1
|
Choutka J, Parkan K, Pohl R, Kaminský J. On the origin of the electronic and magnetic circular dichroism of naphthyl C-glycosides: Anomeric configuration. Carbohydr Res 2024; 535:109021. [PMID: 38171193 DOI: 10.1016/j.carres.2023.109021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Aryl C-glycosides, in which the glycosidic bond is changed to a carbon-carbon bond, are an important family of biologically-active compounds. They often serve as secondary metabolites or exhibit antibiotic and cytostatic activities. Their stability to hydrolysis has made them attractive targets for new drugs. Their conformational behavior often strongly influences the resulting function. Their detailed structural and conformational description is thus highly desirable. This work studies the structure of three different naphthyl C-glycosides using UV-vis absorption as well as electronic and magnetic circular dichroism. It also describes their conformational preferences using a combination of molecular dynamics and DFT calculations. The reliability of these preferences has been verified by simulations of spectral properties and a comparison with their measured spectra. In particular, ECD spectroscopy has been shown to distinguish easily between α- and β-pseudoanomers of aryl C-glycosides. Computer simulations and spectral decomposition have revealed how the resulting ECD patterns of the naphthyl glycosides studied are influenced by different conformer populations. In conclusion, reliable ECD patterns cannot be calculated by separating the naphthyl rotation from other conformational motions. MCD patterns have been similar for all the naphthyl C-glycosides studied. No clear diagnostic features have been found for either the pseudoanomeric configuration or the preferred hydroxymethyl rotamer. Nevertheless, the work has demonstrated the potential of MCD for the study of aryl glycosides interacting with proteins.
Collapse
Affiliation(s)
- Jan Choutka
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic
| | - Kamil Parkan
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic; Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic.
| |
Collapse
|
2
|
Vala D, Mičica M, Cvejn D, Postava K. Broadband Mueller ellipsometer as an all-in-one tool for spectral and temporal analysis of mutarotation kinetics. RSC Adv 2023; 13:6582-6592. [PMID: 36860536 PMCID: PMC9969180 DOI: 10.1039/d3ra00101f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/03/2023] [Indexed: 03/02/2023] Open
Abstract
Spectroscopic Mueller matrix ellipsometry is becoming increasingly routine across physical branches of science, even outside optics. The highly sensitive tracking of the polarization-related physical properties offers a reliable and non-destructive analysis of virtually any sample at hand. If coupled with a physical model, it is impeccable in performance and irreplaceable in versatility. Nonetheless, this method is rarely adopted interdisciplinarily, and when it is, it often plays a supporting role, which does not take benefit of its full potential. To bridge this gap, we present Mueller matrix ellipsometry in the context of chiroptical spectroscopy. In this work, we utilize a commercial broadband Mueller ellipsometer to analyze the optical activity of a saccharides solution. We verify the correctness of the method in the first place by studying the well-known rotatory power of glucose, fructose, and sucrose. By employing a physically meaningful dispersion model, we obtain 2π-unwrapped absolute specific rotations. Besides that, we demonstrate the capability of tracing the glucose mutarotation kinetics from just one set of measurements. Coupling the Mueller matrix ellipsometry with the proposed dispersion model ultimately leads to the precisely determined mutarotation rate constants and spectrally and temporally resolved gyration tensor of individual glucose anomers. In this view, Mueller matrix ellipsometry may stand as an offbeat yet equal technique to those considered classical chiroptical spectroscopy techniques, which may help open new opportunities for broader polarimetric applications in biomedicine and chemistry.
Collapse
Affiliation(s)
- Daniel Vala
- IT4Innovations, National Supercomputing Center, VSB - Technical University of Ostrava 17. listopadu 2172/15 708 00 Ostrava-Poruba Czech Republic
- Faculty of Materials Science and Technology, VSB - Technical University of Ostrava 17. listopadu 2172/15 708 00 Ostrava-Poruba Czech Republic
| | - Martin Mičica
- IT4Innovations, National Supercomputing Center, VSB - Technical University of Ostrava 17. listopadu 2172/15 708 00 Ostrava-Poruba Czech Republic
- Laboratoire de Physique de l'École Normale Supérieure, CNRS UMR 8023 24 rue Lhomond 75005 Paris France
| | - Daniel Cvejn
- ENET Centre, CEET, VSB - Technical University of Ostrava 17. listopadu 2172/15 708 00 Ostrava-Poruba Czech Republic
| | - Kamil Postava
- IT4Innovations, National Supercomputing Center, VSB - Technical University of Ostrava 17. listopadu 2172/15 708 00 Ostrava-Poruba Czech Republic
- Faculty of Materials Science and Technology, VSB - Technical University of Ostrava 17. listopadu 2172/15 708 00 Ostrava-Poruba Czech Republic
| |
Collapse
|
3
|
Palivec V, Johannessen C, Kaminský J, Martinez-Seara H. Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution. PLoS Comput Biol 2022; 18:e1009678. [PMID: 35051172 PMCID: PMC8806073 DOI: 10.1371/journal.pcbi.1009678] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/01/2022] [Accepted: 01/03/2022] [Indexed: 12/13/2022] Open
Abstract
Sugars are crucial components in biosystems and industrial applications. In aqueous environments, the natural state of short saccharides or charged glycosaminoglycans is floating and wiggling in solution. Therefore, tools to characterize their structure in a native aqueous environment are crucial but not always available. Here, we show that a combination of Raman/ROA and, on occasions, NMR experiments with Molecular Dynamics (MD) and Quantum Mechanics (QM) is a viable method to gain insights into structural features of sugars in solutions. Combining these methods provides information about accessible ring puckering conformers and their proportions. It also provides information about the conformation of the linkage between the sugar monomers, i.e., glycosidic bonds, allowing for identifying significantly accessible conformers and their relative abundance. For mixtures of sugar moieties, this method enables the deconvolution of the Raman/ROA spectra to find the actual amounts of its molecular constituents, serving as an effective analytical technique. For example, it allows calculating anomeric ratios for reducing sugars and analyzing more complex sugar mixtures to elucidate their real content. Altogether, we show that combining Raman/ROA spectroscopies with simulations is a versatile method applicable to saccharides. It allows for accessing many features with precision comparable to other methods routinely used for this task, making it a viable alternative. Furthermore, we prove that the proposed technique can scale up by studying the complicated raffinose trisaccharide, and therefore, we expect its wide adoption to characterize sugar structural features in solution.
Collapse
Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
4
|
Kaminský J, Horáčková F, Biačková N, Hubáčková T, Socha O, Kubelka J. Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity. J Phys Chem B 2021; 125:11350-11363. [PMID: 34612644 DOI: 10.1021/acs.jpcb.1c05480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lactic and malic acids are key substances in a number of biochemical processes in living cells and are also utilized in industry. Vibrational spectroscopy represents an efficient and sensitive way to study their structure and interactions. Since water is the natural environment, proper understanding of their molecular dynamics in aqueous solutions is of critical importance. To this end, we employed Raman spectroscopy and Raman optical activity (ROA) to study the conformation of l-lactic and l-malic acids in water (while varying pH, temperature, and concentration), with special emphasis on their double hydrogen bonding dimerization propensity. Raman and ROA experimental data were supported by extensive theoretical calculations of the vibrational properties and by additional experiments (IR absorption, vibrational circular dichroism, and NMR). Conformational behavior of the acids in water was described by molecular dynamics simulations. Reliability of the results was verified by calculating the vibrational properties of populated conformers and by comparing thus obtained spectral features with the experimental data. Calculations estimated the incidence of H-bonded dimers in water to be low in lactic acid and comparable to monomers in malic acid. The "hybrid" approach presented here reveals limitations of relying on the experimental spectra alone to study dimer formation.
Collapse
Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Františka Horáčková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Nina Biačková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Tereza Hubáčková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jan Kubelka
- University of Wyoming, 651 N. 19th Street, Laramie, Wyoming 82072, United States
| |
Collapse
|
5
|
Aerts R, Vanhove J, Herrebout W, Johannessen C. Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity. Chem Sci 2021; 12:5952-5964. [PMID: 35342545 PMCID: PMC8867523 DOI: 10.1039/d1sc01446c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 01/06/2023] Open
Abstract
It is crucial for fundamental physical chemistry techniques to find their application in tackling real-world challenges. Hitherto, Raman optical activity (ROA) spectroscopy is one of the examples where a promising future within the pharmaceutical sector is foreseen, but has not yet been established. Namely, the technique is believed to be able to contribute in investigating the conformational behaviour of drug candidates. We, herein, strive towards the alignment of the ROA analysis outcome and the pharmaceutical expectations by proposing a fresh strategy that ensures a more complete, reliable, and transferable ROA study. The strategy consists of the treatment of the conformational space by means of a principal component analysis (PCA) and a clustering algorithm, succeeded by a thorough ROA spectral analysis and a novel way of estimating the contributions of the different chemical fragments to the total ROA spectral intensities. Here, vancomycin, an antibiotic glycopeptide, has been treated; it is the first antibiotic glycopeptide studied by means of ROA and is a challenging compound in ROA terms. By applying our approach we discover that ROA is capable of independently identifying the correct conformation of vancomycin in aqueous solution. In addition, we have a clear idea of what ROA can and cannot tell us regarding glycopeptides. Finally, the glycopeptide class turns out to be a spectroscopically curious case, as its spectral responses are unlike the typical ROA spectral responses of peptides and carbohydrates. This preludes future ROA studies of this intriguing molecular class. Raman optical activity tackles the complex conformational space of glycopeptide antibiotics.![]()
Collapse
Affiliation(s)
- Roy Aerts
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Jente Vanhove
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171 B-2020 Antwerp Belgium
| |
Collapse
|
6
|
Palivec V, Michal P, Kapitán J, Martinez‐Seara H, Bouř P. Raman Optical Activity of Glucose and Sorbose in Extended Wavenumber Range. Chemphyschem 2020; 21:1272-1279. [DOI: 10.1002/cphc.202000261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Pavel Michal
- Department of OpticsPalacký University Olomouc 17. listopadu 12, 77146 Olomouc Czech Republic
| | - Josef Kapitán
- Department of OpticsPalacký University Olomouc 17. listopadu 12, 77146 Olomouc Czech Republic
| | - Hector Martinez‐Seara
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| |
Collapse
|
7
|
Krupová M, Kessler J, Bouř P. Recent Trends in Chiroptical Spectroscopy: Theory and Applications of Vibrational Circular Dichroism and Raman Optical Activity. Chempluschem 2020; 85:561-575. [DOI: 10.1002/cplu.202000014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and PhysicsCharles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| |
Collapse
|
8
|
Palivec V, Kopecký V, Jungwirth P, Bouř P, Kaminský J, Martinez-Seara H. Simulation of Raman and Raman optical activity of saccharides in solution. Phys Chem Chem Phys 2020; 22:1983-1993. [DOI: 10.1039/c9cp05682c] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All conformers and anomeric forms of sugars in solutions together with the surrounding waters need to be averaged for reliable simulations of vibrational spectra.
Collapse
Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- Prague 6
- Czech Republic
| | - Vladimír Kopecký
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- Prague 2
- Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- Prague 6
- Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- Prague 6
- Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- Prague 6
- Czech Republic
- Gilead Sciences & IOCB Research Center
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- Prague 6
- Czech Republic
| |
Collapse
|
9
|
Tang Y, Cheng F, Feng Z, Jia G, Li C. Stereostructural Elucidation of Glucose Phosphorylation by Raman Optical Activity. J Phys Chem B 2019; 123:7794-7800. [PMID: 31335146 DOI: 10.1021/acs.jpcb.9b05968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phosphorylation of glucose is the prime step in sugar metabolism and energy storage. Two key glucose phosphates are involved, that is, glucose 6-phosphate (G6P) and α-glucose 1-phosphate (αG1P). The chiral conformation of glucose, G6P, and αG1P plays an essential role in enzyme-mediated conversions. However, few techniques were able to give a direct view of the conformational changes from glucose to G6P and αG1P. Here, Raman optical activity (ROA) was used to elucidate the stereochemical evolution of glucose upon phosphorylation. ROA was found to be extremely sensitive to different phosphorylation sites. A characteristic ROA marker of (+)980 cm-1, originated from the phosphate group symmetric stretching vibration, is observed for αG1P with phosphorylation at chiral C1, while no corresponding ROA signal for G6P with phosphorylation at achiral C6 is observed. Phosphorylation-induced gauch-gauch (gg)/gauch-trans (gt) rotamer distribution changes can be sensitively probed by the sign of the ROA band around 1460 cm-1. A positive ROA band at 1465 cm-1 of glucose corresponds to a higher gt ratio, while a negative band at 1455 cm-1 of G6P suggests a dominant gg population, and the disappearance of this ROA band for αG1P indicates a nearly balanced gg/gt distribution. Meanwhile, the phosphorylation at C6 and C1 could cause dramatic reduction of the conformational flexibility of the adjacent C4-OH and C2-OH, respectively. These stereochemical changes revealed by ROA spectra offer a structural basis on the understanding of sugar phosphorylation from the perspective of chirality.
Collapse
Affiliation(s)
- Yuxuan Tang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Feng Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
| | - Zhaochi Feng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
| |
Collapse
|
10
|
Profant V, Johannessen C, Blanch EW, Bouř P, Baumruk V. Effects of sulfation and the environment on the structure of chondroitin sulfate studied via Raman optical activity. Phys Chem Chem Phys 2019; 21:7367-7377. [DOI: 10.1039/c9cp00472f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman optical activity reflects differences in the secondary structure of chondroitin caused by its sulfation.
Collapse
Affiliation(s)
- Václav Profant
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | | | | | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Vladimír Baumruk
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| |
Collapse
|
11
|
Perera AS, Cheramy J, Merten C, Thomas J, Xu Y. IR, Raman, and Vibrational Optical Activity Spectra of Methyl Glycidate in Chloroform and Water: The Clusters-in-a-liquid
Solvation Model. Chemphyschem 2018; 19:2234-2242. [DOI: 10.1002/cphc.201800309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joseph Cheramy
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada T6G 2G2
| | - Christian Merten
- Ruhr-University Bochum; Faculty of Chemistry and Biochemistry; 44801 Bochum Germany
| | - Javix Thomas
- Department of Chemical and Material Engineering; University of Alberta; Edmonton Alberta Canada T6G 1H
| | - Yunjie Xu
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada T6G 2G2
| |
Collapse
|
12
|
Tomobe K, Yamamoto E, Yasui M, Yasuoka K. Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions. Phys Chem Chem Phys 2018; 19:15239-15246. [PMID: 28569306 DOI: 10.1039/c7cp02392h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water-monosaccharide coupled interactions are essential for the function, stability, and dynamics of all glycans. Using molecular dynamics simulations, we investigated the effects of temperature, concentration, and monosaccharide isomer on the hydration structure and water dynamics in the hydration shell of monosaccharides in solution. We found that perturbations of the hydrogen-bond (H-bond) network in the first hydration shell around each monosaccharide molecule can be separated into two regions: one rich in water molecules with donor H-bonds (in the 2.4-2.8 Å region) and the other rich in water molecules with abundant acceptor H-bonds (in the 2.8-3.3 Å region). Moreover, we investigated the dependencies of clustering and conversion of the conformers of the monosaccharides on temperature and concentration. Increasing the concentration enhances monosaccharide clustering in all the monosaccharide solutions, while cluster formation does not depend on temperature. In the clusters, some water molecules in the hydration shell are replaced with monosaccharide oxygen atoms, which contributes to the shrinkage of the hydration shell with increasing monosaccharide concentration. The monosaccharides basically adopt one of two conformers, the stable chair or the unstable boat conformer. We revealed that the hydration structures of the boat and chair conformers were dramatically different. As the temperature increases, the content of the chair conformer decreases. Thus, the conversion of conformers strongly affects the hydration structure around the monosaccharide. These results are critical to understand the important roles of the hydration structure in glycan solutions.
Collapse
Affiliation(s)
- Katsufumi Tomobe
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan.
| | | | | | | |
Collapse
|
13
|
Raich I, Lövyová Z, Trnka L, Parkan K, Kessler J, Pohl R, Kaminský J. Limitations in the description of conformational preferences of C-disaccharides: The (1 → 3)-C-mannobiose case. Carbohydr Res 2017; 451:42-50. [PMID: 28950209 DOI: 10.1016/j.carres.2017.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022]
Abstract
Conformational preferences of two C-glycosyl analogues of Manp-(1 → 3)-Manp, were studied using a combined method of theoretical and experimental chemistry. Molecular dynamics was utilized to provide conformational behavior along C-glycosidic bonds of methyl 3-deoxy-3-C-[(α-d-mannopyranosyl)methyl]-α-d- and l-mannopyranosides. The OPLS2005 and Glycam06 force fields were used. Simulations were performed with explicit water (TIP3P) and methanol. Results were compared with a complete conformational scan at the MM4 level with the dielectric constant corresponding to methanol. In order to verify predicted conformational preferences, vicinal 3JHH NMR coupling constants were calculated by the Karplus equation on simulated potential energy surfaces (PES). A set of new parameters for the Karplus equation was also designed. Predicted 3JHH were compared with experimental data. We also used reverse methodology, in which the 3JHH coupling constants were calculated at the DFT level for each family of (ϕ, ψ)-conformers separately and then experimental values were decomposed onto calculated 3JHH couplings in order to obtain experimentally derived populations of conformers. As an alternative method of evaluation of preferred conformers, analysis of sensitive 13C chemical shifts was introduced. We were able to thoroughly discuss several fundamental issues in predictions of preferred conformers of C-saccharides, such as the solvent effect, reliability of the force field, character of empirical Karplus equation or applicability of NMR parameters in predictions of conformational preferences in general.
Collapse
Affiliation(s)
- Ivan Raich
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Zuzana Lövyová
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Ladislav Trnka
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Kamil Parkan
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| |
Collapse
|
14
|
Jungwirth J, Šebestík J, Šafařík M, Kapitán J, Bouř P. Quantitative Determination of Ala-Ala Conformer Ratios in Solution by Decomposition of Raman Optical Activity Spectra. J Phys Chem B 2017; 121:8956-8964. [DOI: 10.1021/acs.jpcb.7b07154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jakub Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
- Faculty
of Mathematics and Physics, Charles University, Ke Karlovu 3, 12116 Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
| | - Martin Šafařík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department
of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 16610 Prague, Czech Republic
| |
Collapse
|
15
|
Luber S. Raman Optical Activity Spectra from Density Functional Perturbation Theory and Density-Functional-Theory-Based Molecular Dynamics. J Chem Theory Comput 2017; 13:1254-1262. [DOI: 10.1021/acs.jctc.6b00820] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandra Luber
- Department of Chemistry C, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
16
|
Krausbeck F, Autschbach J, Reiher M. Calculated Resonance Vibrational Raman Optical Activity Spectra of Naproxen and Ibuprofen. J Phys Chem A 2016; 120:9740-9748. [DOI: 10.1021/acs.jpca.6b09975] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Krausbeck
- ETH Zürich, Laboratorium für Physikalische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| | - Jochen Autschbach
- Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| |
Collapse
|
17
|
Wu T, Průša J, Kessler J, Dračínský M, Valenta J, Bouř P. Detection of Sugars via Chirality Induced in Europium(III) Compounds. Anal Chem 2016; 88:8878-85. [DOI: 10.1021/acs.analchem.6b02505] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Wu
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, Prague, 16610, Czech Republic
| | - Jiří Průša
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, Prague, 16610, Czech Republic
- Department
of Analytical Chemistry, University of Chemistry and Technology, Technická
5, Prague, 16628, Czech Republic
| | - Jiří Kessler
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, Prague, 16610, Czech Republic
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 12840, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, Prague, 16610, Czech Republic
| | - Jan Valenta
- Faculty
of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 12116, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, Prague, 16610, Czech Republic
| |
Collapse
|