1
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Parra-Santamaria M, Insausti A, Alonso ER, Basterretxea FJ, Cocinero EJ. Structural effects of oxidation on sugars: glucose as a precursor of gluconolactone and glucuronolactone. Chem Commun (Camb) 2024; 60:5302-5305. [PMID: 38661549 DOI: 10.1039/d4cc00735b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Although structural information on sugars is wide, experimental studies on the oxidation products of sugars in the gas phase, free from solvent interactions, have been rarely reported. We present an experimental work on the changes in the structure and interactions of two products of glucose oxidation (D-glucono-1,5-lactone (GlcL) and D-glucurono-6,3-lactone (GlcurL)) with respect to their precursor. Features such as intramolecular interactions, ring puckering and tautomerism were observed.
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Affiliation(s)
- Maider Parra-Santamaria
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, Bilbao 48080, Spain
- Instituto Biofisika (CSIC-UPV/EHU), Bilbao 48080, Spain
| | - Aran Insausti
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, Bilbao 48080, Spain
- Instituto Biofisika (CSIC-UPV/EHU), Bilbao 48080, Spain
| | - Elena R Alonso
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, Bilbao 48080, Spain
| | - Francisco J Basterretxea
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, Bilbao 48080, Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, Bilbao 48080, Spain
- Instituto Biofisika (CSIC-UPV/EHU), Bilbao 48080, Spain
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2
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Phan HT, Tsou PK, Hsu PJ, Kuo JL. A first-principles exploration of the conformational space of sodiated di-saccharides assisted by semi-empirical methods and neural network potentials. Phys Chem Chem Phys 2024; 26:9556-9567. [PMID: 38456454 DOI: 10.1039/d3cp05362h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Previous exploration of the conformational space of sodiated mono-saccharides using a random search algorithm leads to ∼103 structurally distinct conformers covering an energy range of ∼150 kJ mol-1. Thus, it is reasonable to expect that the number of distinct conformers for a given disaccharide would be on the order of 106. Efficient identification of distinct conformers at the first-principles level has been demonstrated with the assistance of neural network potential (NNP) with an accuracy of ∼1 kJ mol-1 compared to DFT. Leveraging a local minima database of neutral and sodiated glucose (Glc), we develop algorithms to systematically explore the conformation landscape of 19 Glc-based sodiated disaccharides. To accelerate the exploration, the NNP method is implemented. The NNP achieves an accuracy of ∼2.3 kJ mol-1 compared to DFT, offering a comparable quality to that of DFT. Through a multi-model approach integrating DFTB3, NNP and DFT, we can rapidly locate low-energy disaccharide conformers at the first-principles level. The methodology we show here can be used to efficiently explore the potential energy landscape of any di-saccharides when first-principles accuracy is required.
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Affiliation(s)
- Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
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3
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Yeni O, Allouche AR, Legentil L, Ferrières V, Compagnon I. Conformational preferences of the flexible galactofuranose sugar in gas-phase. Phys Chem Chem Phys 2023. [PMID: 37465915 DOI: 10.1039/d3cp01671d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
In contrast with the predominant pyranose form of galactose, galactofuranose is known to be highly flexible. Such flexibility poses a remarkable challenge in terms of structural studies, thus hindering the in depth understanding of the structure/function relationship in this rare sugar. A thorough computational study based on molecular dynamics and density functional theory supported by vibrational spectroscopy in the gas phase was carried out to provide a better understanding of the instrinsic conformational preferences of galactofuranose. Based on energetic and spectroscopic criteria, we report a subtantially reduced conformational landscape: methyl α-D-galactofuranose adopts E2/1E conformations and methyl β-D-galactofuranose adopts 1T2/1E conformations.
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Affiliation(s)
- Oznur Yeni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France.
| | - Abdul-Rahman Allouche
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France.
| | - Laurent Legentil
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Vincent Ferrières
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Isabelle Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France.
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4
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Gora N, Weselinski LJ, Begoyan VV, Cooper A, Choe JY, Tanasova M. Discrimination of GLUTs by Fructose Isomers Enables Simultaneous Screening of GLUT5 and GLUT2 Activity in Live Cells. ACS Chem Biol 2023; 18:1089-1100. [PMID: 37116192 PMCID: PMC10566446 DOI: 10.1021/acschembio.2c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Facilitative carbohydrate transporters (GLUTs, SLC2 gene family) are transmembrane proteins transporting hexoses and other sugars based on cellular metabolic demands. While a direct link between GLUTs and metabolic disorders has framed them as important biological and medicinal targets, targeting disease-relevant GLUTs remains challenging. In this study, we aimed to identify substrate-GLUT interactions that would discriminate between major fructose transporters. We examined the uptake distribution for conformational and configurational isomers of fructose using the corresponding conformationally locked fluorescently labeled mimetics as probes for assessing GLUT preferences in real time. Through comparative analysis of the uptake of the probes in the yeast-based single GLUT expression systems and the multi-GLUT mammalian cell environment, we established the ability of fructose transporters to discriminate between fructose conformers and epimers. We demonstrated that recreating the conformational and configurational mixture of fructose with molecular probes allows for the specific probe distribution, with fructofuranose mimetic being taken up preferentially through GLUT5 and β-d-fructopyranose mimetic passing through GLUT2. The uptake of α-d-fructopyranose mimetic was found to be independent of GLUT5 or GLUT2. The results of this study provide a new approach to analyzing GLUT5 and GLUT2 activity in live cells, and the findings can be used as a proof-of-concept for multi-GLUT activity screening in live cells. The research also provides new knowledge on substrate-GLUT interactions and new tools for monitoring alterations in GLUT activities.
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Affiliation(s)
- Nazar Gora
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Lukasz J Weselinski
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Vagarshak V Begoyan
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Andrew Cooper
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Jun-Yong Choe
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina 27834, United States
- Department of Biochemistry and Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois 60064, United States
| | - Marina Tanasova
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
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5
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Pinillos P, Camiruaga A, Torres-Hernández F, Basterrechea FJ, Usabiaga I, Fernández JA. Exploring the interaction sites in glucose and galactose using phenol as a probe. Phys Chem Chem Phys 2023; 25:7205-7212. [PMID: 36846922 DOI: 10.1039/d2cp06036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.
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Affiliation(s)
- Paúl Pinillos
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Ander Camiruaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Fernando Torres-Hernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Francisco J Basterrechea
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Imanol Usabiaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - José A Fernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
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6
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Phan HT, Tsou PK, Hsu PJ, Kuo JL. A first-principles exploration of the conformational space of sodiated pyranose assisted by neural network potentials. Phys Chem Chem Phys 2023; 25:5817-5826. [PMID: 36745400 DOI: 10.1039/d2cp04411k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sampling the conformational space of monosaccharides using the first-principles methods is important and as a database of local minima provides a solid base for interpreting experimental measurements such as infrared photo-dissociation (IRPD) spectroscopy or collision-induced dissociation (CID). IRPD emphasizes low-energy conformers and CID can distinguish conformers with distinct reaction pathways. A typical computational approach is to engage empirical or semi-empirical methods to sample the conformational space first, and only selected minima are reoptimized at first-principles levels. In this work, we propose a computational scheme to explore the configurational space of 12 types of sodiated pyranoses with the assistance of a neural network potential (NNP). We demonstrated that it is possible to train an NNP based on the density functional calculations extracted from a previous study on sodiated glucose (Glc), galactose (Gal), and mannose (Man). This NNP yields a better description of the other five types of aldohexoses than the four types of ketohexoses. We further show that such a discrepancy in the accuracy of NNP can be resolved by an active learning scheme where the NNP model is engaged in generating the data and has itself updated. Through this iterative process, we can locate more than 17 000 distinct local minima at the B3LYP/6-311+G(d,p) level and an NNP with an accuracy of 1 kJ mol-1 was created, which can be used for further studies.
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Affiliation(s)
- Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.,International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
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7
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Huynh HT, Tsai ST, Hsu PJ, Biswas A, Phan HT, Kuo JL, Ni CK, Chiu CC. Collision-induced dissociation of Na +-tagged ketohexoses: experimental and computational studies on fructose. Phys Chem Chem Phys 2022; 24:20856-20866. [PMID: 36043336 DOI: 10.1039/d2cp02313j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Collision-induced dissociation tandem mass spectrometry (CID-MSn) and computational investigation at the MP2/6-311+G(d,p) level of theory have been employed to study Na+-tagged fructose, an example of a ketohexose featuring four cyclic isomers: α-fructofuranose (αFruf), β-fructofuranose (βFruf), α-fructopyranose (αFrup), and β-fructopyranose (βFrup). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MSn can distinguish the different fructose forms. Based on a simulation using a micro-kinetic model, we have obtained an overview of the mechanisms for the different dissociation pathways. It has been demonstrated that the preference for the C-C cleavage over the competing isomerization of linear fructose is the main reason for the previously reported differences between the CID-MS spectra of aldohexoses and ketohexoses. In addition, the kinetic modeling helped to confirm the assignment of the different measured mass spectra to the different fructose isomers. The previously reported assignment based on the peak intensities in the HPLC chromatogram had left some open questions as the preference for the dehydration channels did not always follow trends previously observed for aldohexoses. Setting up the kinetic model further enabled us to directly compare the computational and experimental results, which indicated that the model can reproduce most trends in the differences between the dissociation pathways of the four cyclic fructose isomers.
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Affiliation(s)
- Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Department of Applied Chemistry, National Chiayi University, Chiayi, 60004, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Anik Biswas
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei, 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan. .,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Cheng-Chau Chiu
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan. .,Center for Theoretical and Computational Physics, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
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8
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Saragi RT, Juanes M, Abad JL, Pinacho R, Rubio JE, Lesarri A. Chirality-Puckering correlation and intermolecular interactions in Sphingosines: Rotational spectroscopy of jaspine B3 and its monohydrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120531. [PMID: 34857464 DOI: 10.1016/j.saa.2021.120531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/09/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Chirality is determinant for sphingosine biofunctions and pharmacological activity, yet the reasons for the biological chiral selection are not well understood. Here, we characterized the intra- and intermolecular interactions at the headgroup of the cytotoxic anhydrophytosphingosine jaspine B, revealing chirality-dependent correlations between the puckering of the ring core and the formation of amino-alcohol hydrogen bond networks, both in the monomer and the monohydrate. Following the specific synthesis of a shortened 3-carbon side-chain molecule, denoted jaspine B3, six different isomers were observed in a jet expansion using broadband (chirped-pulsed) rotational spectroscopy. Additionally, a single isomer of the jaspine B3 monohydrate was observed, revealing the insertion of water in between the hydroxy and amino groups and the formation of a network of O-H···N-H···Oring hydrogen bonds. The specific jaspine B3 stereochemistry thus creates a double-faced molecule where the exposed lone-pair electrons may easily catalyze the formation of intermolecular aggregates and determine the sphingosine biological properties.
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Affiliation(s)
- Rizalina T Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
| | - José L Abad
- Research Unit on BioActive Molecules (RUBAM), Departament de Química Biològica, Institut de Química Avançada de Catalunya (IQAC-CSIC), Jordi Girona 18-26, Barcelona 08034, Spain
| | - Ruth Pinacho
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11 Valladolid 47011, Spain
| | - José E Rubio
- Departamento de Electrónica, ETSIT, Universidad de Valladolid, Paseo de Belén 11 Valladolid 47011, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias - I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
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9
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Buschmann P, Lengsfeld KG, Djahandideh J, Grabow JU. From rotational resolved spectra to an extended increment system of planar moments allowing ad-hoc conformational identification – Exemplification by the broadband microwave spectrum of α-hydroxyisobutyric acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Singh H, Pinacho P, Obenchain DA, Quesada-Moreno MM, Schnell M. The many forms of alpha-methoxy phenylacetic acid in the gas phase: flexibility, internal dynamics, and their intramolecular interactions. Phys Chem Chem Phys 2022; 24:27312-27320. [DOI: 10.1039/d2cp03962a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Five conformers of the flexible molecule alpha-methoxy phenylacetic acid were identified using rotational spectroscopy. The conformational landscape, internal dynamics, and intramolecular interactions were investigated.
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Affiliation(s)
- Himanshi Singh
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
| | - Pablo Pinacho
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Daniel A. Obenchain
- Institut fur Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - María Mar Quesada-Moreno
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
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11
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Chirality, structure and hydrogen bonding in dithiols: Rotational spectrum of the chiral and meso 2,3-butanedithiol. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Insausti A, Alonso ER, Tercero B, Santos JI, Calabrese C, Vogt N, Corzana F, Demaison J, Cernicharo J, Cocinero EJ. Laboratory Observation of, Astrochemical Search for, and Structure of Elusive Erythrulose in the Interstellar Medium. J Phys Chem Lett 2021; 12:1352-1359. [PMID: 33507076 DOI: 10.1021/acs.jpclett.0c03050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rotational spectroscopy provides the most powerful means of identifying molecules of biological interest in the interstellar medium (ISM), but despite their importance, the detection of carbohydrates has remained rather elusive. Here, we present a comprehensive Fourier transform rotational spectroscopic study of elusive erythrulose, a sugar building block likely to be present in the ISM, employing a novel method of transferring the hygroscopic oily carbohydrate into the gas phase. The high sensitivity of the experiment allowed the rotational spectra of all monosubstituted isotopologue species of 13C-12C3H8O4 to be recorded, which, together with quantum chemical calculations, enabled us to determine their equilibrium geometries (reSE) with great precision. Searches employing the new experimental data for erythrulose have been undertaken in different ISM regions, so far including the cold areas Barnard 1, the pre-stellar core TMC-1, Sagittarius B2. Although no lines of erythrulose were found, this data will serve to enable future searches and possible detections in other ISM regions.
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Affiliation(s)
- Aran Insausti
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Elena R Alonso
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Belen Tercero
- Observatorio Astronómico Nacional (OAN-IGN), c/Alfonso XII, 3, 28014 Madrid, Spain
- Observatorio de Yebes (IGN), Cerro de la Palera, s/n, 19141 Yebes, Guadalajara Spain
| | - José I Santos
- SGIker UPV/EHU, Centro Joxe Mari Korta, Tolosa Hiribidea 72, 20018 Donostia, Spain
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Natalja Vogt
- Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russian Federation
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Jean Demaison
- Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany
| | - Jose Cernicharo
- Instituto de Física Fundamental (IFF-CSIC), Group of Molecular Astrophysics, c/Serrano 123, 28006 Madrid, Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
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Lei J, Alessandrini S, Chen J, Zheng Y, Spada L, Gou Q, Puzzarini C, Barone V. Rotational Spectroscopy Meets Quantum Chemistry for Analyzing Substituent Effects on Non-Covalent Interactions: The Case of the Trifluoroacetophenone-Water Complex. Molecules 2020; 25:E4899. [PMID: 33113920 PMCID: PMC7660205 DOI: 10.3390/molecules25214899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023] Open
Abstract
The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming a seven-membered ring with 2,2,2-trifluoroacetophenone. Accurate intermolecular parameters featuring one classical O-H···O hydrogen bond and one weak C-H···O hydrogen bond have been determined by means of a semi-experimental approach for equilibrium structure. Furthermore, insights on the nature of the established non-covalent interactions have been unveiled by means of different bond analyses. The comparison with the analogous complex formed by acetophenone with water points out the remarkable role played by fluorine atoms in tuning non-covalent interactions.
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Affiliation(s)
- Juncheng Lei
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy;
| | - Junhua Chen
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Cristina Puzzarini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy;
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
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15
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Dvores MP, Çarçabal P, Maître P, Simons JP, Gerber RB. Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside. Phys Chem Chem Phys 2020; 22:4144-4157. [PMID: 32039431 DOI: 10.1039/c9cp06572e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.
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Affiliation(s)
- M P Dvores
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel.
| | - P Çarçabal
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - P Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - J P Simons
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
| | - R B Gerber
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel. and Department of Chemistry, University of California Irvine, CA 92697, USA
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16
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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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Chiu CC, Lin CK, Kuo JL. Improved agreement between experimental and computational results for collision-induced dissociation mass spectrometry of cation-tagged hexoses. Phys Chem Chem Phys 2020; 22:6928-6941. [DOI: 10.1039/d0cp00286k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low exact exchange DFT methods underestimate the dehydration barriers as the charge localization in such transition states is challenging to describe.
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Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Chih-Kai Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei City 10617
- Taiwan
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Procházková E, Cao C, Rawal A, Dračínský M, Bhattacharyya S, Císařová I, Hook JM, Stenzel MH. Polymorphic Transformation of Drugs Induced by Glycopolymeric Vesicles Designed for Anticancer Therapy Probed by Solid-State NMR Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28278-28288. [PMID: 31290309 DOI: 10.1021/acsami.9b05514] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding the nature of the drug-polymer interactions in micellar drug delivery systems and what happens with the drug and the polymer once the complex has formed is essential for the rational design of the polymeric matrices suitable for a particular drug. In this work, glycopolymeric vesicles-a block copolymer, poly(1-O-methacryloyl-β-d-fructopyranose)-b-poly(methyl methacrylate), (PFru36-PMMA160),-designed to target tumor cells loaded with two drugs, ellipticine and curcumin, were characterized. Advanced solid-state NMR spectroscopy and single-crystal/powder X-ray diffraction (XRD) combined with CASTEP calculations shed light on the nature of the drug, the polymer, and their interactions. While the low drug loading (ca. 5%) ensured that the structure, size, and shape of the polymeric vesicles did not change significantly, the solid-state forms of the drugs changed markedly. Upon loading into the vesicles, ellipticine favored a highly ordered form distinctly different from the bulk drug as indicated by 13C solid-state NMR spectroscopy. A detailed analysis of the CASTEP-calculated 13C spectra derived from crystallographic data based on the lowest mean absolute error showed the best match with form I. Moreover, ellipticine before loading was found as a new polymorph and was described by single-crystal XRD as a new orthorhombic Form III. Likewise, curcumin, originally present in monoclinic Form I was found to recrystallize as metastable orthorhombic Form II inside the vesicles. Intermolecular interactions between the polymeric vesicles and the drugs, ellipticine as well as curcumin, were detected using 2D 1H magic angle spinning experiments, indicating that the drugs are localized in the hydrophobic layer of the vesicles.
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Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Prague 166 10 , Czech Republic
| | | | | | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Prague 166 10 , Czech Republic
| | | | - Ivana Císařová
- Faculty of Science , Charles University , Prague 128 43 , Czech Republic
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20
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Tsai S, Liew CY, Hsu C, Huang S, Weng W, Kuo Y, Ni C. Automatic Full Glycan Structural Determination through Logically Derived Sequence Tandem Mass Spectrometry. Chembiochem 2019; 20:2351-2359. [DOI: 10.1002/cbic.201900228] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shang‐Ting Tsai
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Chia Yen Liew
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
- Molecular Science and Technology International Graduate ProgramAcademia Sinica and National University Taipei 10617 Taiwan
| | - Chen Hsu
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Shih‐Pei Huang
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Wei‐Chien Weng
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Yu‐Hsiang Kuo
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
| | - Chi‐Kung Ni
- Institute of Atomic and Molecular SciencesAcademia Sinica P. O. Box 23-166 Taipei 10617 Taiwan
- Department of ChemistryNational Tsing Hua University Hsinchu 30013 Taiwan
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21
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Chiu CC, Huynh HT, Tsai ST, Lin HY, Hsu PJ, Phan HT, Karumanthra A, Thompson H, Lee YC, Kuo JL, Ni CK. Toward Closing the Gap between Hexoses and N-Acetlyhexosamines: Experimental and Computational Studies on the Collision-Induced Dissociation of Hexosamines. J Phys Chem A 2019; 123:6683-6700. [DOI: 10.1021/acs.jpca.9b04143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Hou-Yu Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Arya Karumanthra
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Undergraduate Programme, Indian Institute of Science, Bangalore, 560012, India
| | - Hayden Thompson
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Yu-Chi Lee
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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22
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Uriarte I, Reviriego F, Calabrese C, Elguero J, Kisiel Z, Alkorta I, Cocinero EJ. Bond Length Alternation Observed Experimentally: The Case of 1H‐Indazole. Chemistry 2019; 25:10172-10178. [DOI: 10.1002/chem.201901666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Iciar Uriarte
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| | - Felipe Reviriego
- Instituto de Ciencia y Tecnología de Polímeros (ICTP)CSIC c/Juan de la Cierva, 3 28006 Madrid Spain
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| | - José Elguero
- Instituto de Química MédicaCSIC C/Juan de la Cierva, 3 28006 Madrid Spain
| | - Zbigniew Kisiel
- Institute of PhysicsPolish Academy of Sciences Al. Lotnikow 32/46 02-668 Warszawa Poland
| | - Ibon Alkorta
- Instituto de Química MédicaCSIC C/Juan de la Cierva, 3 28006 Madrid Spain
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
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23
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Chiu CC, Tsai ST, Hsu PJ, Huynh HT, Chen JL, Phan HT, Huang SP, Lin HY, Kuo JL, Ni CK. Unexpected Dissociation Mechanism of Sodiated N-Acetylglucosamine and N-Acetylgalactosamine. J Phys Chem A 2019; 123:3441-3453. [DOI: 10.1021/acs.jpca.9b00934] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cheng-chau Chiu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Hai Thi Huynh
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jien-Lian Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shih-Pei Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Hou-Yu Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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24
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Fatima M, Steber AL, Poblotzki A, Pérez C, Zinn S, Schnell M. Rotational Signatures of Dispersive Stacking in the Formation of Aromatic Dimers. Angew Chem Int Ed Engl 2019; 58:3108-3113. [DOI: 10.1002/anie.201812556] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/17/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mariyam Fatima
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Amanda L. Steber
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Anja Poblotzki
- Institut für Physikalische ChemieUniversität Göttingen Tammannstrasse 6 37077 Göttingen Germany
| | - Cristóbal Pérez
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Sabrina Zinn
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Melanie Schnell
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
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25
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Fatima M, Steber AL, Poblotzki A, Pérez C, Zinn S, Schnell M. Rotational Signatures of Dispersive Stacking in the Formation of Aromatic Dimers. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812556] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mariyam Fatima
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Amanda L. Steber
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Anja Poblotzki
- Institut für Physikalische ChemieUniversität Göttingen Tammannstrasse 6 37077 Göttingen Germany
| | - Cristóbal Pérez
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Sabrina Zinn
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Melanie Schnell
- FS-SMPDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
- Institut für Physikalische ChemieChristian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
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26
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Tautomeric and epimeric equilibria of aldo- and ketohexoses studied by the MD simulations and QM calculations. Carbohydr Res 2019; 474:8-15. [DOI: 10.1016/j.carres.2019.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/17/2022]
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27
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Deng Z, Wang Y, Mou D, Sun Y, Da H, Gao J. Theoretical investigation on acetylene cyclotrimerization catalysed by TiO2and Ti. J PHYS ORG CHEM 2019. [DOI: 10.1002/poc.3934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Zhe‐Peng Deng
- College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou China
- Running Maintenance DepartmentGansu Computing Center Lanzhou China
| | - Yong‐Cheng Wang
- College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou China
| | - Dan Mou
- Huining, No. 1 Middle School Huining County China
| | - Yu Sun
- Experiment Center of Northwest University for Nationalities Lanzhou China
| | - Hu Da
- Running Maintenance DepartmentGansu Computing Center Lanzhou China
| | - Jian‐De Gao
- Gansu University of Chinese Medicine Lanzhou China
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28
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Schindler B, Legentil L, Allouche AR, Ferrières V, Compagnon I. Spectroscopic diagnostic for the ring-size of carbohydrates in the gas phase: furanose and pyranose forms of GalNAc. Phys Chem Chem Phys 2019; 21:12460-12467. [DOI: 10.1039/c8cp04082f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hexoses are sparingly found in nature in the furanose form (5-membered ring).
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Affiliation(s)
- Baptiste Schindler
- Univ. Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622 Villeurbanne
| | - Laurent Legentil
- Univ. Rennes
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226 – ISCR
- F-35 000 Rennes
| | - Abdul-Rhaman Allouche
- Univ. Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622 Villeurbanne
| | - Vincent Ferrières
- Univ. Rennes
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226 – ISCR
- F-35 000 Rennes
| | - Isabelle Compagnon
- Univ. Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622 Villeurbanne
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29
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Lee KH, Schnupf U, Sumpter BG, Irle S. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution. ACS OMEGA 2018; 3:16899-16915. [PMID: 31458314 PMCID: PMC6643604 DOI: 10.1021/acsomega.8b02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 05/12/2023]
Abstract
Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.
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Affiliation(s)
- Ka Hung Lee
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Bredesen
Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Udo Schnupf
- Department
of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
- E-mail: (U.S.)
| | - Bobby G. Sumpter
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan Irle
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- E-mail: (S.I.)
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30
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Alonso ER, León I, Kolesniková L, Alonso JL. The Structural Signs of Sweetness in Artificial Sweeteners: A Rotational Study of Sorbitol and Dulcitol. Chemphyschem 2018; 19:3334-3340. [DOI: 10.1002/cphc.201800977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Elena R. Alonso
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Iker León
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Lucie Kolesniková
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Jose L. Alonso
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
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31
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Zinn S, Schnell M. Flexibility at the Fringes: Conformations of the Steroid Hormone β-Estradiol. Chemphyschem 2018; 19:2915-2920. [PMID: 30055108 DOI: 10.1002/cphc.201800647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Indexed: 11/09/2022]
Abstract
We present the accurate experimental structure of the steroid hormone β-estradiol obtained with high-resolution rotational spectroscopy under the solvent free, isolated, and cold conditions of a molecular jet. This is the first time that the rotational signature of a steroid hormone is reported. β-Estradiol is a primary female sex hormone and features a rigid steroidal ring system. Three conformers could be identified in the cold environment of a supersonic molecular jet, which only differ in the orientation of the two hydroxy groups attached to the steroidal backbone. The conformers are almost isoenergetic and have very similar rotational constants but still could be clearly resolved and assigned. The high sensitivity of the technique allowed us to record and identify all singly substituted 13 C isotopologues in natural abundance for the dominant conformer. The additional spectroscopic constants led to an accurate determination of its experimental molecular structure. Along with a previous comparison of β-estradiol structures in the solid state and the liquid phase, this study completes the investigations in all three main phases by providing the interaction free gas-phase structure.
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Affiliation(s)
- Sabrina Zinn
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, D-, 22607, Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-, 22761, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, Max-Eyth-Str. 1, D-, 24118, Kiel, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, D-, 22607, Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-, 22761, Hamburg, Germany.,Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, Max-Eyth-Str. 1, D-, 24118, Kiel, Germany
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32
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Domingos SR, Pérez C, Medcraft C, Pinacho P, Schnell M. Flexibility unleashed in acyclic monoterpenes: conformational space of citronellal revealed by broadband rotational spectroscopy. Phys Chem Chem Phys 2018; 18:16682-9. [PMID: 27298210 DOI: 10.1039/c6cp02876d] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational flexibility is intrinsically related to the functionality of biomolecules. Elucidation of the potential energy surface is thus a necessary step towards understanding the mechanisms for molecular recognition such as docking of small organic molecules to larger macromolecular systems. In this work, we use broadband rotational spectroscopy in a molecular jet experiment to unravel the complex conformational space of citronellal. We observe fifteen conformations in the experimental conditions of the molecular jet, the highest number of conformers reported to date for a chiral molecule of this size using microwave spectroscopy. Studies of relative stability using different carrier gases in the supersonic expansion reveal conformational relaxation pathways that strongly favour ground-state structures with globular conformations. This study provides a blueprint of the complex conformational space of an important biosynthetic precursor and gives insights on the relation between its structure and biological functionality.
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Affiliation(s)
- Sérgio R Domingos
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany and The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Cristóbal Pérez
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany and The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Chris Medcraft
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Pablo Pinacho
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Department of Physical Chemistry and Inorganic Chemistry, Universidad de Valladolid, Valladolid, Spain
| | - Melanie Schnell
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany and The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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33
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Huynh HT, Phan HT, Hsu PJ, Chen JL, Nguan HS, Tsai ST, Roongcharoen T, Liew CY, Ni CK, Kuo JL. Collision-induced dissociation of sodiated glucose, galactose, and mannose, and the identification of anomeric configurations. Phys Chem Chem Phys 2018; 20:19614-19624. [DOI: 10.1039/c8cp03753a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Different dehydration barrier heights of cis and trans configurations between O1 and O2 provide a simple and fast anomeric configuration identification.
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Affiliation(s)
- Hai Thi Huynh
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Molecular Science and Technology
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Molecular Science and Technology
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Jien-Lian Chen
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Hock Seng Nguan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Thantip Roongcharoen
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry
| | - Chia Yen Liew
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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34
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Usabiaga I, González J, León I, Arnaiz PF, Cocinero EJ, Fernández JA. Influence of the Anomeric Conformation in the Intermolecular Interactions of Glucose. J Phys Chem Lett 2017; 8:1147-1151. [PMID: 28230998 DOI: 10.1021/acs.jpclett.7b00151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Carbohydrates are, together with amino acids, DNA bases, and lipids, the building blocks of living beings. They play a central role in basic functions such as immunity and signaling, which are governed by noncovalent interactions between sugar units and other biomolecules. To get insights into such interactions between monosaccharide units, we used a combination of mass-resolved laser spectroscopy in supersonic expansions and molecular structure calculations. The results obtained clearly demonstrate that the small stability difference between the α/β anomers of glucopyranose derivatives is reversed and amplified during molecular aggregation, making the complexes of the β-anomers significantly more stable. The amplification mechanism seems to be formation of extensive hydrogen-bond networks extending through the two interacting molecules. The same mechanism must be at play in the interactions of biological and synthetic receptors with glycans, which exhibit, in general, a higher affinity for a specific anomer, usually the beta anomer.
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Affiliation(s)
- Imanol Usabiaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Jorge González
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Iker León
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Pedro F Arnaiz
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Emilio J Cocinero
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Barrio Sarriena s/n, 48940 Leioa, Spain
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Barrio Sarriena s/n, 48940 Leioa, Spain
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35
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Ren LK, Zhu LF, Qi T, Tang JQ, Yang HQ, Hu CW. Performance of Dimethyl Sulfoxide and Brønsted Acid Catalysts in Fructose Conversion to 5-Hydroxymethylfurfural. ACS Catal 2017. [DOI: 10.1021/acscatal.6b01802] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li-Ke Ren
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Liang-Fang Zhu
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Ting Qi
- College
of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, P.R. China
| | - Jin-Qiang Tang
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Hua-Qing Yang
- College
of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, P.R. China
| | - Chang-Wei Hu
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China
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36
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Zeng Z, Bernstein ER. Anionic fructose-related conformational and positional isomers assigned through PES experiments and DFT calculations. Phys Chem Chem Phys 2017; 19:23325-23344. [DOI: 10.1039/c7cp03492j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fructose− exists as an open chain structure with substrate dependent specific conformational isomers. (Fructose-H2O)− evidences two types of positional isomers.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
| | - Elliot R. Bernstein
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
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37
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Diaz-Aguirre V, Velez-Pardo C, Jimenez-Del-Rio M. Fructose sensitizes Jurkat cells oxidative stress-induced apoptosis via caspase-dependent and caspase-independent mechanisms. Cell Biol Int 2016; 40:1162-1173. [DOI: 10.1002/cbin.10653] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/31/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Viviana Diaz-Aguirre
- Neuroscience Research Group; Faculty of Medicine; Medical Research Institute; University of Antioquia (UdeA); Calle 70 No. 52-21 and Calle 62 # 52-59, Building 1, Room 412 SIU Medellin Colombia
| | - Carlos Velez-Pardo
- Neuroscience Research Group; Faculty of Medicine; Medical Research Institute; University of Antioquia (UdeA); Calle 70 No. 52-21 and Calle 62 # 52-59, Building 1, Room 412 SIU Medellin Colombia
| | - Marlene Jimenez-Del-Rio
- Neuroscience Research Group; Faculty of Medicine; Medical Research Institute; University of Antioquia (UdeA); Calle 70 No. 52-21 and Calle 62 # 52-59, Building 1, Room 412 SIU Medellin Colombia
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38
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Zinn S, Medcraft C, Betz T, Schnell M. High‐Resolution Rotational Spectroscopy Study of the Smallest Sugar Dimer: Interplay of Hydrogen Bonds in the Glycolaldehyde Dimer. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sabrina Zinn
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- The Hamburg Centre for Ultrafast Imaging Universität Hamburg Luruper Chaussee 149 22761 Hamburg Germany
| | - Chris Medcraft
- School of Chemistry Newcastle University Newcastle upon Tyne UK
| | - Thomas Betz
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- The Hamburg Centre for Ultrafast Imaging Universität Hamburg Luruper Chaussee 149 22761 Hamburg Germany
| | - Melanie Schnell
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- The Hamburg Centre for Ultrafast Imaging Universität Hamburg Luruper Chaussee 149 22761 Hamburg Germany
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39
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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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40
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Favero LB, Uriarte I, Spada L, Écija P, Calabrese C, Caminati W, Cocinero EJ. Solving the Tautomeric Equilibrium of Purine through Analysis of the Complex Hyperfine Structure of the Four (14)N Nuclei. J Phys Chem Lett 2016; 7:1187-1191. [PMID: 26963732 DOI: 10.1021/acs.jpclett.6b00374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The rotational spectra of two tautomers of purine have been measured by pulsed jet Fourier transform microwave spectroscopy coupled to a UV ultrafast vaporization system. The population ratio of the two main tautomers [N(7)H]/[N(9)H] is about 1/40 in the gas phase. It contrasts with the solid state where only the N(7)H species is present, or in solution where a mixture of both tautomers is observed. For both species, a full quadrupolar hyperfine analysis has been performed. This has led to the determination of the full sets of diagonal quadrupole coupling constants of the four (14)N atoms, which have provided crucial information for the unambiguous identification of both species. This work shows the great potential of microwave spectroscopy to study isolated biomolecules in the gas phase. All the work was supported by theoretical calculations.
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Affiliation(s)
- Laura B Favero
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Sezione di Bologna CNR, Via Gobetti 101, I-40129, Bologna, Italy
| | - Iciar Uriarte
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU) , Apartado 644, E-48080 Bilbao, Spain
| | - Lorenzo Spada
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU) , Apartado 644, E-48080 Bilbao, Spain
- Dipartimento di Chimica, "G. Ciamician" dell'Università , Via Selmi 2, I-40126 Bologna, Italy
| | - Patricia Écija
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU) , Apartado 644, E-48080 Bilbao, Spain
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU) , Apartado 644, E-48080 Bilbao, Spain
- Dipartimento di Chimica, "G. Ciamician" dell'Università , Via Selmi 2, I-40126 Bologna, Italy
| | - Walther Caminati
- Dipartimento di Chimica, "G. Ciamician" dell'Università , Via Selmi 2, I-40126 Bologna, Italy
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU) , Apartado 644, E-48080 Bilbao, Spain
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41
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Zinn S, Medcraft C, Betz T, Schnell M. High‐Resolution Rotational Spectroscopy Study of the Smallest Sugar Dimer: Interplay of Hydrogen Bonds in the Glycolaldehyde Dimer. Angew Chem Int Ed Engl 2016; 55:5975-80. [DOI: 10.1002/anie.201511077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 02/16/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Sabrina Zinn
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- The Hamburg Centre for Ultrafast Imaging Universität Hamburg Luruper Chaussee 149 22761 Hamburg Germany
| | - Chris Medcraft
- School of Chemistry Newcastle University Newcastle upon Tyne UK
| | - Thomas Betz
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- The Hamburg Centre for Ultrafast Imaging Universität Hamburg Luruper Chaussee 149 22761 Hamburg Germany
| | - Melanie Schnell
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- The Hamburg Centre for Ultrafast Imaging Universität Hamburg Luruper Chaussee 149 22761 Hamburg Germany
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42
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Yang G, Li X, Zhou L. Adsorption of fructose in Sn-BEA zeolite from periodic density functional calculations. RSC Adv 2016. [DOI: 10.1039/c5ra25554f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sn-BEA zeolite selects fructose conformers from biochemically relevant polysaccharides rather than gas phase, and dispersion effects contribute significantly during interactions.
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Affiliation(s)
- Gang Yang
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
- Schuit Institute of Catalysis
| | - Xiong Li
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
| | - Lijun Zhou
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
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43
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44
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Vogt N, Demaison J, Cocinero EJ, Écija P, Lesarri A, Rudolph HD, Vogt J. The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations. Phys Chem Chem Phys 2016; 18:15555-63. [PMID: 27212641 DOI: 10.1039/c6cp01842d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mixed estimation method yields very accurate equilibrium structures, as observed in deoxyribose and fructose.
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Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
| | - Jean Demaison
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
| | - Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Heinz Dieter Rudolph
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
| | - Jürgen Vogt
- Section of Chemical Information Systems
- Faculty of Sciences
- University of Ulm
- 89069 Ulm
- Germany
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45
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Écija P, Uriarte I, Spada L, Davis BG, Caminati W, Basterretxea FJ, Lesarri A, Cocinero EJ. Furanosic forms of sugars: conformational equilibrium of methyl β-d-ribofuranoside. Chem Commun (Camb) 2016; 52:6241-4. [DOI: 10.1039/c6cc01180b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rotational spectrum of the isolated ribofuranoside unit, the biologically active sugar form, revealed two structures with a similar puckering to the RNA units in crystals.
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Affiliation(s)
- Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Iciar Uriarte
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Lorenzo Spada
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | | | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 1-40126 Bologna
- Italy
| | - Francisco J. Basterretxea
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
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46
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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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47
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Usabiaga I, González J, Arnáiz PF, León I, Cocinero EJ, Fernández JA. Modeling the tyrosine–sugar interactions in supersonic expansions: glucopyranose–phenol clusters. Phys Chem Chem Phys 2016; 18:12457-65. [DOI: 10.1039/c6cp00560h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present here the structure of glucopyranoe–phenol complexes, as revealed by mass-resolved laser spectroscopy and DFT calculations.
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Affiliation(s)
- Imanol Usabiaga
- Dep. of Physical Chemistry
- Fac. of Science and Technology
- University of the Basque Country (UPV/EHU)
- 48940 Leioa
- Spain
| | - Jorge González
- Dep. of Physical Chemistry
- Fac. of Science and Technology
- University of the Basque Country (UPV/EHU)
- 48940 Leioa
- Spain
| | - Pedro F. Arnáiz
- Dep. of Physical Chemistry
- Fac. of Science and Technology
- University of the Basque Country (UPV/EHU)
- 48940 Leioa
- Spain
| | - Iker León
- Dep. of Physical Chemistry
- Fac. of Science and Technology
- University of the Basque Country (UPV/EHU)
- 48940 Leioa
- Spain
| | - Emilio J. Cocinero
- Dep. of Physical Chemistry
- Fac. of Science and Technology
- University of the Basque Country (UPV/EHU)
- 48940 Leioa
- Spain
| | - José A. Fernández
- Dep. of Physical Chemistry
- Fac. of Science and Technology
- University of the Basque Country (UPV/EHU)
- 48940 Leioa
- Spain
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48
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Szczepaniak M, Moc J. Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study. J Phys Chem A 2015; 119:10946-58. [DOI: 10.1021/acs.jpca.5b07720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek Szczepaniak
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
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49
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Shin JW, Bernstein ER. Vacuum ultraviolet photoionization of carbohydrates and nucleotides. J Chem Phys 2015; 140:044330. [PMID: 25669546 DOI: 10.1063/1.4862829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.
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Affiliation(s)
- Joong-Won Shin
- Division of Science, Governors State University, University Park, Illinois 60484-0975, USA
| | - Elliot R Bernstein
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, USA
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50
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Azofra LM, Quesada-Moreno MM, Alkorta I, Avilés-Moreno JR, Elguero J, López-González JJ. Understanding the Aldo-Enediolate Tautomerism of Glycolaldehyde in Basic Aqueous Solutions. Chemphyschem 2015; 16:2226-36. [DOI: 10.1002/cphc.201500139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 11/12/2022]
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