1
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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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2
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Ponnuchamy V, Sandak A, Sandak J. Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures. ACS OMEGA 2024; 9:25646-25654. [PMID: 38911769 PMCID: PMC11191132 DOI: 10.1021/acsomega.3c08853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/28/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024]
Abstract
Understanding the atomic-scale structure of wood microfibrils is essential for establishing fundamental properties in various wood-based research aspects, including moisture impact, wood modification, and pretreatment. In this study, we employed molecular dynamics simulations to investigate the arrangement of wood polymers, including cellulose, hemicellulose, and lignin, with a primary focus on the composition of softwood, specifically Norway Spruce wood. We assessed the accuracy of our molecular dynamics model by comparing it with available experimental data, such as density, Young's modulus, and glass transition temperature, which ensures the reliability of our approach. A key aspect of our study involved modeling the active sorption site for water interaction with wood polymers. Our findings revealed that the interaction between water and hemicellulose, particularly within the hemicellulose-cellulose interphase, was the most prominent binding site. This observation aligns with prior research in this field, further strengthening the validity of our results.
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Affiliation(s)
- Veerapandian Ponnuchamy
- InnoRenew
CoE, Livade 6a, 6310 Izola, Slovenia
- University
of Primorska, Andrej Marušič Institute, Muzejski trg 2, 6000 Koper, Slovenia
| | - Anna Sandak
- InnoRenew
CoE, Livade 6a, 6310 Izola, Slovenia
- University
of Primorska, Andrej Marušič Institute, Muzejski trg 2, 6000 Koper, Slovenia
- Faculty
of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Jakub Sandak
- InnoRenew
CoE, Livade 6a, 6310 Izola, Slovenia
- University
of Primorska, Andrej Marušič Institute, Muzejski trg 2, 6000 Koper, Slovenia
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3
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Solhi L, Guccini V, Heise K, Solala I, Niinivaara E, Xu W, Mihhels K, Kröger M, Meng Z, Wohlert J, Tao H, Cranston ED, Kontturi E. Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset. Chem Rev 2023; 123:1925-2015. [PMID: 36724185 PMCID: PMC9999435 DOI: 10.1021/acs.chemrev.2c00611] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.
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Affiliation(s)
- Laleh Solhi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Valentina Guccini
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Katja Heise
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Iina Solala
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Elina Niinivaara
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - Wenyang Xu
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Laboratory of Natural Materials Technology, Åbo Akademi University, TurkuFI-20500, Finland
| | - Karl Mihhels
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Marcel Kröger
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Zhuojun Meng
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou325001, China
| | - Jakob Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10044Stockholm, Sweden
| | - Han Tao
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Emily D Cranston
- Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Eero Kontturi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
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4
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Karna NK, Wohlert J, Hjorth A, Theliander H. Capillary forces exerted by a water bridge on cellulose nanocrystals: the effect of an external electric field. Phys Chem Chem Phys 2023; 25:6326-6332. [PMID: 36779301 DOI: 10.1039/d2cp05563e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Capillary forces play an important role during the dewatering and drying of nanocellulosic materials. Traditional moisture removal techniques, such as heating, have been proved to be deterimental to the properties of these materials and hence, there is a need to develop novel dewatering techniques without affecting the desired properties of materials. It is, therefore, important to explore novel methods for dewatering these high-added-value materials without negatively influencing their properties. In this context, we explore the effect of electric field on the capillary forces developed by a liquid-water bridge between two cellulosic surfaces, which may be formed during the water removal process following its displacement from the interfibrillar spaces. All-atom molecular dynamics (MD) simulations have been used to study the influence of an externally applied electric field on the capillary force exerted by a water bridge. Our results suggest that the equilibrium contact angle of water and the capillary force exerted by the water bridge between two nanocellulosic surfaces depend on the magnitude and direction of the externally applied electric fields. Hence, an external electric field can be applied to manipulate the capillary forces between two particles. The close agreement between the capillary forces measured through MD simulations and those calculated through classical equations indicates that, within the range of the electric field applied in this study, Young-Laplace equations can be safely employed to predict the capillary forces between two particles. The present study provides insights into the use of electric fields for drying of nanocellulosic materials.
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Affiliation(s)
- Nabin Kumar Karna
- Chalmers University of Technology, Chalmersplatsen-4, Sweden. .,Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology and Linköping University, SE-10044 Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology and Linköping University, SE-10044 Stockholm, Sweden.,KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Hjorth
- Chalmers University of Technology, Chalmersplatsen-4, Sweden. .,Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology and Linköping University, SE-10044 Stockholm, Sweden
| | - Hans Theliander
- Chalmers University of Technology, Chalmersplatsen-4, Sweden.
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5
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Cellulose Iβ microfibril interaction with pristine graphene in water: Effects of amphiphilicity by molecular simulation. J Mol Graph Model 2023; 118:108336. [PMID: 36182825 DOI: 10.1016/j.jmgm.2022.108336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
Graphene-cellulose interactions have considerable potential in the development of new materials. In previous computational work (Biomacromolecules2016, 16, 1771), we predicted that the model 100 hydrophobic surface of cellulose interacted favourably with pristine graphene in aqueous solution molecular dynamics simulations; conversely, a model of the hydrophilic 010 surface of cellulose exhibited progressive rearrangement to present a more hydrophobic face with the graphene, with weakened hydrogen bonds between cellulose chains and partial permeation of water. Here, we extend this work by simulating the interaction in aqueous solution of the amphiphilic 110 surface of a cellulose Iβ microfibril model, comprising 36 chains of 40 glucosyl residues, with an infinite sheet of pristine graphene. This face of the microfibril is of intermediate hydrophilicity and progressively associates with graphene over replicate simulations. As cellulose chains adhere to the graphene surface, forming interactions via its CH and OH groups, we observe a degree of local and global untwisting of the microfibril. Complementary rippling of the graphene surface is also observed, as it adapts to interaction with the microfibril. This adsorption process is accompanied by increased exclusion of water between cellulose and graphene although some water localises between chains at the immediate interface. The predicted propensity of a cellulose microfibril to adsorb spontaneously on the graphene surface, with mutual structural accommodation, highlights the amphiphilic nature of cellulose and the types of interactions that can be harnessed to design new graphene-carbohydrate biopolymer materials.
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6
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Modi V, Karttunen AJ. Molecular Dynamics Simulations on the Elastic Properties of Polypropylene Bionanocomposite Reinforced with Cellulose Nanofibrils. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3379. [PMID: 36234505 PMCID: PMC9565226 DOI: 10.3390/nano12193379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Cellulose-reinforced polypropylene bionanocomposites can show improved elastic properties over their pure polypropylene counterparts. We have used equilibrium and non-equilibrium molecular dynamics (MD) simulations to study the elastic properties of polypropylene bionanocomposite systems composed of cellulose nanofibrils (CNF), polypropylene (PP) matrix, and maleic anhydride (MAH) coupling agent. The components of the bionanocomposite were parametrized for compatibility with the AMBER14SB force fields. The elastic properties of pure PP systems converge for the chains with at least 20 monomers. The ratio of cellulose in CNF-PP bionanocomposites strongly affects their elastic properties. The elastic modulus of CNF-PP bionanocomposites shows small improvement when the adhesion between hydrophobic and hydrophilic components is facilitated by a MAH coupling agent. The results demonstrate how fully-atomistic MD simulations can be systematically used to evaluate the elastic properties of CNF-PP bionanocomposites and to make predictions that are in agreement with experiments.
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7
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Cosgrove DJ. Building an extensible cell wall. PLANT PHYSIOLOGY 2022; 189:1246-1277. [PMID: 35460252 PMCID: PMC9237729 DOI: 10.1093/plphys/kiac184] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/21/2022] [Indexed: 05/15/2023]
Abstract
This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model's mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose-cellulose interactions in forming a strong yet extensible network.
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8
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Gupta A, Khodayari A, van Duin ACT, Hirn U, Van Vuure AW, Seveno D. Cellulose Nanocrystals: Tensile Strength and Failure Mechanisms Revealed Using Reactive Molecular Dynamics. Biomacromolecules 2022; 23:2243-2254. [PMID: 35549173 DOI: 10.1021/acs.biomac.1c01110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellulose nanocrystals (CNCs) offer excellent mechanical properties. However, measuring the strength by performing reliable experiments at the nanoscale is challenging. In this paper, we model Iβ crystalline cellulose using reactive molecular dynamics simulations. Taking the fibril twist into account, structural changes and hydrogen-bonding characteristics of CNCs during the tensile test are inspected and the failure mechanism of CNCs is analyzed down to the scale of individual bonds. The C4-O4 glycosidic bond is found to be responsible for the failure of CNCs. Finally, the effect of strain rate on ultimate properties is analyzed and a nonlinear model is used to predict the ultimate strength of 9.2 GPa and ultimate strain of 8.5% at a 1 s-1 strain rate. This study sheds light on the applications of cellulose in nanocomposites and further modeling of cellulose nanofibres.
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Affiliation(s)
- Aman Gupta
- Indian Institute of Science, Bangalore 560012, India
| | - Ali Khodayari
- Department of Materials Engineering, KU Leuven, Leuven 3000, Belgium
| | - Adri C T van Duin
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ulrich Hirn
- Institute of Bioproducts and Paper Technology, TU Graz, Graz 8010, Austria
| | - Aart W Van Vuure
- Department of Materials Engineering, KU Leuven, Leuven 3000, Belgium
| | - David Seveno
- Department of Materials Engineering, KU Leuven, Leuven 3000, Belgium
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9
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Krichen F, Walha S, Abdelmouleh M. Hirshfeld surface analysis of the intermolecular interaction networks in cellulose Iα and Iβ. Carbohydr Res 2022; 518:108600. [DOI: 10.1016/j.carres.2022.108600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
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10
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11
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An Y, Lu W, Li W, Pan L, Lu M, Cesarino I, Li Z, Zeng W. Dietary Fiber in Plant Cell Walls—The Healthy Carbohydrates. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyab037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Dietary fiber (DF) is one of the major classes of nutrients for humans. It is widely distributed in the edible parts of natural plants, with the cell wall being the main DF-containing structure. The DF content varies significantly in different plant species and organs, and the processing procedure can have a dramatic effect on the DF composition of plant-based foods. Given the considerable nutritional value of DF, a deeper understanding of DF in food plants, including its composition and biosynthesis, is fundamental to the establishment of a daily intake reference of DF and is also critical to molecular breeding programs for modifying DF content. In the past decades, plant cell wall biology has seen dramatic progress, and such knowledge is of great potential to be translated into DF-related food science research and may provide future research directions for improving the health benefits of food crops. In this review, to spark interdisciplinary discussions between food science researchers and plant cell wall biologists, we focus on a specific category of DF—cell wall carbohydrates. We first summarize the content and composition of carbohydrate DF in various plant-based foods, and then discuss the structure and biosynthesis mechanism of each carbohydrate DF category, in particular the respective biosynthetic enzymes. Health impacts of DF are highlighted, and finally, future directions of DF research are also briefly outlined.
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Affiliation(s)
| | | | | | | | | | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, São Paulo, Brazil
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12
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Lazar RD, Akher FB, Ravenscroft N, Kuttel MM. Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse. J Chem Theory Comput 2022; 18:1156-1172. [PMID: 35015958 DOI: 10.1021/acs.jctc.1c00534] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although the quality of current additive all-atom force fields for carbohydrates has been demonstrated in many applications, occasional significant differences reported for the hydrodynamic behavior of specific polysaccharides modeled with different force fields is a cause for concern. In particular, irreversible conformational collapse has been noted for some polysaccharide simulations with the GLYCAM06j force field. Here, we investigate the cause of this phenomenon through comparative simulations of a range of saccharides with both the GLYCAM06j and the CHARMM36 carbohydrate force fields. We find that conformational collapse in GLYCAM06j occurs for saccharide chains containing the deoxy sugar α-l-rhamnose after relatively long simulation intervals. Further, we explore the mechanism of conformational collapse and show that this phenomenon arises because of the anomalous low energy in GLYCAM06j (as compared to quantum mechanical calculations) of a specific orientation of α-l-Rha to α-l-Rha glycosidic linkages, which are subsequently sustained by intramolecular interactions in the saccharide chain. We identify the lack of partial charges on aliphatic hydrogens in GLYCAM as the source of this anomaly, demonstrating that addition of small partial atomic charges on the aliphatic protons in rhamnose removes the conformational collapse phenomenon. This work reveals the large cumulative impact that small partial charges may have on the dynamic behavior of polysaccharides and indicates that future reparameterization of the GLYCAM06j force field should investigate the addition of partial charges on all aliphatic hydrogens.
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Affiliation(s)
- Ryan D Lazar
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Farideh B Akher
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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13
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French AD. Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose. Adv Carbohydr Chem Biochem 2021; 80:15-93. [PMID: 34872656 DOI: 10.1016/bs.accb.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially, the molecular shape is inferred from the crystal structures of many small molecules that have β-(1→4) linkages. Then, conformational analyses with potential energy calculations of cellobiose are covered, followed by the use of Atoms-In-Molecules theory to learn about interactions in experimental and theoretical structures. The last section covers models of cellulose nanoparticles. Controversies addressed include the stability of twofold screw-axis conformations, the influence of different computational methods, the predictability of crystalline conformations by studies of isolated molecules, and the twisting of model cellulose crystals.
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Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U.S. Department of Agriculture, New Orleans, Louisiana, USA
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14
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Karna NK, Lidén A, Wohlert J, Theliander H. Electroassisted Filtration of Microfibrillated Cellulose: Insights Gained from Experimental and Simulation Studies. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nabin Kumar Karna
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology, Linköping University, SE-100 44 Stockholm, Sweden
| | - Anna Lidén
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology, Linköping University, SE-100 44 Stockholm, Sweden
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Hans Theliander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology, Linköping University, SE-100 44 Stockholm, Sweden
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15
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Khodayari A, Thielemans W, Hirn U, Van Vuure AW, Seveno D. Cellulose-hemicellulose interactions - A nanoscale view. Carbohydr Polym 2021; 270:118364. [PMID: 34364609 DOI: 10.1016/j.carbpol.2021.118364] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023]
Abstract
In this work, we study interactions of five different hemicellulose models, i.e. Galactoglucomannan, O-Acetyl-Galactoglucomannan, Fuco-Galacto-Xyloglucan, 4-O-Methylglucuronoxylan, and 4-O-Methylglucuronoarabinoxylan, and their respective binding strength to cellulose nanocrystals by molecular dynamics simulations. Glucuronoarabinoxylan showed the highest free energy of binding, whereas Xyloglucan had the lowest interaction energies amongst the five models. We further performed simulated shear tests and concluded that failure mostly happens at the inter-molecular interaction level within the hemicellulose fraction, rather than at the interface with cellulose. The presence of water molecules seems to have a weakening effect on the interactions of hemicellulose and cellulose, taking up the available hydroxyl groups on the surface of the cellulose for hydrogen bonding. We believe that these studies can shed light on better understanding of plant cell walls, as well as providing evidence on variability of the structures of different plant sources for extractions, purification, and operation of biorefineries.
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Affiliation(s)
- Ali Khodayari
- Department of Materials Engineering, KU Leuven, Leuven, Belgium.
| | - Wim Thielemans
- Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Ulrich Hirn
- Institute of Bioproducts and Paper Technology, TU Graz, Graz, Austria
| | | | - David Seveno
- Department of Materials Engineering, KU Leuven, Leuven, Belgium
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16
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Hou Y, Guan QF, Xia J, Ling ZC, He Z, Han ZM, Yang HB, Gu P, Zhu Y, Yu SH, Wu H. Strengthening and Toughening Hierarchical Nanocellulose via Humidity-Mediated Interface. ACS NANO 2021; 15:1310-1320. [PMID: 33372752 DOI: 10.1021/acsnano.0c08574] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Undoubtedly humidity is a non-negligible and sensitive problem for cellulose, which is usually regarded as one disadvantage to cellulose-based materials because of the uncontrolled deformation and mechanical decline. But the lack of an in-depth understanding of the interfacial behavior of nanocellulose in particular makes it challenging to maintain anticipated performance for cellulose-based materials under varied relative humidity (RH). Starting from multiscale mechanics, we herein carry out first-principles calculations and large-scale molecular dynamics simulations to demonstrate the humidity-mediated interface in hierarchical cellulose nanocrystals (CNCs) and associated deformation modes. More intriguingly, the simulations and subsequent experiments reveal that water molecules (moisture) as the interfacial media can strengthen and toughen nanocellulose simultaneously within a suitable range of RH. From the perspective of interfacial design in materials, the anomalous mechanical behavior of nanocellulose with humidity-mediated interfaces indicates that flexible hydrogen bonds (HBs) play a pivotal role in the interfacial sliding. The difference between CNC-CNC HBs and CNC-water-CNC HBs triggers the humidity-mediated interfacial slipping in nanocellulose, resulting in the arising of a pronounced strain hardening stage and the suppression of strain localization during uniaxial tension. This inelastic deformation of nanocellulose with humidity-mediated interfaces is similar to the Velcro-like behavior of a wet wood cell wall. Our investigations give evidence that the humidity-mediated interface can promote the mechanical enhancement of nanocellulose, which would provide a promising strategy for the bottom-up design of cellulose-based materials with tailored mechanical properties.
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Affiliation(s)
- YuanZhen Hou
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei 230027, China
| | - Qing-Fang Guan
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Comprehensive National Science Center, Department of Chemistry, Institute of Biomimetic Materials & Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Jun Xia
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei 230027, China
| | - Zhang-Chi Ling
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Comprehensive National Science Center, Department of Chemistry, Institute of Biomimetic Materials & Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - ZeZhou He
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei 230027, China
| | - Zi-Meng Han
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Comprehensive National Science Center, Department of Chemistry, Institute of Biomimetic Materials & Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Huai-Bin Yang
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Comprehensive National Science Center, Department of Chemistry, Institute of Biomimetic Materials & Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Ping Gu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei 230027, China
| | - YinBo Zhu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei 230027, China
| | - Shu-Hong Yu
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Comprehensive National Science Center, Department of Chemistry, Institute of Biomimetic Materials & Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - HengAn Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei 230027, China
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17
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Karna NK, Wohlert J, Lidén A, Mattsson T, Theliander H. Wettability of cellulose surfaces under the influence of an external electric field. J Colloid Interface Sci 2021; 589:347-355. [PMID: 33476890 DOI: 10.1016/j.jcis.2021.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/12/2020] [Accepted: 01/01/2021] [Indexed: 11/15/2022]
Abstract
HYPOTHESIS Interfacial tensions play an important role in dewatering of hydrophilic materials like nanofibrillated cellulose, and are affected by the molecular organization of water at the interface. Application of an electric field influences the orientation of water molecules along the field direction. Hence, it should be possible to alter the interfacial free energies to tune the wettability of cellulose surface through application of an external electric field thus, aiding the dewatering process. SIMULATIONS Molecular dynamics simulations of cellulose surface in contact with water under the influence of an external electric field have been conducted with GLYCAM-06 forcefield. The effect of variation in electric field intensity and directions on the spreading coefficient has been addressed via orientational preference of water molecules and interfacial free energy analyses. FINDINGS The application of electric field influences the interfacial free energy difference at the cellulose-water interface. The spreading coefficient increases with the electric field directed parallel to the cellulose-water interface while it decreases in the perpendicular electric field. Variation in interfacial free energies seems to explain the change in contact angle adequately in presence of an electric field. The wettability of cellulose surface can be tuned by the application of an external electric field.
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Affiliation(s)
- Nabin Kumar Karna
- Division of Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Göteborg, Sweden; Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044, Sweden.
| | - Jakob Wohlert
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044, Sweden; Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-10044, Sweden.
| | - Anna Lidén
- Division of Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Göteborg, Sweden.
| | - Tuve Mattsson
- Division of Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Göteborg, Sweden; Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044, Sweden.
| | - Hans Theliander
- Division of Forest Products and Chemical Engineering, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Göteborg, Sweden; Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044, Sweden.
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18
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Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000Res 2020; 9:Chem Inf Sci-1390. [PMID: 33604023 PMCID: PMC7863993 DOI: 10.12688/f1000research.27141.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.
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Affiliation(s)
- Victoria T. Lim
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | | | - David L. Mobley
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
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19
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Aguilera-Segura SM, Di Renzo F, Mineva T. Molecular Insight into the Cosolvent Effect on Lignin-Cellulose Adhesion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:14403-14416. [PMID: 33202139 DOI: 10.1021/acs.langmuir.0c02794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding and controlling the physical adsorption of lignin compounds on cellulose pulp are key parameters in the successful optimization of organosolv processes. The effect of binary organic-aqueous solvents on the coordination of lignin to cellulose was studied with molecular dynamics simulations, considering ethanol and acetonitrile to be organic cosolvents in aqueous solutions in comparison to their monocomponent counterparts. The structures of the solvation shells around cellulose and lignin and the energetics of lignin-cellulose adhesion indicate a more effective disruption of lignin-cellulose binding by binary solvents. The synergic effect between solvent components is explained by their preferential interactions with lignin-cellulose complexes. In the presence of pure water, long-lasting H-bonds in the lignin-cellulose complex are observed, promoted by the nonfavorable interactions of lignin with water. Ethanol and acetonitrile compete with water and lignin for cellulose oxygen binding sites, causing a nonlinear decrease in the lignin-cellulose interactions with the amount of the organic component. This effect is modulated by the water exclusion from the cellulose solvation shell by the organic solvent component. The amount and rate of water exclusion depend on the type of organic cosolvent and its concentration.
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Affiliation(s)
| | | | - Tzonka Mineva
- ICGM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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20
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Bregado JL, Tavares FW, Secchi AR, Segtovich ISV. Thermophysical Properties of Amorphous‐Paracrystalline Celluloses by Molecular Dynamics. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jurgen Lange Bregado
- Programa de Engenharia Química/COPPEUniversidade Federal do Rio de JaneiroCidade Universitária Rio de Janeiro CP 21941‐914 Brazil
| | - Frederico Wanderley Tavares
- Programa de Engenharia Química/COPPEUniversidade Federal do Rio de JaneiroCidade Universitária Rio de Janeiro CP 21941‐914 Brazil
- Escola de QuímicaDepartamento de Engenharia QuímicaUniversidade Federal do Rio de JaneiroCidade Universitária Rio de Janeiro CP 21941‐972 Brazil
| | - Argimiro Resende Secchi
- Programa de Engenharia Química/COPPEUniversidade Federal do Rio de JaneiroCidade Universitária Rio de Janeiro CP 21941‐914 Brazil
- Escola de QuímicaDepartamento de Engenharia QuímicaUniversidade Federal do Rio de JaneiroCidade Universitária Rio de Janeiro CP 21941‐972 Brazil
| | - Iuri Soter Viana Segtovich
- Programa de Engenharia Química/COPPEUniversidade Federal do Rio de JaneiroCidade Universitária Rio de Janeiro CP 21941‐914 Brazil
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21
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Wu Z, Beltran-Villegas DJ, Jayaraman A. Development of a New Coarse-Grained Model to Simulate Assembly of Cellulose Chains Due to Hydrogen Bonding. J Chem Theory Comput 2020; 16:4599-4614. [DOI: 10.1021/acs.jctc.0c00225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Daniel J. Beltran-Villegas
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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22
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Crawford B, Ismail AE. Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride-Water Mixture using Molecular Dynamics Simulations. Polymers (Basel) 2020; 12:polym12030627. [PMID: 32182932 PMCID: PMC7183325 DOI: 10.3390/polym12030627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/31/2022] Open
Abstract
All-atom molecular dynamics simulations are utilized to determine the properties and mechanisms of cellulose dissolution using the ionic liquid tetrabutylphosphonium chloride (TBPCl)–water mixture, from 63.1 to 100 mol % water. The hydrogen bonding between small and large cellulose bundles with 18 and 88 strands, respectively, is compared for all concentrations. The Cl, TBP, and water enable cellulose dissolution by working together to form a cooperative mechanism capable of separating the cellulose strands from the bundle. The chloride anions initiate the cellulose breakup, and water assists in delaying the cellulose strand reformation; the TBP cation then more permanently separates the cellulose strands from the bundle. The chloride anion provides a net negative pairwise energy, offsetting the net positive pairwise energy of the peeling cellulose strand. The TBP–peeling cellulose strand has a uniquely favorable and potentially net negative pairwise energy contribution in the TBPCl–water solution, which may partially explain why it is capable of dissolving cellulose at moderate temperatures and high water concentrations. The cellulose dissolution declines rapidly with increasing water concentration as hydrogen bond lifetimes of the chloride–cellulose hydroxyl hydrogens fall below the cellulose’s largest intra-strand hydrogen bonding lifetime.
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23
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DFT approach to the pathway of conformational changes of cellulose C6-hydroxymethyl group with simple cellotetraose model involving the mechanism of mercerization process. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Chen P, Terenzi C, Furó I, Berglund LA, Wohlert J. Quantifying Localized Macromolecular Dynamics within Hydrated Cellulose Fibril Aggregates. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00472] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Pan Chen
- Beijing Engineering Research Center of Cellulose and its Derivatives, School of Materials Science and Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Camilla Terenzi
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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25
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Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines. FORESTS 2019. [DOI: 10.3390/f10080628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This paper aims at providing a methodological framework for investigating wood polymers using atomistic modeling, namely, molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. Atomistic simulations are used to mimic water adsorption and desorption in amorphous polymers, make observations on swelling, mechanical softening, and on hysteresis. This hygromechanical behavior, as observed in particular from the breaking and reforming of hydrogen bonds, is related to the behavior of more complex polymeric composites. Wood is a hierarchical material, where the origin of wood-moisture relationships lies at the nanoporous material scale. As water molecules are adsorbed into the hydrophilic matrix in the cell walls, the induced fluid–solid interaction forces result in swelling of these cell walls. The interaction of the composite polymeric material, that is the layer S2 of the wood cell wall, with water is known to rearrange its internal material structure, which makes it moisture sensitive, influencing its physical properties. In-depth studies of the coupled effects of water sorption on hygric and mechanical properties of different polymeric components can be performed with atomistic modeling. The paper covers the main components of knowledge and good practice for such simulations.
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26
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Molecular insight into the wetting behavior and amphiphilic character of cellulose nanocrystals. Adv Colloid Interface Sci 2019; 267:15-25. [PMID: 30884357 DOI: 10.1016/j.cis.2019.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 02/05/2023]
Abstract
The study of nanocellulose is a field of growing interest due to its many applications and its use in the development of biocompatible and eco-friendly materials. In spite of the vast number of studies in the field, many questions about the role of the molecular structure in the properties of cellulose are still subject of debate. One of these fundamental questions is the possible amphiphilic nature of cellulose and the relative role of hydrogen bonding and hydrophobic effect on the interactions of cellulose. In this work we present an extensive molecular dynamics simulation study of this question by analyzing the wetting of cellulose with water and organic solvent, its interaction with hydrophilic and hydrophobic ions and its interaction with a protein (human epidermal growth factor, hEGF). We consider two characteristic cellulose crystal planes of Iβ cellulose with very different roughness, different hydrogen bonding capability and different exposure of cellulose hydrophobic groups (the (010) plane which has exposed -OH groups and the (100) plane with buried -OH groups). Our results show that both surfaces are simultaneously hydrophilic and lipophilic, with both surfaces having very similar contact angles. In spite of the global similarity of wetting of both surfaces, the molecular details of wetting are very different and substantial local wetting heterogeneities (which strongly depend on the surface) appear for both solvents. We also observe a weak interaction of both surfaces with hydrophobic and hydrophilic solutes. These weak interactions are attributed to the simultaneous lipophilic and hydrophilic character of both (100) and (010) cellulose surfaces. Interestingly, we found a substantial interaction of both cellulose planes with polar and apolar residues of the hEGF protein.
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27
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Morozova S, Schmidt PW, Bates FS, Lodge TP. Effect of Poly(ethylene glycol) Grafting Density on Methylcellulose Fibril Formation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01899] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Gurtovenko AA, Mukhamadiarov EI, Kostritskii AY, Karttunen M. Phospholipid–Cellulose Interactions: Insight from Atomistic Computer Simulations for Understanding the Impact of Cellulose-Based Materials on Plasma Membranes. J Phys Chem B 2018; 122:9973-9981. [DOI: 10.1021/acs.jpcb.8b07765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg, 199004 Russia
| | - Evgenii I. Mukhamadiarov
- Faculty of Physics, St. Petersburg State University, Ulyanovskaya str. 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Andrei Yu. Kostritskii
- Faculty of Physics, St. Petersburg State University, Ulyanovskaya str. 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg, 199004 Russia
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 3K7
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
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29
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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30
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Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study. Pharmaceutics 2018; 10:pharmaceutics10030101. [PMID: 30037083 PMCID: PMC6161151 DOI: 10.3390/pharmaceutics10030101] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/13/2018] [Accepted: 07/18/2018] [Indexed: 11/29/2022] Open
Abstract
Amorphous solid dispersions are considered a promising formulation strategy for the oral delivery of poorly soluble drugs. The limiting factor for the applicability of this approach is the physical (in)stability of the amorphous phase in solid samples. Minimizing the risk of reduced shelf life for a new drug by establishing a suitable excipient/polymer-type from first principles would be desirable to accelerate formulation development. Here, we perform Molecular Dynamics simulations to determine properties of blends of eight different polymer–small molecule drug combinations for which stability data are available from a consistent set of literature data. We calculate thermodynamic factors (mixing energies) as well as mobilities (diffusion rates and roto-vibrational fluctuations). We find that either of the two factors, mobility and energetics, can determine the relative stability of the amorphous form for a given drug. Which factor is rate limiting depends on physico-chemical properties of the drug and the excipients/polymers. The methods outlined here can be readily employed for an in silico pre-screening of different excipients for a given drug to establish a qualitative ranking of the expected relative stabilities, thereby accelerating and streamlining formulation development.
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31
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Gebhardt J, Kleist C, Jakobtorweihen S, Hansen N. Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution. J Phys Chem B 2018; 122:1608-1626. [PMID: 29287148 DOI: 10.1021/acs.jpcb.7b11808] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6GLYC instead of 53A6 and 56A6CARBO_R or 2016H66 instead of 56A6CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.
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Affiliation(s)
- Julia Gebhardt
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Catharina Kleist
- Institute of Thermal Separation Processes, Hamburg University of Technology , D-21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology , D-21073 Hamburg, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany
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32
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Kannam SK, Oehme DP, Doblin MS, Gidley MJ, Bacic A, Downton MT. Hydrogen bonds and twist in cellulose microfibrils. Carbohydr Polym 2017; 175:433-439. [PMID: 28917886 DOI: 10.1016/j.carbpol.2017.07.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 06/23/2017] [Accepted: 07/29/2017] [Indexed: 10/19/2022]
Abstract
There is increasing experimental and computational evidence that cellulose microfibrils can exist in a stable twisted form. In this study, atomistic molecular dynamics (MD) simulations are performed to investigate the importance of intrachain hydrogen bonds on the twist in cellulose microfibrils. We systematically enforce or block the formation of these intrachain hydrogen bonds by either constraining dihedral angles or manipulating charges. For the majority of simulations a consistent right handed twist is observed. The exceptions are two sets of simulations that block the O2-O6' intrachain hydrogen bond, where no consistent twist is observed in multiple independent simulations suggesting that the O2-O6' hydrogen bond can drive twist. However, in a further simulation where exocyclic group rotation is also blocked, right-handed twist still develops suggesting that intrachain hydrogen bonds are not necessary to drive twist in cellulose microfibrils.
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Affiliation(s)
- Sridhar Kumar Kannam
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Daniel P Oehme
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Monika S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael J Gidley
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Matthew T Downton
- IBM Research Australia, Level 5, 204 Lygon Street, 3053 Carlton, Victoria, Australia.
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33
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Kearns FL, Hudson PS, Woodcock HL, Boresch S. Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities. J Comput Chem 2017; 38:1376-1388. [PMID: 28272811 DOI: 10.1002/jcc.24706] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/29/2016] [Indexed: 01/09/2023]
Abstract
We demonstrate that Jarzynski's equation can be used to reliably compute free energy differences between low and high level representations of systems. The need for such a calculation arises when employing the so-called "indirect" approach to free energy simulations with mixed quantum mechanical/molecular mechanical (QM/MM) Hamiltonians; a popular technique for circumventing extensive simulations involving quantum chemical computations. We have applied this methodology to several small and medium sized organic molecules, both in the gas phase and explicit solvent. Test cases include several systems for which the standard approach; that is, free energy perturbation between low and high level description, fails to converge. Finally, we identify three major areas in which the difference between low and high level representations make the calculation of ΔAlow→high difficult: bond stretching and angle bending, different preferred conformations, and the response of the MM region to the charge distribution of the QM region. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Fiona L Kearns
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE205, Tampa, Florida, 33620-5250
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE205, Tampa, Florida, 33620-5250
| | - Henry L Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE205, Tampa, Florida, 33620-5250
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 17, Vienna, A-1090, Austria
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34
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Liu W, Jia X, Wang M, Li P, Wang X, Hu W, Zheng J, Mei Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv 2017. [DOI: 10.1039/c7ra06215j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, both a molecular mechanical (MM) method and a hybrid quantum mechanical/molecular mechanical (QM/MM) method have been applied in the study of the binding affinities of methyl-α-l-fucoside to Ralstonia solanacearum lectins.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Meiting Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Wenxin Hu
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Jun Zheng
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
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35
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Murillo JD, Biernacki JJ, Northrup S, Mohammad AS. BIOMASS PYROLYSIS KINETICS: A REVIEW OF MOLECULAR-SCALE MODELING CONTRIBUTIONS. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2017. [DOI: 10.1590/0104-6632.20170341s20160086] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- J. D. Murillo
- Tennessee Technological University, USA; Tennessee Technological University, USA
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36
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Lindh EL, Bergenstråhle-Wohlert M, Terenzi C, Salmén L, Furó I. Non-exchanging hydroxyl groups on the surface of cellulose fibrils: The role of interaction with water. Carbohydr Res 2016; 434:136-142. [DOI: 10.1016/j.carres.2016.09.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022]
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37
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Zhang Y, Inouye H, Crowley M, Yu L, Kaeli D, Makowski L. Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716013297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.
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38
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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39
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Feng T, Zhu X, Campanella O. Molecular modeling tools to characterize the structure and complexation behavior of carbohydrates. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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40
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Chin SL, Lu Q, Dane EL, Dominguez L, McKnight CJ, Straub JE, Grinstaff MW. Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides. J Am Chem Soc 2016; 138:6532-40. [DOI: 10.1021/jacs.6b01837] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Qing Lu
- Division
of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States
| | | | | | | | - John E. Straub
- Division
of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States
| | - Mark W. Grinstaff
- Division
of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States
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41
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Hadden JA, French AD, Woods RJ. Unraveling cellulose microfibrils: a twisted tale. Biopolymers 2016; 99:746-56. [PMID: 23681971 DOI: 10.1002/bip.22279] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 12/26/2022]
Abstract
Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface.
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Affiliation(s)
- Jodi A Hadden
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602
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42
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Lay WK, Miller MS, Elcock AH. Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements. J Chem Theory Comput 2016; 12:1401-7. [PMID: 26967542 DOI: 10.1021/acs.jctc.5b01136] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields.
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Affiliation(s)
- Wesley K Lay
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Mark S Miller
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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43
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Miyamoto H, Schnupf U, Crowley MF, Brady JW. Comparison of the simulations of cellulosic crystals with three carbohydrate force fields. Carbohydr Res 2016; 422:17-23. [DOI: 10.1016/j.carres.2016.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 01/12/2023]
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44
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Lukasheva NV, Tolmachev DA. Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:125-134. [PMID: 26652774 DOI: 10.1021/acs.langmuir.5b03953] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed. The structural characteristics of cellulose nanofibrils (in particular, of the surface layer) are found to be nearly independent of the solvation models used in the simulation and on the presence of ions in the solutions. It is shown that ionic clusters are formed in the solution rather than on the fibril surface. The cluster sizes are slightly different for the two water models. The effect of the ion-ion interaction parameters on the results is discussed. The main conclusion is that the activity of hydroxyl groups on the BC fibril surface is not high enough to cause adsorption of Ca(2+) ions from the solution. Therefore, the nucleation of CP crystals takes place initially in solution, and then the crystallites formed can be adsorbed on BC nanofibril surfaces.
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Affiliation(s)
- N V Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences , Bol'shoi pr. 31, St. Petersburg, 199004 Russia
| | - D A Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences , Bol'shoi pr. 31, St. Petersburg, 199004 Russia
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45
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Střelcová Z, Kulhánek P, Friák M, Fabritius HO, Petrov M, Neugebauer J, Koča J. The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations. RSC Adv 2016. [DOI: 10.1039/c6ra00107f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure–property relations reveal the typical size of chitin nanofibrils observed in natural systems.
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Affiliation(s)
- Zora Střelcová
- CEITEC – Central European Institute of Technology
- Masaryk University
- 625 00 Brno
- Czech Republic
- National Centre for Biomolecular Research
| | - Petr Kulhánek
- CEITEC – Central European Institute of Technology
- Masaryk University
- 625 00 Brno
- Czech Republic
- National Centre for Biomolecular Research
| | - Martin Friák
- CEITEC – Central European Institute of Technology
- Masaryk University
- 625 00 Brno
- Czech Republic
- Max-Planck-Institut für Eisenforschung GmbH
| | | | - Michal Petrov
- Max-Planck-Institut für Eisenforschung GmbH
- 40237 Düsseldorf
- Germany
| | - Jörg Neugebauer
- Max-Planck-Institut für Eisenforschung GmbH
- 40237 Düsseldorf
- Germany
| | - Jaroslav Koča
- CEITEC – Central European Institute of Technology
- Masaryk University
- 625 00 Brno
- Czech Republic
- National Centre for Biomolecular Research
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46
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Conley K, Godbout L, Whitehead M(T, van de Ven TG. Origin of the twist of cellulosic materials. Carbohydr Polym 2016; 135:285-99. [DOI: 10.1016/j.carbpol.2015.08.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 08/03/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
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47
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Batista MLS, Pérez-Sánchez G, Gomes JRB, Coutinho JAP, Maginn EJ. Evaluation of the GROMOS 56ACARBO Force Field for the Calculation of Structural, Volumetric, and Dynamic Properties of Aqueous Glucose Systems. J Phys Chem B 2015; 119:15310-9. [DOI: 10.1021/acs.jpcb.5b08155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marta L. S. Batista
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
- Department
of Chemical and Biomolecular Engineering, 182 Fitzpatrick Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Germán Pérez-Sánchez
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
| | - Edward J. Maginn
- Department
of Chemical and Biomolecular Engineering, 182 Fitzpatrick Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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48
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Meng C, Lu H, Cao GP, Yao CW, Liu Y, Zhang QM, Bai YB, Wang H. Activation of Cellulose by Supercritical Tetrafluoroethane and Its Application in Synthesis of Cellulose Acetate. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b03418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Chen Meng
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hui Lu
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Gui-Ping Cao
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chen-Wei Yao
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yue Liu
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qi-Ming Zhang
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yun-Bo Bai
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hua Wang
- UNILAB,
State Key Lab of
Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
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49
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Bu L, Himmel ME, Crowley MF. The molecular origins of twist in cellulose I-beta. Carbohydr Polym 2015; 125:146-52. [DOI: 10.1016/j.carbpol.2015.02.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/01/2015] [Accepted: 02/12/2015] [Indexed: 10/24/2022]
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50
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Lyubimova O, Stoyanov SR, Gusarov S, Kovalenko A. Electric Interfacial Layer of Modified Cellulose Nanocrystals in Aqueous Electrolyte Solution: Predictions by the Molecular Theory of Solvation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7106-7116. [PMID: 26053228 DOI: 10.1021/acs.langmuir.5b00680] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The X-ray crystal structure-based models of Iα cellulose nanocrystals (CNC), both pristine and containing surface sulfate groups with negative charge 0-0.34 e/nm(2) produced by sulfuric acid hydrolysis of softwood pulp, feature a highly polarized "crystal-like" charge distribution. We perform sampling using molecular dynamics (MD) of the structural relaxation of neutral pristine and negatively charged sulfated CNC of various lengths in explicit water solvent and then employ the statistical mechanical 3D-RISM-KH molecular theory of solvation to evaluate the solvation structure and thermodynamics of the relaxed CNC in ambient aqueous NaCl solution at a concentration of 0.0-0.25 mol/kg. The MD sampling induces a right-hand twist in CNC and rearranges its initially ordered structure with a macrodipole of high-density charges at the opposite faces into small local spots of alternating charge at each face. This surface charge rearrangement observed for both neutral and charged CNC significantly affects the distribution of ions around CNC in aqueous electrolyte solution. The solvation free energy (SFE) of charged sulfated CNC has a minimum at a particular electrolyte concentration depending on the surface charge density, whereas the SFE of neutral CNC increases linearly with NaCl concentration. The SFE contribution from Na(+) counterions exhibits behavior similar to the NaCl concentration dependence of the whole SFE. An analysis of the 3D maps of Na(+) density distributions shows that these model CNC particles exhibit the behavior of charged nanocolloids in aqueous electrolyte solution: an increase in electrolyte concentration shrinks the electric interfacial layer and weakens the effective repulsion between charged CNC particles. The 3D-RISM-KH method readily treats solvent and electrolyte of a given nature and concentration to predict effective interactions between CNC particles in electrolyte solution. We provide CNC structural models and a modeling procedure for studies of effective interactions and the formation of ordered phases of CNC suspensions in electrolyte solution.
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Affiliation(s)
- Olga Lyubimova
- †National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- ‡Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
| | - Stanislav R Stoyanov
- †National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- ‡Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
- §Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Sergey Gusarov
- †National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Andriy Kovalenko
- †National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- ‡Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
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