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Yong WCM, Devi A, Lin TF, Chappell HF. First principles modelling of the ion binding capacity of finger millet. NPJ Sci Food 2024; 8:28. [PMID: 38744951 PMCID: PMC11094100 DOI: 10.1038/s41538-024-00270-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Finger millet, a cereal grain widely consumed in India and Africa, has gained more attention in recent years due to its high dietary fibre (arabinoxylan) and trace mineral content, and its climate resilience. The aim of this study was to understand the interactions between potassium (K+), calcium (Ca2+) and zinc (Zn2+) ions and the arabinoxylan structure and determine its ion-binding capacity. Three variations of a proposed model of the arabinoxylan structure were constructed and first principles Density Functional Theory calculations were carried out to determine the cation-binding capacity of the arabinoxylan complexes. Zn2+-arabinoxylan complexes were highly unstable and thermodynamically unfavourable in all three models. Ca2+ and K+ ions, however, form thermodynamically stable complexes, particularly involving two glucuronic acid residues as a binding pocket. Glucuronic acid residues are found to play a key role in stabilising the cation-arabinoxylan complex, and steric effects are more important to the stability than charge density. Our results highlight the most important structural features of the millet fibre regarding ion-storage capacity, and provide valuable preliminary data for confirmatory experimental studies and for the planning of clinical trials where the bioavailability of bound ions following digestion may be tested.
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Affiliation(s)
| | - Apramita Devi
- Department of Viticulture and Enology, University of California, Davis, CA, USA
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Tsair-Fuh Lin
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Helen F Chappell
- School of Food Science and Nutrition, University of Leeds, Leeds, UK.
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2
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Dash S, Gutti P, Behera B, Mishra D. Anionic species from multivalent metal salts are differentially retained during aqueous ionic gelation of sodium alginate and could fine-tune the hydrogel properties. Int J Biol Macromol 2024; 265:130767. [PMID: 38471601 DOI: 10.1016/j.ijbiomac.2024.130767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/20/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
The role of anionic counterions of divalent metal salts in alginate gelation and hydrogel properties has been thoroughly investigated. Three anions were selected from the Hofmeister series, namely sulphate, acetate and chloride, paired in all permutations and combinations with divalent metal cations like calcium, zinc and copper. Spectroscopic analysis revealed the presence of anions and their interaction with the respective metal cations in the hydrogel. The data showed that the gelation time and other hydrogel properties were largely controlled by cations. However, subtle yet significant variations in viscoelasticity, water uptake, drug release and cytocompatibility properties were anion dependent in each cationic group. Computational modelling based study showed that metal-anion-alginate configurations were energetically more stable than the metal-alginate models. The in vitro and in silico studies concluded that acetate anions preceded chlorides in the drug release, swelling and cytocompatibility fronts, followed by sulphate anions in each cationic group. Overall, the data confirmed that anions are an integral part of the metal-alginate complex. Furthermore, anions offer a novel option to further fine-tune the properties of alginate hydrogels for myriads of applications. In addition, full exploration of this novel avenue would enhance the usability of alginate polymers in the pharmaceutical, environmental, biomedical and food industries.
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Affiliation(s)
- Subhasis Dash
- Bioinspired Design Lab, School of BioSciences and Technology (SBST), Vellore Institute of Technology (VIT) Vellore, Tamil Nadu, India
| | - Pavan Gutti
- Bioinspired Design Lab, School of BioSciences and Technology (SBST), Vellore Institute of Technology (VIT) Vellore, Tamil Nadu, India
| | - Birendra Behera
- Department of Biotechnology and Bioinformatics, Sambalpur University, Burla, Odisha, India
| | - Debasish Mishra
- Bioinspired Design Lab, School of BioSciences and Technology (SBST), Vellore Institute of Technology (VIT) Vellore, Tamil Nadu, India.
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3
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Zouaoui-Rabah M, Bekri L, Hedidi M, Elhorri AM, Madaoui Y. Characteristics of new pyrrolic derivatives and their oligomers using DFT and TD-DFT calculations. J Mol Model 2023; 29:364. [PMID: 37945908 DOI: 10.1007/s00894-023-05763-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT This article is based on the study of pyrrolic derivatives and their oligomers. Knowing that, pyrrolic derivatives are widely studied on an industrial scale. The aim of this work is to find pyrrolic derivatives having the same physicochemical characteristics such as the pyrrolic edifice. Six derivatives were studied by substituting the hydrogens in the β position of the pyrroles with the following radicals: -CHO, -Cl, -CN, -NO, and -OH. The study was carried out theoretically using ab initio and density functional of theory (DFT) methods. In the first step, molecules of four units were taken into consideration in order to make the comparison between them. This comparison showed that the majority of molecules exhibited high intramolecular charge transfer (ICT) compared to the molecule composed of four pyrrolic units (OP4), and also exhibited strong nucleophilic and electrophilic characteristics. Natural bond orbital (NBO) analysis has shown continuous ICT mechanisms for certain molecules. The studied derivatives showed good solvation in several solvents compared to OP4. The molecules substituted by the radicals -CHO, -CN, -OH, and -NO generated several peaks in the excited states, which is the opposite case for the other molecules with a single peak. The effects of chain elongation revealed exponential equations generated by the two parameters energy gaps (ΔEH-L) and maximum wavelengths (λmax) as a function of the number of units (n). These equations were used to predict the maximum and minimum values of the above parameters for more elongated oligomers. METHOD The software used to make the calculations is Gaussian 16. All geometries were calculated by B3LYP functional and 6-31++G(d,p) basis set. The electronic parameters ΔEH-L were calculated by the following functionals: B3LYP, CAM-B3LYP, LC-wPBE, LC-BLYP, wB97X, M062X, M06HF, and M11 in addition to the second-order Møller-Plesset method (MP2) while always keeping the basis set mentioned before. An effect of basis set variation was studied by the optimal functional in combination with the following basis sets: 6-31G(d,p), 6-31++G(d,p), cc-pVDZ, AUG-cc-pVDZ, 6-311G(d,p), 6-311++G(d,p), cc-pVTZ, and AUG-cc-pVTZ. The NBO study was carried out with the M06HF/6-31++G(d,p) functional using the NBO method. The solvation parameters were calculated by M06HF/6-31++G(d,p) in the presence of the implicit solvation model Solvation Model based on Density (SMD). The excited states were calculated by M06HF/6-31++G(d,p) by the implicit solvation model Conductor Polarizable Continuum Model (CPCM).
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Affiliation(s)
- Mourad Zouaoui-Rabah
- Department of Preparatory Education in Science and Technology, National Polytechnic School of Oran Maurice Audin, P.O. Box 1523, Oran, El M'naouer, Algeria
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
| | - Lahcène Bekri
- Departement of Chemistry, Faculty of Exact Sciences, Mustapha Stambouli, University of Mascara, Av. Cheikh El Khaldi, 29000, Mascara, Algeria
| | - Madani Hedidi
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
| | - Abdelkader M Elhorri
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria.
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria.
| | - Yemouna Madaoui
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
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4
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Fonseca RG, Kuster A, Fernandes PP, Tavakoli M, Pereira P, Fernandes JR, De Bon F, Serra AC, Fonseca AC, Coelho JFJ. Facile Synthesis of Highly Stretchable, Tough, and Photodegradable Hydrogels. Adv Healthc Mater 2023; 12:e2300918. [PMID: 37133868 DOI: 10.1002/adhm.202300918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 05/04/2023]
Abstract
Recently, highly stretchable and tough hydrogels that are photodegradable on-demand have been reported. Unfortunately, the preparation procedure is complex due to the hydrophobic nature of the photocrosslinkers. Herein, a simple method is reported to prepare photodegradable double-network (DN) hydrogels that exhibit high stretchability, toughness, and biocompatibility. Hydrophilic ortho-nitrobenzyl (ONB) crosslinkers incorporating different poly(ethylene glycol) (PEG) backbones (600, 1000, and 2000 g mol-1 ) are synthesized. These photodegradable DN hydrogels are prepared by the irreversible crosslinking of chains by using such ONB crosslinkers, and the reversible ionic crosslinking between sodium alginate and divalent cations (Ca2+ ). Remarkable mechanical properties are obtained by combining ionic and covalent crosslinking and their synergistic effect, and by reducing the length of the PEG backbone. The rapid on-demand degradation of these hydrogels is also demonstrated by using cytocompatible light wavelength (λ = 365 nm) that degrades the photosensitive ONB units. The authors have successfully used these hydrogels as skin-worn sensors for monitoring human respiration and physical activities. A combination of excellent mechanical properties, facile fabrication, and on-demand degradation holds promise for their application as the next generation of substrates or active sensors eco-friendly for bioelectronics, biosensors, wearable computing, and stretchable electronics.
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Affiliation(s)
- Rita G Fonseca
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
| | - Aline Kuster
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
| | - Pedro P Fernandes
- Soft and Printed Microelectronics Lab, Department of Electrical Engineering, University of Coimbra, Coimbra, 3030-194, Portugal
| | - Mahmoud Tavakoli
- Soft and Printed Microelectronics Lab, Department of Electrical Engineering, University of Coimbra, Coimbra, 3030-194, Portugal
| | - Patrícia Pereira
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
- IPN - Instituto Pedro Nunes, Associação para a Inovação e Desenvolvimento em Ciência e Tecnologia, Rua Pedro Nunes, Coimbra, 3030-199, Portugal
| | - José R Fernandes
- Chemical Centre - Vila Real (CQVR), Physics Department, School of Science and Technology, University of Trás-os-Montes e Alto Douro, Vila Real, 5000-801, Portugal
| | - Francesco De Bon
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
| | - Arménio C Serra
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
| | - Ana C Fonseca
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
| | - Jorge F J Coelho
- CEMMPRE - Department of Chemical Engineering, University of Coimbra, Coimbra, 3030-790, Portugal
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Beheshtizadeh N, Farzin A, Rezvantalab S, Pazhouhnia Z, Lotfibakhshaiesh N, Ai J, Noori A, Azami M. 3D printing of complicated GelMA-coated Alginate/Tri-calcium silicate scaffold for accelerated bone regeneration. Int J Biol Macromol 2023; 229:636-653. [PMID: 36586652 DOI: 10.1016/j.ijbiomac.2022.12.267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Polymer-based composite scaffolds are an attractive class of biomaterials due to their suitable physical and mechanical performance as well as appropriate biological properties. When such composites contain osteoinductive ceramic nanopowders, it is possible, in principle, to stimulate the seeded cells to differentiate into osteoblasts. However, reproducibly fabricating and developing an appropriate niche for cells' activities in three-dimensional (3D) scaffolds remains a challenge using conventional fabrication techniques. Additive manufacturing provides a new strategy for the fabrication of complex 3D structures. Here, an extrusion-based 3D printing method was used to fabricate the Alginate (Alg)/Tri-calcium silicate (C3S) bone scaffolds. To improve physical and biological attributes, scaffolds were coated with gelatin methacryloyl (GelMA), a biocompatible viscose hydrogel. Conducting a combination of experimental techniques and molecular dynamics simulations, it is found that the composition ratio of Alg/C3S governs intermolecular interactions among the polymer and ceramic, affecting the product performance. Investigating the effects of various C3S amounts in the bioinks, the 90/10 composition ratio of Alg/C3S is known as the optimum content in developed bioinks. Accordingly, the printability of high-viscosity inks is boosted by improved hierarchical interactions among assemblies, which in turn leads to better nanoscale alignment in extruded macroscopic filaments. Conducting multiple tests on specimens, the GelMA-coated Alg/C3S scaffolds (with a composition ratio of 90/10) were shown to have improved mechanical qualities and cell adhesion, spreading, proliferation, and osteogenic differentiation, compared to the bare scaffolds, making them better candidates for further future research. Overall, the in-silico and in vitro studies of GelMA-coated 3D-printed Alg/C3S scaffolds open new aspects for biomaterials aimed at the regeneration of large- and complicated-bone defects through modifying the extrusion-based 3D-printed constructs.
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Affiliation(s)
- Nima Beheshtizadeh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ali Farzin
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sima Rezvantalab
- Renewable Energies Department, Faculty of Chemical Engineering, Urmia University of Technology, 57166-419 Urmia, Iran
| | - Zahra Pazhouhnia
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nasrin Lotfibakhshaiesh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Jafar Ai
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Noori
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mahmoud Azami
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Joint Reconstruction Research Center (JRRC), Tehran University of Medical Sciences, Tehran, Iran.
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6
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The effect of alkali metals, carbocations, and metallocenes substitutes on two ν-carrabiose disaccharide derivatives: a density functional study. Struct Chem 2022. [DOI: 10.1007/s11224-022-02114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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7
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Anugrah DSB, Darmalim LV, Polanen MRI, Putro PA, Sasongko NA, Siahaan P, Ramadhan ZR. Quantum Chemical Calculation for Intermolecular Interactions of Alginate Dimer-Water Molecules. Gels 2022; 8:703. [PMID: 36354611 PMCID: PMC9689446 DOI: 10.3390/gels8110703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 07/22/2023] Open
Abstract
The abundance of applications of alginates in aqueous surroundings created by their interactions with water is a fascinating area of research. In this paper, computational analysis was used to evaluate the conformation, hydrogen bond network, and stabilities for putative intermolecular interactions between alginate dimers and water molecules. Two structural forms of alginate (alginic acid, alg, and sodium alginate, SA) were evaluated for their interactions with water molecules. The density functional theory (DFT-D3) method at the B3LYP functional and the basis set 6-31++G** was chosen for calculating the data. Hydrogen bonds were formed in the Alg-(H2O)n complexes, while the SA-(H2O)n complexes showed an increase in Van der Walls interactions and hydrogen bonds. Moreover, in the SA-(H2O)n complexes, metal-nonmetal bonds existed between the sodium atom in SA and the oxygen atom in water (Na…O). All computational data in this study demonstrated that alginate dimers and water molecules had moderate to high levels of interaction, giving more stability to their complex structure.
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Affiliation(s)
- Daru Seto Bagus Anugrah
- Biotechnology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang 15345, Indonesia
| | - Laura Virdy Darmalim
- Biotechnology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang 15345, Indonesia
| | - Muhammad Rifky Irwanto Polanen
- Food Technology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, BSD Campus, Tangerang 15345, Indonesia
| | - Permono Adi Putro
- Department of Physics, Faculty of Science, Universitas Mandiri, Subang 41211, Indonesia
| | - Nurwarrohman Andre Sasongko
- Department of Chemistry, Faculty of Science and Mathematics, Diponegoro University, Semarang 50275, Indonesia
- Department of Chemistry, Pukyong National University, Busan 48513, Korea
| | - Parsaoran Siahaan
- Department of Chemistry, Faculty of Science and Mathematics, Diponegoro University, Semarang 50275, Indonesia
| | - Zeno Rizqi Ramadhan
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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Benchehaima FZ, Springborg M, Rahal MS. Nonlinear optical properties DFT calculations of polyacethylene and copolymers models substituted with aldimines chromophores as side chains. J Comput Chem 2022; 43:1701-1718. [PMID: 35938777 DOI: 10.1002/jcc.26971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 11/05/2022]
Abstract
Aldimine derivatives chromophores grafted on polyacetylene oligomers were first designed to investigate the nonlinear optical (NLO) response of the resulting materials using CAMB3LYP method. The effects of different factors such as the chain length separating the substitutions as well as the configurations and the orientations of these latter, were examined and discussed. In a second part of this paper, NLO responses, in particular the static hyperpolarizabilities of polyvinyl oligomers substituted by aldimine chromophores via carboxylic groups and by pyrrolidone groups were calculated for different configurations. The stability and the hydrogen bonding in each oligomer were also discussed.
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Affiliation(s)
- Fatima-Zohra Benchehaima
- Laboratoire de Chimie Théorique de Bio- et Nanosystèmes (LCTBN), Faculty of Exact Sciences, University Djillali Liabes of Sidi Bel Abbès, Sidi Bel Abbes, Algeria
| | - Michael Springborg
- Physikalische und Theoretische Chemie, Universität des Saarlandes, Saarbrücken, Germany
| | - Majda Sekkal Rahal
- Laboratoire de Chimie Théorique de Bio- et Nanosystèmes (LCTBN), Faculty of Exact Sciences, University Djillali Liabes of Sidi Bel Abbès, Sidi Bel Abbes, Algeria
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9
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Li ZJ, Srebnik S, Rojas OJ. Competing Effects of Hydration and Cation Complexation in Single-Chain Alginate. Biomacromolecules 2022; 23:1949-1957. [PMID: 35362969 DOI: 10.1021/acs.biomac.1c01591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alginic acid, a naturally occurring anionic polyelectrolyte, forms strong physically cross-linked hydrogels in the presence of metal cations. The latter engage in electrostatic interactions that compete with intra- and intermolecular hydrogen bonds, determining the gel structure and properties of the system in aqueous media. In this study, we use all-atom molecular dynamics simulations to systematically analyze the interactions between alginic acid chains and Na+ and Ca2+ counterions. The formed alginates originate from the competition of intramolecular hydrogen bonding and water coordination around the polyelectrolyte. In contrast to the established interpretation, we show that calcium cations strongly bind to alginate by disrupting hydrogen bonds within (1 → 4)-linked β-d-mannuronate (M) residues. On the other hand, Na+ cations enhance intramolecular hydrogen bonds that stabilize a left-hand, fourfold helical chain structure in poly-M alginate, resulting in stiffer chains. Hence, the traditionally accepted flexible flat-chain model for poly-M sequence is not valid in the presence of Na+. The two cations have a distinct effect on water coordination around alginate and therefore on its solubility. While Ca+ disrupts water coordination directly around the alginate chains, mobile Na+ cations significantly disrupt the second hydration layer.
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Affiliation(s)
- Zezhong John Li
- Department of Chemical and Biological Engineering University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Laboratory of Sustainable and Catalytic Processing, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Simcha Srebnik
- Department of Chemical and Biological Engineering University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Orlando J Rojas
- Department of Chemical and Biological Engineering University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Bioproducts Institute, Department of Chemistry and Department of Wood Science, University of British Columbia, 2385 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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10
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Makshakova O, Zykwinska A, Cuenot S, Colliec-Jouault S, Perez S. Three-dimensional structures, dynamics and calcium-mediated interactions of the exopolysaccharide, Infernan, produced by the deep-sea hydrothermal bacterium Alteromonas infernus. Carbohydr Polym 2022; 276:118732. [PMID: 34823768 DOI: 10.1016/j.carbpol.2021.118732] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 01/09/2023]
Abstract
The exopolysaccharide Infernan, from the bacterial strain GY785, has a complex repeating unit of nine monosaccharides established on a double-layer of sidechains. A cluster of uronic and sulfated monosaccharides confers to Infernan functional and biological activities. We characterized the 3-dimensional structures and dynamics along Molecular Dynamics trajectories and clustered the conformations in extended two-fold and five-fold helical structures. The electrostatic potential distribution over all the structures revealed negatively charged cavities explored for Ca2+ binding through quantum chemistry computation. The transposition of the model of Ca2+complexation indicates that the five-fold helices are the most favourable for interactions. The ribbon-like shape of two-fold helices brings neighbouring chains in proximity without steric clashes. The cavity chelating the Ca2+ of one chain is completed throughout the interaction of a sulfate group from the neighbouring chain. The resulting is a 'junction zone' based on unique chain-chain interactions governed by a heterotypic binding mode.
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Affiliation(s)
- Olga Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russian Federation.
| | - Agata Zykwinska
- Ifremer, Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies, 44311 Nantes, France.
| | - Stephane Cuenot
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
| | - Sylvia Colliec-Jouault
- Ifremer, Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies, 44311 Nantes, France.
| | - Serge Perez
- Centre de Recherches sur les Macromolécules Végétales, Université de Grenoble Alpes, Centre National de la Recherche Scientifique, Grenoble, France.
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11
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Rowbotham JS, Christopher Greenwell H, Dyer PW. Opening the Egg Box: NMR spectroscopic analysis of the interactions between s-block cations and kelp monosaccharides. Dalton Trans 2021; 50:13246-13255. [PMID: 34617523 DOI: 10.1039/d0dt04375c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The best-known theory accounting for metal-alginate complexation is the so-called "Egg Box" model. In order to gain greater insight into the metal-saccharide interactions that underpin this model, the coordination chemistry of the corresponding monomeric units of alginate, L-guluronate (GulA) and D-mannuronate (ManA) have been studied herein. GulA and ManA were exposed to solutions of different s-block cations and then analysed by 1H and 13C NMR spectroscopy. It was found that the α/β ratio of the pyranose anomeric equilibria of GulA showed large pertubations from the starting value (α/β = 0.21 ± 0.01) upon contact with 1.0 M Ca2+, Sr2+, and Ba2+ (α/β = 1.50 ± 0.03, 1.20 ± 0.02, and 0.58 ± 0.02, respectively) at pD 7.9, but remained almost constant in the presence of Na+, K+, and Mg2+ (α/β = 0.24 ± 0.01, 0.19 ± 0.01, and 0.26 ± 0.01, respectively). By comparison, no significant changes were observed in the α/β ratios of ManA and related mono-uronates D-glucuronate (GlcA) and D-galacturonate (GalA) in the presence of all of the metal ions surveyed. Analysis of the 1H and 13C coordination chemical shift patterns indicate that the affinity of α-GulA for larger divalent cations is a consequence of the unique ax-eq-ax arrangement of hydroxyl groups found for this uronate anomer.
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Affiliation(s)
- Jack S Rowbotham
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK. .,Current address: Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - H Christopher Greenwell
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK. .,Department of Earth Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Philip W Dyer
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.
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Ardiles CS, Rodríguez CC. Theoretical study for determining the type of interactions between a GG block of an alginate chain with metals Cu2+, Mn2+, Ca2+ and Mg2+. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Theoretical investigation on the improper hydrogen bond in κ-carrabiose⋯Y (Y = HF, HCl, HBr, NH 3, H 2O, and H 2S) complexes. J Mol Model 2021; 27:292. [PMID: 34546413 DOI: 10.1007/s00894-021-04904-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
The nature of H-bonds in κ-carrabiose⋯Y (Y = HF, HCl, HBr, NH3, H2O, and H2S) complexes was studied. For this aim, the structure of isolated κ-carrabiose was optimized using three global hybrids functional: B3LYP, PBE0, and M06-2X combined with 6-311G** basis set. Subsequently, the κ-carrabiose in the presence of HF, HCl, HBr, NH3, H2O, and H2S was optimized using the CBS-4 M method. NBO analyses were then carried out at the MP2/6-311G** level of theory. A particular interest was focused on C(18)-H(34)⋯Y bond. The results reveal that the C(18)-H(34)⋯Y bond is an improper H-bond since a significant contraction of C(18)-H(34) was observed during the complexation leading to a significant blueshifted stretching frequency. The NBO analyses have shown that the formation of the improper H-bonds C(18)-H(34)⋯Y (Y = F, Cl, Br, N, O, and S) is principally due to the increase of the s-character of the hybrid orbital in carbon atom (rehybridization) in κ-carrabiose⋯Y complexes. Regarding the polarization, it was proved that more the H-bond center (carbon in C(18)-H(34)⋯Y) becomes less positive, the hydrogen more positive, and Y more negative; more the contraction of the C(18)-H(34) bond is important. It was also confirmed for intramolecular H-bonds in κ-carrabiose⋯Y complexes that the rehybridization is responsible for H-bonds nature either proper or improper.
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Li ZJ, Srebnik S, Rojas OJ. Revisiting Cation Complexation and Hydrogen Bonding of Single-Chain Polyguluronate Alginate. Biomacromolecules 2021; 22:4027-4036. [PMID: 34461721 DOI: 10.1021/acs.biomac.1c00840] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Modifying the properties of bio-based materials has garnered increasing interest in recent years. In related applications, the ability of alginates to complex with metal ions has been shown to be effective in liquid-to-gel transitions, useful in the development of foodstuff and pharma products as well as biomaterials, among others. However, despite its ubiquitous use, alginate behavior as far as interactions with cations is not fully understood. Hence, this study presents a detailed comparison of alginate's complexation with Na+ and Ca2+ and the involved intramolecular hydrogen bonding and biomolecular chain geometry. Using all-atom molecular dynamics simulations, we find that in contrast to accepted models, calcium cations strongly bind to alginate chains by disruption of hydrogen bonds between neighboring residues, stabilizing a left-hand, 3-fold helical chain structure that enhances chain stiffness. Hence, while present, the traditionally accepted egg-box binding mode was a minor subset of possible conformations. For a single chain, most of the cation binding occurred as single-cation interaction with a carboxyl group, without the coordination of other alginate oxygens. The monovalent Na+ ions were found to be mostly nonlocalized around alginate and therefore do not compete with intramolecular hydrogen bonding. The different binding modes observed for Na+ and Ca2+ contribute toward explaining the different solubility of sodium and calcium alginate.
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Affiliation(s)
- Zezhong John Li
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia, Canada V6T 1Z3.,Laboratory of Sustainable and Catalytic Processing, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Simcha Srebnik
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Orlando J Rojas
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia, Canada V6T 1Z3.,Bioproducts Institute and Departments of Chemistry and Wood Science, University of British Columbia, 2385 East Mall, Vancouver, British Columbia, Canada V6T 1Z4
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Cation complexation by mucoid Pseudomonas aeruginosa extracellular polysaccharide. PLoS One 2021; 16:e0257026. [PMID: 34473773 PMCID: PMC8412252 DOI: 10.1371/journal.pone.0257026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mucoid Pseudomonas aeruginosa is a prevalent cystic fibrosis (CF) lung colonizer, producing an extracellular matrix (ECM) composed predominantly of the extracellular polysaccharide (EPS) alginate. The ECM limits antimicrobial penetration and, consequently, CF sufferers are prone to chronic mucoid P. aeruginosa lung infections. Interactions between cations with elevated concentrations in the CF lung and the anionic EPS, enhance the structural rigidity of the biofilm and exacerbates virulence. In this work, two large mucoid P. aeruginosa EPS models, based on β-D-mannuronate (M) and β-D-mannuronate-α-L-guluronate systems (M-G), and encompassing thermodynamically stable acetylation configurations–a structural motif unique to mucoid P. aeruginosa–were created. Using highly accurate first principles calculations, stable coordination environments adopted by the cations have been identified and thermodynamic stability quantified. These models show the weak cross-linking capability of Na+ and Mg2+ ions relative to Ca2+ ions and indicate a preference for cation binding within M-G blocks due to the smaller torsional rearrangements needed to reveal stable binding sites. The geometry of the chelation site influences the stability of the resulting complexes more than electrostatic interactions, and the results show nuanced chemical insight into previous experimental observations.
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Characterization and functional assessment of alginate fibers prepared by metal-calcium ion complex coagulation bath. Carbohydr Polym 2020; 232:115693. [DOI: 10.1016/j.carbpol.2019.115693] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 11/17/2022]
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Makshakova O, Faizullin D, Zuev Y. Interplay between secondary structure and ion binding upon thermoreversible gelation of κ-carrageenan. Carbohydr Polym 2020; 227:115342. [DOI: 10.1016/j.carbpol.2019.115342] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 01/03/2023]
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