| 1. |
- Angles d'Ortoli, Thibault, et al.
(författare)
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Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:30, s. 9559-9570
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Tidskriftsartikel (refereegranskat)abstract
- Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.
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| 2. |
- Bergenstråhle-Wohlert, Malin, et al.
(författare)
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Concentration enrichment of urea at cellulose surfaces : results from molecular dynamics simulations and NMR spectroscopy
- 2012
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 19:1, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- A combined solid-state NMR and Molecular Dynamics simulation study of cellulose in urea aqueous solution and in pure water was conducted. It was found that the local concentration of urea is significantly enhanced at the cellulose/solution interface. There, urea molecules interact directly with the cellulose through both hydrogen bonds and favorable dispersion interactions, which seem to be the driving force behind the aggregation. The CP/MAS (13)C spectra was affected by the presence of urea at high concentrations, most notably the signal at 83.4 ppm, which has previously been assigned to C4 atoms in cellulose chains located at surfaces parallel to the (110) crystallographic plane of the cellulose I beta crystal. Also dynamic properties of the cellulose surfaces, probed by spin-lattice relaxation time (13)CT (1) measurements of C4 atoms, are affected by the addition of urea. Molecular Dynamics simulations reproduce the trends of the T (1) measurements and lends new support to the assignment of signals from individual surfaces. That urea in solution is interacting directly with cellulose may have implications on our understanding of the mechanisms behind cellulose dissolution in alkali/urea aqueous solutions.
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| 3. |
- Berglund, Jennie, et al.
(författare)
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A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility
- 2016
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Ingår i: The Plant Journal. - : John Wiley & Sons Ltd.. - 0960-7412 .- 1365-313X. ; 88:1, s. 56-70
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Tidskriftsartikel (refereegranskat)abstract
- The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by NMR spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated and free energy maps of the φ - ψ space and hydrogen bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of hemicelluloses’ function both in the cell wall and in technical products.
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| 4. |
- Tolonen, Lasse K., et al.
(författare)
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Solubility of Cellulose in Supercritical Water Studied by Molecular Dynamics Simulations
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:13, s. 4739-4748
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Tidskriftsartikel (refereegranskat)abstract
- The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm(-3)) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 x 4 x 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water-water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water.
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| 5. |
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| 6. |
- Wang, Yan, 1987-, et al.
(författare)
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Hydration and dimensional stability of the intercalated galleries in xyloglucan/montmorillonite nanocomposites studied by molecular dynamics simulations
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The outstanding properties of biological composite nacre materials have for a long time inspired research and development of man-made bionanocomposites. One of the most recent nacre-mimetic bionanocomposites comprising xygloglucan (XG) and montmorillonite (Mnt) clay has been investigated by related model systems through Molecular dynamics (MD) simulations. The expansion of the inter-gallery of the XG-Mnt composites when exposed to water, has been found to be a key issue for the material property. In order to shed light on the mechanism for this swelling behavior we have investigated the relation between the hydration and the dimensional stability of the inter-gallery in XG-Mnt composites, exploring also the role of the dynamic state of the polymer XG for the dimensional change. We find that at a hydration level below 50%, XG-Mnt possesses good dimensional stability, suggesting a constant performance of the material, while at a hydration level of 75%, the expansion ratio of the composite is found to be slightly smaller than the swelling of Mnt clay. At the four-layer hydrate formation with a hydration level of 100%, the swelling ratios of clay and the2composite reach the same value, suggesting a critical point of losing dimensional stability. We conclude that the strong adhesion between the polymer XG and the Mnt clay is the main driving force for the preservation of the stability at lower hydration conditions, while the dynamics of the XG polymer is related to the losing of dimensional stability for the composite at higher hydration levels. The ramification of these results in terms of moisture sensitivity of the material is briefly discussed.
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| 7. |
- Wang, Yan, et al.
(författare)
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Molecular Adhesion at Clay Nanocomposite Interfaces Depends on Counterion Hydration-Molecular Dynamics Simulation of Montmorillonite/Xyloglucan
- 2015
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Ingår i: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 16:1, s. 257-265
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Tidskriftsartikel (refereegranskat)abstract
- Nacre-mimetic clay/polymer nanocomposites with clay platelet orientation parallel to the film surface show interesting gas barrier and mechanical properties. In moist conditions, interfacial adhesion is lowered and mechanical properties are reduced. Molecular dynamic simulations (MD) have been performed to investigate the effects of counterions on molecular adhesion at montmorillonite clay (Mnt)-xyloglucan (XG) interfaces. We focus on the role of monovalent cations K+, Na+, and Li+ and the divalent cation Ca2+ for mediating and stabilizing the Mnt/XG complex formation. The conformation of adsorbed XG is strongly influenced by the choice of counterion and so is the simulated work of adhesion. Free energy profiles that are used to estimate molecular adhesion show stronger interaction between XG and clay in the monovalent cation system than in divalent cation system, following a decreasing order of K-Mnt, Na-Mnt, Li-Mnt, and Ca-Mnt. The Mnt clay hydrates differently in the presence of different counterions, leading to a chemical potential of water that is highest in the case of K-Mnt, followed by Na-Mnt and Li-Mnt, and lowest in the case of Ca-Mnt. This means that water is most easily displaced from the interface in the case of K-Mnt, which contributes to the relatively high work of adhesion. In all systems, the penalty of replacing polymer with water at the interface gives a positive contribution to the work of adhesion of between 19 and 35%. Our work confirms the important role of counterions in mediating the adsorption of biopolymer XG to Mnt clays and predicts potassium or sodium as the best choice of counterions for a Mnt-based biocomposite design.
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| 8. |
- Wang, Yan, 1987-, et al.
(författare)
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Molecular mechanisms for the adhesion of chitin and chitosan to montmorillonite clay
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Molecular dynamics simulations have been performed to investigate molecular adhesion of chitin and chitosan oligomers to montmorillonite (Mnt) clay at different degrees of acetylation (DA, 0%, 20%, 40%, 60%, 80% and 100%) and different degree of protonation (DPr, 0%, 50%, 100% mimicking pH > 6.5, pH = 6.5, pH < 4, respectively) under fully hydrated conditions. Although the Mnt surface is negatively charged and a variation in DA also implies going from a positively charged oligomer at DA = 0% to a neutral oligomer at DA = 100%, the simulations show unexpectedly variation of the total molecular adhesion as a function of DA. From our analysis we propose that this quantitatively similar adhesion arise from two different mechanisms. At low DA, the oligomer is rich in positively charged amino groups interacting strongly with the negatively charged surface by direct electrostatic interaction. On the other hand, at high DA, electrically neutral acetyl groups are strongly correlated with the Na+ counter ions, which are in all cases stuck at the surface and the counter ions seem to act as ‘glue’ between the acetyl groups and the Mnt. However, when protonation was decreased, adhesion was significantly lowered. The reason is conclued by differences in charge distributions of the respective functional groups. A further investigation on the intramolecular hydrogen bonds formed in CHT or CHS shows that the adsorbed conformation of the polymer is also highly affected by DA. This work provides fundamental insights into adhesion mechanisms and is, of potential importance for the development of polymer-clay based composite materials.
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| 9. |
- Wang, Yan, et al.
(författare)
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Molecular mechanisms for the adhesion of chitin and chitosan to montmorillonite clay
- 2015
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Ingår i: RSC Advances. - : RSC Publishing. - 2046-2069. ; 5:67, s. 54580-54588
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations have been performed to investigate molecular adhesion of chitin and chitosan oligomers to montmorillonite (Mnt) clay at different degrees of acetylation (DA, 0%, 20%, 40%, 60%, 80% and 100%) and different degree of protonation (DPr, 0%, 50%, 100% mimicking pH > 6.5, pH = 6.5, pH < 4, respectively) under fully hydrated conditions. Although the Mnt surface is negatively charged and a variation in DA also implies going from a positively charged oligomer at DA = 0% to a neutral oligomer at DA = 100%, the simulations show unexpectedly small variation of the total molecular adhesion as a function of DA. From our analysis we propose that this quantitatively similar adhesion arises from two different mechanisms. At low DA, the oligomer is rich in positively charged amino groups interacting strongly with the negatively charged surface by direct electrostatic interaction. On the other hand, at high DA, electrically neutral acetyl groups are strongly correlated with the Na+ counter ions, which are in all cases stuck at the surface and the counter ions seem to act as 'glue' between the acetyl groups and the Mnt. However, when protonation was decreased, adhesion was affected and significantly lowered at neutral conditions (DPr = 0%). The reason is concluded to be differences in charge distributions of the respective functional groups. A further investigation on the intramolecular hydrogen bonds formed in CHT or CHS shows that the adsorbed conformation of the polymer is also highly affected by DA. This work provides fundamental insights into adhesion mechanisms and is of potential importance for the development of polymer-clay based composite materials.
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| 10. |
- Wang, Yan, et al.
(författare)
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Swelling and dimensional stability of xyloglucan/montmorillonite nanocomposites in moist conditions from molecular dynamics simulations
- 2017
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Ingår i: Computational Materials Science. - : Elsevier. - 0927-0256. ; 128, s. 191-197
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Tidskriftsartikel (refereegranskat)abstract
- Nacre-mimetic biocomposites made from the combination of montmorillonite clay and the hemicellulose xyloglucan give materials that retain much of their material properties even at high relative humidity. Here, a model composite system consisting of two clay platelets intercalated by xyloglucan oligomers was studied at different levels of hydration using molecular dynamics simulations, and compared to the pure clay. It was found that xyloglucan inhibits swelling of the clay at low water contents by promoting the formation of nano-sized voids that fill with water without affecting the material's dimensions. At higher water contents the XG itself swells, but at the same time maintaining contact with both platelets across the gallery, thereby acting as a physical cross-linker in a manner similar to the role of XG in the plant cell wall.
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| 11. |
- Wohlert, Jakob, et al.
(författare)
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A simple model for cellulose solubility in supercritical water
- 2015
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Ingår i: Nordic Pulp & Paper Research Journal. - : Walter de Gruyter GmbH. - 0283-2631 .- 2000-0669. ; 30:1, s. 14-19
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Tidskriftsartikel (refereegranskat)abstract
- A simple model for the hydration of a polar molecule is developed in order to provide a description of cellulose solubility in water under ambient and supercritical conditions. The change in free energy upon hydration is regarded as the sum of the energy cost of forming a cavity and a polar contribution. The model is able to predict the existence of an optimal density for dissolution of polar solutes in supercritical water. Those results are in line with earlier experiments and simulations showing that water at high temperature and pressure dissolves cellulose, and that an optimal density for dissolution exists. The present study shows that the density dependence comes from the fact that both the cavity formation energy and the polar energy are highly density dependent but with opposing behaviour. The cavity formation energy increases with density, whereas the polar energy decreases. Based on the present model, it is possible to rationalize a few basic strategies regarding cellulose dissolution in aqueous media. To increase solubility, one can either increase the polar/electrostatic contribution, or more importantly, one can decrease the cost of cavity formation, e.g. by introducing co-solvents, changing temperature and/or pressure.
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| 12. |
- Wohlert, Jakob, et al.
(författare)
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Deformation of cellulose nanocrystals : entropy, internal energy and temperature dependence
- 2012
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 19:6, s. 1821-1836
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Tidskriftsartikel (refereegranskat)abstract
- An in-depth analysis was performed of the molecular deformation mechanisms in cellulose during axial stretching. For the first time, it was demonstrated that entropy affects the stiffness of cellulose nanocrystals significantly. This was achieved through Molecular Dynamics simulations of model nanocrystals subject to constant stress in the axial direction, for nanocrystals of varying lateral dimensions and at different temperatures. The simulations were analyzed in terms of Young's modulus E, which is a measure of the elastic response to applied stress. A weak but significant temperature dependence was shown, with partial derivative E/partial derivative T = -0.05 Gpa K-1 at room temperature, in agreement with experimental numbers. In order to analyze the respective contributions from internal energy and entropy, a decomposition of the total response of the free energy with respect to strain was made. It was shown that the decrease in E with increasing T is due to entropy, and that the magnitude of the decrease is 6-9 % at room temperature compared to the value at 0 K. This was also shown independently by a direct calculation of the vibrational entropy of the cellulose crystal. Finally, it was found that internal hydrogen bonds are contributing to the stiffness by 20 %, mainly by stabilizing the cellulose internal structure.
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| 13. |
- Beckham, Gregg T., et al.
(författare)
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The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 99:11, s. 3773-3781
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Tidskriftsartikel (refereegranskat)abstract
- Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose Cellulose degrading enzymes (cellulases) are often modular with catalytic domains for cellulose hydrolysis and carbohydrate binding modules connected by linkers rich in serine and threonine with O-glycosylation Few studies have probed the role that the linker and O-glycans play in catalysis Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity the structure function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms Here the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation Contrary to the predominant view the O-glycosylation does not change the stiffness of the linker as measured by the relative fluctuations in the end to end distance rather it provides a 16 A extension thus expanding the operating range of Cel7A We explain observations from previous biochemical experiments in the light of results obtained here and compare the Cel7A linker with linkers from other cellulases with sequence based tools to predict disorder This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T reesei may not be as disordered warranting further study
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| 14. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Dynamics of Cellulose-Water Interfaces : NMR Spin-Lattice Relaxation Times Calculated from Atomistic Computer Simulations
- 2008
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Ingår i: Journal of Physical Chemistry B. - Washington : ACS Publications. - 1520-6106 .- 1520-5207. ; 112:9, s. 2590-2595
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Tidskriftsartikel (refereegranskat)abstract
- Solid-state nuclear magnetic resonance (CP/MAS 13C NMR) spectroscopy has often been used to study cellulose structure, but some features of the cellulose NMR spectrum are not yet fully understood. One such feature is a doublet around 84 ppm, a signal that has been proposed to originate from C4 atoms at cellulose fibril surfaces. The two peaks yield different T1, differing by approximately a factor of 2 at 75 MHz. In this study, we calculate T1 from C4-H4 vector dynamics obtained from molecular dynamics computer simulations of cellulose Iβ-water interfacial systems. Calculated and experimentally obtained T1 values for C4 atoms in surface chains fell within the same order of magnitude, 3-20 s. This means that the applied force field reproduces relevant surface dynamics for the cellulose-water interface sufficiently well. Furthermore, a difference in T1 of about a factor of 2 in the range of Larmor frequencies 25-150 MHz was found for C4 atoms in chains located on top of two different crystallographic planes, namely, (110) and (10). A previously proposed explanation that the C4 peak doublet could derive from surfaces parallel to different crystallographic planes is herewith strengthened by computationally obtained evidence. Another suggested basis for this difference is that the doublet originates from C4 atoms located in surface anhydro-glucose units with hydroxymethyl groups pointing either inward or outward. This was also tested within this study but was found to yield no difference in calculated T1.
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| 15. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Simulation studies of the insolubility of cellulose
- 2010
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Ingår i: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 345:14, s. 2060-2066
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations have been used to calculate the potentials of mean force for separating short cellooligomers in aqueous solution as a means of estimating the contributions of hydrophobic stacking and hydrogen bonding to the insolubility of crystalline cellulose. A series of four potential of mean force (pmf) calculations for glucose, cellobiose, cellotriose, and cellotetraose in aqueous solution were performed for situations in which the molecules were initially placed with their hydrophobic faces stacked against one another, and another for the cases where the molecules were initially placed adjacent to one another in a co-planar, hydrogen-bonded arrangement, as they would be in cellulose ID. From these calculations, it was found that hydrophobic association does indeed favor a crystal-like structure over solution, as might be expected. Somewhat more surprisingly, hydrogen bonding also favored the crystal packing, possibly in part because of the high entropic cost for hydrating glucose hydroxyl groups, which significantly restricts the configurational freedom of the hydrogen-bonded waters. The crystal was also favored by the observation that there was no increase in chain configurational entropy upon dissolution, because the free chain adopts only one conformation, as previously observed, but against intuitive expectations, apparently due to the persistence of the intramolecular O3-O5 hydrogen bond.
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| 16. |
- Chen, Pan, et al.
(författare)
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Alternative hydrogen bond models of cellulose II and IIII based on molecular force-fields and density functional theory
- 2015
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 22:3, s. 1485-1493
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Tidskriftsartikel (refereegranskat)abstract
- Alternative hydrogen-bond structures were found for cellulose II and IIII based on molecular dynamics simulations using four force fields and energy optimization based on density functional theory. All the modeling results were in support to the new hydrogen-bonding network. The revised structures of cellulose II and IIII differ with the fiber diffraction models mainly in the orientation of two hydroxyl groups, namely, OH2 and OH6 forming hydrogen-bond chains perpendicular to the cellulose molecule. In the alternative structures, the sense of hydrogen bond is inversed but little difference can be seen in hydrogen bond geometries. The preference of these alternative hydrogen bond structures comes from the local stabilization of hydroxyl groups with respect to the beta carbon. On the other hand when simulated fiber diffraction patterns were compared with experimental ones, the current structure of cellulose II with higher energy and the alternative structure of cellulose IIII with lower energy were in better agreement.
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| 17. |
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| 18. |
- Joby Kochumalayil, Jose, et al.
(författare)
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Bioinspired and highly oriented clay nanocomposites with a xyloglucan biopolymer matrix : Extending the range of mechanical and barrier properties
- 2013
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Ingår i: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 14:1, s. 84-91
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Tidskriftsartikel (refereegranskat)abstract
- The development of clay bionanocomposites requires processing routes with nanostructural control. Moreover, moisture durability is a concern with water-soluble biopolymers. Here, oriented bionanocomposite coatings with strong in-plane orientation of clay platelets are for the first time prepared by continuous water-based processing. Montmorillonite (MTM) and a "new" unmodified biological polymer (xyloglucan (XG)) are combined. The resulting nanocomposites are characterized by FE-SEM, TEM, and XRD. XG adsorption on MTM is measured by quartz crystal microbalance analysis. Mechanical and gas barrier properties are measured, also at high relative humidity. The reinforcement effects are modeled. XG dimensions in composites are estimated using atomistic simulations. The nanostructure shows highly oriented and intercalated clay platelets. The reinforcement efficiency and effects on barrier properties are remarkable and are likely to be due to highly oriented and well-dispersed MTM and strong XG-MTM interactions. Properties are well preserved in humid conditions and the reasons for this are discussed.
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| 19. |
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| 20. |
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| 21. |
- Lindh, Erik L., et al.
(författare)
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Non-exchanging hydroxyl groups on the surface of cellulose fibrils : The role of interaction with water
- 2016
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Ingår i: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 434, s. 136-142
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Tidskriftsartikel (refereegranskat)abstract
- The interaction of water with cellulose stages many unresolved questions. Here 2H MAS NMR and IR spectra recorded under carefully selected conditions in 1H-2H exchanged, and re-exchanged, cellulose samples are presented. It is shown here, by a quantitative and robust approach, that only two of the three available hydroxyl groups on the surface of cellulose fibrils are exchanging their hydrogen with the surrounding water molecules. This finding is additionally verified and explained by MD simulations which demonstrate that the 1HO(2) and 1HO(6) hydroxyl groups of the constituting glucose units act as hydrogen-bond donors to water, while the 1HO(3) groups behave exclusively as hydrogen-bond acceptors from water and donate hydrogen to their intra-chain neighbors O(5). We conclude that such a behavior makes the latter hydroxyl group unreactive to hydrogen exchange with water.
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| 22. |
- Matthews, James F., et al.
(författare)
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Comparison of Cellulose I beta Simulations with Three Carbohydrate Force Fields
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:2, s. 735-748
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose I beta microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose 1 beta crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.
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