Supplementary data for the mechanism research for depolymerization of cellulose induced by hydroxyl radical using GC-MS, reaction kinetics simulation and quantum chemistry computation.

This data article contains the chemical structure of cellobiose, which was chosen as the model molecule of cellulose. A brief diagram of the reaction system established by Packmol containing celluloses, hydroxyl radicals and water for ReaxFF kinetic simulation as well as the energy change curve obtained during the optimization process were provided. The total ion current (TIC) and product species of the reaction of cellobiose with Fenton's regent given by GC-MS were displayed, respectively. A brief diagram of the OH-abstraction of cellobiose triggered by hydrated hydrogen radical was shown. Additionally, chemical structures of all transition states in pathways 1-4 of the reaction of cellobiose with •OH carried out by means of quantum calculation using Gaussian 09 are shown. Some key frames in reaction pathway 1 obtained by ReaxFF simulation and the thermodynamic parameters for reaction pathways 1-4 were also listed successively. Interpretation of this data can be found in a research article titled "Study on Cellulose Degradation Induced by Hydroxyl Radical with Cellobiose as a Model Using GC-MS, ReaxFF Simulation and DFT Computation" (Shao et al., 2020) [1].

Data

Data provided in this article are based on GC-MS, ReaxFF kinetics simulation and DFT computation. The computation performed applying Gaussian 09 [1] at B3LYP/6-31 + G (d,p) level and are treated using ChemBioDraw Ultra 12.0 [2], Origin 9.0 or BIOVIA Discovery Studio Visualizer 2016 [3]. Cellobiose was chosen as the model molecule and its chemical structure is shown in Fig. 1. The ReaxFF kinetics system established by Packmol [4] as well as the energy curve during the geometry optimization process by Materials Studio 8.0 [5] are shown in Fig. 2. In Fig. 3, the total ion current obtained by gas chromatography – mass spectra (GC-MS) and the product species based on different carbon atoms are displayed, the latter figure is done by origin 9.0. And in Fig. 4, a brief diagram of the hydroxyl group abstraction process induced by hydrated hydrogen radical is shown. Fig. 5, Fig. 6, Fig. 7, Fig. 8 show the 3D structures of transition states in the reaction pathways 1 to 4.

Fig. 1

Cellobiose was chosen as the model of cellulose, the pyran rings were labelled A and B while the carbon atoms were labelled 1 to 6 and 1′ to 6'.

Fig. 2

The molecular system for ReaxFF kinetics simulation. (a) The system established by packmol; (b) the energy curve during geometry optimization (The green molecules refer to cellobiose while others are hydroxyl radicals and water molecules). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

GC-MS results of the reaction of cellobiose with Fenton's regent. (a)Total ion current (TIC) given by GC-MS; (b) the product species with different carbon atoms, 27 compounds, including 25 carbon containing components and a couple of inorganic acids (compound 4 and 6), were identified by means of NIST 11.

Fig. 4

A brief diagram of the OH-abstraction of cellobiose triggered by hydrated hydrogen radical.

Fig. 5

The chemical structures of all the transition states of reaction pathway 1.

Fig. 6

The chemical structure of all the transition states of reaction pathway 2.

Fig. 7

The chemical structure of all the transition states of reaction pathway 3.

Fig. 8

The chemical structure of all the transition states of reaction pathway 4.

Some key frames during reaction pathway 1 given by the ReaxFF kinetics simulation with Materials Studio 8.0, such as the H-abstraction, the formation of aldehyde groups as well as breakage of the glycosidic bond are listed in Fig. 9.

Fig. 9

Some key frames in reaction pathway 1 obtained from ReaxFF simulation given by Materials Strudio 8.0.

Thermodynamic parameters of pathways given by quantum calculation are listed in Table 1.

Table 1

Thermodynamic parameters of reaction pathway 1 given by quantum calculation.

Species	E (A.U.)	ΔE (kcal/mol)	Imaginary frequencies
Reaction pathway 1
Cellobiose + •OH	−1373.80018994
TSI1	−1373.79517894	2.79	−254.8448
IM1	−1297.37289889
TSI2	−1297.36573672	3.84	−181.7516
IM2	−1297.30024826
TSI3	−1297.29356259	4.18	−1210−6476
IM3 + •OH	−1372.40518022
TSI4	−1372.39133055	8.69	−578.2651
IM4	−1296.15615717
TSI5	−1296.15593283	10.40	−372.2592
IM5	−610.07969778
TSI6	−610.06100125	11.76	−177.7205
IM6	−382.200029716
TSI7	−382.198054016	1.57	−88.4025
Reaction pathway 2
Cellobiose + •OH	−1373.79706884
TSII1	−1373.79117764	1.02	−888.4194
IM7	−1373.80515267
TSII2	−1373.80129746	1.44	−362.4149
P6	−1374.97667174
TSII3	−1374.97189175	3.79	−15.3957
IM8	−1222.11611902
TSII4	−1222.0538359	2.45	−26.6661
IM9	−1297.35048791
TSII5	−1297.34439439	2.91	−54.8196
IM10 + P7	−1106.37433006
TSII6	−1106.36437043	6.33	−394.7160
IM11 + P8	−915.662806851
TSII7	−915.6594552	3.15	−183.7358
IM12	−992.033632568
TSII8	−992.019196563	14.87	−98.9341
IM13 + P4 + P8	−228.357657028
TSII9	−228.33836401	5.33	−981.8451
Reaction pathway 3
Cellobiose + •OH	−1374.99075606
TSIII1	−1374.96156176	19.52	−20.6975
IM14	−1374.98418693
TSIII2	−1222.11844387	12.46	−539.2050
IM15	−1222.14881312
TSIII3	−954.922663476	1.37	−823.4358
IM17	−954.950996012
TSIII4	−878.492664121	4.01	−132.1112
IM18	−878.500865162
TSIII5	−878.491636879	4.82	−154.0470
IM19	−878.495438060
TSIII6	−954.883306720	13.52	−364.0099
IM20 + P9	−954.894062195
TSIII7	−610.124246923	9.59	−55.0716
IM21 + P2	−610.148031871
TSIII8	−382.198292315	1.96	−609.7246
Reaction pathway 4 (cellobiose to P10 + P11)
Cellobiose + •OH	−1373.83149075
TSIV1	−1373.82600309	3.41	−18.6029
IM22	−1373.83363056
TSIV2	−1297.37321738	7.62	−21.4493
IM23 + P10	−1297.37560601
TSIV3	−611.331097178	9.94	−70.3568
IM24	−611.343289532
TSIV4	−610.773383274	2.31	−4.9432
Reaction pathway 4 (cellobiose to P8)
Cellobiose + •OH	−1373.83149075
TSIV1	−1373.82600309	3.41	−18.6029
IM22	−1373.83363056
TSIV2	−1297.37321738	7.62	−21.4493
IM23 + IM25	−1297.37560601
TSIV5	−761.772136432	1.24	−32.1187
IM26	−761.803346865
TSIV6	−685.329217242	13.79	−416.2850
IM27 + P12	−685.346966712
TSIV7	−456.253820055	4.08	−330.7715
IM28 + P13	−456.260315463
TSIV8	−342.953813877	8.98	−46.5245

Experimental design, materials and methods

A Trace 1310 gas chromatograph (Thermo, USA) equipped with an ISQ single quadrupole mass spectrometer (Thermo, USA) and a MP–5 ms gas chromatographic column (0.25 mm × 30 m × 0.25 μm, Agilent, USA) was used for the GC-MS analysis. Analysis of GC-MS was performed using the Thermo Xcalibur Qual software [6]. Identification of compounds was carried out by comparing the mass spectra to the standard library NIST11 [[7], [8]].

The chemical structure schemes were generated by using BIOVIA Discovery Studio Visualizer 2016 based on the TS optimization of the corresponding transition states with Gaussian 09 at B3LYP/6-31 + G (d,p) level.

Specifications Table

Subject	Chemistry, Physical and Theoretical Chemistry
Specific subject area	Radical degradation mechanism of carbohydrate
Type of data	Table, Figure, Graph, Chart, Schematic diagram, Image.
How data were acquired	Schematic diagram from ChemBioDraw Ultra 12.0.GC-MS spectra collected using Thermo Trace 1310 with MS standard library NIST11 and the bar charts made by Origin 9.0.Structures of transition states and energy data from Gaussion09.ReaxFF reaction kinetics simulation using Material Studio 8.0.
Data format	Data of current article
Parameters for data collection	The MS samples were derived with O-methyl hydroxylamine hydrochloride/pyridine and N-methyl-N-(trimethylsilyl) trifluoroacetamide. The temperature of the injector was set at 250 °C, the flow rate of the carrier gas (helium) was 1.00 mL/min and the split ratio was 10:1. The temperature of the column was set to keep at 110 °C for 2 min at first, then raised to 160 °C at 8 °C/min, to 230 °C at 2 °C/min, to 250 °C at 5 °C/min and kept for 10 min. The injection volume was 1.0 μL.Quantum chemistry calculation with B3LYP/6-31 + G (d,p) level and PCM solvent model.ReaxFF reaction kinetics simulation using Reaxff 6.0 forcefield in GULP module of Material Studio 8.0.
Description of data collection	The structure of Fig. 1, Fig. 4 were drawn using ChemBioDraw Ultra 12.0. Fig. 2 was collected by Material Studio 8.0. Fig. 3(a) was given by Trace 1310 GC-MS and the data in Fig. 3(b) was collected from the identification of compounds in MS by comparing the mass spectra to the standard library NIST11 and the bar chart was made by Origin 9.0. Fig. 5, Fig. 6, Fig. 7, Fig. 8 were the transition states in the reaction pathways 1 to 4 from DFT calculation at B3LYP/6-31 + G (d,p) using G09 and the images were made by BIOVIA Discovery Studio Visualizer 2016. Fig. 9 was made by Material Studio 8.0. The data in Table 1 were obtained from the quantum chemistry calculation using Gaussion09 at B3LYP/6-31 + G (d,p) level with PCM aqueous solvent model.
Data source location	Tianjin, China Latitude and longitude:117.715812E, 39.093244 N.
Data accessibility	With the article
Related research article	C. Shao, Q. Shao, X. Wang, J. Ling, X. Guo, Y. Ning, Y. Dai, S. Jia, Y. Qiao, C. Li, K. Zhao. Study on cellulose degradation induced by hydroxyl radical with cellobiose as a model using GC–MS, ReaxFF simulation and DFT computation, Carbohydrate Polymers, 233 (2020) 115,677.https://doi.org/10.1016/j.carbpol.2019.115677

Value of the Data• These data provide some details which can facilitate the readers' understanding of the related research article. • All researchers and investigators who focused on the related research field can benefit from these data. • These data could extend the readers' knowledge about the free radical degradation of cellulose.