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Ubbink J. Recent advances in carbohydrate phase behavior and rheology. ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 114:353-414. [PMID: 40155088 DOI: 10.1016/bs.afnr.2024.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2025]
Abstract
The past decades have seen major advances in the understanding of the role of phase and state transitions of food carbohydrates on the behavior during processing and on product characteristics. Specifically, the awareness of the importance of the glass transition temperature and the plasticization by water and its study for a variety of food system is having major impact on the formulation and processing of foods, and in defining shelf-life conditions. This has led to the use of phase and state diagrams in the analysis and prediction of the behavior of food systems during processing and storage. This review first summarizes the current understanding of the food carbohydrate phase behavior and rheology, with emphasis on the concentrated states close to the glass transition and in the glassy state. Several pertinent topics, including the modeling of the rheological properties close to the glass transition, the strongly non-linear diffusion of water in the rubbery and glassy states, the aging and antiplasticization of glassy carbohydrate matrices, and consequences of amorphous-amorphous phase separation for the behavior of carbohydrate blends in concentrated states are discussed. Applications in food processing and product development are discussed, including the spray drying and freeze drying, powder agglomeration of food powders, powder caking, encapsulation, baked goods, crystallization and extrusion.
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Affiliation(s)
- Job Ubbink
- Department of Food Science and Nutrition, University of Minnesota, Eckles Ave., St. Paul, MN, United States.
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2
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Gomez A, Piskulich ZA, Thompson WH, Laage D. Water Diffusion Proceeds via a Hydrogen-Bond Jump Exchange Mechanism. J Phys Chem Lett 2022; 13:4660-4666. [PMID: 35604934 DOI: 10.1021/acs.jpclett.2c00825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The self-diffusion of water molecules plays a key part in a broad range of essential processes in biochemistry, medical imaging, material science, and engineering. However, its molecular mechanism and the role played by the water hydrogen-bond network rearrangements are not known. Here we combine molecular dynamics simulations and analytic modeling to determine the molecular mechanism of water diffusion. We establish a quantitative connection between the water diffusion coefficient and hydrogen-bond jump exchanges, and identify the features that determine the underlying energetic barrier. We thus provide a unified framework to understand the coupling between translational, rotational, and hydrogen-bond dynamics in liquid water. It explains why these different dynamics do not necessarily exhibit identical temperature dependences although they all result from the same hydrogen-bond exchange events. The consequences for the understanding of water diffusion in supercooled conditions and for water transport in complex aqueous systems, including ionic, biological, and confined solutions, are discussed.
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Affiliation(s)
- Axel Gomez
- PASTEUR, Department of Chemistry, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Zeke A Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Damien Laage
- PASTEUR, Department of Chemistry, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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3
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Bama JA, Dudognon E, Affouard F. Impact of Low Concentration of Strongly Hydrogen-Bonded Water Molecules on the Dynamics of Amorphous Terfenadine: Insights from Molecular Dynamics Simulations and Dielectric Relaxation Spectroscopy. J Phys Chem B 2021; 125:11292-11307. [PMID: 34590855 DOI: 10.1021/acs.jpcb.1c06087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The impact of low water concentration of strongly hydrogen-bonded water molecules on the dynamical properties of amorphous terfenadine (TFD) is investigated through complementary molecular dynamics (MD) simulations and dielectric relaxation spectroscopy (DRS) experiments. In this article, we especially highlight the important role played by some residual water molecules in the concentration of 1-2% (w/w) trapped in the TFD glassy matrix, which are particularly difficult to remove experimentally without a specific heating/drying process. From MD computations and analyses of the hydrogen bonding (HB) interactions, different categories of water molecules are revealed and particularly the presence of strongly HB water molecules. These latter localize themselves in small pockets in empty spaces existing in between the TFD molecules due to the poor packing of the glassy state and preferentially interact with the polar groups close to the flexible central part of the TFD molecules. We present a simple model which rationalizes at the molecular scale the effect of these strongly HB water molecules on dynamics and how they give rise to a supplementary relaxation process (namely process S) which is detected for the first time in the glassy state of TFD annealed at room temperature while this process is completely absent in a non-annealed glass. It also explains how this supplementary relaxation is coupled with the intramolecular motion (namely process γ) of the very flexible central part of the TFD molecule. The present findings help to understand more generally the microscopic origin of the secondary relaxations often detected by DRS in the glassy states of molecular compounds for which the exact nature is still debated.
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Affiliation(s)
- Jeanne-Annick Bama
- University Lille, CNRS, INRAE, Centrale Lille, UMR 8207-UMET-Unité Matériaux et Transformations, Lille F-59000, France
| | - Emeline Dudognon
- University Lille, CNRS, INRAE, Centrale Lille, UMR 8207-UMET-Unité Matériaux et Transformations, Lille F-59000, France
| | - Frédéric Affouard
- University Lille, CNRS, INRAE, Centrale Lille, UMR 8207-UMET-Unité Matériaux et Transformations, Lille F-59000, France
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4
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Tuning the Johari-Goldstein β-Relaxation and Its Separation from α-Relaxation of Poly(n-alkyl methacrylate)s by Small Molecule-bridged Hydrogen Bonds. CHINESE JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1007/s10118-021-2595-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Abstract
Cellulose is the most common biopolymer and widely used in our daily life. Due to its unique properties and biodegradability, it has been attracting increased attention in the recent years and various new applications of cellulose and its derivatives are constantly being found. The development of new materials with improved properties, however, is not always an easy task, and theoretical models and computer simulations can often help in this process. In this review, we give an overview of different coarse-grained models of cellulose and their applications to various systems. Various coarse-grained models with different mapping schemes are presented, which can efficiently simulate systems from the single cellulose fibril/crystal to the assembly of many fibrils/crystals. We also discuss relevant applications of these models with a focus on the mechanical properties, self-assembly, chiral nematic phases, conversion between cellulose allomorphs, composite materials and interactions with other molecules.
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6
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Song YC, Ingram S, Arbon RE, Topping DO, Glowacki DR, Reid JP. Transient cavity dynamics and divergence from the Stokes-Einstein equation in organic aerosol. Chem Sci 2020; 11:2999-3006. [PMID: 34122802 PMCID: PMC8157714 DOI: 10.1039/c9sc06228a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/15/2020] [Indexed: 12/26/2022] Open
Abstract
The diffusion of small molecules through viscous matrices formed by large organic molecules is important across a range of domains, including pharmaceutical science, materials chemistry, and atmospheric science, impacting on, for example, the formation of amorphous and crystalline phases. Here we report significant breakdowns in the Stokes-Einstein (SE) equation from measurements of the diffusion of water (spanning 5 decades) and viscosity (spanning 12 decades) in saccharide aerosol droplets. Molecular dynamics simulations show water diffusion is not continuous, but proceeds by discrete hops between transient cavities that arise and dissipate as a result of dynamical fluctuations within the saccharide lattice. The ratio of transient cavity volume to solvent volume increases with size of molecules making up the lattice, increasing divergence from SE predictions. This improved mechanistic understanding of diffusion in viscous matrices explains, for example, why organic compounds equilibrate according to SE predictions and water equilibrates more rapidly in aerosols.
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Affiliation(s)
- Young-Chul Song
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Stephen Ingram
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - Robert E Arbon
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - David O Topping
- School of Earth and Environmental Science, University of Manchester Manchester M13 9PL UK
| | - David R Glowacki
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, University of Bristol Cantock's Close BS8 1TS UK
- Department of Computer Science, University of Bristol UK
| | - Jonathan P Reid
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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7
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Nadler KA, Kim P, Huang DL, Xiong W, Continetti RE. Water diffusion measurements of single charged aerosols using H2O/D2O isotope exchange and Raman spectroscopy in an electrodynamic balance. Phys Chem Chem Phys 2019; 21:15062-15071. [DOI: 10.1039/c8cp07052k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report water diffusion measurements on single charged aerosols using isotope exchange in an electrodynamic balance.
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Affiliation(s)
- Katherine A. Nadler
- Department of Chemistry and Biochemistry
- University of California San Diego
- La Jolla
- USA
| | - Pyeongeun Kim
- Department of Chemistry and Biochemistry
- University of California San Diego
- La Jolla
- USA
| | - Dao-Ling Huang
- Department of Chemistry and Biochemistry
- University of California San Diego
- La Jolla
- USA
| | - Wei Xiong
- Department of Chemistry and Biochemistry
- University of California San Diego
- La Jolla
- USA
| | - Robert E. Continetti
- Department of Chemistry and Biochemistry
- University of California San Diego
- La Jolla
- USA
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8
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Kindlein M, Elts E, Briesen H. Phospholipids in chocolate: Structural insights and mechanistic explanations of rheological behavior by coarse-grained molecular dynamics simulations. J FOOD ENG 2018. [DOI: 10.1016/j.jfoodeng.2018.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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10
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Haddadian EJ, Zhang H, Freed KF, Douglas JF. Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles. Sci Rep 2017; 7:41671. [PMID: 28176808 PMCID: PMC5296861 DOI: 10.1038/srep41671] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.
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Affiliation(s)
- Esmael J Haddadian
- Biological Sciences Collegiate Division, University of Chicago, Chicago, IL 60637, USA
| | - Hao Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Alberta, T6G 1H9 Canada
| | - Karl F Freed
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, IL 60637, USA
| | - Jack F Douglas
- Materials Science and Engineering Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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11
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Price HC, Mattsson J, Murray BJ. Sucrose diffusion in aqueous solution. Phys Chem Chem Phys 2016; 18:19207-16. [PMID: 27364512 PMCID: PMC5044753 DOI: 10.1039/c6cp03238a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/02/2022]
Abstract
The diffusion of sugar in aqueous solution is important both in nature and in technological applications, yet measurements of diffusion coefficients at low water content are scarce. We report directly measured sucrose diffusion coefficients in aqueous solution. Our technique utilises a Raman isotope tracer method to monitor the diffusion of non-deuterated and deuterated sucrose across a boundary between the two aqueous solutions. At a water activity of 0.4 (equivalent to 90 wt% sucrose) at room temperature, the diffusion coefficient of sucrose was determined to be approximately four orders of magnitude smaller than that of water in the same material. Using literature viscosity data, we show that, although inappropriate for the prediction of water diffusion, the Stokes-Einstein equation works well for predicting sucrose diffusion under the conditions studied. As well as providing information of importance to the fundamental understanding of diffusion in binary solutions, these data have technological, pharmaceutical and medical implications, for example in cryopreservation. Moreover, in the atmosphere, slow organic diffusion may have important implications for aerosol growth, chemistry and evaporation, where processes may be limited by the inability of a molecule to diffuse between the bulk and the surface of a particle.
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Affiliation(s)
- Hannah C. Price
- School of Earth and Environment , University of Leeds , Leeds , UK .
| | - Johan Mattsson
- School of Physics and Astronomy , University of Leeds , Leeds , UK .
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12
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Schammé B, Mignot M, Couvrat N, Tognetti V, Joubert L, Dupray V, Delbreilh L, Dargent E, Coquerel G. Molecular Relaxations in Supercooled Liquid and Glassy States of Amorphous Quinidine: Dielectric Spectroscopy and Density Functional Theory Approaches. J Phys Chem B 2016; 120:7579-92. [PMID: 27391029 DOI: 10.1021/acs.jpcb.6b04242] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this article, we conduct a comprehensive molecular relaxation study of amorphous Quinidine above and below the glass-transition temperature (Tg) through broadband dielectric relaxation spectroscopy (BDS) experiments and theoretical density functional theory (DFT) calculations, as one major issue with the amorphous state of pharmaceuticals is life expectancy. These techniques enabled us to determine what kind of molecular motions are responsible, or not, for the devitrification of Quinidine. Parameters describing the complex molecular dynamics of amorphous Quinidine, such as Tg, the width of the α relaxation (βKWW), the temperature dependence of α-relaxation times (τα), the fragility index (m), and the apparent activation energy of secondary γ relaxation (Ea-γ), were characterized. Above Tg (> 60 °C), a medium degree of nonexponentiality (βKWW = 0.5) was evidenced. An intermediate value of the fragility index (m = 86) enabled us to consider Quinidine as a glass former of medium fragility. Below Tg (< 60 °C), one well-defined secondary γ relaxation, with an apparent activation energy of Ea-γ = 53.8 kJ/mol, was reported. From theoretical DFT calculations, we identified the most reactive part of Quinidine moieties through exploration of the potential energy surface. We evidenced that the clearly visible γ process has an intramolecular origin coming from the rotation of the CH(OH)C9H14N end group. An excess wing observed in amorphous Quinidine was found to be an unresolved Johari-Goldstein relaxation. These studies were supplemented by sub-Tg experimental evaluations of the life expectancy of amorphous Quinidine by X-ray powder diffraction and differential scanning calorimetry. We show that the difference between Tg and the onset temperature for crystallization, Tc, which is 30 K, is sufficiently large to avoid recrystallization of amorphous Quinidine during 16 months of storage under ambient conditions.
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Affiliation(s)
- Benjamin Schammé
- Normandie Univ, Laboratoire SMS - EA3233, Univ Rouen , F-76821 Mont Saint Aignan, France.,AMME-LECAP EA 4528 International Lab, Avenue de l'Université, BP12, Normandie Univ, Université de Rouen Normandie , 76801 St Etienne du Rouvray, France
| | - Mélanie Mignot
- Normandie Univ, Laboratoire SMS - EA3233, Univ Rouen , F-76821 Mont Saint Aignan, France
| | - Nicolas Couvrat
- Normandie Univ, Laboratoire SMS - EA3233, Univ Rouen , F-76821 Mont Saint Aignan, France
| | - Vincent Tognetti
- COBRA UMR 6014 and FR 3038, Normandie Univ, Université de Rouen, INSA Rouen, CNRS , F-76821 Mont Saint Aignan, Cedex, France
| | - Laurent Joubert
- COBRA UMR 6014 and FR 3038, Normandie Univ, Université de Rouen, INSA Rouen, CNRS , F-76821 Mont Saint Aignan, Cedex, France
| | - Valérie Dupray
- Normandie Univ, Laboratoire SMS - EA3233, Univ Rouen , F-76821 Mont Saint Aignan, France
| | - Laurent Delbreilh
- AMME-LECAP EA 4528 International Lab, Avenue de l'Université, BP12, Normandie Univ, Université de Rouen Normandie , 76801 St Etienne du Rouvray, France
| | - Eric Dargent
- AMME-LECAP EA 4528 International Lab, Avenue de l'Université, BP12, Normandie Univ, Université de Rouen Normandie , 76801 St Etienne du Rouvray, France
| | - Gérard Coquerel
- Normandie Univ, Laboratoire SMS - EA3233, Univ Rouen , F-76821 Mont Saint Aignan, France
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13
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Ubbink J. Structural and thermodynamic aspects of plasticization and antiplasticization in glassy encapsulation and biostabilization matrices. Adv Drug Deliv Rev 2016; 100:10-26. [PMID: 26748258 DOI: 10.1016/j.addr.2015.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 01/21/2023]
Abstract
The structural and thermodynamic properties of glassy carbohydrate matrices for the encapsulation and biostabilization of sensitive bioactive compounds, such as pharmaceutically active proteins and oxidation-sensitive compounds, are reviewed in the context of the plasticization and antiplasticization of glassy carbohydrates of intermediate and high molecular weight by low molecular weight diluents. Plasticization and antiplasticization may be monitored either by dynamic measures or by structural and thermodynamic features of the glassy matrices. Specifically, it is demonstrated that the decrease in size of the molecular free volume holes with increasing diluent content, as determined by positron annihilation lifetime spectroscopy (PALS), is related to the antiplasticization of glassy carbohydrate matrices, resulting in increased barrier properties of the glassy matrix. As far as could be ascertained from the available data, the regimes as identified by PALS map on those detected by neutron scattering and dielectric spectroscopy for glassy matrices consisting of trehalose and the diluent glycerol. The review is concluded by a survey of the published results on the stability of bioactive compounds encapsulated in carbohydrate glasses and an overview of outstanding questions.
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14
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Davies JF, Wilson KR. Raman Spectroscopy of Isotopic Water Diffusion in Ultraviscous, Glassy, and Gel States in Aerosol by Use of Optical Tweezers. Anal Chem 2016; 88:2361-6. [DOI: 10.1021/acs.analchem.5b04315] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James F. Davies
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94611, United States
| | - Kevin R. Wilson
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94611, United States
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15
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Stabilization of proteins in solid form. Adv Drug Deliv Rev 2015; 93:14-24. [PMID: 25982818 DOI: 10.1016/j.addr.2015.05.006] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 05/07/2015] [Accepted: 05/09/2015] [Indexed: 12/15/2022]
Abstract
Immunogenicity of aggregated or otherwise degraded protein delivered from depots or other biopharmaceutical products is an increasing concern, and the ability to deliver stable, active protein is of central importance. We review characterization approaches for solid protein dosage forms with respect to metrics that are intended to be predictive of protein stability against aggregation and other degradation processes. Each of these approaches is ultimately motivated by hypothetical connections between protein stability and the material property being measured. We critically evaluate correlations between these properties and stability outcomes, and use these evaluations to revise the currently standing hypotheses. Based on this we provide simple physical principles that are necessary (and possibly sufficient) for generating solid delivery vehicles with stable protein loads. Essentially, proteins should be strongly coupled (typically through H-bonds) to the bulk regions of a phase-homogeneous matrix with suppressed β relaxation. We also provide a framework for reliable characterization of solid protein forms with respect to stability.
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16
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Cecotka A, Tripathy SN, Paluch M. Evidence of pressure induced intermolecular proton transfer via mutarotation: the case of supercooled d-fructose. Phys Chem Chem Phys 2015; 17:19394-400. [PMID: 26144525 DOI: 10.1039/c5cp02044a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This paper describes a systematic investigation on the role of pressure in mutarotation kinetics of supercooled d-fructose using dielectric spectroscopy. The structural relaxation time acts as a suitable dynamical observable to monitor the mutarotation process that enables the construction of the kinetic curves. The reaction kinetic shapes have been analyzed using the Avrami model. At low temperature, sigmoidal kinetic curves are noted, which correspond to the high concentration of furanosidic forms. The magnitude of activation energy of the process significantly decreases with increasing pressure and is comparable to the solvated systems at 100 MPa. A potential connection between cooperative motion and the origin of intermolecular proton transfer via mutarotation at elevated pressure is also discussed. These experimental observations have fundamental significance on theoretical explanation of the mechanism involving mutarotation in sugars.
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Affiliation(s)
- Adam Cecotka
- Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice, Poland.
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17
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Sauter J, Grafmüller A. Solution Properties of Hemicellulose Polysaccharides with Four Common Carbohydrate Force Fields. J Chem Theory Comput 2015; 11:1765-74. [PMID: 26574386 DOI: 10.1021/ct500924f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemicellulose polysaccharides play an important role in the swelling behavior of the primary plant cell wall, and molecular dynamics simulations provide the means of gaining a concise understanding of the interactions of hemicellulose polysaccharides with water. Here, we compare four of the main polysaccharide force fields (CHARMM36 TIP3P, GROMOS56A6(CARBO) SPC, GLYCAM06h TIP3P, and GLYCAM06h TIP5P) for the most abundant hemicellulose backbone components. In particular, we compare aggregation, diffusion coefficients, system density, and investigate the free energy of hydration of saccharides in water. We find that the saccharides show nonphysical aggregation at low concentrations with the GLYCAM06h TIP3P force field, which can be rectified by the use of the TIP5P water model. As a result of the aggregation, GLYCAM06h TIP3P does not lead to reasonable diffusion coefficients whereas the diffusion coefficients, as well as the system density, agrees best with experimental data for the GLYCAM06h TIP5P force field. Overall, GLYCAM06h TIP5P gives good agreement with experimental free energy of hydration data for small saccharides. In addition, the free energy of hydration for short polysaccharides calculated with the GLYCAM06h TIP5P force field is consistent with the radial distribution functions between the polysaccharides and water, the hydration number of the polysaccharides, and the hydrogen bonds formed in the system.
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Affiliation(s)
- Jörg Sauter
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces , Potsdam, Germany
| | - Andrea Grafmüller
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces , Potsdam, Germany
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18
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Qian KK, Grobelny PJ, Tyagi M, Cicerone MT. Using the fluorescence red edge effect to assess the long-term stability of lyophilized protein formulations. Mol Pharm 2015; 12:1141-9. [PMID: 25786057 DOI: 10.1021/mp500641f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanosecond relaxation processes in sugar matrices are causally linked through diffusional processes to protein stability in lyophilized formulations. Long-term protein degradation rates track mean-squared displacement (⟨u(2)⟩) of hydrogen atoms in sugar glasses, a parameter describing dynamics on a time scale of picoseconds to nanoseconds. However, measurements of ⟨u(2)⟩ are usually performed by neutron scattering, which is not conducive to rapid formulation screening in early development. Here, we present a benchtop technique to derive a ⟨u(2)⟩ surrogate based on the fluorescence red edge effect. Glycerol, lyophilized trehalose, and lyophilized sucrose were used as model systems. Samples containing 10(-6) mole fraction of rhodamine 6G, a fluorophore, were excited at either 532 nm (main peak) or 566 nm (red edge), and the ⟨u(2)⟩ surrogate was determined based the corresponding Stokes shifts. Results showed reasonable agreement between ⟨u(2)⟩ from neutron scattering and the surrogate from fluorescence, although deviations were observed at very low temperatures. We discuss the sources of the deviations and suggest technique improvements to ameliorate these. We expect that this method will be a valuable tool to evaluate lyophilized sugar matrices with respect to their ability to protect proteins from diffusion-limited degradation processes during long-term storage. Additionally, the method may have broader applications in amorphous pharmaceutical solids.
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Affiliation(s)
- Ken K Qian
- †National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Pawel J Grobelny
- ‡University of Connecticut, Storrs, Connecticut 06269, United States
| | - Madhusudan Tyagi
- †National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Marcus T Cicerone
- †National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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19
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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: 0.7] [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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20
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Lienhard DM, Huisman AJ, Bones DL, Te YF, Luo BP, Krieger UK, Reid JP. Retrieving the translational diffusion coefficient of water from experiments on single levitated aerosol droplets. Phys Chem Chem Phys 2014; 16:16677-83. [DOI: 10.1039/c4cp01939c] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Hydrogen bonding in maltooligomer–glycerol–water matrices: Relation to physical state and molecular free volume. Carbohydr Polym 2014; 102:566-75. [DOI: 10.1016/j.carbpol.2013.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/28/2013] [Accepted: 12/03/2013] [Indexed: 11/23/2022]
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22
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PARTANEN R, MURTOMÄKI L, MOISIO T, LÄHTEENMÄKI M, TOIKKANEN O, HARTIKAINEN R, FORSSELL P. Routes to Control Oxygen Transfer Across Biomatrix. ACTA ACUST UNITED AC 2014. [DOI: 10.11301/jsfe.15.61] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Greiner M, Sonnleitner B, Mailänder M, Briesen H. Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching. Food Funct 2014; 5:235-42. [DOI: 10.1039/c3fo60355e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Kossack W, Adrjanowicz K, Tarnacka M, Kiprop Kipnusu W, Dulski M, Mapesa EU, Kaminski K, Pawlus S, Paluch M, Kremer F. Glassy dynamics and physical aging in fucose saccharides as studied by infrared- and broadband dielectric spectroscopy. Phys Chem Chem Phys 2013; 15:20641-50. [DOI: 10.1039/c3cp52551a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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van der Sman RGM, Meinders MBJ. Moisture diffusivity in food materials. Food Chem 2012; 138:1265-74. [PMID: 23411242 DOI: 10.1016/j.foodchem.2012.10.062] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/01/2012] [Indexed: 11/30/2022]
Abstract
This paper investigates whether moisture diffusion can be predicted for food materials. We focus especially on mixtures of glucose homopolymers and water. The predictions are based on three theories: (1) the Darken relation, linking the mutual diffusivity to the self diffusivities, (2) the generalised Stokes-Einstein relation for the solute self diffusivity, and (3) the free volume theory for water self diffusivity. Using literature data obtained for the whole class of glucose homopolymer, we show that these theories predict the moisture diffusivity for the whole range of volume fractions, from zero to one, and a broad range of temperatures. Furthermore, we show that the theories equally holds for other hydrophilic biopolymers one finds in food. In the concentrated regime, all experimental data collapse to a single curve. This universal behaviour arises because these biopolymers form a hydrogen bonded network, where water molecules move via rearrangement of the free volume.
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Affiliation(s)
- R G M van der Sman
- Agrotechnology and Food Sciences Group, Wageningen University & Research, The Netherlands.
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26
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Hatch HW, Debenedetti PG. Molecular modeling of mechanical stresses on proteins in glassy matrices: Formalism. J Chem Phys 2012; 137:035103. [DOI: 10.1063/1.4734007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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27
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Kaminski K, Adrjanowicz K, Zakowiecki D, Kaminska E, Wlodarczyk P, Paluch M, Pilch J, Tarnacka M. Dielectric Studies on Molecular Dynamics of Two Important Disaccharides: Sucrose and Trehalose. Mol Pharm 2012; 9:1559-69. [DOI: 10.1021/mp2004498] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. Kaminski
- Institute of Physics, University
of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - K. Adrjanowicz
- Institute of Physics, University
of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - D. Zakowiecki
- Preformulation Department R&D, Pharmaceutical Works Polpharma SA, Pelplinska 19, 83-200 Starogard Gdanski, Poland
| | - E. Kaminska
- Department
of Pharmacognosy and
Phytochemistry, Medical University of Silesia, ul. Jagiellonska 4,
41-200 Sosnowiec, Poland
| | - P. Wlodarczyk
- Institute of Physics, University
of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - M. Paluch
- Institute of Physics, University
of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - J. Pilch
- Department of Biological Sciences
Academy of Physical Education, Raciborska 1, 40-074 Katowice, Poland
| | - M. Tarnacka
- Institute of Physics, University
of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland
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28
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Hynninen AP, Matthews JF, Beckham GT, Crowley MF, Nimlos MR. Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water. J Chem Theory Comput 2011; 7:2137-50. [DOI: 10.1021/ct200092t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Gregg T. Beckham
- Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
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30
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Kaminski K, Adrjanowicz K, Kaminska E, Paluch M. Probing of structural relaxation times in the glassy state of sucrose and trehalose based on dynamical properties of two secondary relaxation processes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:061502. [PMID: 21797367 DOI: 10.1103/physreve.83.061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 05/31/2023]
Abstract
Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the β process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the γ relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determine structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett. 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. Solids 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.
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Affiliation(s)
- K Kaminski
- Institute of Physics, Silesian University, Katowice, Poland
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31
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Zhu L, Cai T, Huang J, Stringfellow TC, Wall M, Yu L. Water Self-Diffusion in Glassy and Liquid Maltose Measured by Raman Microscopy and NMR. J Phys Chem B 2011; 115:5849-55. [DOI: 10.1021/jp202663r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lei Zhu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Ting Cai
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Jun Huang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Thomas C. Stringfellow
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
| | - Mark Wall
- Thermo Fisher Scientific, 5225 Verona Road, Madison, Wisconsin 53711, United States
| | - Lian Yu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53706, United States
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32
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Zobrist B, Soonsin V, Luo BP, Krieger UK, Marcolli C, Peter T, Koop T. Ultra-slow water diffusion in aqueous sucrose glasses. Phys Chem Chem Phys 2011; 13:3514-26. [DOI: 10.1039/c0cp01273d] [Citation(s) in RCA: 218] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Meso-Scale Modeling of Polysaccharides in Plant Cell Walls: An Application to Translation of CBMs on the Cellulose Surface. ACTA ACUST UNITED AC 2010. [DOI: 10.1021/bk-2010-1052.ch005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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34
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Kaminski K, Kaminska E, Wlodarczyk P, Adrjanowicz K, Wojnarowska Z, Grzybowska K, Paluch M. Dynamics of the slow mode in the family of six-carbon monosaccharides monitored by dielectric spectroscopy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:365103. [PMID: 21386531 DOI: 10.1088/0953-8984/22/36/365103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Broadband dielectric measurements performed on D-glucose, L-sorbose, D-fructose and D-galactose revealed that, except for the structural relaxation process, one can detect in the liquid phase of these carbohydrates a much slower relaxation mode. Recently we have demonstrated that in D-glucose this relaxation mode might be related to the long range correlation of density fluctuations (LRCDF), also called Fischer clusters (FC). Based on the dielectric data obtained for the four monosaccharides we were able to make a more general conclusion about the characteristic dielectric features of the slow mode in the whole family of carbohydrates. We found out that the timescale separation between structural and considered relaxation reaches up to six decades at the glass transition temperature and the dielectric strength decreases significantly with lowering temperature. Another very interesting feature of the slow process is that it can be described by an almost exponential response function. We have found out that the fragility of the slow process lies within the range m = 44-50. Finally, we have also shown that there is a close link between structural and slow relaxation.
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Affiliation(s)
- K Kaminski
- Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice, Poland
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35
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Kaminski K, Wlodarczyk P, Adrjanowicz K, Kaminska E, Wojnarowska Z, Paluch M. Origin of the Commonly Observed Secondary Relaxation Process in Saccharides. J Phys Chem B 2010; 114:11272-81. [DOI: 10.1021/jp1034773] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. Kaminski
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - P. Wlodarczyk
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - K. Adrjanowicz
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - E. Kaminska
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - Z. Wojnarowska
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - M. Paluch
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
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36
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Wlodarczyk P, Kaminski K, Haracz S, Dulski M, Paluch M, Ziolo J, Wygledowska-Kania M. Kinetic processes in supercooled monosaccharides upon melting: Application of dielectric spectroscopy in the mutarotation studies of D-ribose. J Chem Phys 2010; 132:195104. [DOI: 10.1063/1.3408286] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Townrow S, Roussenova M, Giardiello MI, Alam A, Ubbink J. Specific Volume−Hole Volume Correlations in Amorphous Carbohydrates: Effect of Temperature, Molecular Weight, and Water Content. J Phys Chem B 2010; 114:1568-78. [DOI: 10.1021/jp908462k] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sam Townrow
- H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Mina Roussenova
- H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Maria-Isabelle Giardiello
- H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Ashraf Alam
- H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Job Ubbink
- H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom, and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
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38
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Kaminski K, Kaminska E, Adrjanowicz K, Wojnarowska Z, Wlodarczyk P, Grzybowska K, Dulski M, Wrzalik R, Paluch M. Observation of the dynamics of clusters in d-glucose with the use of dielectric spectroscopy. Phys Chem Chem Phys 2010; 12:723-30. [DOI: 10.1039/b916699h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Transformation of the Strongly Hydrogen Bonded System into van der Waals one Reflected in Molecular Dynamics. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-90-481-3408-3_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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40
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Kaminski K, Kaminska E, Pawlus S, Wlodarczyk P, Paluch M, Ziolo J, Kasprzycka A, Szeja W, Ngai K, Pilch J. Dielectric properties of two diastereoisomers of the arabinose and their equimolar mixture. Carbohydr Res 2009; 344:2547-53. [DOI: 10.1016/j.carres.2009.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 09/22/2009] [Accepted: 10/02/2009] [Indexed: 11/30/2022]
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41
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Bu L, Beckham GT, Crowley MF, Chang CH, Matthews JF, Bomble YJ, Adney WS, Himmel ME, Nimlos MR. The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds. J Phys Chem B 2009; 113:10994-1002. [PMID: 19594145 DOI: 10.1021/jp904003z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A multiscale simulation model is used to construct potential and free energy surfaces for the carbohydrate-binding module [CBM] from an industrially important cellulase, Trichoderma reesei cellobiohydrolase I, on the hydrophobic face of a coarse-grained cellulose Ibeta polymorph. We predict from computation that the CBM alone exhibits regions of stability on the hydrophobic face of cellulose every 5 and 10 A, corresponding to a glucose unit and a cellobiose unit, respectively. In addition, we predict a new role for the CBM: specifically, that in the presence of hydrolyzed cellulose chain ends, the CBM exerts a thermodynamic driving force to translate away from the free cellulose chain ends. This suggests that the CBM is not only required for binding to cellulose, as has been known for two decades, but also that it has evolved to both assist the enzyme in recognizing a cellulose chain end and exert a driving force on the enzyme during processive hydrolysis of cellulose.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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42
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Wlodarczyk P, Kaminski K, Adrjanowicz K, Wojnarowska Z, Czarnota B, Paluch M, Ziolo J, Pilch J. Identification of the slower secondary relaxation’s nature in maltose by means of theoretical and dielectric studies. J Chem Phys 2009; 131:125103. [DOI: 10.1063/1.3224856] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Maiti PK, Li Y, Cagin T, Goddard WA. Structure of polyamidoamide dendrimers up to limiting generations: a mesoscale description. J Chem Phys 2009; 130:144902. [PMID: 19368466 DOI: 10.1063/1.3105338] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polyamidoamide (PAMAM) class of dendrimers was one of the first dendrimers synthesized by Tomalia and co-workers at Dow. Since its discovery the PAMAMs have stimulated many discussions on the structure and dynamics of such hyperbranched polymers. Many questions remain open because the huge conformation disorder combined with very similar local symmetries have made it difficult to characterize experimentally at the atomistic level the structure and dynamics of PAMAM dendrimers. The higher generation dendrimers have also been difficult to characterize computationally because of the large size (294,852 atoms for generation 11) and the huge number of conformations. To help provide a practical means of atomistic computational studies, we have developed an atomistically informed coarse-grained description for the PAMAM dendrimer. We find that a two-bead per monomer representation retains the accuracy of atomistic simulations for predicting size and conformational complexity, while reducing the degrees of freedom by tenfold. This mesoscale description has allowed us to study the structural properties of PAMAM dendrimer up to generation 11 for time scale of up to several nanoseconds. The gross properties such as the radius of gyration compare very well with those from full atomistic simulation and with available small angle x-ray experiment and small angle neutron scattering data. The radial monomer density shows very similar behavior with those obtained from the fully atomistic simulation. Our approach to deriving the coarse-grain model is general and straightforward to apply to other classes of dendrimers.
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Affiliation(s)
- Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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44
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Wlodarczyk P, Kaminski K, Paluch M, Ziolo J. Mutarotation in d-Fructose Melt Monitored by Dielectric Spectroscopy. J Phys Chem B 2009; 113:4379-83. [DOI: 10.1021/jp8095902] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Wlodarczyk
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - K. Kaminski
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - M. Paluch
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - J. Ziolo
- Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
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45
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Lombardo TG, Giovambattista N, Debenedetti PG. Structural and mechanical properties of glassy water in nanoscale confinement. Faraday Discuss 2009; 141:359-76; discussion 443-65. [DOI: 10.1039/b805361h] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Shinyashiki N, Shinohara M, Iwata Y, Goto T, Oyama M, Suzuki S, Yamamoto W, Yagihara S, Inoue T, Oyaizu S, Yamamoto S, Ngai KL, Capaccioli S. The Glass Transition and Dielectric Secondary Relaxation of Fructose−Water Mixtures. J Phys Chem B 2008; 112:15470-7. [DOI: 10.1021/jp807038r] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Shinyashiki
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - M. Shinohara
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - Y. Iwata
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - T. Goto
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - M. Oyama
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - S. Suzuki
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - W. Yamamoto
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - S. Yagihara
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - T. Inoue
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - S. Oyaizu
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - S. Yamamoto
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - K. L. Ngai
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
| | - S. Capaccioli
- Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan, Research & Development Division, Nichirei Foods INC, 9, Shinminato, Mihama-ku, Chiba 261-8545, Japan, Naval Research Laboratory, Washington, D.C. 20375-5320, and Dipartimento di Fisica, Università di Pisa and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127 Pisa, Italy
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47
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Kaminski K, Kaminska E, Hensel-Bielowka S, Pawlus S, Paluch M, Ziolo J. High pressure study on molecular mobility of leucrose. J Chem Phys 2008; 129:084501. [DOI: 10.1063/1.2969816] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Ubbink J, Burbidge A, Mezzenga R. Food structure and functionality: a soft matter perspective. SOFT MATTER 2008; 4:1569-1581. [PMID: 32907147 DOI: 10.1039/b802183j] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure and functionality of foods are described from the perspective of recent advances in soft condensed matter physics. An overview is given of the structure and properties of food materials in terms of the physically relevant length scales. Recent developments in the understanding of the physics of gels, micelles, liquid crystals, biopolymer complexes and amorphous carbohydrates are presented.
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Affiliation(s)
- Job Ubbink
- Nestlé Research Center, CH-1000 Lausanne 26, Switzerland.
| | - Adam Burbidge
- Nestlé Research Center, CH-1000 Lausanne 26, Switzerland. and School of Engineering, University of Wales Singleton Park, Swansea, United KingdomSA2 8PP.
| | - Raffaele Mezzenga
- Nestlé Research Center, CH-1000 Lausanne 26, Switzerland. and University of Fribourg and Fribourg Center for Nanomaterials, CH-1700, Fribourg, Switzerland.
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49
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Kaminski K, Kaminska E, Hensel-Bielowka S, Chelmecka E, Paluch M, Ziolo J, Wlodarczyk P, Ngai KL. Identification of the Molecular Motions Responsible for the Slower Secondary (β) Relaxation in Sucrose. J Phys Chem B 2008; 112:7662-8. [DOI: 10.1021/jp711502a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Kaminski
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - E. Kaminska
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - S. Hensel-Bielowka
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - E. Chelmecka
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - M. Paluch
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - J. Ziolo
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - P. Wlodarczyk
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
| | - K. L. Ngai
- Institute of Physics, University of Silesia, ul. Uniwersytecka 4, 40-007 Katowice, Poland, Statistical Division, Department of Instrumental Analysis, Medical University of Silesia, ul. Ostrogórska 30, Sosnowiec, Poland, and Naval Research Laboratory, Washington, D.C. 20375-5320
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50
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Townrow S, Kilburn D, Alam A, Ubbink J. Molecular Packing in Amorphous Carbohydrate Matrixes. J Phys Chem B 2007; 111:12643-8. [DOI: 10.1021/jp074884l] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sam Townrow
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K., and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Duncan Kilburn
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K., and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Ashraf Alam
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K., and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
| | - Job Ubbink
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K., and Nestlé Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland
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