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Khodayari A, Hirn U, Spirk S, Ogawa Y, Seveno D, Thielemans W. Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review. Carbohydr Polym 2024; 343:122415. [PMID: 39174111 DOI: 10.1016/j.carbpol.2024.122415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/27/2024] [Accepted: 06/16/2024] [Indexed: 08/24/2024]
Abstract
The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.
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Affiliation(s)
- Ali Khodayari
- Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, Leuven 3001, Belgium.
| | - Ulrich Hirn
- Institute of Bioproducts and Paper Technology, TU Graz, Inffeldgasse 23, Graz 8010, Austria
| | - Stefan Spirk
- Institute of Bioproducts and Paper Technology, TU Graz, Inffeldgasse 23, Graz 8010, Austria
| | - Yu Ogawa
- Centre de recherches sur les macromolécules végétales, CERMAV-CNRS, CS40700, 38041 Grenoble cedex 9, France
| | - David Seveno
- Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, Leuven 3001, Belgium
| | - Wim Thielemans
- Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, Campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
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Mohan M, Jetti KD, Smith MD, Demerdash ON, Kidder MK, Smith JC. Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents. J Chem Theory Comput 2024; 20:3911-3926. [PMID: 38387055 DOI: 10.1021/acs.jctc.3c01163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Deep eutectic solvents (DESs) are emerging as environmentally friendly designer solvents for mass transport and heat transfer processes in industrial applications; however, the lack of accurate tools to predict and thus control their viscosities under both a range of environmental factors and formulations hinders their general application. While DESs may serve as designer solvents, with nearly unlimited combinations, this unfortunately makes it experimentally infeasible to comprehensively measure the viscosities of all DESs of potential industrial interest. To assist in the design of DESs, we have developed several new machine learning (ML) models that accurately and rapidly predict the viscosities of a diverse group of DESs at different temperatures and molar ratios using, to date, one of the most comprehensive data sets containing the properties of over 670 DESs over a wide range of temperatures (278.15-385.25 K). Three ML models, including support vector regression (SVR), feed forward neural networks (FFNNs), and categorical boosting (CatBoost), were developed to predict DES viscosity as a function of temperature and molar ratio and contrasted with multilinear and two-factor polynomial regression baselines. Quantum chemistry-based, COSMO-RS-derived sigma profile (σ-profile) features were used as inputs for the ML models. The CatBoost model is excellent at externally predicting DES viscosity, as indicated by high R2 (0.99) and low root-mean-square-error (RMSE) and average absolute relative deviations (AARD) (5.22%) values for the testing data sets, and 98% of the data points lie within the 15% of AARD deviations. Furthermore, SHapley additive explanation (SHAP) analysis was employed to interpret the ML results and rationalize the viscosity predictions. The result is an ML approach that accurately predicts viscosity and will aid in accelerating the design of appropriate DESs for industrial applications.
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Affiliation(s)
- Mood Mohan
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Karuna Devi Jetti
- Department of Biotechnology, GIS, GITAM,Vishakhapatnam, Andhra Pradesh 530045, India
| | - Micholas Dean Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Omar N Demerdash
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michelle K Kidder
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States
| | - Jeremy C Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Zhu B, Xu Y, Ge H, Wang S, Wang W, Li B, Xu H. Theoretical study of lactic acid-based deep eutectic solvents dissociation of hemicellulose with different hydrogen bonding acceptors. Int J Biol Macromol 2023; 244:125342. [PMID: 37321434 DOI: 10.1016/j.ijbiomac.2023.125342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/04/2023] [Accepted: 06/10/2023] [Indexed: 06/17/2023]
Abstract
This paper explored the mechanism of dissociation of hemicellulose using lactic acid (LA)-based deep eutectic solvents (DESs) synthesized with different hydrogen bond acceptors (HBAs) via simulations. Density functional theory (DFT) calculations and molecular dynamics (MD) simulations revealed that DESs synthesized with guanidine hydrochloride (GuHCl) as hydrogen bond acceptor (HBA) demonstrated better hemicellulose solubilization compared to the conventional DESs synthesized using choline chloride (ChCl) as HBA. The best interaction with hemicellulose was achieved at GuHCl:LA = 1:1. The results showed that CL- played a dominant role in the dissolution of hemicellulose by DESs. Unlike ChCl, the guanidine group in GuHCl had the delocalized π bond, which made CL- have stronger coordination ability and promoted dissolution of hemicellulose by DESs. Moreover, multivariable analysis was employed to establish the correlation between the effects of different DESs on hemicellulose and the molecular simulation results. Additionally, the influence of different HBAs functional groups and carbon chain length on the solubilization of hemicellulose by DESs were analyzed.
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Affiliation(s)
- Baoping Zhu
- College of chemical engineering, Qingdao University of science and technology, Qingdao 266042, China
| | - Yang Xu
- College of chemical engineering, Qingdao University of science and technology, Qingdao 266042, China
| | - Hanwen Ge
- College of chemical engineering, Qingdao University of science and technology, Qingdao 266042, China
| | - Shenglin Wang
- College of chemical engineering, Qingdao University of science and technology, Qingdao 266042, China
| | - Weixian Wang
- College of chemical engineering, Qingdao University of science and technology, Qingdao 266042, China
| | - Bin Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Huanfei Xu
- College of chemical engineering, Qingdao University of science and technology, Qingdao 266042, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
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Mohan M, Simmons BA, Sale KL, Singh S. Multiscale molecular simulations for the solvation of lignin in ionic liquids. Sci Rep 2023; 13:271. [PMID: 36609448 PMCID: PMC9822913 DOI: 10.1038/s41598-022-25372-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023] Open
Abstract
Lignin, the second most abundant biopolymer found in nature, has emerged as a potential source of sustainable fuels, chemicals, and materials. Finding suitable solvents, as well as technologies for efficient and affordable lignin dissolution and depolymerization, are major obstacles in the conversion of lignin to value-added products. Certain ionic liquids (ILs) are capable of dissolving and depolymerizing lignin but designing and developing an effective IL for lignin dissolution remains quite challenging. To address this issue, the COnductor-like Screening MOdel for Real Solvents (COSMO-RS) model was used to screen 5670 ILs by computing logarithmic activity coefficients (ln(γ)) and excess enthalpies (HE) of lignin, respectively. Based on the COSMO-RS computed thermodynamic properties (ln(γ) and HE) of lignin, anions such as acetate, methyl carbonate, octanoate, glycinate, alaninate, and lysinate in combination with cations like tetraalkylammonium, tetraalkylphosphonium, and pyridinium are predicted to be suitable solvents for lignin dissolution. The dissolution properties such as interaction energy between anion and cation, viscosity, Hansen solubility parameters, dissociation constants, and Kamlet-Taft parameters of selected ILs were evaluated to assess their propensity for lignin dissolution. Furthermore, molecular dynamics (MD) simulations were performed to understand the structural and dynamic properties of tetrabutylammonium [TBA]+-based ILs and lignin mixtures and to shed light on the mechanisms involved in lignin dissolution. MD simulation results suggested [TBA]+-based ILs have the potential to dissolve lignin because of their higher contact probability and interaction energies with lignin when compared to cholinium lysinate.
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Affiliation(s)
- Mood Mohan
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Bioresource and Environmental Security Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
| | - Blake A. Simmons
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Kenneth L. Sale
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Department of Computational Biology and Biophysics, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
| | - Seema Singh
- grid.451372.60000 0004 0407 8980Deconstruction Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Bioresource and Environmental Security Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
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Grewal J, Khare SK, Drewniak L, Pranaw K. Recent perspectives on microbial and ionic liquid interactions with implications for biorefineries. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Zhao J, Zhou G, Fang T, Ying S, Liu X. Screening ionic liquids for dissolving hemicellulose by COSMO-RS based on the selective model. RSC Adv 2022; 12:16517-16529. [PMID: 35754873 PMCID: PMC9169070 DOI: 10.1039/d2ra02001g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
The utilization of biomass resources has attracted more and more attention due to the consumption of non-renewable resources. Compared with cellulose and lignin, hemicellulose has been less studied. Some ionic liquids (ILs) have been proved to be excellent solvents for lignocellulosic pretreatment. However, screening of more efficient ILs is difficult due to numerous possible ILs. Computational chemistry has been proved effective in solvent screening, but a precise model is indispensable. In this work, we focused on building several appropriate models and selected the most suitable one. According to the structure of hemicellulose, six hemicellulose models were constructed and the mid-dimer of the xylan chain hemicellulose (MDXC) model was proved to be the best compared with the reported experimental results. Based on the MDXC model, 1368 ILs were screened to evaluate their ability to dissolve hemicellulose by Conductor-like Screening Model for Real Solvents (COSMO-RS). The activity coefficient (γ), excess enthalpy (HE), and σ-profile indicated that the hydrogen-bond (H-bond) played a vital role in the dissolution of hemicellulose. Anions played a more critical role than cations, where small anions with H-bond acceptor groups could enhance the molecular interactions with hemicellulose. This work provided a thermodynamic understanding of hemicellulose and IL solvent systems. It highlights the importance of building appropriate solute models, which may be necessary to predict of the other thermodynamic properties in the future.
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Affiliation(s)
- Jinzheng Zhao
- School of Chemistry and Chemical Engineering, Qingdao University 308 Ningxia Road Shinan District Qingdao Shandong 266071 P. R. China
| | - Guohui Zhou
- School of Chemistry and Chemical Engineering, Qingdao University 308 Ningxia Road Shinan District Qingdao Shandong 266071 P. R. China
| | - Timing Fang
- School of Chemistry and Chemical Engineering, Qingdao University 308 Ningxia Road Shinan District Qingdao Shandong 266071 P. R. China
| | - Shengzhe Ying
- School of Chemistry and Chemical Engineering, Qingdao University 308 Ningxia Road Shinan District Qingdao Shandong 266071 P. R. China
| | - Xiaomin Liu
- School of Chemistry and Chemical Engineering, Qingdao University 308 Ningxia Road Shinan District Qingdao Shandong 266071 P. R. China
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Rajamani S, Santhosh R, Raghunath R, Jadhav SA. Value-added chemicals from sugarcane bagasse using ionic liquids. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01732-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wang Y, Tian F, Guo P, Fu D, Heeres HJ, Tang T, Yuan H, Wang B, Li J. Catalytic liquefaction of sewage sludge to small molecular weight chemicals. Sci Rep 2020; 10:18929. [PMID: 33144686 PMCID: PMC7609695 DOI: 10.1038/s41598-020-75980-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/19/2020] [Indexed: 11/09/2022] Open
Abstract
The catalytic hydrotreatment of sewage sludge, the wet solid byproducts from wastewater treatment plants, using supported Ir, Pt, Pd, Ru catalysts had been investigated with different solvent conditions. Reactions were carried out in a batch set-up at elevated temperatures (400 °C) using a hydrogen donor (formic acid (FA) in isopropanol (IPA) or hydrogen gas), with sewage sludge obtained from different sampling places. Sewage sludge conversions of up to 83.72% were achieved using Pt/C, whereas the performance for the others catalysts is different and solvent had a strong effect on the conversion rate and product constitution. The sewage sludge oils were characterised using a range of analytical techniques (GC, GC-MS, GCxGC, GPC) and were shown to consist of monomers, mainly alkanes and higher oligomers.
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Affiliation(s)
- Yuehu Wang
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China. .,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China.
| | - Feihong Tian
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
| | - Peimei Guo
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
| | - Dazhen Fu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
| | - Hero Jan Heeres
- Chemical Engineering Department, ENTEG, University of Groningen, Nijenborg 4, 9747 AG, Groningen, The Netherlands
| | - Taotao Tang
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
| | - Huayu Yuan
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
| | - Bing Wang
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China.,Observation and Research Station for Guizhou Karst Environmental Ecosystems, Guiyang, 550025, China
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Mohan M, Deshavath NN, Banerjee T, Goud VV, Dasu VV. Ionic Liquid and Sulfuric Acid-Based Pretreatment of Bamboo: Biomass Delignification and Enzymatic Hydrolysis for the Production of Reducing Sugars. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b00914] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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