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Seo Y, Song Y, Schatz GC, Hwang H. Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study. J Phys Chem B 2018; 122:8174-8184. [DOI: 10.1021/acs.jpcb.8b05591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yongil Seo
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Yeonho Song
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - George C. Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hyonseok Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
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Liu J, Cukier RI, Bu Y, Shang Y. Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation. J Chem Theory Comput 2014; 10:4189-97. [PMID: 26588118 DOI: 10.1021/ct500238k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ab initio molecular dynamics simulations reveal that an excess electron (EE) can be more efficiently localized as a cavity-shaped state in aqueous glucose solution (AGS) than in water. Compared with that (∼1.5 ps) in water, the localization time is shortened by ∼0.7-1.2 ps in three AGSs (0.56, 1.12, and 2.87 M). Although the radii of gyration of the solvated EEs are all close to 2.6 Å in the four solutions, the solvated EE cavities in the AGSs become more compact and can localize ∼80% of an EE, which is considerably larger than that (∼40-60% and occasionally ∼80%) in water. These observations are attributed to a modification of the hydrogen-bonded network by the introduction of glucose molecules into water. The water acts as a promoter and stabilizer, by forming voids around glucose molecules and, in this fashion, favoring the localization of an EE with high efficiency. This study provides important information about EEs in physiological AGSs and suggests a new strategy to efficiently localize an EE in a stable cavity for further exploration of biological function.
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Affiliation(s)
- Jinxiang Liu
- Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University , Jinan, 250100, China
| | - Robert I Cukier
- Department of Chemistry, Michigan State University , East Lansing, 48224-1322, United States
| | - Yuxiang Bu
- Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University , Jinan, 250100, China
| | - Yuan Shang
- National Supercomputer Center in Jinan, Jinan, 250101, China
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Mahadevan T, Kojic M, Ferrari M, Ziemys A. Mechanisms of reduced solute diffusivity at nanoconfined solid–liquid interface. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Cheema U, Rong Z, Kirresh O, MacRobert AJ, Vadgama P, Brown RA. Oxygen diffusion through collagen scaffolds at defined densities: implications for cell survival in tissue models. J Tissue Eng Regen Med 2011; 6:77-84. [DOI: 10.1002/term.402] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 11/19/2010] [Indexed: 11/10/2022]
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Lerbret A, Lelong G, Mason PE, Saboungi ML, Brady JW. Molecular dynamics and neutron scattering study of glucose solutions confined in MCM-41. J Phys Chem B 2011; 115:910-8. [PMID: 21214282 PMCID: PMC3033472 DOI: 10.1021/jp1097519] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glucose aqueous solutions confined in MCM-41 cylindrical pores of diameter 3.2 nm have been studied by molecular dynamics (MD) simulations and quasielastic neutron scattering (QENS). MD simulations reveal a strong preferential interaction of glucose molecules with the silica walls, which induces significant concentration gradients within the pore. The influence of glucose on the structural and dynamical properties of water strongly depends on the region of the pore considered. The distortion of the hydrogen bond network (HBN) and of the tetrahedral organization of interfacial water molecules induced by silica is much stronger than that induced by glucose molecules. The interfacial glucose molecules diffuse about 1 order of magnitude slower than those in the core region. Differences in affinities for silica of the different species in confined hydrogen-bonded mixtures induce significant structural and dynamical heterogeneities not present in bulk solutions.
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Affiliation(s)
- Adrien Lerbret
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
| | - Gérald Lelong
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
- Centre de Recherche sur la Matière Divisée, CNRS – Université d'Orléans, 1b, rue de la Férollerie, 45071 Orléans Cedex 2, France
- Institut de Minéralogie et Physique des Milieux Condensés, Université Paris 6 / CNRS-UMR 7590/Université Paris 7/IPGP/IRD, 140, Rue de Lourmel 75015 Paris, France
| | - Philip E. Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
| | - Marie-Louise Saboungi
- Centre de Recherche sur la Matière Divisée, CNRS – Université d'Orléans, 1b, rue de la Férollerie, 45071 Orléans Cedex 2, France
| | - John W. Brady
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
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Ziemys A, Grattoni A, Fine D, Hussain F, Ferrari M. Confinement effects on monosaccharide transport in nanochannels. J Phys Chem B 2010; 114:11117-26. [PMID: 20738139 DOI: 10.1021/jp103519d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transport theories based on the continuum hypothesis may not be appropriate at the nanoscale in view of surface effects. We employed molecular dynamics simulations to study the effects of confinement and concentration on diffusive transport of glucose in silica nanochannels (10 nm or smaller). We found that glucose modifies the electrical properties of nanochannels and that, below 5 nm in channel height, glucose adsorption and diffusivity are significantly reduced. With increasing concentration, the diffusivity is reduced linearly in the bulk, while it is reduced nonlinearly at the interface. The effective diffusivity reduction is related to the interface thickness, which can be 2-4 nm depending on concentration, and has an unexpected reduction at low concentrations. Results suggest that nanochannels present a one-dimensional cage environment that affects diffusivity in a fashion similar to cage-breaking diffusion. Our simulation results, consistent with the experimental observations presented here, suggest that nanoconfinement is the essential cause of the observed altered fluid diffusive transport, not accounted for by classical theories, because of coupling of confinement and concentration effects.
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Affiliation(s)
- A Ziemys
- Department of Nanomedicine and Biomedical Engineering, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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Lelong G, Howells WS, Brady JW, Talón C, Price DL, Saboungi ML. Translational and rotational dynamics of monosaccharide solutions. J Phys Chem B 2010; 113:13079-85. [PMID: 19739660 DOI: 10.1021/jp905001q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics computer simulations have been carried out on aqueous solutions of glucose at concentrations bracketing those previously measured with quasi-elastic neutron scattering (QENS), in order to investigate the motions and interactions of the sugar and water molecules. In addition, QENS measurements have been carried out on fructose solutions to determine whether the effects previously observed for glucose apply to monosaccharide solutions. The simulations indicate a dynamical analogy between higher solute concentration and lower temperature that could provide a key explanation of the bioprotective phenomena observed in many living organisms. The experimental results on fructose solutions show qualitatively similar behavior to the glucose solutions. The dynamics of the water molecules are essentially the same, while the translational diffusion of the sugar molecules is slightly faster in the fructose solutions.
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Affiliation(s)
- Gérald Lelong
- Centre de Recherche sur la Matiere Divisee, Universite d'Orleans/CNRS-UMR 6619, 45071 Orleans, France.
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Luo G, Zhang Q, Del Castillo AR, Urban V, O'Neill H. Characterization of sol-gel-encapsulated proteins using small-angle neutron scattering. ACS APPLIED MATERIALS & INTERFACES 2009; 1:2262-2268. [PMID: 20355861 DOI: 10.1021/am900430v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Entrapment of biomolecules in silica-derived sol-gels has grown into a vibrant area of research since it was originally demonstrated. However, accessing the consequences of entrapment on biomolecules and the gel structure remains a major challenge in characterizing these biohybrid materials. We present the first demonstration that it is possible with small-angle neutron scattering (SANS) to study the conformation of dilute proteins that are entrapped in transparent and dense sol-gels. Using deuterium-labeled green fluorescent protein (GFP) and SANS with contrast variation, we demonstrate that the scattering signatures of the sol-gel and the protein can be separated. Analysis of the scattering curves of the sol-gels using a mass-fractal model shows that the size of the colloidal silica particles and the fractal dimensions of the gels were similar in the absence and presence of protein, demonstrating that GFP did not influence the reaction pathway for the formation of the gel. The major structural difference in the gels was that the pore size was increased 2-fold in the presence of the protein. At the contrast match point for silica, the scattering signal from GFP inside the gel became distinguishable over a wide q range. Simulated scattering curves representing a monomer, end-to-end dimer, and parallel dimer of the protein were calculated and compared to the experimental data. Our results show that the most likely structure of GFP is that of an end-to-end dimer. This approach can be readily applied and holds great potential for the structural characterization of complex biohybrid and other materials.
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Affiliation(s)
- Guangming Luo
- Center for Structural Molecular Biology, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Pomata MHH, Sonoda MT, Skaf MS, Elola MD. Anomalous Dynamics of Hydration Water in Carbohydrate Solutions. J Phys Chem B 2009; 113:12999-3006. [DOI: 10.1021/jp904019c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matías H. H. Pomata
- Departamento de Física, Comisión Nacional de Energía Atómica-CNEA, Avenida Gral. Paz 1499 (1650) San Martín, Buenos Aires, Argentina
| | - Milton T. Sonoda
- Universidade Federal de Uberlandia, Avenida Jose Joao Dib, 2545 Ituiutaba, MG, 38302-000 Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas—UNICAMP, P. O. Box 6154, Campinas, SP, 13084-862 Brazil
| | - M. Dolores Elola
- Departamento de Física, Comisión Nacional de Energía Atómica—CNEA, Avenida Libertador 8250, (1429) Buenos Aires, Argentina
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Lelong G, Price DL, Brady JW, Saboungi ML. Dynamics of trehalose molecules in confined solutions. J Chem Phys 2007; 127:065102. [PMID: 17705626 DOI: 10.1063/1.2753841] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamics of trehalose molecules in aqueous solutions confined in silica gel have been studied by quasielastic neutron scattering (QENS). Small-angle neutron scattering measurements confirmed the absence of both sugar clustering and matrix deformation of the gels, indicating that the results obtained are representative of homogeneous trehalose solutions confined in a uniform matrix. The pore size in the gel is estimated to be 18 nm, comparable to the distances in cell membranes. For the QENS measurements, the gel was prepared from D2O in order to accentuate the scattering from the trehalose. Values for the translational diffusion constant and effective jump distance were derived from model fits to the scattering function. Comparison with QENS and NMR results in the literature for bulk trehalose shows that confinement on a length scale of 18 nm has no significant effect on the translational diffusion of trehalose molecules.
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Affiliation(s)
- Gérald Lelong
- Centre de Recherche sur la Matière Divisée, 45071 Orleans Cedex 2, France
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Sonoda MT, Skaf MS. Carbohydrate Clustering in Aqueous Solutions and the Dynamics of Confined Water. J Phys Chem B 2007; 111:11948-56. [PMID: 17887790 DOI: 10.1021/jp0749120] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.
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Affiliation(s)
- Milton T Sonoda
- Institute of Chemistry, State University of Campinas-UNICAMP, Campinas, SP, Brazil
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