2D IR Spectra Research Articles

Theory of rotationally resolved two-dimensional infrared spectroscopy including polarization dependence and rotational coherence dynamics

Two-dimensional infrared (2DIR) spectroscopy is widely used to study molecular dynamics but it is typically restricted to solid and liquid phase samples and modest spectral resolution. Only recently, its potential to study gas-phase dynamics is beginning to be realized. Moreover, the recently proposed technique of cavity-enhanced 2D spectroscopy using frequency combs and developments in multi-comb spectroscopy are expected to dramatically advance capabilities for acquisition of rotationally-resolved 2DIR spectra. This demonstrates the need for rigorous and quantitative treatment of rotationally-resolved, polarization-dependent third-order response of gas-phase samples. In this article, we provide a rigorous and quantitative description of rotationally-resolved 2DIR spectroscopy using density-matrix, time-dependent perturbation theory and angular momentum algebra techniques. We describe the band and branch structure of 2D spectra, decompose the molecular response into polarization-dependence classes, use this decomposition to derive and explain special polarization conditions and relate the liquid-phase polarization conditions to gas-phase ones. Furthermore, we discuss the rotational coherence dynamics during waiting time.

Molecular photothermal effects on time-resolved IR spectroscopy.

Time-resolved IR pump-probe (IR-PP) and two-dimensional IR (2D-IR) spectroscopy are valuable techniques for studying various ultrafast chemical and biological processes in solutions. The time-dependent changes of nonlinear IR signals reflecting fast molecular processes such as vibrational energy transfer and chemical exchange provide invaluable information on the rates and mechanisms of solvation dynamics and structural transitions of multispecies vibrationally interacting molecular systems. However, due to the intrinsic difficulties in distinguishing the contributions of molecule-specific processes to the time-resolved IR signals from those resulting from local heating, it becomes challenging to interpret time-resolved IR-PP and 2D-IR spectra exhibiting transient growing-in spectral components and cross-peaks unambiguously. Here, theoretical considerations of various effects of vibrational coupling, energy transfer, chemical exchange, the generation of hot ground states, molecular photothermal process, and their combinations on the line shapes and time-dependent intensities of IR-PP spectra and 2D-IR diagonal peaks and cross-peaks are presented. We anticipate that the present work will help researchers using IR pump-probe and 2D-IR techniques to distinguish local heating-induced photothermal signals from genuine nonlinear IR signals.

Application of FT-IR spectroscopy and chemometric technique for the identification of three different parts of Camellia nitidissima and discrimination of its authenticated product.

Camellia nitidissima C.W. Chi is a golden camellia recognized in Chinese herbology and widely used as tea and essential oil in Chinese communities. Due to its diverse pharmacological properties, it can be used to treat various diseases. However, unethical sellers adulterated the flower with other parts of Camellia nitidissima in their product. This study used an integrated tri-step infrared spectroscopy method and a chemometric approach to distinguish C. nitidissima’s flowers, leaves, and seeds. The three different parts of C. nitidissima were well distinguished using Fourier transform infrared spectroscopy (FT-IR), second-derivative infrared (SD-IR) spectra, and two-dimensional correlation infrared (2D-IR) spectra. The FT-IR and SD-IR spectra of the samples were subjected to principal component analysis (PCA), PCA-class, and orthogonal partial least square discriminant analysis (OPLS-DA) for classification and discrimination studies. The three parts of C. nitidissima were well separated and discriminated by PCA and OPLS-DA. The PCA-class model’s sensitivity, accuracy, and specificity were all >94%, indicating that PCA-class is the good model. In addition, the RMSEE, RMSEP, and RMSECV values for the OPLS-DA model were low, and the model’s sensitivity, accuracy, and specificity were all 100%, showing that it is the excellent one. In addition, PCA-class and OPLS-DA obtained scores of 27/32 and 26/32, respectively, for detecting adulterated and other TCM reference flower samples from C. nitidissima. Combining an infrared spectroscopic method with a chemometric approach proved that it is possible to differentiate distinct sections of C. nitidissima and discriminate adulterated samples of C.nitidissima flower.

Multiple Ensembles of the Hydrogen-bonded Network in Ethylammonium Nitrate versus Water from Vibrational Spectral Dynamics of SCN- Probe.

We performed classical molecular dynamics simulations to monitor the structural interactions and ultrafast dynamical and spectral response in the protic ionic liquid, ethylammonium nitrate (EAN) and water using the nitrile stretching mode of thiocyanate ion (SCN- ) as the vibrational probe. The normalized frequency distribution of the nitrile stretch in SCN- attains an asymmetric shape in EAN, indicating the existence of more than one hydrogen-bonding environment in EAN. Further, we computed the 2D IR spectrum from classical trajectories, applying the response function formalism. Spectral diffusion dynamics in EAN undergo an initial rattling of the SCN- inside the local ion-cage occurring at a timescale of 0.10 ps, followed by the breakup of the ion-cage activating molecular diffusion at 7.86 ps timescale. In contrast, the dynamics of structural reorganization occur at a timescale of 0.58 ps in H2 O. Hence, the time dependence of the frequency-frequency correlation function decay hints at the local molecular structure and ultrafast ion dynamics of the SCN- probe. The loss of frequency correlation read from the peak shape changes in the 2D correlation spectrum as a function of waiting time is faster in H2 O than in EAN due to the enhanced structural ordering and higher viscosity of the latter. We provide an atomic-level interpretation of the solvation environment around SCN- in EAN and water, which indicates multiple ensembles of the hydrogen bond network in EAN.

Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study

[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (H2), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and CN− ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump-IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.

Rotationally-Resolved Two-Dimensional Infrared Spectroscopy of CO2(g): Rotational Wavepackets and Angular Momentum Transfer.

Angular momentum transfer and wavepacket dynamics of CO2(g) were measured on the picosecond time scale using polarization-resolved two-dimensional infrared (2D-IR) spectroscopy. The dynamics of rotational levels up to Jmax ≈ 50 are observed simultaneously at room temperature. Rotational wavepackets launched by the pump pulses cause oscillations in the intensity of individual peaks and beating patterns in the 2D-IR spectra. The structure of the rotationally resolved 2D-IR spectrum is explained using nonlinear response function theory. Spectral diffusion of the rotationally resolved 2D-IR peaks reveals information about angular momentum transfer. We demonstrate the ability to directly measure inelastic angular momentum dynamics simultaneously across the ∼50 thermally excited rotational levels over several hundred picoseconds.

Measuring Protein Conformation at Aqueous Interfaces with 2D Infrared Spectroscopy of Emulsions.

Determining the secondary and tertiary structures of proteins at aqueous interfaces is crucial for understanding their function, but measuring these structures selectively at the interface is challenging. Here we demonstrate that two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions offers a new route to measuring interfacial protein structure with high levels of detail. We prepared hexadecane/water oil-in-water emulsions stabilized by model LK peptides that are known to fold into either α-helix or β-sheet conformations at hydrophobic interfaces and measured 2D-IR spectra in a transmission geometry. We saw clear spectral signatures of the peptides folding at the interface, with no detectable residue from remaining bulk peptides. Using 2D spectroscopy gives us access to correlation and dynamics data, which enables structural assignment in cases where linear spectroscopy fails. Using the emulsions allows one to study interfacial spectra with standard transmission geometry spectrometers, bringing the richness of 2D-IR to the interface with no additional optical complexity.

Rapid Identification for the Pterocarpus Bracelet by Three-Step Infrared Spectrum Method

In order to explore a rapid identification method for the anti-counterfeit of commercial high value collections, a three-step infrared spectrum method was used for the pterocarpus collection identification to confirm whether a commercial pterocarpus bracelet (PB) was made from the precious species of Pterocarpus santalinus (P. santalinus). In the first step, undertaken by Fourier transform infrared spectroscopy (FTIR) spectrum, the absorption peaks intensity of PB was slightly higher than that of P. santalinus only at 1594 cm−1, 1205 cm−1, 1155 cm−1 and 836 cm−1. In the next step of second derivative IR spectra (SDIR), the FTIR features of the tested samples were further amplified, and the peaks at 1600 cm−1, 1171 cm−1 and 1152 cm−1 become clearly defined in PB. Finally, by means of two-dimensional correlation infrared (2DIR) spectrum, it revealed that the response of holocellulose to thermal perturbation was stronger in P. santalinus than that in PB mainly at 977 cm−1, 1008 cm−1, 1100 cm−1, 1057 cm−1, 1190 cm−1 and 1214 cm−1, while the aromatic functional groups of PB were much more sensitive to the thermal perturbation than those of P. santalinus mainly at 1456 cm−1, 1467 cm−1, 1518 cm−1, 1558 cm−1, 1576 cm−1 and 1605 cm−1. In addition, fluorescence microscopy was used to verify the effectiveness of the above method for wood identification and the results showed good consistency. This study demonstrated that the three-step IR method could provide a rapid and effective way for the anti-counterfeit of pterocarpus collections.

Structure, Organization, and Heterogeneity of Water-Containing Deep Eutectic Solvents.

The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN- anions as the reporter) and THz spectroscopy. Molecular dynamics simulations correctly describe the nontrivial dependence of both spectroscopic signatures depending on water content. For the 2D IR spectra, the MD simulations relate the steep increase in the cross-relaxation rate at high water content to the parallel alignment of packed SCN- anions. Conversely, the nonlinear increase of the THz absorption with increasing water content is mainly attributed to the formation of larger water clusters. The results demonstrate that a combination of structure-sensitive spectroscopies and molecular dynamics simulations provides molecular-level insights into the emergence of heterogeneity of such mixtures by modulating their composition.

Preparation, Crystallization Behavior, Simultaneous Spectroscopic and Rheological Characterization of Polyphenylene Sulfide/Graphene Quantum Dots Nanocomposites

AbstractGraphene quantum dots are prepared conveniently and quickly with brown‐black humic acid as raw material by green oxidation process. The average size of GQDs is about 12 nm with a lattice spacing of 0.26 nm and GQDs have hydroxyl and carboxyl functional groups on their surface. Moreover, photoluminescence testing shows that GQDs have excellent photoluminescence properties with maximum excitation/emission wavelength at 347/478 nm. Next, polyphenylene sulfide (PPS)/GQDs nanocomposites are prepared by melt blending with GQDs and PPS. Mechanical tests show that the tensile strength and the impact strength of PPS can be greatly improved when the amount of GQDs is 0.5 wt% and tensile strength and the impact strength are increased by 53.38% and 375%, respectively. The nonisothermal crystallization of PPS/GQDs nanocomposites is investigated by differential scanning calorimetry, which shows that GQDs effectively increase the crystallization rate of PPS. The crystallization of PPS/GQDs nanocomposites during cooling are studied by Rheonaut technology analysis. The rheological results show that the storage modulus of PPS/GQDs (0.5 wt%) nanocomposites is increased by about 1.04 times than that of pure PPS, and 2D IR spectrum confirms that GQDs accelerate crystallization of PPS. Rheological studies present that GQDs have good compatibility with PPS.

Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra.

Ultrafast spectroscopy often involves measuring weak signals and long data acquisition times. Spectra are typically collected as a "pump-probe" spectrum by measuring differences in intensity across laser shots. Shot-to-shot intensity fluctuations are most often the primary source of noise in ultrafast spectroscopy. Here, we present a novel approach for denoising ultrafast two-dimensional infrared (2D IR) spectra using conditional generative adversarial neural networks (cGANNs). The cGANN approach is able to eliminate shot-to-shot noise and reconstruct the line shapes present in the noisy input spectrum. We present a general approach for training the cGANN using matched pairs of noisy and clean synthetic 2D IR spectra based on the Kubo-line shape model for a three-level system. Experimental shot-to-shot laser noise is added to synthetic spectra to recreate the noise profile present in measured experimental spectra. The cGANNs can recover line shapes from synthetic 2D IR spectra with signal-to-noise ratios as low as 2:1, while largely preserving the key features such as center frequencies, line widths, and diagonal elongation. In addition, we benchmark the performance of the cGANN using experimental 2D IR spectra of an ester carbonyl vibrational probe and demonstrate that, by applying the cGANN denoising approach, we can extract the frequency-frequency time correlation function (FFCF) from reconstructed spectra using a nodal-line slope analysis. Finally, we provide a set of practical guidelines for extending the denoising method to other coherent multidimensional spectroscopies.

Dynamics in tris(pentafluoroethyl)trifluorophosphate (FAP) anion based ionic liquids: A 2D-IR study with tungsten hexacarbonyl

Ultrafast two-dimensional infrared spectroscopy (2D-IR) measurements for tungsten hexacarbonyl, W(CO)6, has been performed in two fluoroalkylphosphate ([FAP])-based ultrahigh hydrophobic, ionic liquids, namely, 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)-trifluorophosphate ([EMIM][FAP]) and 1-(hexyl)-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([HMIM][FAP]) to probe their local structure and dynamics. To understand the effect of FAP anion on the dynamics, a relatively less hydrophobic [PF6-] anion has been introduced in the form of [HMIM][PF6]. While the linear IR spectra records some influence of anion in terms of spectral shifts, the alkyl chain length of the cation seems to have no significant influence on the spectral peak position; and even the spectral broadening is found to be in the similar range. Further, vibrational population relaxation dynamics and vibrational anisotropy decay also does not show any significant variation due to difference in constituent of these ionic liquids as well as its solvent properties, such as, viscosity. Finally, 2D-IR spectra show large variation in the spectral shapes with waiting times, which qualitatively remains similar in all the tested ionic liquids. The frequency-fluctuation correlation function measured from 2D-IR spectra displays a bi-exponential decay with the shorter time-constant dependent on the identity of the anion, and has been attributed to the ion-rattling motion, whereas, the longer component has been found to be invariant with the identity of ionic liquid, and has been attributed to ion-cage motions which is in line with previous MD simulations as well as previous experimental measurements, using ionic vibrational probe. Overall, 2D-IR spectroscopy, in combination with this neutral and hydrophobic probe, W(CO)6 provides a unique opportunity to understand the local structural dynamics of this ultrahigh hydrophobic ionic liquid which are otherwise not accessible by hitherto explored ionic vibrational probes.

Ainslides A-F, Six Sesquiterpenoids Isolated from Ainsliaea pertyoides and Their NLRP3-Inflammasome Inhibitory Activity.

Six new sesquiterpenoids, named as ainslides A-F (1-6), including one carotene-type sesquiterpene (1), one eudesmane (2), four guaianolides (3-6), together with eight known sesquiterpenoids (7-14), were purified from the whole plants of Ainsliaea pertyoides. The structures of these sesquiterpenoids were characterized based on spectroscopic methods including 1D and 2D NMR, HR-ESI-MS, UV, and IR spectra, together with ECD calculations and X-ray diffraction experiments. The anti-inflammatory activity of all the isolated compounds was screened and compounds 3 and 7-13 exhibited NLRP3-inflammasome inhibitory activity with IC50 values of 1.80-4.33 μM.

Intermolecular Vibration Energy Transfer Process in Two CL-20-Based Cocrystals Theoretically Revealed by Two-Dimensional Infrared Spectra.

Inspired by the recent cocrystallization and theory of energetic materials, we theoretically investigated the intermolecular vibrational energy transfer process and the non-covalent intermolecular interactions between explosive compounds. The intermolecular interactions between 2,4,6-trinitrotoluene (TNT) and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) and between 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) and CL-20 were studied using calculated two-dimensional infrared (2D IR) spectra and the independent gradient model based on the Hirshfeld partition (IGMH) method, respectively. Based on the comparison of the theoretical infrared spectra and optimized geometries with experimental results, the theoretical models can effectively reproduce the experimental geometries. By analyzing cross-peaks in the 2D IR spectra of TNT/CL-20, the intermolecular vibrational energy transfer process between TNT and CL-20 was calculated, and the conclusion was made that the vibrational energy transfer process between CL-20 and TNTII (TNTIII) is relatively slower than between CL-20 and TNTI. As the vibration energy transfer is the bridge of the intermolecular interactions, the weak intermolecular interactions were visualized using the IGMH method, and the results demonstrate that the intermolecular non-covalent interactions of TNT/CL-20 include van der Waals (vdW) interactions and hydrogen bonds, while the intermolecular non-covalent interactions of HMX/CL-20 are mainly comprised of vdW interactions. Further, we determined that the intermolecular interaction can stabilize the trigger bond in TNT/CL-20 and HMX/CL-20 based on Mayer bond order density, and stronger intermolecular interactions generally indicate lower impact sensitivity of energetic materials. We believe that the results obtained in this work are important for a better understanding of the cocrystal mechanism and its application in the field of energetic materials.

Revealing the Relationship between Electric Fields and the Conformation of Oxytocin Using Quasi-Static Amide-I Two-Dimensional Infrared Spectra.

It is reported that the cis/trans conformation change of the peptide hormone oxytocin plays an important role in its receptors and activation and the cis conformation does not lead to antagonistic activity. Motivated by recent experiments and theories, the quasi-static amide-I 2D IR spectra of oxytocin are investigated using DFT/B3LYP (D3)/6-31G (d, p) in combination with the isotope labeling method under different electric fields. The theoretical amide-I IR spectra and bond length of the disulfide bond are consistent with the experimental values, which indicates that the theoretical modes are reasonable. Our theoretical results demonstrate that the oxytocin conformation is transformed from the cis conformation to the trans conformation with the change of the direction of the electric field, which is confirmed by the distance of the backbone carbonyl oxygen of Cys6 and Pro7, the Ramachandran plot of Cys6 and Pro7, the dihedral angle of Cβ-S-S-Cβ, and the rmsd of the oxytocin backbone. Moreover, the trans conformation as the result of the turn in the vicinity of Pro7 has a tighter secondary spatial structure than the cis conformation, including stronger hydrogen bonds, longer γ-turn geometry involving five amino acids, and a more stable disulfide bond. Our work provides new insights into the relationship between the conformation, the activation of the peptide hormone oxytocin, and the electric fields.

A theoretical analysis of coherent cross-peaks in polarization selective 2DIR for detection of cross-α fibrils.

The coupled amide-I vibrational modes in peptide systems such as fibrillar aggregates can often provide a wealth of structural information, although the associated spectra can be difficult to interpret. Using exciton scattering calculations, we characterized the polarization selective 2DIR peak patterns for cross-α peptide fibrils, a challenging system given the similarity between the monomeric and fibrillar structures, and interpret the results in light of recently collected 2D data on the cross-α peptide phenol soluble modulin α3. We find that stacking of α-helices into fibrils couples the bright modes across helical subunits, generating three new Bloch-like extended excitonic states that we designate A⊥, E∥, and E⊥. Coherent superpositions of these states in broadband 2DIR simulations lead to characteristic signals that are sensitive to fibril length and match the experimental 2DIR spectra.

2D IR spectra of the intrinsic vibrational probes of ionic liquid from dispersion corrected DFT-MD simulations

We present the vibrational spectral profile of the intrinsic cationic (N-H) and anionic (C-O) probe stretch modes in methylammonium formate (MAF) using first principles molecular dynamics simulations in conjunction with the density functional theory (DFT) approaches. All simulations were performed employing Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) functionals, using three types of van der Waals (vdW) dispersion-corrected representations (D2, D3, and dispersion-corrected atom-centered one-electron potentials) and two values of plane-wave cut-off (300 and 600 Ry). The long-range electrostatic interactions, directional hydrogen bonds and non-directional van der Waals (vdW) dispersion forces are required to accurately interpret the interionic interactions in the protic ionic liquid, MAF. We compute the 2D IR correlation spectra from the wavelet-derived instantaneous frequencies obtained at each timeframe applying the cumulant expansion truncated at the second order to measure the dynamics of vibrational spectral diffusion. Here, we investigate the effects of electronic structure parameters on the spectral bands of the 2D IR contour plot. The spectral bands for both the N-H and CO stretching vibrations attain a round shape by 1 ps, indicating the loss of frequency correlation irrespective of the type of BLYP or PBE-based functionals. Further, the diagonal linewidth of the 2D IR spectral band agrees with the FWHM (full width at half maxima) of the calculated normalized vibrational stretch frequency distribution. Moreover, this study also finds the reason behind the coalescence of the symmetric and antisymmetric C-O stretches in the computed 2D IR spectra. Besides, these computational results may attract the attention of the experimental spectroscopists as it provides molecular-level interpretation and detailed ultrafast time-resolved spectral information of the intrinsic stretching vibrations and associated dynamics of the protic ionic liquid (PIL). Herein, we inspect the quality of different density functionals along with vdW dispersion corrections. However, even though the experimental data is not available for direct comparison of the results, we finally conclude that the inclusion of the effects of dispersion interactions provides a better estimation of the spectroscopic properties.

Isolating Polaritonic 2D-IR Transmission Spectra.

Strong coupling between vibrational transitions in molecules within a resonant optical microcavity leads to the formation of collective, delocalized vibrational polaritons. There are many potential applications of "polaritonic chemistry", ranging from modified chemical reactivity to quantum information processing. One challenge in obtaining the polaritonic response is removing a background contribution due to the uncoupled molecules that generate an ordinary 2D-IR spectrum whose amplitude is filtered by the polariton transmission spectrum. We show that most features in 2D-IR spectra of vibrational polaritons can be explained by a linear superposition of this background signal and the true polariton response. Through a straightforward correction procedure, in which the filtered bare-molecule 2D-IR spectrum is subtracted from the measured cavity response, we recover the polaritonic spectrum.

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein.

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

Study on the chemical changes of Quercus acuttisima by Ganoderma lucidum cultivation after different years by FTIR analysis

The popularmedicinal mushroomGanodermalucidum was often cultivated by the natural-log. Generally the short log after cultivation were discarded and became pollutant. Rapid and less destructive method of analysis technical by Fourier Transform Infrared (FTIR) and Two-dimension Infrared (2DIR) correlation spectroscopy were selected to determine the composition changes of the logs after G.lucidum cultivation after first year to fifth year. The FTIR accumulated spectra formed without processed baseline showed the samples relied upon a sequenced increase of higher level than spectrum control Q (Q = Quercus acuttisima) from L + Q-5 (L = Lingzhi), L + Q-3, L + Q-1 to L + Q-2. The spectrum L + Q-4 has the optimum highest peak at box B, C and E from this lumped spectral view. The split spectra pinpointed on the fingerprint region of a sample begins from peak 1737 cm−1. ascribed C = O stretching vibration on acetyl and carboxyl hemicellulose group bonding gradually faded from L + Q-1 to L + Q-4 but appeared again on L + Q-5, possibly due to the degradation of hemicellulose. The absorption of peak around 1626 cm−1,1318 cm−1 and 781 cm−1 could be the characteristic absorption peak of calcium oxalate monohydrate. The correlation table indicated, most of the original structure of the building block of the wooden part was deteriorated and marked the lowest correlation value of the 4th year sample with control Q. The sudden changing pattern of 2nd derivative spectrum L + Q-3 to more flatten pattern spectrum L + Q-4 ascribed the changing contents of cellulose and hemicellulose included the lignin within one year during the G. lucidum cultivation. The 2DIR spectrum of the raw material sample precisely showed that the active site with red color was clustered with the area around 1800–1700 cm−1, 1450–800 cm−1 and 750–400 cm−1. In between, the range 1450–800 cm−1 was the most active cluster. Each of the sample showed the different sequence of autopeak comparison. This study has examined the impact of G. lucidum on the degradation of Q. acuttisima in term of their ecosystem life chain. The components of healthy Q. acuttisima wood including lignin, cellulose, hemicellulose and calcium oxalate monohydrate underwent changes after different years of G. lucidum cultivation.