JP7589460B2 - Information processing system, information processing method, and information processing program - Google Patents

Description

One aspect of the present disclosure relates to an information processing system, an information processing method, and an information processing program.

A method is known for estimating the reaction pathway from multiple reactants to the product using the Nudged Elastic Band (NEB) method. For example, Patent Document 1 describes the use of the NEB method to search for exhaust gas purification catalysts.

JP 2009-189915 A

The NEB method can accurately search for the reaction path with the lowest activation energy, but on the other hand, it has the disadvantage that the search takes time. Therefore, a method that can more quickly estimate the reaction path from multiple reactants to the product is desired.

An information processing system according to one aspect of the present disclosure analyzes a chemical reaction between a plurality of reactants. The information processing system includes at least one processor. For each of the plurality of reactants, the at least one processor extracts a portion of the atoms involved in the chemical reaction from among all atoms of the reactant as target atoms, sets constraint conditions for the NEB method limited to the target atoms, and executes the NEB method under the constraint conditions to estimate a reaction path from the plurality of reactants to a product.

An information processing method according to one aspect of the present disclosure is executed by an information processing system having at least one processor and analyzing a chemical reaction between a plurality of reactants. This information processing method includes the steps of: extracting, for each of the plurality of reactants, a portion of the atoms involved in the chemical reaction from among all atoms of the reactant as target atoms; setting constraint conditions for the NEB method limited to the target atoms; and executing the NEB method under the constraint conditions to estimate a reaction path from the plurality of reactants to a product.

An information processing program according to one aspect of the present disclosure causes a computer to function as an information processing system that analyzes chemical reactions between multiple reactants. This information processing program causes a computer to execute the steps of: extracting, for each of the multiple reactants, a portion of the atoms involved in the chemical reaction from among all atoms of the reactant as target atoms; setting constraint conditions for the NEB method limited to the target atoms; and executing the NEB method under the constraint conditions to estimate the reaction path from the multiple reactants to the product.

In this aspect, constraint conditions of the NEB method are set for only a portion of all atoms in a compound that are involved in a chemical reaction. Then, the reaction path is estimated by the NEB method under those constraint conditions. In this way, by limiting the atoms for which constraint conditions are set, the calculation time of the NEB method is shortened, making it possible to estimate the reaction path from multiple reactants to the product more quickly.

According to one aspect of the present disclosure, it is possible to more quickly estimate the reaction path from multiple reactants to the product.

FIG. 2 is a diagram illustrating an example of a hardware configuration of a computer that configures the information processing system according to the embodiment. FIG. 1 is a diagram illustrating an example of a functional configuration of an information processing system according to an embodiment. 4 is a flowchart illustrating an example of an operation of the information processing system according to the embodiment. FIG. 13 is a diagram showing an example of extracting a target atom.

Embodiments of the present disclosure will be described in detail below with reference to the accompanying drawings. In the description of the drawings, identical or equivalent elements are given the same reference numerals, and duplicate descriptions will be omitted.

[System Configuration]
The information processing system 10 according to the embodiment is a computer system that analyzes a chemical reaction between a plurality of reactants (also referred to as "starting materials"). More specifically, the information processing system 10 estimates a reaction path from a plurality of reactants to a product (also referred to as "final product"). The reaction path refers to a process from the reactants to the product. Neither the reactants nor the product are limited in any way.

In this embodiment, the information processing system 10 estimates the reaction path using the NEB method. In the NEB method, the structures of the reactants (initial structures) and products (final structures) are processed as input data, and n intermediate structures that connect these two structures are generated. These intermediate structures are also called images. Each intermediate structure is connected to another adjacent structure by a spring that runs along the reaction path. The NEB method finds the force acting on each intermediate structure, and performs structural optimization while taking into account the perpendicular component to the reaction path and the restoring force of the springs, thereby finding the reaction path with the smallest activation energy as the most stable path.

[System Configuration]
The information processing system 10 is composed of one or more computers. When multiple computers are used, a single information processing system 10 is logically constructed by connecting these computers via a communication network such as the Internet or an intranet.

Figure 1 is a diagram showing an example of a general hardware configuration of a computer 100 constituting an information processing system 10. For example, the computer 100 includes a processor (e.g., a CPU) 101 that executes an operating system, application programs, etc., a main memory unit 102 consisting of ROM and RAM, an auxiliary memory unit 103 consisting of a hard disk, flash memory, etc., a communication control unit 104 consisting of a network card or wireless communication module, input devices 105 such as a keyboard and mouse, and an output device 106 such as a monitor.

Each functional element of the information processing system 10 is realized by loading a predetermined program onto the processor 101 or the main memory unit 102 and having the processor 101 execute the program. In accordance with the program, the processor 101 operates the communication control unit 104, the input device 105, or the output device 106, and reads and writes data in the main memory unit 102 or the auxiliary memory unit 103. Data or databases required for processing are stored in the main memory unit 102 or the auxiliary memory unit 103.

Figure 2 is a diagram showing an example of the functional configuration of the information processing system 10. The information processing system 10 includes functional elements including a structure calculation unit 11, an atom extraction unit 12, and a path search unit 13. The structure calculation unit 11 is a functional element that calculates the optimal structure for each of a plurality of reactants and products. The optimal structure refers to the structure of the substance when the substance is in the minimum energy state, and is also called the most stable structure. The atom extraction unit 12 is a functional element that extracts atoms related to a chemical reaction as target atoms for each of a plurality of reactants. The path search unit 13 is a functional element that estimates the reaction path from a plurality of reactants to products by at least the NEB method. The path search unit 13 sets constraint conditions for the NEB method limited to the target atoms, and executes the NEB method under the constraint conditions to estimate the reaction path.

[System Operation]
The operation of the information processing system 10 and the information processing method according to the present embodiment will be described with reference to Fig. 3. Fig. 3 is a flow chart showing an example of the operation of the information processing system 10 as a process flow S1.

In step S11, the structure calculation unit 11 calculates the optimal structure for each of the multiple reactants and products. The structure calculation unit 11 accepts data indicating the reactants and products, and calculates the optimal structure for each substance by first-principles calculation. First-principles calculation refers to a method of calculating the physical properties of a substance based on quantum mechanics without using empirical parameters (i.e., experimental data). The specific method of first-principles calculation is not limited. In one example, the structure calculation unit 11 is implemented using Gaussian's computational chemistry software "Gaussian16", and the optimal structure may be calculated under the calculation conditions of B3LYP/6-31G(d).

In step S12, the atom extraction unit 12 extracts atoms involved in a chemical reaction as target atoms. "Atoms involved in a chemical reaction" are atoms that constitute a partial structure of a reactant that changes due to the chemical reaction (in other words, participates in the reaction pathway). Therefore, for each reactant, the atoms extracted as target atoms are only a portion of all atoms of the reactant. There are no limitations on the method of extracting atoms involved in a chemical reaction (atoms involved in the reaction pathway), and the atom extraction unit 12 may extract target atoms by any method.

In one example, the atom extraction unit 12 may select an atom whose interatomic distance changes to straddle a given threshold Ta due to a chemical reaction, and extract this atom as a target atom. There are two types of "atoms whose interatomic distance changes to straddle a threshold (Ta)". One is an atom whose distance with a partner atom changes from a value exceeding the threshold Ta to a value below the threshold Ta due to a chemical reaction. Such a reduction in the interatomic distance means that a bond (more specifically, a covalent bond) has been formed. The other is an atom whose distance with a partner atom changes from a value below the threshold Ta to a value exceeding the threshold Ta due to a chemical reaction. Such an increase in the interatomic distance means that a bond (covalent bond) has been cleaved. In other words, an atom whose interatomic distance changes to straddle a threshold is an atom involved in the formation or cleavage of a bond. An "atom involved in the formation or cleavage of a bond" is an example of an atom involved in a chemical reaction (an atom involved in a reaction path).

In one example, the threshold value Ta for a combination of two atoms is the product of the bond distance d of the combination and a coefficient α greater than 1. That is, Ta = d × α. The bond distance refers to the average distance between the two atoms that make up the covalent bond (more specifically, between the two atomic nuclei). The bond distance is determined by the combination of the two atoms. The coefficient α is a common value that does not depend on the type of combination of the two atoms. Therefore, the threshold value Ta depends on the bond distance d. The common coefficient α may be determined according to any policy, and may be, for example, 1.2.

The atom extraction unit 12 refers to the optimal structures of each of the multiple reactants and products, and extracts as target atoms those atoms whose interatomic distances change to cross the threshold value Ta.

In another example, the atom extraction unit 12 may select an atom in which at least one bond angle changes to straddle a given threshold Tb due to a chemical reaction, and extract this atom as a target atom. A bond angle refers to the angle between two chemical bonds extending from an atom. There are two types of "atoms in which at least one bond angle changes to straddle a threshold (Tb)". One is an atom in which the angle between two chemical bonds extending from the atom changes from a value that exceeds the threshold Tb to a value that is less than the threshold Tb due to a chemical reaction. The other is an atom in which the angle between two chemical bonds extending from the atom changes from a value that is less than the threshold Tb to a value that exceeds the threshold Tb due to a chemical reaction. An atom in which a bond angle changes to straddle the threshold Tb may also be involved in a reaction path.

In another example, the atom extraction unit 12 may select a group of atoms whose dihedral angle changes by a given threshold Tc or more due to a chemical reaction, and extract this group of atoms as target atoms. The "group of atoms whose dihedral angle changes by a threshold (Tc) or more" may be two atoms common to the two faces that form the dihedral angle, and an atom bonded to each of the two atoms. A group of atoms whose dihedral angle changes by a threshold Tc or more may also be involved in the reaction pathway.

In the present disclosure, an atom whose interatomic distance changes to straddle the threshold Ta, an atom whose bond angle changes to straddle the threshold Tb, and a group of atoms whose dihedral angle changes to equal to or greater than the threshold Tc are also referred to as a "first atom". The atom extraction unit 12 may also extract an atom located near the first atom in the reactant (referred to as a "second atom" in the present disclosure) as a target atom. The second atom is close to a position where bond formation or cleavage occurs or is close to a position where such formation or cleavage may occur, so the second atom may also be an atom related to a chemical reaction (an atom involved in a reaction path). In one example, the atom extraction unit 12 selects an atom that bonds to the first atom in the reactant as the second atom, and extracts this second atom as a target atom.

Figure 4 shows an example of extracting a target atom, and more specifically, an example of extracting a target atom in a reaction between an amine compound and an epoxy compound. In this example, n-butylamine is shown as the amine compound, and 1,2-epoxyhexane is shown as the epoxy compound. In this example, the atom extraction unit 12 selects an atom whose interatomic distance changes by a chemical reaction to straddle a given threshold value Ta as the first atom 201. Specifically, the atom extraction unit 12 selects the nitrogen atom and one hydrogen atom of n-butylamine, and the oxygen atom and the tip carbon atom of 1,2-epoxyhexane as the first atom 201. Furthermore, the atom extraction unit 12 selects an atom bonded to the first atom 201 as the second atom 202. Specifically, the atom extraction unit 12 selects another hydrogen atom and one carbon atom, each bonded to a nitrogen atom, as the second atom 202 for n-butylamine. Furthermore, for 1,2-epoxyhexane, the atom extraction unit 12 selects the carbon atom bonded to both the oxygen atom and the tip carbon atom, and the two hydrogen atoms bonded to the tip carbon atom, as the second atom 202. Therefore, the atom extraction unit 12 extracts a total of nine atoms as target atoms.

Returning to FIG. 3, in step S13, the path search unit 13 sets constraint conditions for the NEB method limited to each target atom. That is, the path search unit 13 sets constraint conditions limited to some atoms for each reactant. Specifically, the path search unit 13 sets constraint conditions that limit the reaction direction of each target atom to the direction of the reaction path. This constraint condition includes a restriction that each target atom is connected to an adjacent intermediate structure by a spring along the reaction path. The spring constant included in the constraint condition may be set based on any policy.

In step S14, the path search unit 13 executes the NEB method under the set constraint conditions to search for a tentative most stable path. Specifically, the path search unit 13 generates an arbitrary reaction path (initial reaction path) that indicates the coordinate changes of each atom between the reactant and the product. Then, the path search unit 13 sets multiple intermediate structures on the reaction path. Each intermediate structure can be said to be a waypoint on the reaction path. Then, for each of the multiple intermediate structures, the path search unit 13 calculates the potential energy of the intermediate structure and the force, which is the first derivative of the potential energy. Then, the path search unit 13 performs structural optimization of each intermediate structure based on the calculation result, and updates the coordinates of each atom of each intermediate structure. As a result, a new reaction path is obtained. The path search unit 13 executes a series of processes including calculation of potential energy and force, structural optimization, and updating of the coordinates of each atom under the constraint conditions. The path search unit 13 repeatedly executes the series of processes until the amount of change in potential energy in each intermediate structure becomes equal to or less than a given threshold value. If the change in potential energy for the last reaction path obtained is equal to or less than a given threshold, the path search unit 13 ends the iterative process and estimates the path as the provisional most stable path.

In this embodiment, the path search unit 13 uses the CI-NEB method to calculate a transition state (TS) in a chemical reaction from the path obtained by the NEB method, and the most stable path that passes through that transition state. Therefore, in this embodiment, the path obtained by the NEB method is expressed as a "tentative most stable path." A transition state is the state with the highest energy in a chemical reaction. The CI-NEB method is an improved method of the NEB method.

In step S15, the path search unit 13 executes the CI-NEB method under the set constraint conditions to search for the most stable path and transition state. Specifically, the path search unit 13 reads data indicating the tentative most stable path obtained by the NEB method. Next, for each of the multiple intermediate structures, the path search unit 13 calculates the potential energy of the intermediate structure and the force, which is the first derivative of the potential energy. In this calculation, the path search unit 13 does not introduce the concept of a spring for the intermediate structure (image) with the highest energy, but considers the force with which the intermediate structure climbs the potential surface. For the other intermediate structures, the path search unit 13 executes the same calculation as the NEB method. Thus, the difference between the CI-NEB method and the NEB method lies in the calculation method for the intermediate structure with the highest energy. The path search unit 13 executes structural optimization of each intermediate structure based on the calculation results, thereby updating the coordinates of each atom of each intermediate structure. As a result, a new reaction path is obtained. The path search unit 13 executes a series of processes, including calculation of potential energy and force, structure optimization, and updating of the coordinates of each atom, under constraint conditions. The path search unit 13 repeatedly executes the series of processes until the change in potential energy in each intermediate structure becomes equal to or less than a given threshold. If the change in potential energy for the last obtained reaction path is equal to or less than a given threshold, the path search unit 13 ends the repeated process and estimates the path as the most stable path.

In step S16, the route search unit 13 outputs the most stable route as an estimated result. There are no limitations on the method of outputting the estimated result. For example, the route search unit 13 may store the estimated result in a given database, may transmit it to another computer or computer system, or may display it on a display device. Alternatively, the route search unit 13 may output the estimated result to another functional element for subsequent processing in the information processing system 10.

[program]
An information processing program for causing a computer or computer system to function as the information processing system 10 includes program codes for causing the computer system to function as a structure calculation unit 11, an atom extraction unit 12, and a path search unit 13. This information processing program may be provided after being non-temporarily recorded on a tangible recording medium such as a CD-ROM, a DVD-ROM, or a semiconductor memory. Alternatively, the information processing program may be provided via a communication network as a data signal superimposed on a carrier wave. The provided information processing program is stored in, for example, the auxiliary storage unit 103. The processor 101 reads out the information processing program from the auxiliary storage unit 103 and executes it, thereby realizing each of the above-mentioned functional elements.

[effect]
As described above, an information processing system according to one aspect of the present disclosure analyzes a chemical reaction between a plurality of reactants. The information processing system includes at least one processor. For each of the plurality of reactants, the at least one processor extracts a portion of atoms involved in the chemical reaction from among all atoms of the reactant as target atoms, sets constraint conditions for the NEB method by limiting the target atoms, and executes the NEB method under the constraint conditions to estimate a reaction path from the plurality of reactants to a product.

An information processing method according to one aspect of the present disclosure is executed by an information processing system having at least one processor and analyzing a chemical reaction between a plurality of reactants. This information processing method includes the steps of: extracting, for each of the plurality of reactants, a portion of the atoms involved in the chemical reaction from among all atoms of the reactant as target atoms; setting constraint conditions for the NEB method limited to the target atoms; and executing the NEB method under the constraint conditions to estimate a reaction path from the plurality of reactants to a product.

An information processing program according to one aspect of the present disclosure causes a computer to function as an information processing system that analyzes chemical reactions between multiple reactants. This information processing program causes a computer to execute the steps of: extracting, for each of the multiple reactants, a portion of the atoms involved in the chemical reaction from among all atoms of the reactant as target atoms; setting constraint conditions for the NEB method limited to the target atoms; and executing the NEB method under the constraint conditions to estimate the reaction path from the multiple reactants to the product.

In this aspect, constraint conditions of the NEB method are set only for a portion of all atoms in a compound that are involved in a chemical reaction. Then, the reaction path is estimated by the NEB method under those constraint conditions. In this way, by limiting the atoms for which constraint conditions are set, the calculation time of the NEB method is shortened (in other words, the structural optimization converges more quickly), making it possible to estimate the reaction path from multiple reactants to the product more quickly.

In an information processing system according to another aspect, at least one processor may select, for each of a plurality of reactants, an atom whose interatomic distance changes by a chemical reaction so as to cross a given threshold as a first atom, and extract the first atom as a target atom. A change in interatomic distance indicates the creation or cleavage of a bond. Therefore, by taking this interatomic distance into consideration, it is possible to appropriately extract a target atom for which a constraint condition is set. This in turn makes it possible to estimate a reaction path with higher accuracy.

In an information processing system according to another aspect, the threshold value may be a product of the bond distance and a coefficient greater than 1. By setting the threshold value in this manner, atoms involved in the creation or cleavage of bonds can be accurately selected based on the interatomic distance. As a result, it becomes possible to appropriately extract target atoms for which constraint conditions are set, and to estimate the reaction path with higher accuracy.

In an information processing system according to another aspect, at least one processor may select, for each of a plurality of reactants, an atom whose bond angle changes to cross a given threshold value as a result of a chemical reaction as a first atom, and extract the first atom as a target atom. A change in the bond angle indicates that the atom may be involved in the reaction pathway. Therefore, by taking this bond angle into consideration, it is possible to appropriately extract a target atom for which a constraint condition is set. This in turn makes it possible to estimate the reaction pathway with higher accuracy.

In an information processing system according to another aspect, at least one processor may select, for each of a plurality of reactants, a group of atoms whose dihedral angle changes by a given threshold or more due to a chemical reaction as a first atom, and extract the first atom as a target atom. The change in the dihedral angle indicates that the group of atoms may be involved in the reaction path. Therefore, by taking this dihedral angle into consideration, it is possible to appropriately extract a target atom for which a constraint condition is set. This in turn makes it possible to estimate the reaction path with higher accuracy.

In an information processing system according to another aspect, the target atoms may include a second atom bonded to the first atom. By setting constraint conditions not only on the first atom involved in the bond creation or cleavage, but also on the second atom adjacent to the first atom, the reaction path can be estimated with higher accuracy.

[Modification]
The present invention has been described in detail above based on the embodiments. However, the present invention is not limited to the above embodiments. The present invention can be modified in various ways without departing from the spirit and scope of the present invention.

In the above embodiment, the path search unit 13 estimates the reaction path using the NEB method and the CI-NEB method. However, the information processing system may estimate the reaction path by the NEB method without using the CI-NEB method. For example, the information processing system may output the "tentative most stable path" estimated in step S14 in the above embodiment as the final estimation result.

The processing procedure of the information processing method executed by at least one processor is not limited to the example in the above embodiment. For example, some of the steps (processing) described above may be omitted, or each step may be executed in a different order. In addition, any two or more of the steps described above may be combined, or some of the steps may be modified or deleted. Alternatively, other steps may be executed in addition to each of the steps described above.

When comparing the magnitude relationship of two numerical values within an information processing system, either of the two criteria "greater than or equal to" and "greater than" may be used, or either of the two criteria "less than or equal to" and "less than". The choice of such criteria does not change the technical significance of the process of comparing the magnitude relationship of two numerical values.

In this disclosure, the expression "at least one processor executes a first process, executes a second process, ... executes an nth process" or a corresponding expression indicates a concept including cases where the entity executing the n processes from the first process to the nth process (i.e., the processor) changes midway. In other words, this expression indicates a concept including both cases where all n processes are executed by the same processor and cases where the processor changes among the n processes according to an arbitrary policy.

10...information processing system, 11...structure calculation unit, 12...atom extraction unit, 13...path search unit.

Claims (5)

An information processing system for analyzing a chemical reaction between a plurality of reactants, comprising:
At least one processor;
the at least one processor:
For each of the plurality of reactants, of all atoms of the reactant,
Atoms whose interatomic distance changes by the chemical reaction so as to cross a given threshold value;
An atom whose bond angle changes by the chemical reaction so as to cross a given threshold;
A group of atoms whose dihedral angle changes by a given threshold or more as a result of the chemical reaction;
Selecting at least one of the first atoms as a first atom that is a part of atoms involved in the chemical reaction, and extracting the first atom as a target atom;
Setting constraints for the NEB method limited to the target atoms,
Executing the NEB method under the constraint conditions to predict reaction paths from the plurality of reactants to products;
Information processing system. the threshold for the interatomic distance is the product of the bond distance and a coefficient greater than 1;
The information processing system according to claim 1 . the target atom includes a second atom bonded to the first atom;
3. The information processing system according to claim 1 or 2 . 1. An information processing method executed by an information processing system for analyzing a chemical reaction between a plurality of reactants, the information processing system including at least one processor, the method comprising:
For each of the plurality of reactants, of all atoms of the reactant,
Atoms whose interatomic distance changes by the chemical reaction so as to cross a given threshold value;
An atom whose bond angle changes by the chemical reaction so as to cross a given threshold;
A group of atoms whose dihedral angle changes by a given threshold or more as a result of the chemical reaction;
a step of selecting at least one of the first atoms as a first atom which is a part of atoms involved in the chemical reaction, and extracting the first atom as a target atom;
setting constraint conditions for the NEB method limited to the target atoms;
executing the NEB method under the constraint conditions to predict reaction paths from the plurality of reactants to products;
An information processing method comprising: An information processing program that causes a computer to function as an information processing system that analyzes a chemical reaction between a plurality of reactants, comprising:
For each of the plurality of reactants, of all atoms of the reactant,
Atoms whose interatomic distance changes by the chemical reaction so as to cross a given threshold value;
An atom whose bond angle changes by the chemical reaction so as to cross a given threshold;
A group of atoms whose dihedral angle changes by a given threshold or more as a result of the chemical reaction;
a step of selecting at least one of the first atoms as a first atom that is a part of atoms involved in the chemical reaction, and extracting the first atom as a target atom;
setting constraint conditions for the NEB method limited to the target atoms;
executing the NEB method under the constraint conditions to predict reaction paths from the plurality of reactants to products;
An information processing program that causes the computer to execute the above.

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