Calculation methods, systems and devices for bond lengths and bond angles of hydrogen bonds at different frequencies

Abstract

The present invention provides a method, a system and a device for calculating the bond length and bond angle of hydrogen bonds at different frequencies. The method includes the following steps: calculating the coordinates of each atom in the unit cell at the maximum displacement and the equilibrium position during vibration at each frequency; calculating the bond length and bond angle of the hydrogen bond at the maximum displacement and the equilibrium position of the atom during vibration at each frequency based on the frequency and the coordinates; and judging based on the change amount between the bond length and bond angle of the hydrogen bond at the maximum displacement of the atom at each frequency and the bond length and bond angle of the hydrogen bond at the equilibrium position. The method, the system and the device for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to the present invention are used to evaluate the response of hydrogen bonds to different frequencies. If the change amount is large, the response is intense; if the change amount is small, the response is gentle.

Description

Technical Field

[0001] The present invention relates to the technical field of vibration spectrum analysis of hydrogen-bonded molecular crystal systems, and particularly to a method, system and device for calculating the bond length and bond angle of hydrogen bonds at different frequencies. Background Art

[0002] Terahertz spectroscopy technology is widely used in the fields of material structure research, molecular specific recognition, chemical composition detection and analysis, etc. The terahertz vibration spectrum of molecules contains rich physical and chemical information, which is of great help for the specific recognition of molecules and the understanding of diverse biological functions. In particular, the low-frequency vibration of molecules is closely related to biological functions. In the terahertz vibration spectrum, the low-frequency phonons in the low-frequency range are mainly dominated by intermolecular vibrations with small force constants and large reduced masses. These intermolecular vibrations include many important intermolecular interactions, including hydrogen bonds, van der Waals forces, ion-π, ion-dipole, dipole-dipole, induction forces and dispersion forces, etc. Among them, as a relatively strong intermolecular interaction, hydrogen bonds have an important impact on the stacking form of molecules, the intermolecular connection strength, the crystal structure, etc. in the hydrogen-bonded crystal system. Especially when a ligand molecule binds to a receptor such as a protein, hydrogen bonds are formed between the ligand molecule and the receptor residues to enhance the binding strength and even activate its active site to achieve corresponding biological functions. Therefore, studying the response of hydrogen bonds to terahertz is helpful for a deeper understanding of the terahertz vibration spectrum and is crucial for the study of the low-frequency vibration of molecules.

[0003] At present, in the analysis of terahertz spectra of crystals at home and abroad, there are few studies on the response of hydrogen bonds in crystals to terahertz. Generally, it only involves the description of the bond length and bond angle of each hydrogen bond in the equilibrium state to prove that the unit cell structure optimized in the density functional theory calculation meets the requirements; or the change of hydrogen bond angle is calculated to illustrate the influence of hydrogen bonds on the vibration of molecular skeletons. The form of hydrogen bonds is generally expressed as XH···Y, where X and Y are atoms with large electronegativity, such as N, O, F and other atoms. Bond parameters generally include bond energy, bond length and bond angle. The energy of hydrogen bonds is about 10 to 30 kJ / mol, which is close to van der Waals forces. The strength of the hydrogen bond XH···Y is determined not only by the bond length, that is, the distance between H···Y, but also by the angle formed by XH···Y. The shorter the bond length, the greater the strength of the hydrogen bond; the bond angle often presents a bending state in the range of 150 to 180°. Different types of hydrogen bonds have different bond length and bond angle conditions. In general, bond energy generally requires complex quantum chemical calculation methods for fitting and calculation, which is not suitable for quickly measuring the changes in hydrogen bond strength in each specific vibration in the spectrum. By locating the coordinates of the relevant atoms that form the hydrogen bond, the bond length and bond angle of the hydrogen bond can be quickly calculated, thereby achieving the characterization of the changes in the hydrogen bond. In terahertz spectroscopy analysis, the calculation of the hydrogen bond length and bond angle can quantify the response of the hydrogen bond to terahertz, analyze its contribution to the absorption peak and the characteristic frequency of its vibration, and then analyze the vibration characteristics of the hydrogen bond. However, due to the large number of hydrogen bonds in the crystal, it is often difficult to analyze the changes in hydrogen bonds in multiple vibration modes. The huge amount of calculation is the biggest difficulty hindering quantitative analysis.

[0004] Python is a concise and effective programming language with rich packages that can realize various functions. Python programming can be used to analyze and process big data.

[0005] Therefore, it is hoped that the difficulty in analyzing hydrogen bond changes in multiple vibrational modes can be solved. Summary of the invention

[0006] In view of the above-mentioned shortcomings of the prior art, the purpose of the present invention is to provide a method, system and device for calculating the bond length and bond angle of hydrogen bonds at different frequencies, so as to solve the problem of difficulty in analyzing the changes of hydrogen bonds under multiple vibration modes in the prior art.

[0007] To achieve the above and other related objectives, the present invention provides a method for calculating the bond length and bond angle of hydrogen bonds at different frequencies, including the following steps: calculating the coordinates of each atom in the unit cell at the maximum displacement and equilibrium position of vibration at each frequency; calculating the bond length and bond angle of the hydrogen bond of the atom at the maximum displacement and equilibrium position of vibration at each frequency based on the frequency and coordinates; judging based on the change amount between the bond length and bond angle of the hydrogen bond at the maximum displacement of the atom at each frequency and the bond length and bond angle of the hydrogen bond at the equilibrium position, so as to evaluate the response of the hydrogen bond to different frequencies.

[0008] To achieve the above objective, the present invention also provides a system for calculating the bond length and bond angle of hydrogen bonds at different frequencies, including: a calculation module and a judgment module; the calculation module is used to calculate the coordinates of each atom in the unit cell at the maximum displacement and equilibrium position of vibration at each frequency; the judgment module is used to calculate the bond length and bond angle of the hydrogen bond of the atom at the maximum displacement and equilibrium position of vibration at each frequency based on the frequency and coordinates; judging based on the change amount between the bond length and bond angle of the hydrogen bond at the maximum displacement of the atom at each frequency and the bond length and bond angle of the hydrogen bond at the equilibrium position, so as to evaluate the response of the hydrogen bond to different frequencies.

[0009] To achieve the above objective, the present invention also provides a computer-readable storage medium, on which a computer program is stored, and when the computer program is executed by a processor, it implements any of the above methods for calculating the bond length and bond angle of hydrogen bonds at different frequencies.

[0010] To achieve the above objective, the present invention also provides a device for calculating the bond length and bond angle of hydrogen bonds at different frequencies, including: a processor and a memory; the memory is used to store a computer program; the processor is connected to the memory and is used to execute the computer program stored in the memory, so that the device for calculating the bond length and bond angle of hydrogen bonds at different frequencies executes any of the above methods for calculating the bond length and bond angle of hydrogen bonds at different frequencies.

[0011] As described above, a method, system and device for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to the present invention have the following beneficial effects: used to evaluate the response of hydrogen bonds to different frequencies. Description of the Drawings

[0012] Figure 1 It shows a flowchart of the method for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to the present invention in an embodiment;

[0013] Figure 2 It shows a schematic structural diagram of the system for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to the present invention in an embodiment;

[0014] Figure 3 It shows a schematic structural diagram of the device for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to the present invention in an embodiment.

[0015] Component Label Explanation

[0016] 21 Calculation Module

[0017] 22 Judgment Module

[0018] 31 Processor

[0019] 32 Memory Detailed Implementation Manner

[0020] The following uses specific specific examples to illustrate the implementation manners of the present invention. Those skilled in the art can easily understand other advantages and effects of the present invention from the content disclosed in this specification. The present invention can also be implemented or applied through other different specific implementation manners. Various details in this specification can also be modified or changed based on different viewpoints and applications without departing from the spirit of the present invention. It should be noted that, without conflict, the following embodiments and the features in the embodiments can be combined with each other.

[0021] It should be noted that the diagrams provided in the following embodiments only illustrate the basic concept of the present invention in a schematic manner. Therefore, only the components related to the present invention are shown in the diagrams, rather than being drawn according to the number, shape, and size of the components in actual implementation. The type, quantity, and ratio of each component in actual implementation can be an arbitrary change, and the component layout type may also be more complex.

[0022] The method, system, and device for calculating the bond length and bond angle of hydrogen bonds at different frequencies of the present invention are used for analyzing the changes of hydrogen bonds in multiple vibration modes and judging the responses of hydrogen bonds at different frequencies.

[0023] As Figure 1 shown, in an embodiment, the method for calculating the bond length and bond angle of hydrogen bonds at different frequencies of the present invention includes the following steps:

[0024] Step S11: Calculate and obtain the coordinates of the maximum displacement and equilibrium position of each atom in the unit cell at each frequency.

[0025] Specifically, the calculation of obtaining the coordinates of the maximum displacement and equilibrium position of each atom in the unit cell at each frequency includes:

[0026] Step S111: Obtain a unit cell from the data center and perform structural optimization on the unit cell. Specifically, obtain the unit cell structure of a certain substance downloaded from the Cambridge Crystallographic Data Centre (CCDC). The unit cell structure is saved in the cif format. Import the unit cell structure into the Masterial studio (MS) software. Adjust the display mode to display all the molecules and hydrogen bonds in the unit cell. The structural optimization of the unit cell includes: click on the calculation option in the CASTEP module of the Masterial studio (MS) software to perform the structural optimization of the unit cell of the above-mentioned substance, such as unit cell parameters, conformations, bond angles, etc. The calculation option is set as follows:

[0027]

[0028] Select the unit cell structure file after structural optimization and perform energy optimization. The parameters are set as follows:

[0029]

[0030]

[0031] Step S112: Calculate the frequencies and corresponding intensities of the infrared-active normal vibration modes of the unit cell. Select the unit cell file after structural and energy optimization. The unit cell file is in the xsd format. Click on Vibrational Analysis in the Tools menu of the MS software, and then click Calculate to obtain the vibration frequencies and corresponding intensities of the infrared-active normal vibration modes. Double-click on each frequency to obtain the corresponding xtd file of the vibration. A dynamic vibration diagram can be seen in the visualization window. Click the stop button to make the dynamic diagram stationary. The frequencies of the infrared-active normal vibration modes cover all frequency ranges from far-infrared, mid-infrared to near-infrared.

[0032] Step S113: Calculate the coordinates of the atoms at the maximum displacement of atomic vibration and the coordinates of the atoms at the equilibrium position in each unit cell at each frequency. The calculation of the coordinates of the atoms at the maximum displacement of atomic vibration and the equilibrium position in each unit cell at each frequency includes: Based on the atomic coordinate calculation script running in the Masterial studio software, obtain the coordinates of the atoms at the preset number of frames obtained in the atomic motion trajectory at each frequency. Input the obtained xtd file names into the Perl script of the MS software respectively, set the output file name, click F5 to run the script, and obtain the atomic coordinates (including the equilibrium position coordinates, at the position of the tenth frame) at the preset number of 20 frames obtained in the atomic motion trajectory in this vibration mode and the final position coordinates after vibration (at the position of the fifth frame, that is, the atomic coordinates at the maximum displacement in the vibration mode). The coordinates at the remaining frames are the coordinates during the vibration process and are not calculated here), and output a txt file. Operate on the xtd file of each vibration mode in this way to obtain the txt file of the atomic coordinates in each vibration mode.

[0033] The content of the atomic coordinate calculation script is as follows:

[0034]

[0035]

[0036]

[0037] Step S12: Calculate the bond lengths and bond angles of the hydrogen bonds of the atoms at the maximum displacement of vibration and the equilibrium position at each frequency based on the frequency and coordinates; judge based on the change amounts between the bond lengths and bond angles of the hydrogen bonds at the maximum displacement of the atoms at each frequency and the bond lengths and bond angles of the hydrogen bonds at the equilibrium position, and use it to evaluate the response of the hydrogen bonds to different frequencies.

[0038] Specifically, the calculation of the bond lengths and bond angles of the hydrogen bonds of the atoms at the maximum displacement of vibration and the equilibrium position at each frequency based on the frequency and coordinates means running the bond length and bond angle calculation script of the hydrogen bond to obtain the bond lengths and bond angles of the hydrogen bonds of the atoms at the maximum displacement of vibration and the equilibrium position at each frequency. Obtain the change amounts of the bond lengths and bond angles of the hydrogen bonds at the maximum displacement of vibration at each frequency and the bond lengths and bond angles at the equilibrium position in each vibration mode. If the difference between the bond lengths and bond angles of the hydrogen bonds at the maximum displacement of vibration at a certain frequency and the bond lengths and bond angles at the equilibrium position in the vibration mode of this frequency is relatively large, it indicates that the vibration of the molecule at this frequency is very intense and the conformation is easy to change, indicating the resonance response of the hydrogen bond at different frequencies.

[0039] Specifically, the hydrogen bond is a hydrogen bond, and the hydrogen bond includes intramolecular hydrogen bonds and intermolecular hydrogen bonds. Specifically, the bond length and bond angle calculation script of the hydrogen bond is as follows:

[0040] I. Input of Initial Parameters

[0041] import numpy as np

[0042] from glob import glob

[0043] import pandas as pd

[0044] import math

[0045] a1 = int(input('Please enter the atomic coordinates in the first molecule'))

[0046] a2 = int(input('Please enter the atomic coordinates in the second molecule'))

[0047] a3 = int(input('Please enter the atomic coordinates in the third molecule'))

[0048] II. Calculation

[0049]

[0050]

[0051]

[0052]

[0053]

[0054] As Figure 2 shown, in an embodiment, the hydrogen bond bond length and bond angle calculation system at different frequencies of the present invention includes a calculation module 21 and a judgment module 22; the calculation module is used to calculate the coordinates of the maximum displacement and equilibrium position of each atom in the unit cell at each frequency; the judgment module is used to calculate the hydrogen bond bond length and bond angle of the atom at the maximum displacement and equilibrium position of each frequency vibration based on the frequency and coordinates; and the change amount between the hydrogen bond bond length and bond angle at the maximum displacement of the atom at each frequency and the hydrogen bond bond length and bond angle at the equilibrium position is judged to evaluate the response of the hydrogen bond to different frequencies. Specifically, the calculation module is used to calculate the coordinates of the maximum displacement and equilibrium position of each atom in the unit cell at each frequency, including: obtaining the unit cell from the data center, optimizing the structure of the unit cell; calculating the frequencies and corresponding intensities of the infrared active normal vibration modes of the unit cell; and calculating the coordinates of the atoms at the maximum displacement and the coordinates of the atoms at the equilibrium position of the vibration of the atoms contained in the unit cell at each frequency.

[0055] Specifically, calculating the coordinates of the maximum displacement of atomic vibration and the coordinates of the atoms at the equilibrium position in each unit cell at each frequency includes: running an atomic coordinate calculation script based on the Masterial studio software to obtain the coordinates of the atoms at a preset number of frames obtained in the atomic motion trajectory at each frequency.

[0056] It should be noted that the structures and principles of the calculation module 21 and the judgment module 22 correspond one by one to the steps in the above methods for calculating the bond lengths and bond angles of hydrogen bonds at different frequencies, so they will not be elaborated here.

[0057] It should be noted that it should be understood that the division of each module of the above system is only a division of logical functions. In actual implementation, it can be fully or partially integrated into a physical entity, or physically separated. And these modules can all be implemented in the form of software called by a processing element; they can also all be implemented in the form of hardware; they can also be partially implemented in the form of software called by a processing element and partially implemented in the form of hardware. For example, the x module can be a separately established processing element, or can be integrated in a certain chip of the above device. In addition, it can also be stored in the memory of the above device in the form of program code and called and executed by a certain processing element of the above device to perform the functions of the above x module. The implementation of other modules is similar. In addition, all or part of these modules can be integrated together or can be independently implemented. The processing element mentioned here can be an integrated circuit with signal processing capabilities. In the implementation process, each step of the above method or each of the above modules can be completed by the integrated logic circuit in the processor element or the instructions in the form of software.

[0058] For example, the above modules can be one or more integrated circuits configured to implement the above method, such as: one or more application specific integrated circuits (ASICs), or, one or more microprocessor units (MPUs), or, one or more field programmable gate arrays (FPGAs), etc. Again, when a certain module above is implemented in the form of a processing element scheduling program code, the processing element can be a general-purpose processor, such as a central processing unit (CPU) or other processors that can call program code. Again, these modules can be integrated together and implemented in the form of a system-on-a-chip (SOC).

[0059] In an embodiment of the present invention, the present invention further includes a computer-readable storage medium, on which a computer program is stored, and when the program is executed by a processor, the method for calculating the bond length and bond angle of hydrogen bonds at different frequencies described above is implemented.

[0060] Those of ordinary skill in the art can understand that all or part of the steps of implementing the above method embodiments can be completed by hardware related to a computer program. The foregoing computer program can be stored in a computer-readable storage medium. When the program is executed, it executes the steps including the above method embodiments; and the foregoing storage medium includes: various media such as ROM, RAM, magnetic disk, or optical disc that can store program codes.

[0061] As Figure 3 shown, in an embodiment, the apparatus for calculating the bond length and bond angle of hydrogen bonds at different frequencies of the present invention includes: a processor 31 and a memory 32; the memory 32 is used to store a computer program; the processor 31 is connected to the memory 32 and is used to execute the computer program stored in the memory 32, so that the apparatus for calculating the bond length and bond angle of hydrogen bonds at different frequencies executes any one of the methods for calculating the bond length and bond angle of hydrogen bonds at different frequencies.

[0062] Specifically, the memory 32 includes: various media such as ROM, RAM, magnetic disk, USB flash drive, memory card, or optical disc that can store program codes.

[0063] Preferably, the processor 31 can be a general-purpose processor, including a central processing unit (Central Processing Unit, abbreviated as CPU), a network processor (Network Processor, abbreviated as NP), etc.; it can also be a digital signal processor (Digital Signal Processor, abbreviated as DSP), an application specific integrated circuit (Application Specific Integrated Circuit, abbreviated as ASIC), a field programmable gate array (Field Programmable Gate Array, abbreviated as FPGA), or other programmable logic devices, discrete gate or transistor logic devices, discrete hardware components.

[0064] In summary, the method, system, and apparatus for calculating the bond length and bond angle of hydrogen bonds at different frequencies of the present invention are used to determine whether a hydrogen bond is broken. Therefore, the present invention effectively overcomes various disadvantages in the prior art and has high industrial utilization value.

[0065] The above embodiments are only illustrative of the principles and effects of the present invention and are not intended to limit the present invention. Any person familiar with this technology can modify or change the above embodiments without departing from the spirit and scope of the present invention. Therefore, all equivalent modifications or changes made by those with ordinary knowledge in the technical field without departing from the spirit and technical idea disclosed by the present invention should still be covered by the claims of the present invention.

Claims

1. A method for calculating the bond length and bond angle of hydrogen bonds at different frequencies, characterized in that, it includes the following steps: Calculating the coordinates of each atom in the unit cell at the maximum displacement and equilibrium position of vibration at each frequency; Calculating the bond length and bond angle of the hydrogen bond at the maximum displacement and equilibrium position of the atom's vibration at each frequency based on the frequency and coordinates; wherein, the method for calculating the bond length and bond angle of the hydrogen bond at the maximum displacement and equilibrium position of the atom's vibration at each frequency is: running a script for calculating the bond length and bond angle of the hydrogen bond to obtain the bond length and bond angle of the hydrogen bond at the maximum displacement and equilibrium position of the atom's vibration at each frequency; Judging based on the change amount between the bond length and bond angle of the hydrogen bond at the maximum displacement of the atom at each frequency and the bond length and bond angle of the hydrogen bond at the equilibrium position, so as to evaluate the response of the hydrogen bond to different frequencies.

2. The method for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to claim 1, characterized in that, The calculating the coordinates of each atom in the unit cell at the maximum displacement and equilibrium position of vibration at each frequency includes: Obtaining the unit cell from the data center and performing structure optimization on the unit cell; Calculating the frequencies and corresponding intensities of each infrared active normal vibration mode of the unit cell; Calculating the coordinates of the atoms at the maximum displacement of vibration of the atoms contained in the unit cell at each frequency and the coordinates of the atoms at the equilibrium position.

3. The method for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to claim 2, characterized in that, The calculating the coordinates of the atoms at the maximum displacement of vibration of the atoms contained in the unit cell at each frequency and the coordinates of the atoms at the equilibrium position includes: Based on the Masterial studio software, running an atomic coordinate calculation script to obtain the coordinates of the atoms at a preset number of frames obtained in the atomic movement trajectory at each frequency.

4. A system for calculating the bond length and bond angle of hydrogen bonds at different frequencies, characterized in that, it includes: A calculation module and a judgment module; The calculation module is used to calculate the coordinates of each atom in the unit cell at the maximum displacement and equilibrium position of vibration at each frequency; The judgment module is used to calculate the bond length and bond angle of the hydrogen bond at the maximum displacement and equilibrium position of the atom's vibration at each frequency based on the frequency and coordinates; wherein, the method for calculating the bond length and bond angle of the hydrogen bond at the maximum displacement and equilibrium position of the atom's vibration at each frequency is: running a script for calculating the bond length and bond angle of the hydrogen bond to obtain the bond length and bond angle of the hydrogen bond at the maximum displacement and equilibrium position of the atom's vibration at each frequency; judging based on the change amount between the bond length and bond angle of the hydrogen bond at the maximum displacement of the atom at each frequency and the bond length and bond angle of the hydrogen bond at the equilibrium position, so as to evaluate the response of the hydrogen bond to different frequencies.

5. The system for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to claim 4, characterized in that, The calculation module is used to calculate the coordinates of each atom in the unit cell at the maximum displacement and equilibrium position of vibration at each frequency includes: Obtaining the unit cell from the data center and performing structure optimization on the unit cell; Calculating the frequencies and corresponding intensities of each infrared active normal vibration mode of the unit cell; Calculating the coordinates of the atoms at the maximum displacement of vibration of the atoms contained in the unit cell at each frequency and the coordinates of the atoms at the equilibrium position.

6. The system for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to claim 4, wherein, the calculation of the coordinates at the maximum displacement of atomic vibration and the coordinates of atoms at the equilibrium position included in each unit cell at each frequency comprises: running an atomic coordinate calculation script based on the Masterial studio software to obtain the coordinates of atoms in a preset number of frames obtained in the atomic motion trajectory at each frequency.

7. A computer-readable storage medium, on which a computer program is stored, wherein, the computer program is executed by a processor to implement the method for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to any one of claims 1 to 3.

8. A device for calculating the bond length and bond angle of hydrogen bonds at different frequencies, wherein, it comprises: a processor and a memory; the memory is used for storing a computer program; the processor is connected to the memory and is used for executing the computer program stored in the memory, so that the device for calculating the bond length and bond angle of hydrogen bonds at different frequencies executes the method for calculating the bond length and bond angle of hydrogen bonds at different frequencies according to any one of claims 1 to 3.

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