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Ab initio investigation of the first hydration shell of glucose. Carbohydr Res 2020; 496:108114. [DOI: 10.1016/j.carres.2020.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/15/2020] [Accepted: 08/03/2020] [Indexed: 11/23/2022]
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Tomobe K, Yamamoto E, Kojić D, Sato Y, Yasui M, Yasuoka K. Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds. SCIENCE ADVANCES 2017; 3:e1701400. [PMID: 29282448 PMCID: PMC5741398 DOI: 10.1126/sciadv.1701400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 11/17/2017] [Indexed: 05/29/2023]
Abstract
Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules.
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Affiliation(s)
- Katsufumi Tomobe
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Eiji Yamamoto
- Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Dušan Kojić
- Department of Pharmacology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
| | - Yohei Sato
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Department of System Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masato Yasui
- Department of Pharmacology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio University Global Research Institute, Keio University, Mita, Minato-ku 108-8345, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Keio Advanced Research Institute for Water Biology and Medicine, Keio University, Shinanomachi, Shinjuku-ku 160-8582, Japan
- Keio University Global Research Institute, Keio University, Mita, Minato-ku 108-8345, Japan
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Quesada-Moreno MM, Azofra LM, Avilés-Moreno JR, Alkorta I, Elguero J, López-González JJ. Conformational preference and chiroptical response of carbohydrates D-ribose and 2-deoxy-D-ribose in aqueous and solid phases. J Phys Chem B 2013; 117:14599-614. [PMID: 24134404 DOI: 10.1021/jp405121s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work targets the structural preferences of D-ribose and 2-deoxy-D-ribose in water solution and solid phase. A theoretical DFT (B3LYP and M06-2X) and MP2 study has been undertaken considering the five possible configurations (open-chain, α-furanose, β-furanose, α-pyranose, and β-pyranose) of these two carbohydrates with a comparison of the solvent treatment using only a continuum solvation model (PCM) and the PCM plus one explicit water molecule. In addition, experimental vibrational studies using both nonchiroptical (IR-Raman) and chiroptical (VCD) techniques have been carried out. The theoretical and experimental results show that α- and β-pyranose forms are the dominant configurations for both compounds. Moreover, it has been found that 2-deoxy-D-ribose presents a non-negligible percentage of open-chain forms in aqueous solution, while in solid phase this configuration is absent.
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Affiliation(s)
- María Mar Quesada-Moreno
- Department of Physical and Analytical Chemistry, University of Jaén , Campus Las Lagunillas, E-23071 Jaén, Spain
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Verdel N, Jerman I, Bukovec P. The "autothixotropic" phenomenon of water and its role in proton transfer. Int J Mol Sci 2011; 12:7481-94. [PMID: 22174612 PMCID: PMC3233418 DOI: 10.3390/ijms12117481] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/16/2011] [Accepted: 10/20/2011] [Indexed: 01/25/2023] Open
Abstract
In an experimental study, significantly higher conductivity values than those of freshly prepared chemically analogous solutions were found in aged (~one year old) aqueous solutions, except for those stored frozen. The results surprisingly resemble a previously noticed phenomenon in liquid water, which develops when water is stored in closed vessels. This was observed as a disturbing phenomenon in gravimetric measurements and in luminescence spectroscopy measurements. The phenomenon was termed “autothixotropy of water” due to the weak gel-like behavior which develops spontaneously over time, in which ions seem to play an important role. Here, according to experimental results we propose that contact with hydrophilic surfaces also plays an important role. The role of the “autothixotropy of water” in proton transfer is also discussed.
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Affiliation(s)
- Nada Verdel
- Institute Bion, Stegne 21, 1000 Ljubljana, Slovenia; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +386-41-959-546; Fax: +386-1-513-1147
| | - Igor Jerman
- Institute Bion, Stegne 21, 1000 Ljubljana, Slovenia; E-Mail:
| | - Peter Bukovec
- Department of Inorganic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia; E-Mail:
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Esquivelzeta-Rabell M, Peon J, Cuevas G. Rotational Diffusion of Dihydroxy Coumarins: Effect of OH Groups and Their Relative Position on Solute−Solvent Interactions. J Phys Chem B 2009; 113:8599-606. [DOI: 10.1021/jp9010058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariana Esquivelzeta-Rabell
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, 04510 México, D.F., México
| | - Jorge Peon
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, 04510 México, D.F., México
| | - Gabriel Cuevas
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, 04510 México, D.F., México
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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Suzuki T. The hydration of glucose: the local configurations in sugar-water hydrogen bonds. Phys Chem Chem Phys 2007; 10:96-105. [PMID: 18075687 DOI: 10.1039/b708719e] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydration of a simple sugar is an essential model for understanding interactions between hydrophilic groups and interfacial water molecules. Here I perform first-principles molecular dynamics simulations on a glucose-water system and investigate how individual hydroxyl groups are locally hydrated. I demonstrate that the hydroxyl groups are less hydrated and more incompatible with a locally tetrahedral network of hydrogen bonds than previously thought. The results suggest that the hydroxyl groups form roughly two hydrogen bonds. Further, I find that the local hydration of the hydroxyl groups is sensitively affected by seemingly small variations in the local electronic structure and bond polarity of the groups. My findings offer insight into an atomic-level understanding of sugar-water interactions.
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Affiliation(s)
- Teppei Suzuki
- Advanced Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo, 169-8555, Japan.
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Suzuki T, Kawashima H, Sota T. Conformational Properties of and a Reorientation Triggered by Sugar−Water Vibrational Resonance in the Hydroxymethyl Group in Hydrated β-Glucopyranose. J Phys Chem B 2006; 110:2405-18. [PMID: 16471832 DOI: 10.1021/jp052993z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we discuss the conformational properties of the hydroxymethyl group of beta-glucopyranose in aqueous solution and its reorientation mechanism. First, using the values for the hydroxymethyl torsion (O5-C5-C6-O6) angle obtained by our ab initio simulations, we reestimate the experimental ratio of the hydroxymethyl rotamer populations. The reestimated ratio is found to be in agreement with those previously reported in several computational studies, which probably partly explains the discrepancies between theoretical and experimental studies that have been discussed in the literature. Second, our time-frequency analysis on a reorientation in the hydroxymethyl group in an ab initio molecular dynamics trajectory suggests that, before the reorientation, the O6-H6 stretching mode is vibrationally coupled with a proton-accepting first-hydration-shell water molecule, whereas the C6-O6 stretching mode is vibrationally coupled with a proton-donating one. The amount of the total vibrational energy induced by these vibrational couplings is estimated to be comparable to typical values for the potential barriers between hydroxymethyl rotamers. To elucidate the vibrational couplings, we investigate the hydrogen-bonding properties around the hydroxymethyl group during the pretransition period. The implications, validity, and limitation of a possible reorientation mechanism based on these findings are also discussed.
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Affiliation(s)
- Teppei Suzuki
- Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.
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Biarnés X, Nieto J, Planas A, Rovira C. Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase. J Biol Chem 2006; 281:1432-41. [PMID: 16260784 DOI: 10.1074/jbc.m507643200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.
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Affiliation(s)
- Xevi Biarnés
- Centre especial de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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