A method for analyzing vibrational modes and weak interactions of vitamin C stereoisomers based on terahertz spectroscopy and periodic boundary conditions.

Abstract

This invention discloses a method for analyzing vibrational modes and weak interactions of vitamin C stereoisomers based on terahertz spectroscopy and periodic boundary conditions, belonging to the fields of molecular spectroscopy and computational chemistry. The method includes: mixing L-ascorbic acid or D-isoascorbic acid with polytetrafluoroethylene (PTFE), grinding, sieving, weighing, tableting, and drying; obtaining experimental absorption spectra of L-ascorbic acid and D-isoascorbic acid in the range of 0.5–2.5 THz using terahertz time-domain spectroscopy; calculating theoretical spectra of L-ascorbic acid and D-isoascorbic acid using density functional theory (DFT) with periodic boundary conditions; verifying the accuracy and reliability of the theoretical spectra by comparing them with experimental spectra; quantitatively assigning the vibrational modes of each characteristic absorption peak using the automatic vibrational mode correlation determination (VMARD) analysis method; and visualizing the type, range, and intensity of various weak interactions using the region of interaction indicator (IRI) method. This invention applies periodic boundary conditions to the terahertz spectral analysis of vitamin C stereoisomers, achieving quantitative assignment of vibrational modes and visualization of weak interactions, providing a reliable method for understanding the differences in the microscopic properties of stereoisomers.

Description

Technical Field

[0001] This invention belongs to the field of molecular spectroscopy and computational chemistry, specifically involving a method that utilizes terahertz time-domain spectroscopy experiments, density functional theory (DFT) calculations based on periodic boundary conditions, quantitative assignment of vibrational modes, and visualization analysis of weak interactions to analyze the low-frequency vibrational modes and weak interactions of two stereoisomers, L-ascorbic acid and D-isoascorbic acid. Background Technology

[0002] Vitamin C, also known as L-ascorbic acid, with the molecular formula C6H8O6, is an essential nutrient for the human body. It is used to prevent and treat scurvy, and as an adjunct treatment for coronary heart disease and various acute and chronic infectious diseases. It is also an antioxidant, protecting the body from free radical damage, and is widely used in the pharmaceutical, food, and cosmetic industries. D-isoascorbic acid is a stereoisomer of L-ascorbic acid. While its physicochemical properties are similar to L-ascorbic acid, D-isoascorbic acid has almost no physiological activity and strong reducing properties. It can be used for antioxidant and preservative purposes in general foods, and also as a color-fixing agent. Although they are similar in macroscopic properties, their differences in physiological function suggest fundamental differences in their microscopic molecular structure and intermolecular interactions.

[0003] The frequencies corresponding to weak intermolecular interactions (such as hydrogen bonds and van der Waals forces), skeletal vibrations (configurational bending) of macromolecules, low-frequency vibrational absorption of crystal lattices, and vibrational and rotational energy levels of a large number of biomolecules are located within the terahertz frequency band. Therefore, terahertz time-domain spectroscopy can be used to study substances with similar structures, providing new evidence and assistance for revealing the structure, properties, and functions of molecules.

[0004] Existing technologies have the following shortcomings: most theoretical calculations use isolated molecule models or finite cluster models, neglecting the periodic environment of the crystal and long-range interactions between molecules, resulting in inaccurate simulations of lattice vibrations and collective modes; the attribution of vibrational modes is mostly qualitative, lacking quantitative decomposition methods based on internal coordinates, and cannot accurately characterize the contribution rate of each internal coordinate; the analysis of weak interactions lacks visualization; for the two stereoisomers L-ascorbic acid and D-isoascorbic acid, there is still no method that can achieve a comprehensive analysis of theoretical calculations under periodic boundary conditions, quantitative attribution of vibrational modes, and visualization of weak interactions.

[0005] To address the aforementioned problems, this invention proposes a comprehensive analysis method that combines terahertz experimental spectroscopy, DFT calculation based on periodic boundary conditions, quantitative attribution of vibrational modes, and visualization of weak interactions. Summary of the Invention

[0006] (a) Purpose of the invention

[0007] This invention aims to provide a method for analyzing the vibrational modes and weak interactions of vitamin C stereoisomers based on terahertz spectroscopy and periodic boundary conditions. This method overcomes the problems of existing isolated molecular models that ignore crystal periodicity, lack quantitative assignment of vibrational modes, and lack visualization of weak interactions. It enables quantitative assignment of vibrational modes and visualized characterization of weak interactions between L-ascorbic acid and D-isoascorbic acid.

[0008] (II) Technical Solution

[0009] The present invention provides a method for analyzing the vibrational modes and weak interactions of vitamin C stereoisomers based on terahertz spectroscopy and periodic boundary conditions, which specifically includes the following steps:

[0010] Step 1: Sample preparation: Take L-ascorbic acid standard (purity ≥98%) and D-isoascorbic acid standard (purity ≥98%) respectively, mix them with polytetrafluoroethylene (PTFE) powder at a mass ratio of 1:1, grind them into uniform powder using an agate mortar, pass them through a 200-mesh sieve, weigh out 200mg of mixed sample using an electronic balance, press them into circular thin sheets with a diameter of 13 mm and a thickness of 1 mm using a tablet press under 10 tons of pressure for 30 seconds, place the pressed sample sheets in a vacuum drying oven, and dry them at 55℃ for 2 hours to remove moisture from the sample.

[0011] Step 2: Terahertz time-domain spectroscopy measurement: The time-domain spectral signal of the sample is acquired using a transmission terahertz time-domain spectroscopy system. The time-domain signal is subjected to Fast Fourier Transform (FFT) to obtain the frequency-domain spectral data. According to the absorbance formula, the experimental absorption spectrum of the sample in the range of 0.5~2.5 THz is obtained. Savitzky-Golay filtering (window length 11, polynomial order 3) is used to smooth the spectrum and filter out clutter in the system.

[0012] Step 3: Theoretical Calculation: Obtain the crystal structure parameters of L-ascorbic acid and D-isoascorbic acid from the Cambridge Data Centre for Crystallography (CCDC); construct a three-dimensional periodic unit cell model using the Quickstep module in the first-principles calculation software CP2K, applying periodic boundary conditions in all three directions to simulate an infinite crystal environment, and using the mixed Gaussian plane wave (GPW) method to describe the electron density; use PBE as the exchange-correlation functional, employ D3(BJ) dispersion correction to describe the weak interaction, and select 6-311G** as the basis set to optimize the unit cell structure until the energy is lowest and there are no imaginary frequencies; based on the optimized structure, calculate the vibrational frequencies to obtain the theoretical absorption spectrum in the range of 0.5–2.5 THz.

[0013] Step 4: Comparative Analysis: Compare the peak positions of the theoretical spectrum and the experimental spectrum to verify the accuracy and reliability of the theoretical calculation model.

[0014] Step 5: Vibrational Mode Analysis: The Vibrational Mode Automatic Correlation Determination (VMARD) method is used to quantitatively decompose the complex collective molecular vibrations into the contribution rates of basic internal coordinates such as bond length stretching, bond angle bending, exterior angle bending, and dihedral torsion. The type of internal coordinate with the largest contribution rate is determined as the dominant vibrational mode. Using VMD software, a vibrational mode vector diagram is drawn based on the vibrational characteristic vectors. Arrows represent the atomic displacement direction and relative amplitude, and different colors are used to distinguish the atomic types (H in white, C in cyan, O in red).

[0015] Step Six: Weak Interaction Analysis: Based on the optimized periodic cell model from Step Three, calculate the electron density ρ(r) and its gradient ∇ρ(r); use the Interaction Region Indication (IRI) method to visualize the weak interactions, introducing the sign(λ2)ρ function to project different colors onto the IRI isosurface. When the value is greater than 0, the projection surface appears red, representing steric hindrance. When the value is less than 0, the projected surface appears blue, representing hydrogen bonds where electrostatic interaction dominates. The green color of the projected surface indicates that this region is either a van der Waals interaction region or a hydrogen bond dominated by dispersive interactions, thus allowing us to determine the type, strength, and spatial distribution of weak interactions.

[0016] (III) Beneficial Effects

[0017] Compared with the prior art, the present invention has the following beneficial effects:

[0018] 1. Applying periodic boundary conditions to terahertz spectral calculations of vitamin C stereoisomers: Compared with traditional isolated molecule or finite cluster models, periodic boundary conditions can accurately reflect the vibrational modes and weak interactions of crystals, significantly improving the agreement between theoretical and experimental spectra.

[0019] 2. Achieve quantitative attribution of vibration modes: The VMARD method is used to decompose vibration modes into the contribution percentage of internal coordinates such as bond length, bond angle, exterior angle, and dihedral angle, overcoming the subjectivity of traditional qualitative attribution.

[0020] 3. Visualization of weak interactions: The IRI method is used to visualize and analyze weak interactions. The type, strength and spatial distribution of weak interactions are determined by isosurfaces, and van der Waals forces, hydrogen bonds and steric hindrance effects are distinguished.

[0021] 4. Method universality: The method described in this invention is not only applicable to L-ascorbic acid and D-isoascorbic acid, but can also be extended to the analysis of terahertz spectral vibrational modes and weak interactions of other small organic molecule crystals, providing an analytical method for the fields of molecular spectroscopy and computational chemistry. Attached Figure Description

[0022] Figure 1 Comparison of terahertz absorption spectra of L-ascorbic acid and D-isoascorbic acid, where green represents L-ascorbic acid and purple represents D-isoascorbic acid.

[0023] Figure 2 Comparison of experimental and theoretical spectra of L-ascorbic acid, where blue represents the experimental spectrum and red represents the theoretical spectrum.

[0024] Figure 3 : Comparison of experimental and theoretical spectra of D-isoascorbic acid, where blue represents the experimental spectrum and red represents the theoretical spectrum.

[0025] Figure 4 : Vector diagrams of terahertz vibrational modes of L-ascorbic acid unit cells at frequencies of (a) 1.39 THz, (b) 1.79 THz, (c) 1.97 THz, and (d) 2.32 THz.

[0026] Figure 5 : Vector diagrams of terahertz vibrational modes of D-isoascorbic acid unit cells at (a) 1.79 THz and (b) 2.40 THz frequencies

[0027] Figure 6 IRI analysis results of L-ascorbic acid: (a) Three-dimensional isosurface plot (b) Two-dimensional scatter plot

[0028] Figure 7 IRI analysis results of D-isoascorbic acid: (a) Three-dimensional isosurface plot (b) Two-dimensional scatter plot Detailed Implementation

[0029] Example 1: Vibrational Modes and Weak Interactions of L-Ascorbic Acid

[0030] In this embodiment, L-ascorbic acid is analyzed according to steps one through six of the technical solution.

[0031] Step 1: Sample preparation: Take L-ascorbic acid standard (purity ≥98%, CAS 50-81-7), mix it with PTFE at a ratio of 1:1 and press it.

[0032] Step 2: Terahertz time-domain spectroscopy measurement: The L-ascorbic acid sample was measured using a CCT-1800 system to obtain the experimental absorption spectrum. Figure 2(Blue curve) The characteristic peaks of the terahertz spectrum are located at 0.94 THz, 1.80 THz, 2.01 THz and 2.24 THz.

[0033] Step 3: Theoretical Calculation: The L-ascorbic acid crystal structure was obtained from CCDC. Periodic boundary conditions were set using CP2K software. Structure optimization and frequency calculations were performed using the PBE-D3(BJ) functional and the 6-311G** basis set. The calculation results showed no imaginary frequencies, and the theoretical absorption spectrum was obtained. Figure 2 (Red curve) The characteristic peaks of the terahertz spectrum are located at 1.39 THz, 1.79 THz, 1.97 THz and 2.32 THz.

[0034] Step 4: Comparative Analysis: By comparing the experimental absorption spectrum with the theoretical absorption spectrum of L-ascorbic acid, it was found that the peak position deviations of the experimental and theoretical terahertz absorption spectra were +0.45THz, -0.01THz, -0.04THz, and +0.08THz, respectively.

[0035] Step 5: Vibrational Mode Analysis: The VMARD method was used to assign vibrational modes of L-ascorbic acid. The results showed that the vibrational modes of each peak were dominated by dihedral torsion (τ) and bond bending (σ). The L-ascorbic acid vibrational mode vector diagram (…) Figure 4 The atomic motion is mainly concentrated in the five-membered lactone ring and the hydroxyl side chain.

[0036] Step Six: Weak Interaction Analysis: The weak interactions of L-ascorbic acid were visualized using the IRI method. The results showed that green isosurfaces (van der Waals forces) were widely distributed in L-ascorbic acid crystals, blue isosurfaces (hydrogen bonds) appeared between adjacent molecular hydroxyl groups, and a small number of reddish-brown isosurfaces (steric hindrance) were found near the center of the five-membered lactone ring. In the two-dimensional scatter plot, sign(λ2)ρ showed blue peaks (hydrogen bonds) at -0.036 and -0.025, and multiple green peaks (van der Waals forces) appeared in the range of -0.01 to +0.005.

[0037] Example 2: Vibrational Modes and Weak Interactions of D-Isoascorbic Acid

[0038] In this embodiment, D-isoascorbic acid was analyzed following the same steps as in Example 1.

[0039] Step 1: Sample preparation: Take D-isoascorbic acid standard (purity ≥98%, CAS 89-65-6), mix it with PTFE at a ratio of 1:1 and press it.

[0040] Step 2: Terahertz time-domain spectroscopy measurement: The D-isoascorbic acid sample was measured using the CCT-1800 system to obtain the experimental absorption spectrum. Figure 3(Blue curve) The characteristic absorption peaks of the terahertz spectrum are located at 1.36 THz and 2.01 THz.

[0041] Step 3: Theoretical Calculation: The crystal structure of D-isoascorbic acid was obtained from CCDC. Periodic boundary conditions were set using CP2K software. Structure optimization and frequency calculations were performed using the PBE-D3(BJ) functional and the 6-311G** basis set. The calculation results showed no imaginary frequencies, and the theoretical absorption spectrum was obtained. Figure 3 (Red curve) The characteristic absorption peaks of the terahertz spectrum are located at 1.79 THz and 2.40 THz.

[0042] Step 4: Comparative Analysis: By comparing the experimental absorption spectrum with the theoretical absorption spectrum of D-isoascorbic acid, it was found that the peak position deviations of the experimental and theoretical terahertz absorption spectra were +0.43THz and +0.39THz, respectively.

[0043] Step 5: Vibrational Mode Analysis: The VMARD method was used to assign vibrational modes of D-isoascorbic acid. The results showed that the vibrational modes of each peak were dominated by dihedral torsion (τ) and bond bending (σ). The D-isoascorbic acid vibrational mode vector diagram (…) Figure 5 This shows that atomic motion is mainly concentrated in the carbon skeleton.

[0044] Step Six: Weak Interaction Analysis: The weak interactions of D-isoascorbic acid were visualized using the IRI method. The results showed that D-isoascorbic acid was also dominated by green isosurfaces (van der Waals forces), but the blue region (hydrogen bonds) was stronger. In the two-dimensional scatter plot, sign(λ2)ρ showed blue spikes (hydrogen bonds) at -0.03 and -0.02, which was wider than that of L-ascorbic acid.

Claims

1. A method for analyzing the vibrational modes and weak interactions of vitamin C stereoisomers based on terahertz spectroscopy and periodic boundary conditions, characterized in that, Includes the following steps: Step Step 1: Sample Preparation: L-ascorbic acid or D-isoascorbic acid was mixed with polytetrafluoroethylene (PTFE), ground, sieved, weighed, pressed into sheets, and dried. Step 2: Terahertz Time-Domain Spectroscopy Measurement: Spectroscopic measurements were performed using a transmission terahertz time-domain spectrometer to obtain experimental absorption spectra. Step 3: Theoretical Calculation: The crystal structures of L-ascorbic acid and D-isoascorbic acid were obtained from the Cambridge Crystal Data Center. Then, density functional theory (DFT) with periodic boundary conditions was used for structural optimization and frequency calculation to obtain theoretical absorption spectra. Step 4: Comparative Analysis: The experimental absorption spectra were compared with the theoretical absorption spectra to verify the accuracy and reliability of the theoretical absorption spectra. Step 5: Vibrational Mode Assignment: The vibrational modes of the characteristic absorption peaks in the terahertz spectrum were quantitatively decomposed into the contribution rates of bond length stretching, bond angle bending, exterior angle bending, and dihedral torsion using the Vibrational Mode Correlation Determination (VMARD) analysis method. Step 6: Weak Interaction Analysis: The weak interactions between L-ascorbic acid and D-isoascorbic acid were visualized and analyzed.

2. The method according to claim 1, characterized in that, The specific preparation method of the sample sheet described in step one is as follows: the sample and PTFE are mixed at a mass ratio of 1:1, ground through a 200-mesh sieve, and each 200mg of mixed sample is weighed using an electronic balance. The sample is pressed into a disc with a diameter of 13 mm and a thickness of 1 mm under a pressure of 10 tons for 30 seconds, and then vacuum dried at 55℃ for 2 hours.

3. The method according to claim 1, characterized in that, The measurement range of the terahertz time-domain spectroscopy system described in step two is 0.5~2.5THz.

4. The method according to claim 1, characterized in that, The DFT calculation of the periodic boundary conditions described in step three uses the PBE-D3(BJ) exchange-correlated functional and the 6-311G** basis set, and the calculation software is CP2K.

5. The method according to claim 1, characterized in that, The VMARD analysis method described in step five is based on Bayesian linear regression, which calculates the contribution rate of the interior coordinates through the posterior probability distribution.

6. The method according to claim 1, characterized in that, Step six uses the IRI analysis method to perform a visual analysis of weak interactions. The type, strength, and spatial distribution of weak interactions are determined by isosurfaces, and van der Waals forces, hydrogen bonds, and steric hindrance effects are distinguished.

7. The method according to claim 1, characterized in that, The method described above is used for comparative analysis of the vibrational modes and weak interactions of two stereoisomers, L-ascorbic acid and D-isoascorbic acid.

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