uranyl ion-ligand coordination structure coordinates, enabling the regular and automated construction of uranyl ion coordination structures. The constructed model is an inference model, avoiding the problems of strong subjectivity, low modeling efficiency, and poor structural consistency caused by traditional reliance on manual experience to build coordination configurations one by one. This significantly improves the efficiency and repeatability of uranyl ion coordination structure modeling, and is particularly suitable for multi-coordination systems containing multiple coordination functional groups or a large number of candidate ligands. It has good application value in large-scale structure generation, computational screening, and coordination law research, and can be used for ligand screening, coordination structure analysis, and related computational research. Attached Figure Description

[0033] Figure 1 This is a flowchart of the automatic generation method for uranyl ion coordination structure coordinates of the present invention;

[0034] Figure 2 This is a schematic diagram of the initial coordination structure of Embodiment 2 of the present invention. Detailed Implementation

[0035] The technical solution of the present invention will now be clearly and completely described with reference to the accompanying drawings. Obviously, the described embodiments are only some, not all, of the embodiments of the present invention. All other embodiments obtained by those skilled in the art based on the embodiments of the present invention without creative effort are within the scope of protection of the present invention.

[0036] The present invention provides an automatic method for generating coordinates of uranyl ion coordination structures for quantum chemical calculations, comprising the following steps: taking the molecular structure of the ligand to be coordinated as input, performing structural analysis on the ligand molecule to identify the element types, connectivity relationships, and spatial distribution information of atoms in the molecule; based on this, determining the functional groups in the ligand molecule according to a preset functional group identification rule, and screening out functional groups with potential coordination capabilities and their corresponding coordinating atoms; subsequently, based on the identified functional group types and coordinating atom information, introducing uranyl ions and constructing an initial coordination relationship between them and the ligands, and generating the coordinates of the uranyl ion coordination structure model under the condition of satisfying the linear structure constraint of uranyl ions. The coordination number of the central metal ion in the structure model is N, and its vacant coordination sites are filled by water molecules.

[0037] The functional group identification process described above is influenced by factors such as functional group type, atomic composition characteristics, bond connections, and local geometric configuration.

[0038] In the above methods, the functional group types include, but are not limited to, oxygen- or nitrogen-containing functional groups such as carbonyl, amide, phosphoryl, and amino groups.

[0039] In the above method, functional group identification is based on the functional group matching rules described by SMARTS.

[0040] In the above method, the potential coordinating atom is an oxygen or nitrogen atom in the functional group that can form a coordination interaction with uranyl ions.

[0041] In the above method, the coordination mode includes monodentate coordination, bidentate coordination or polydentate coordination, and the coordination mode is determined by the spatial arrangement of functional groups and the coordination preference of uranyl ions.

[0042] In the above method, the construction process of uranyl ion coordination structure includes influencing factors such as the selection of coordinating atoms, the setting of initial coordination distance, and the adjustment of spatial orientation.

[0043] In the above method, uranyl ions are introduced in the form of a linear structure of O=U=O, and their linear structure remains unchanged during the modeling process.

[0044] In the above method, the initial coordination distance is set to a reasonable value within a predetermined range according to different functional group types, so as to avoid atomic overlap or unreasonable spatial configuration.

[0045] In the above method, spatial orientation adjustment is used to ensure that a reasonable coordination geometry is formed between uranyl ions and ligand molecules.

[0046] The above method can be repeated to generate coordinates for uranyl ion coordination structure models of various ligands in batches.

[0047] The coordinates of the uranyl ion coordination structure model automatically generated using the above method can be directly used as the initial structure input for density functional theory calculations or molecular simulations.

[0048] Example 1

[0049] This embodiment provides an automatic modeling method for uranyl ion coordination structures based on functional group recognition, including the following steps:

[0050] Step 1: Obtain the ligand molecular structure and perform functional group recognition.

[0051] For the target uranyl ion coordination system, the structural information of the ligand molecule to be modeled is obtained, and the ligand molecule is subjected to functional group identification processing to determine the types of functional groups that may participate in metal coordination in the ligand molecule, such as carbonyl, hydroxyl, aldehyde, phosphoryl, nitro, amino and other oxygen- or nitrogen-containing functional groups.

[0052] In this embodiment, the ligand molecule structure information may be derived from molecular formula, two-dimensional structural formula or three-dimensional initial configuration; the functional group identification is used to classify and label the functional groups contained in the ligand molecule, wherein the structural rules may be implemented by a functional group matching rule judgment method based on SMARTS description.

[0053] This step enables the preliminary identification of potential coordination functional regions in ligand molecules, providing basic structural information for subsequent coordination site analysis.

[0054] Step 2: Construct a functional group-based representation of coordination site information.

[0055] The identified functional groups are further analyzed to determine the types of atoms that can serve as metal coordinating atoms in each functional group and their spatial positions, thereby constructing a representation of coordination site information to characterize the coordination ability of ligands.

[0056] In this embodiment, the coordination site information includes at least: functional group category information; the type of atom that can participate in coordination within the functional group; and the spatial position of the atom in the ligand molecule.

[0057] Step 3: Generate the initial coordination structure of uranyl ion-ligand.

[0058] Based on the coordination site information constructed in step two, an initial coordination structure is generated between the uranyl ion center and the ligand molecule, which is used as the input configuration for subsequent quantum chemical calculations; wherein, the construction process of the initial coordination structure is based on the coordination ability of functional groups, and key coordination parameters are set in a regular manner.

[0059] (1) Determination of axial structural parameters

[0060] Uranyl ions are represented using a linear axial structure, and their axial oxygen-uranium-oxygen configuration satisfies:

[0061] O=U=O

[0062] The axial uranium-oxygen bond length is denoted as (where ax represents the axial direction).

[0063] To reflect the influence of equatorial plane coordination on axial bonding, this invention will Represented as a parametric function related to coordination functional groups:

[0064]

[0065] in:

[0066] The reference axial bond length is 1.75 Å under ligand-free or weakly ligand conditions.

[0067] Functional group coordination capacity factor;

[0068] The modulation coefficient is used to control the intensity of the influence of equatorial plane coordination on axial bond length, and its preferred value is 0.02~0.05 Å.

[0069] income The range of 1.7 to 1.9 Å is limited to a reasonable range to ensure the physical rationality of the structure and the convergence of the calculation.

[0070] Axial uranium-oxygen bond length In basic bond length The functional group coordination ability factor is introduced to modulate the electron feedback effect of changes in the equatorial coordination environment on the axial U=O bond order, thereby reflecting the response relationship of axial bond length to changes in equatorial coordination electronic structure: when strong ligands appear in the equatorial plane, equatorial electron donation is enhanced, the occupancy of axial U=O antibonding orbitals increases slightly, and axial bonds are slightly elongated.

[0071] (2) Determination of the initial distance of equatorial coordination

[0072] For the coordination structure at the equatorial plane, let the initial coordination distance between the coordinating atom and the uranium atom be . .

[0073] This invention is the first to explicitly represent the initial equatorial coordination distance as a functional group-related calculation parameter, and its expression is as follows:

[0074]

[0075] in:

[0076] For reference to the equatorial coordination distance, 2.6 Å is preferred;

[0077] Functional group coordination capacity factor;

[0078] The coordination contraction coefficient is preferably taken as 0.1~0.2Å.

[0079] The The value of is restricted to the range of 2.3 to 2.7 Å.

[0080] Equatorial Coordination Distance At the base distance A coordination ability factor is introduced for negative correction to characterize the coordination bond distance contraction effect caused by the enhanced electron-donating ability of ligands, resulting in electrostatic attraction between metal and coordinating atoms and the enhancement of covalent composition.

[0081] (3) Definition of functional group coordination ability factor

[0082] The functional group coordination ability factor The relative coordination strength between different functional groups and uranyl ions is used to characterize the relative coordination strength between them. The values ​​are discretized based on the type of functional group and the properties of the donor atom. In this embodiment:

[0083] carbonyl group:

[0084] Phosphoryl group:

[0085] Nitro:

[0086] Hydroxyl group:

[0087] The above values ​​are not unique and can be replaced or adjusted according to the needs of the system, but they all follow the basic principle that "strong coordination functional groups correspond to smaller equatorial coordination distances".

[0088] (4) Parameter extension in the case of multiple coordination

[0089] When multiple coordinating atoms participate in coordination simultaneously, the coordination ability factor of the functional group is taken as an average or weighted sum:

[0090]

[0091] The parameters are then substituted into the above formula to determine a uniform initial coordination parameter, thereby generating initial coordination configurations under different coordination number conditions.

[0092] Based on the adjusted initial coordination configuration, the output satisfies the axial coordination distance. Constraints and equatorial coordination distance The coordinates of the constrained uranyl ion-ligand coordination structure; during the adjustment of the coordination distance, the relative spatial relationships between atoms within the ligand molecule remain unchanged.

[0093] Step 4: Geometric normalization and validity determination of coordination configurations

[0094] After obtaining the initial coordination configuration of the uranyl ion and ligand, the configuration undergoes geometric adjustment and discrimination processing to ensure that it meets the structural rationality requirements for subsequent quantum chemical calculations. Specifically, this includes the following steps:

[0095] (1) Configuration alignment and spatial adjustment

[0096] Using the uranium atom U in the uranyl ion as the origin of the coordinate system, and taking the coordinating atom as the center, the ligand as a whole is subjected to rigid translation and rotation operations to ensure that the distance between it and the uranium atom meets the set coordination distance range.

[0097] The translation and rotation operations do not change the bonding relationships and relative geometry within the ligand.

[0098] (2) Key geometric parameter constraints

[0099] For the adjusted configuration, define and check the following geometric parameters:

[0100] Non-bonded interatomic distance: (Any two non-bonding atoms i and j)

[0101] Parameter of the angle between adjacent coordinating atoms:

[0102] Where X = oxygen atom or nitrogen atom.

[0103] (3) Criteria for judging the rationality of structure

[0104] A configuration is considered valid only if it simultaneously meets the following conditions:

[0105] The distance between any non-bonding atom pairs is not less than a given threshold. To avoid unreasonable overlap between atoms, the settings are based on the combination of atom types. The preferred Å value is 1.2~2.0 Å; this is used to avoid unreasonable spatial overlap or strong repulsive interactions between non-bonding atoms, so as to ensure that the generated structure satisfies the van der Waals repulsion boundary conditions.

[0106] Depending on the coordination number, the coordination angle Not less than a given threshold To ensure the geometric rationality of the coordination direction, The preferred angle is 60° to 90°. This is used to ensure the proper arrangement of equatorial coordinating atoms on the equatorial plane of uranyl ions, maintaining the rationality of the coordination environment and the stability of the coordination polyhedron.

[0107] Step 5: Output and calculate the uranyl ion coordination structure

[0108] The uranyl ion-ligand coordination structure obtained in step four and screened for geometric and coordination rationality is output. Based on this, quantum chemical calculations are performed on the coordination structure to quickly verify the rationality of its geometric configuration. The calculations use density functional theory to perform low-cost structural optimization or single-point energy calculations on the uranyl ion-ligand coordination system.

[0109] The preliminary calculations confirmed that the coordinates of the uranyl ion coordination structure model with a reasonable structure can be used as the input structure for subsequent high-precision structure optimization calculations, coordination bond parameter analysis, or large-scale ligand screening applications.

[0110] In this embodiment, the uranyl ion coordination structure model can be used as the initial input structure for quantum chemical structure optimization, which significantly reduces the workload of manual modeling and improves modeling consistency.

[0111] In this embodiment, the coordination system is a uranyl ion coordination system, and the ligand includes organic molecules containing oxygen or nitrogen functional groups, including but not limited to carbonyl, hydroxyl, aldehyde, phosphoryl, nitro, and amino groups.

[0112] In this embodiment, by automatically generating uranyl ion coordination structures based on functional group identification, the problems of strong subjectivity and poor repeatability in the traditional manual construction of coordination models are avoided, thereby improving the efficiency and reliability of uranyl ion coordination structure modeling.

[0113] The results show that the uranyl ion coordination structures automatically generated by the method of this invention have good geometric rationality and can stably converge to reasonable coordination configurations, which significantly reduces the cost of manual modeling and improves the efficiency of modeling and screening large-scale uranyl ion coordination systems.

[0114] Example 2

[0115] In this specific embodiment, to verify the applicability of the method of the present invention to actual ligand sets, organic molecules from a publicly available chemical database were selected as the initial ligand set, and the following procedure was followed. The coordination number of the central metal ion is 5, and the vacant coordination sites are filled by water molecules to form a stable coordination structure.

[0116] (1) Ligand set acquisition and preprocessing

[0117] Organic molecules containing oxygen- or nitrogen-containing functional groups are obtained from publicly available molecular databases as the initial set of ligands, and the initial number of molecules is denoted as N0.

[0118] Preprocessing operations are performed on the ligand set, including but not limited to:

[0119] Remove inorganic molecules, metal complexes, and repeating molecules;

[0120] Remove molecules that do not contain potential coordinating functional groups;

[0121] The molecular structure is standardized.

[0122] After preprocessing, a subset of ligands that meets the basic modeling conditions is obtained, and the number of molecules is denoted as N1.

[0123] (2) Functional group identification and coordination site analysis

[0124] Steps one and two of Example 1 were performed sequentially on the N1 ligand molecules to identify their functional groups and analyze their coordination sites.

[0125] Molecules that do not contain effective coordinating atoms are eliminated, and the number of remaining ligands after screening is denoted as N2.

[0126] (3) Initial coordination structure generation

[0127] For the N2 ligand molecules, based on the functional group coordination ability factor and coordination parameter rules described in step three, the initial coordination structure of the uranyl ion-ligand is automatically generated, as follows: Figure 2 As shown.

[0128] In this step, for each ligand molecule, based on the number of its coordinateable atoms, initial coordination configurations of monocoordinate, dicoordinate, or multicoordinate are generated, and the total number of initial structures generated is denoted as M0.

[0129] (4) Geometric normalization and effectiveness screening

[0130] Perform the geometric normalization and rationality judgment operations described in step four on the generated M0 initial coordination structures.

[0131] Configurations that do not meet the minimum distance constraint or coordination angle constraint of non-bonded atoms are automatically eliminated, and the number of effective coordination structures retained after screening is denoted as M1.

[0132] (5) Rapid quantum chemical verification calculations

[0133] Low-cost quantum chemical calculations were performed on the M1 effective coordination structures to verify the rationality of their geometric configurations.

[0134] In this step, configurations that fail to converge stably or exhibit significant structural distortions are eliminated, ultimately yielding a set of uranyl ion coordination structures that can be used for subsequent high-precision calculations or screening analyses. The number of structures is denoted as M2.

[0135] Through the above process, the automatic modeling, parameterization, and step-by-step screening of ligand sets to uranyl ion coordination structures were achieved.

[0136] In particular, in some preferred embodiments of the present invention, a computer device is also provided, including a memory and a processor and a computer program stored in the memory, wherein the processor executes the computer program to implement the steps of the automatic generation method for uranyl ion coordination structure coordinates described in any of the above embodiments.

[0137] In some other preferred embodiments of the present invention, a computer-readable storage medium is also provided, on which a computer program / instruction is stored, wherein when the computer program is executed by a processor, the steps of the automatic generation method for uranyl ion coordination structure coordinates described in any of the above embodiments are implemented.

[0138] Those skilled in the art will understand that all or part of the processes in the above embodiments can be implemented by a computer program instructing related hardware. The computer program can be stored in a non-volatile computer-readable storage medium. When the computer program is executed, it can include the processes of the above embodiments of the automatic generation method for uranyl ion coordination structure coordinates, which will not be repeated here.

[0139] Those skilled in the art will understand that embodiments of the present invention can be provided as methods, systems, or computer program products. Therefore, the present invention can take the form of a completely hardware embodiment, a completely software embodiment, or an embodiment combining software and hardware aspects. Furthermore, the present invention can take the form of a computer program product embodied on one or more computer-usable storage media (including, but not limited to, disk storage, CD-ROM, optical storage, etc.) containing computer-usable program code.

[0140] This invention is described with reference to flowchart illustrations and / or block diagrams of methods, apparatus (systems), and computer program products according to embodiments of the invention. It will be understood that each block of the flowchart illustrations and / or block diagrams, and combinations of blocks in the flowchart illustrations and / or block diagrams, can be implemented by computer program instructions. These computer program instructions can be provided to a processor of a general-purpose computer, special-purpose computer, embedded processor, or other programmable data processing apparatus to produce a machine, such that the instructions, which execute via the processor of the computer or other programmable data processing apparatus, generate instructions for implementing the flowchart illustrations and / or block diagrams. Figure 1 One or more processes and / or boxes Figure 1 A device that provides the functions specified in one or more boxes.

[0141] These computer program instructions may also be stored in a computer-readable storage medium that can direct a computer or other programmable data processing device to function in a particular manner, such that the instructions stored in the computer-readable storage medium produce an article of manufacture including instruction means, which are implemented in a process Figure 1 One or more processes and / or boxes Figure 1 The function specified in one or more boxes.

[0142] These computer program instructions may also be loaded onto a computer or other programmable data processing equipment to cause a series of operational steps to be performed on the computer or other programmable equipment to produce a computer-implemented process, thereby providing instructions that execute on the computer or other programmable equipment for implementing the process. Figure 1 One or more processes and / or boxes Figure 1 The steps of the function specified in one or more boxes.

[0143] In a typical configuration, a computing device includes one or more processors (CPU), input / output interfaces, network interfaces, and memory.

[0144] Memory may include non-persistent storage in computer-readable media, such as random access memory (RAM) and / or non-volatile memory, such as read-only memory (ROM) or flash RAM. Memory is an example of computer-readable media.

[0145] Computer-readable media includes both permanent and non-permanent, removable and non-removable media that can store information by any method or technology. Information can be computer-readable instructions, data structures, modules of programs, or other data. Examples of computer storage media include, but are not limited to, phase-change memory (PRAM), static random access memory (SRAM), dynamic random access memory (DRAM), other types of random access memory (RAM), read-only memory (ROM), electrically erasable programmable read-only memory (EEPROM), flash memory or other memory technologies, CD-ROM, digital versatile optical disc (DVD) or other optical storage, magnetic tape, magnetic disk storage or other magnetic storage devices, or any other non-transferable medium that can be used to store information accessible by a computing device. As defined herein, computer-readable media does not include transient computer-readable media, such as modulated data signals and carrier waves.

[0146] It should also be noted that the terms "comprising," "including," or any other variations thereof are intended to cover non-exclusive inclusion, such that a process, method, article, or apparatus that comprises a list of elements includes not only those elements but also other elements not expressly listed, or elements inherent to such process, method, article, or apparatus. Unless otherwise specified, an element defined by the phrase "comprising one..." does not exclude the presence of other identical elements in the process, method, article, or apparatus that includes that element.

[0147] The above are merely embodiments of this application and are not intended to limit the scope of this application. Various modifications and variations can be made to this application by those skilled in the art. Any modifications, equivalent substitutions, improvements, etc., made within the spirit and principles of this application should be included within the scope of the claims of this application.

Claims

1. A method for automatically generating coordinates of uranyl ion coordination structures for quantum chemical calculations, characterized in that, Includes the following steps: Step 1: Obtain the structural information of uranyl ion ligand molecules and identify and analyze the functional groups of the ligand molecules; Functional groups in ligand molecules are screened to obtain functional groups with potential coordination ability; Step 2: Analyze the functional groups with potential coordination ability, determine the types of atoms in each functional group that can act as metal coordinating atoms and their spatial position information, and construct a coordination site information representation to characterize the coordination ability of ligands. Step 3: Based on the constructed coordination site information representation, an initial coordination structure is generated between the uranyl ion center and the ligand molecule; Step 4: After obtaining the initial coordination configuration of uranyl ions and ligands, perform geometric adjustments to satisfy the distance constraints between non-bonded atoms and the angle constraints between adjacent coordinating atoms; Step 5: Based on the adjusted initial coordination configuration, output the coordinates of the uranyl ion-ligand coordination structure.

2. The method for automatically generating coordinates of uranyl ion coordination structures according to claim 1, characterized in that, Before obtaining the structural information, the molecular structure of the uranyl ion ligand is standardized; the molecular structure information of the ligand comes from the molecular formula, two-dimensional structural formula or three-dimensional initial configuration of the uranyl ion ligand molecule; the functional group identification and analysis of the ligand molecule includes functional group type, atomic composition characteristics, bond connection relationship and local geometric configuration.

3. The method for automatically generating coordinates of uranyl ion coordination structures according to claim 1, characterized in that, The functional group screening is based on the functional group matching rules described in SMARTS.

4. The method for automatically generating coordinates of uranyl ion coordination structures according to claim 1, characterized in that, The coordination site information includes information on the functional group category, the type of atom that can participate in coordination within the functional group, and the spatial position of the atom in the ligand molecule.

5. The method for automatically generating coordinates of uranyl ion coordination structures according to claim 1, characterized in that, The axial uranium-oxygen bond length of the uranyl ion in the initial coordination structure It is 1.7~1.9 Å; in, The axial uranium-oxygen bond length under ligand-free or weakly ligand conditions; The modulation coefficient; Functional group coordination capacity factor; In the initial coordination structure, the initial coordination distance between the coordinating atom and the uranium atom in the equatorial plane is... It is 2.3~2.7 Å; in, The equatorial coordination distance under conditions of no ligand or weak ligand; The coordination shrinkage coefficient; in, For the first Coordination ability factor of functional groups of each ligand.

6. The method for automatically generating coordinates of uranyl ion coordination structures according to claim 1, characterized in that, The geometric adjustment is performed by rigidly translating and rotating the entire ligand with the uranium atom U in the uranyl ion as the origin and the coordinating atom as the center.

7. The method for automatically generating coordinates of uranyl ion coordination structures according to claim 1, characterized in that, The adjusted geometry satisfies the following conditions: Non-bonded atom distance constraint: any two non-bonded atoms and Distance between Not less than the set threshold , It is 1.2~2 Å; Angle constraint between adjacent coordinating atoms: Angle between adjacent coordinating atoms Not less than the set threshold , The angle is 60° to 90°. , and These are coordinating atoms.

8. A computer device, comprising a memory, a processor, and a computer program stored in the memory, characterized in that, The processor executes the computer program to implement the steps of the method according to any one of claims 1 to 7.

9. A computer-readable storage medium having a computer program stored thereon, characterized in that, When executed by a processor, the computer program implements the steps of the method according to any one of claims 1 to 7.

10. A computer program product, comprising a computer program, characterized in that, When executed by a processor, the computer program implements the steps of the method according to any one of claims 1 to 7.

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