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Yeole SD. Quantum chemical study of molecular hydration of phenylxylopyranose sugar. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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2
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Lowe JM, Seo Y, Clarke JJ, Gagné MR. Precyclization Conformer Profiles of -SiR 3+- and -Bcat +-Activated Linear Si-Protected Hexitols Explain Condensative Cyclization Selectivities. J Org Chem 2022; 87:12065-12071. [PMID: 36053236 DOI: 10.1021/acs.joc.2c01151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The condensative cyclization of sp3 C-O bonds in per-silylated hexitols is investigated by computation. Conformer searches using the Monte Carlo algorithm, followed by successively higher levels of theory (MMFF, PM3, and B3LYP), of -SiR3+- and -Bcat+-activated substrates lead to structures primed for intramolecular chemistry. Silane activation features O4 to C1 attack, while borane activation suggests boronium ions that activate O5 to C2 reactivity. This, in conjunction with Boltzmann population analysis, parallels reported reactivity for sorbitol, mannitol, and galactitol. Calculations using the meta-hybrid M06-2X functional additionally provide free-energy profiles for each cyclization event. In most of the cases presented, precyclization conformers that position a nucleophilic oxygen less than 3.0 Å from the C-O leaving group correlate to efficient experimental reactivities. Two examples of galactitol containing bridging silyl groups are analyzed computationally, and the experimental outcomes match predictions. The computational regime presented is a step closer to providing predictive power for the reduction of per-functionalized molecules.
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Affiliation(s)
- Jared M Lowe
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Youngran Seo
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua J Clarke
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michel R Gagné
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Prokhorov E, Luna-Barcenas G, Kumar-Krishnan S, Mauricio Sánchez R, Castillo Reyes B, Hernández Vargas J. Probing molecular interactions of polysaccharides in the presence of water. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Palacio J, Monsalve Y, Ramírez-Rodríguez F, López B. Study of encapsulation of polyphenols on succinyl-chitosan nanoparticles. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2020.101610] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Matsuo K, Gekko K. Vacuum Ultraviolet Electronic Circular Dichroism Study of d-Glucose in Aqueous Solution. J Phys Chem A 2020; 124:642-651. [DOI: 10.1021/acs.jpca.9b09210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
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Dong Q, Guo X, Li L, Yu C, Nie L, Tian W, Zhang H, Huang S, Zang H. Understanding hyaluronic acid induced variation of water structure by near-infrared spectroscopy. Sci Rep 2020; 10:1387. [PMID: 31992833 PMCID: PMC6987104 DOI: 10.1038/s41598-020-58417-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/03/2020] [Indexed: 01/26/2023] Open
Abstract
In order to understand the hydration effect of hyaluronic acid (HA) in aqueous solution, near-infrared (NIR) spectroscopy was used to investigate the HA aqueous solutions at different concentrations and temperature. As HA concentration was raised, there was a nonlinear change in absorption value in the first overtone region of OH, indicating the changes of hydration water. A reconstructed spectrum based on principal component analysis (PCA) was established and analyzed with the concept of aquaphotomics. The results showed that HA acted as a structure maker to make water molecules arranged in order. Water species with two hydrogen bonds (S2) and three hydrogen bonds (S3) showed the decrease at low concentration range of 0-40 mg/mL, but increased at higher concentration, indicating the difference in water species at different HA concentration. Meanwhile, HA had the ability to improve the thermal stability of water structure, suggesting a potential bio-protective function. This study provides a unique perspective on the molecular interactions between HA and water molecules, which is helpful for understanding the role of HA in life process and may serve as the basis for HA applications.
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Affiliation(s)
- Qin Dong
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Xueping Guo
- Bloomage Biotechnology Corporation Limited, Tianchen Street 678, Jinan, 250012, China
| | - Lian Li
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Chen Yu
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Lei Nie
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Weilu Tian
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Hui Zhang
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Siling Huang
- Bloomage Biotechnology Corporation Limited, Tianchen Street 678, Jinan, 250012, China
| | - Hengchang Zang
- School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China.
- Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Wenhuaxi Road 44, Jinan, 250012, China.
- National Glycoengineering Research Center, Shandong University, Binhai Road 72, Qingdao, 266200, China.
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Vickman AE, Pohl NLB. Probing deoxysugar conformational preference: A comprehensive computational study investigating the effects of deoxygenation. Carbohydr Res 2018; 475:17-26. [PMID: 30771703 DOI: 10.1016/j.carres.2018.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Deoxysugars are intrinsic components in a number of antibiotics, antimicrobials, and therapeutic agents that often dictate receptor binding, improve efficacy, and provide a diverse toolbox in modifying glycoconjugate function due to an extensive number of unique isomers and inherent conformational flexibility. Hence, this work provides a comprehensive examination of the conformational effects associated with deoxygenation of the pyranose ring. Both the location and degree of deoxygenation were evaluated by interrogating the energetic landscape for a number of mono- and dideoxyhexopyranose derivatives using DFT methods (M05-2X/cc-pVTZ(-f)). Both anomeric forms and in some cases, the alternate chair form, have been investigated in the gas phase. As was documented in a preceding study, variation of the C-6 oxidation state has been shown to affect the anomeric preference of select glucose stereoisomers. Similar results were also observed for several deoxysugar isomers in this work, wherein the alternate anomer was favored upon reduction to the 6-deoxyhexose derivative or oxidation to the hexonic acid. Additionally, comparison of relative Gibbs free energies revealed C-3 deoxygenation imparts greater instability compared to C-2 or C-4 deoxygenation, as indicated by an increase in free energy for 3-deoxysugars. A polarizable continuum solvation model was also applied to empirically validate theoretical results for several deoxysugars, wherein good agreement with both carbon (σ = 1.6 ppm) and proton (σ = 0.20 ppm) NMR shifts was observed for the majority of isomers. Solvated and gas phase anomeric ratios were also calculated and compared favorably to reported literature values, although some discrepancies are noted.
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Affiliation(s)
- Alison E Vickman
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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Oliveira LB, Colherinhas G. TD-DFT and GIAO-NMR spectroscopy studies for maltose and (α- and β)-glucose in water solution using S-MC/QM polarization methodology. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.04.108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers. J Mol Model 2017; 23:214. [PMID: 28656484 DOI: 10.1007/s00894-017-3385-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/04/2017] [Indexed: 01/25/2023]
Abstract
Knowledge of multi-dimensional carbohydrate structure is essential when delineating structure-function relationships in the development of analytical techniques such as ion mobility-mass spectrometry and of carbohydrate-based therapeutics, as well as in rationally modifying the chemical and physical properties of drugs and materials based on sugars. Although monosaccharides are conventionally presumed to adopt the canonical 4C1 chair conformation, it is not well known how altering the substituent identity around the pyranose ring affects the favored conformational state. This work provides a comprehensive and systematic computational comparison of all eight aldohexose isomers in the gas phase with reduction and oxidation at the C-6 position using density functional theory (M05-2X/cc-pVTZ(-f)//B3LYP/6-31G**) to determine the conformational and anomeric preference for each sugar in the gas phase. All 6-deoxyhexose and aldohexose isomers favored the 4C1 chair conformation, while oxidation at C-6 showed a shift in equilibrium to favor the 1C4 chair for β-alluronic acid, β-guluronic acid, and β-iduronic acid. The anomeric preference was found to be significantly affected by a remote change in oxidation state, with the alternate anomer favored for several isomers. These findings provide a fundamental platform to empirically test steric and electronic effects of pyranose substituents, with the goal of formulating straightforward rules that govern carbohydrate reactivity and drive quicker, more efficient syntheses. Graphical abstract A systematic comparative conformational analysis of all eight aldohexose isomers using DFT methods (M05-2X/cc-pVTZ(-f)) reveals changes in anomeric and ring conformational preference upon reduction or oxidation at the C-6 position for several sugars.
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Pandey P, Mallajosyula SS. Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields. J Phys Chem B 2016; 120:6621-33. [PMID: 27266974 DOI: 10.1021/acs.jpcb.6b05546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.
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Affiliation(s)
- Poonam Pandey
- Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India
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Yang G, Zhu C, Zhou L. Deprotonation and acidity characterization of biomass sugars: a first-principles study. J Mol Model 2016; 22:104. [DOI: 10.1007/s00894-016-2972-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/24/2016] [Indexed: 11/24/2022]
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13
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Cui X, Cai W, Shao X. Glucose induced variation of water structure from temperature dependent near infrared spectra. RSC Adv 2016. [DOI: 10.1039/c6ra18912a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The different effects of glucose on water species provide evidence to explain the bioprotective function of carbohydrates in aqueous solutions.
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Affiliation(s)
- Xiaoyu Cui
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Wensheng Cai
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Xueguang Shao
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
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Kosaka A, Aida M, Katsumoto Y. Reconsidering the activation entropy for anomerization of glucose and mannose in water studied by NMR spectroscopy. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.03.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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