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Novelli F. Terahertz spectroscopy of thick and diluted water solutions. OPTICS EXPRESS 2024; 32:11041-11056. [PMID: 38570962 DOI: 10.1364/oe.510393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 04/05/2024]
Abstract
While bright terahertz sources are used to perform nonlinear experiments, they can be advantageous for high-precision linear measurements of opaque samples. By placing the sample away from the focus, nonlinearities can be suppressed, and sizeable amounts of transmitted radiation detected. Here, this approach is demonstrated for a 0.5 mm thick layer of liquid water in a static sample holder. Variations of the index of refraction as small as (7 ± 2) · 10-4 were detected at 0.58 THz for an aqueous salt solution containing ten millimoles of sodium chloride. To my knowledge, this precision is unprecedented in time-domain spectroscopy studies of diluted aqueous systems or other optically thick and opaque materials.
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Penkov NV. Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules. Biophys Rev 2023; 15:833-849. [PMID: 37974994 PMCID: PMC10643733 DOI: 10.1007/s12551-023-01131-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.
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Affiliation(s)
- Nikita V. Penkov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics RAS, 142290 Pushchino, Russia
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Ge H, Sun Z, Jiang Y, Wu X, Jia Z, Cui G, Zhang Y. Recent Advances in THz Detection of Water. Int J Mol Sci 2023; 24:10936. [PMID: 37446112 DOI: 10.3390/ijms241310936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The frequency range of terahertz waves (THz waves) is between 0.1 and 10 THz and they have properties such as low energy, penetration, transients, and spectral fingerprints, which are especially sensitive to water. Terahertz, as a frontier technology, have great potential in interpreting the structure of water molecules and detecting biological water conditions, and the use of terahertz technology for water detection is currently frontier research, which is of great significance. Firstly, this paper introduces the theory of terahertz technology and summarizes the current terahertz systems used for water detection. Secondly, an overview of theoretical approaches, such as the relaxation model and effective medium theory related to water detection, the relationship between water molecular networks and terahertz spectra, and the research progress of the terahertz detection of water content and water distribution visualization, are elaborated. Finally, the challenge and outlook of applications related to the terahertz wave detection of water are discussed. The purpose of this paper is to explore the research domains on water and its related applications using terahertz technology, as well as provide a reference for innovative applications of terahertz technology in moisture detection.
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Affiliation(s)
- Hongyi Ge
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Zhenyu Sun
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yuying Jiang
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- School of Artificial Intelligence and Big Data, Henan University of Technology, Zhengzhou 450001, China
| | - Xuyang Wu
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Zhiyuan Jia
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Guangyuan Cui
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yuan Zhang
- Key Laboratory of Grain Information Processing & Control, Ministry of Education, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Grain Photoelectric Detection and Control, Zhengzhou 450001, China
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
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Suzuki M, Tsuchiko A, Tanaka Y, Matubayasi N, Mogami G, Uozumi N, Takahashi S. Hyper-mobile Water and Raman 2900 cm -1 Peak Band of Water Observed around Backbone Phosphates of Double Stranded DNA by High-Resolution Spectroscopies and MD Structural Feature Analysis of Water. J Phys Chem B 2023; 127:285-299. [PMID: 36573838 DOI: 10.1021/acs.jpcb.2c06952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High-resolution measurements of microwave dielectric relaxation and Raman spectroscopies for waters in double-stranded (ds) 10-mer DNA solution revealed the presence of hyper-mobile water (HMW) and a marked OH stretching band appearing in the range from 2500 to 3100 cm-1, here called the LA band, at the low wavenumber tail of the major OH stretching band of water. Quantitation of the Raman scattering intensity for ds 10-mer DNA in phosphate or tris(hydroxymethyl)aminomethane (TRIS) buffers showed that the LA band was formed by 2000-3000 water molecules per ds 10-mer DNA, indicating collective OH stretching vibrations of water molecules around the backbone phosphate oxygen atoms. The LA band intensity of ds 10-mer DNA in 10 mM TRIS increased and decreased by 30% with the addition of 2 mM MgCl2 and 2 mM CaCl2, respectively. The LA band intensity and the effect of adding Mg(II) or Ca(II) ions to the band intensity were maintained in the presence of 0.14 M KCl; however, the changes induced by the divalent cations were reduced by half. Molecular dynamics calculations of water molecules around the backbone phosphate groups of ds 10-mer DNA indicate the presence of high-density water and broad regions of fluctuating water density, suggesting that they correspond to HMW and the LA band, respectively.
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Affiliation(s)
- Makoto Suzuki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira Aobaku, Sendai980-8577, Japan.,Graduate School of Engineering, Tohoku University, 6-6 Aoba Aramaki Aobaku, Sendai980-8579, Japan
| | - Akira Tsuchiko
- Graduate School of Engineering, Tohoku University, 6-6 Aoba Aramaki Aobaku, Sendai980-8579, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji Yamashirocho, Tokushima770-8514, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka560-8531, Japan
| | - George Mogami
- Graduate School of Engineering, Tohoku University, 6-6 Aoba Aramaki Aobaku, Sendai980-8579, Japan
| | - Nobuyuki Uozumi
- Graduate School of Engineering, Tohoku University, 6-6 Aoba Aramaki Aobaku, Sendai980-8579, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira Aobaku, Sendai980-8577, Japan
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Waszkiewicz R, Ranasinghe M, Fogg JM, Catanese DJ, Ekiel-Jeżewska ML, Lisicki M, Demeler B, Zechiedrich L, Szymczak P. DNA supercoiling-induced shapes alter minicircle hydrodynamic properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522747. [PMID: 36711572 PMCID: PMC9881935 DOI: 10.1101/2023.01.04.522747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.
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Affiliation(s)
- Radost Waszkiewicz
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maduni Ranasinghe
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Alberta, T1K3M4, Canada
| | - Jonathan M. Fogg
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Daniel J. Catanese
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX 77005-1827, USA
| | - Maria L. Ekiel-Jeżewska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, A. Pawińskiego 5B, 02-106 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Maciej Lisicki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Borries Demeler
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Alberta, T1K3M4, Canada,University of Montana, Dept. of Chemistry and Biochemistry, Missoula, MT 59812, USA,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
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Campo MG, Corral GM. Structural, dynamic, and hydration properties of quercetin and its aggregates in solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:294001. [PMID: 35472688 DOI: 10.1088/1361-648x/ac6a99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Quercetin is a flavonoid present in the human diet with multiple health benefits. Quercetin solutions are inhomogeneous even at very low concentrations due to quercetin's tendency to aggregate. We simulate, using molecular dynamics, three systems of quercetin solutions: infinite dilution, 0.22 M, and 0.46 M. The systems at the two highest concentrations represent regions of the quercetin aggregates, in which the concentration of this molecule is unusually high. We study the behavior of this molecule, its aggregates, and the modifications in the surrounding water. In the first three successive layers of quercetin hydration, the density of water and the hydrogen bonds formations between water molecules are smaller than that of bulk. Quercetin has a hydrophilic surface region that preferentially establishes donor hydrogen bonds with water molecules with relative frequencies from 0.12 to 0.46 at infinite dilution. Also, it has two hydrophobic regions above and below the planes of its rings, whose first hydration layers are further out from quercetin (≈0.3 Å) and their water molecules do not establish hydrogen bonds with it. Water density around the hydrophobic regions is smaller than that of the hydrophilic. Quercetin molecules aggregate inπ-stacking configurations, with a distance of ≈0.37 nm between the planes of their rings, and form bonds between their hydroxyl groups. The formation of quercetin aggregates decreases the hydrogen bonds between quercetin and the surrounding water and produces a subdiffusive behavior in water molecules. Quercetin has a subdiffusive behavior even at infinite dilution, which increases with the number of molecules within the aggregates and the time they remain within them.
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Affiliation(s)
- M G Campo
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Uruguay 151, (6300) Santa Rosa, Argentina
| | - G M Corral
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Uruguay 151, (6300) Santa Rosa, Argentina
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Relationships between Molecular Structure of Carbohydrates and Their Dynamic Hydration Shells Revealed by Terahertz Time-Domain Spectroscopy. Int J Mol Sci 2021; 22:ijms222111969. [PMID: 34769399 PMCID: PMC8584907 DOI: 10.3390/ijms222111969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Despite more than a century of research on the hydration of biomolecules, the hydration of carbohydrates is insufficiently studied. An approach to studying dynamic hydration shells of carbohydrates in aqueous solutions based on terahertz time-domain spectroscopy assay is developed in the current work. Monosaccharides (glucose, galactose, galacturonic acid) and polysaccharides (dextran, amylopectin, polygalacturonic acid) solutions were studied. The contribution of the dissolved carbohydrates was subtracted from the measured dielectric permittivities of aqueous solutions based on the corresponding effective medium models. The obtained dielectric permittivities of the water phase were used to calculate the parameters describing intermolecular relaxation and oscillatory processes in water. It is established that all of the analyzed carbohydrates lead to the increase of the binding degree of water. Hydration shells of monosaccharides are characterized by elevated numbers of hydrogen bonds and their mean energies compared to undisturbed water, as well as by elevated numbers and the lifetime of free water molecules. The axial orientation of the OH(4) group of sugar facilitates a wider distribution of hydrogen bond energies in hydration shells compared to equatorial orientation. The presence of the carboxylic group affects water structure significantly. The hydration of polysaccharides is less apparent than that of monosaccharides, and it depends on the type of glycosidic bonds.
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