1
|
Matamoros E, Pérez EMS, Light ME, Cintas P, Martínez RF, Palacios JC. A True Reverse Anomeric Effect Does Exist After All: A Hydrogen Bonding Stereocontrolling Effect in 2-Iminoaldoses. J Org Chem 2024; 89:7877-7898. [PMID: 38752850 PMCID: PMC11165589 DOI: 10.1021/acs.joc.4c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
Abstract
The reverse anomeric effect is usually associated with the equatorial preference of nitrogen substituents at the anomeric center. Once postulated as another anomeric effect with explanations ranging from electrostatic interactions to delocalization effects, it is now firmly considered to be essentially steric in nature. Through an extensive research on aryl imines from 2-amino-2-deoxyaldoses, spanning nearly two decades, we realized that such substances often show an anomalous anomeric behavior that cannot easily be rationalized on the basis of purely steric grounds. The apparent preference, or stabilization, of the β-anomer takes place to an extent that not only neutralizes but also overcomes the normal anomeric effect. Calculations indicate that there is no stereoelectronic effect opposing the anomeric effect, resulting from the repulsion between electron lone pairs on the imine nitrogen and the endocyclic oxygen. Such data and compelling structural evidence unravel why the exoanomeric effect is largely inhibited. We are now confident, as witnessed by 2-iminoaldoses, that elimination of the exo-anomeric effect in the α-anomer is due to the formation of an intramolecular hydrogen bond between the anomeric hydroxyl and the iminic nitrogen, thereby accounting for a true electronic effect. In addition, discrete solvation may help justify the observed preference for the β-anomer.
Collapse
Affiliation(s)
- Esther Matamoros
- Departamento
de Química Orgánica e Inorgánica, Facultad de
Ciencias, and Instituto del Agua, Cambio Climático y Sostenibilidad
(IACYS), Universidad de Extremadura, 06006 Badajoz, Spain
- Departamento
de Química Orgánica, Universidad
de Málaga, Campus
Teatinos s/n, 29071 Málaga, Spain
- Instituto
de Investigación Biomédica de Málaga y Plataforma
en Nanomedicina − IBIMA, Plataforma Bionand, Parque Tecnológico de Andalucía, 29590 Málaga, Spain
| | - Esther M. S. Pérez
- Departamento
de Química Orgánica e Inorgánica, Facultad de
Ciencias, and Instituto del Agua, Cambio Climático y Sostenibilidad
(IACYS), Universidad de Extremadura, 06006 Badajoz, Spain
| | - Mark E. Light
- Department
of Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Pedro Cintas
- Departamento
de Química Orgánica e Inorgánica, Facultad de
Ciencias, and Instituto del Agua, Cambio Climático y Sostenibilidad
(IACYS), Universidad de Extremadura, 06006 Badajoz, Spain
| | - R. Fernando Martínez
- Departamento
de Química Orgánica e Inorgánica, Facultad de
Ciencias, and Instituto del Agua, Cambio Climático y Sostenibilidad
(IACYS), Universidad de Extremadura, 06006 Badajoz, Spain
| | - Juan C. Palacios
- Departamento
de Química Orgánica e Inorgánica, Facultad de
Ciencias, and Instituto del Agua, Cambio Climático y Sostenibilidad
(IACYS), Universidad de Extremadura, 06006 Badajoz, Spain
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Deljuie F, Rouhani M, Saeidian H. Exceptional design of super/hyperbases based on spiro‐alleneic structures in gas phase: A DFT study. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fatemeh Deljuie
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
| | - Morteza Rouhani
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
| | - Hamid Saeidian
- Department of Science Payame Noor University (PNU) Tehran Iran
| |
Collapse
|
4
|
Mosapour Kotena Z, Razi M, Ahmadi S. Evaluation of hydrogen bonds formation in the selected rare sugars based on 6-31G* and 6-311 + + G(d,p) basis sets. J Mol Model 2021; 27:315. [PMID: 34625848 DOI: 10.1007/s00894-021-04916-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6-311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6-311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced between 158 and 164 (kcal.mol-1). The overall effect of basis set enhancement is to decrease H-bond energies in the range of 1.25 to 2.51 (kcal.mol-1) and stabilization energies between 2 and 5 (kcal.mol-1) in the selected rare sugars at the DFT level of theory. The intramolecular H-bond distances, H-bond energies obtained from the AIM analysis, and also the second-order stabilization energies obtained from the NBO analysis were fluctuated largely depending on the basis set. In summary, it was found that the use of 6-311 ++ G(d,p) basis set to be more efficient results in rare sugars geometry than the 6-31G* basis set.
Collapse
Affiliation(s)
- Zahrabatoul Mosapour Kotena
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Chemistry, Sharif University & Technology, P.O. Box 11365-9516, Tehran, Iran.
| | - Mozhan Razi
- Department of Agricultural Science & Food Industries, Science & Research Branch, Islamic Azad University, Tehran, Iran
| | - Sara Ahmadi
- Department of Chemistry, Firoozabad Branch, Islamic Azad University, Firoozabad, Iran
| |
Collapse
|
5
|
Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry Sharif University of Technology Tehran Iran
| |
Collapse
|
6
|
Lomas JS. Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H … OH and C─H … OH bonding interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:666-684. [PMID: 32201981 DOI: 10.1002/mrc.5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.
Collapse
Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Université de Paris, Paris, France
| |
Collapse
|
7
|
Bojarski KK, Becher J, Riemer T, Lemmnitzer K, Möller S, Schiller J, Schnabelrauch M, Samsonov SA. Synthesis and in silico characterization of artificially phosphorylated glycosaminoglycans. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
8
|
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]
|
9
|
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.
Collapse
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.)
| |
Collapse
|
10
|
Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
Collapse
Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
| |
Collapse
|
11
|
Lomas JS. Intramolecular O-H⋯O and C-H⋯O hydrogen bond cooperativity in D-glucopyranose and D-galactopyranose-A DFT/GIAO, QTAIM/IQA, and NCI approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:748-766. [PMID: 29498091 DOI: 10.1002/mrc.4728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom-atom interaction energies, and atomic charges for partial structures and conformers of α-D-glucopyranose, β-D-glucopyranose, and α-D-galactopyranose built up by introducing OH groups into 2-methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3-diol motif. Variations in the interaction energies reveal that a "new" hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C-H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O-H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O-H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom-atom distances are shorter, and interaction energies are enhanced.
Collapse
Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Paris Diderot University, Sorbonne Paris Cité, F-75205, Paris, France
| |
Collapse
|
12
|
Brzyska A, Płaziński W, Woliński K. Force-induced structural changes in non-sulfated carrageenan based oligosaccharides - a theoretical study. SOFT MATTER 2018; 14:6264-6277. [PMID: 30004100 DOI: 10.1039/c8sm00319j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work we use the Enforced Geometry Optimization (EGO) approach to simulate force-induced structural changes in the monomer, and di- up to pentameric oligomers of neutral and non-sulfated carrageenan based oligosaccharides. Our results indicate that the monosaccharide unit sequence in the oligomeric structure determines: (i) the type(s) of the enforced conformational transition(s), and (ii) the mechanical resistance to external forces. It is a direct consequence of the different glycosidic bonding types in the examined carregeenan based oligosaccharides.
Collapse
Affiliation(s)
- A Brzyska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland.
| | | | | |
Collapse
|
13
|
Bestaoui-Berrekhchi-Berrahma N, Springborg M, Berrekhchi-Berrahma C, Sekkal-Rahal M. DFT and MP2 conformational study of 3,6-anhydro-α-d-galactose in gas phase and in aqueous solvent. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
14
|
Lomas JS, Joubert L. On the importance of intramolecular hydrogen bond cooperativity in d-glucose - an NMR and QTAIM approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:893-901. [PMID: 28432857 DOI: 10.1002/mrc.4599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/15/2017] [Accepted: 04/18/2017] [Indexed: 05/16/2023]
Abstract
The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of d-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules. Association of OH1 in the counterclockwise conformers with a strong acceptor, pyridine, is accompanied by cooperative participation from OH2, but there is no significant change in the bonding of the two following 1,2-diol motifs. The OH6... O5 (G-g+/cc/t and G+g-/cc/t conformers) or OH6... O4 (Tg+/cc/t conformer) distance is reduced, and the OH6 proton is slightly deshielded. In the latter case, this shortening and the associated increase in the OH6-O4 interaction energy may be interpreted as a small cooperative effect, but intermolecular interaction energies are practically the same for all three conformers. In most of the pyridine complexes, one ortho proton interacts with the endocyclic oxygen O5. Analogous results are obtained when the clockwise conformer, G-g+/cl/g-, detected for the α anomer, and a hypothetical conformer, Tt/cl/g-, are complexed with pyridine through OH6. Generally, the cooperative effect does not go beyond the first two OH groups of a chain. Copyright © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Univ Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, F-76821, Mont St Aignan Cedex, France
| |
Collapse
|
15
|
Del Vigo EA, Marino C, Stortz CA. Exhaustive rotamer search of the 4C1 conformation of α- and β-d-galactopyranose. Carbohydr Res 2017; 448:136-147. [DOI: 10.1016/j.carres.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
|
16
|
Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers. J Mol Model 2017; 23:214. [PMID: 28656484 DOI: 10.1007/s00894-017-3385-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/04/2017] [Indexed: 01/25/2023]
Abstract
Knowledge of multi-dimensional carbohydrate structure is essential when delineating structure-function relationships in the development of analytical techniques such as ion mobility-mass spectrometry and of carbohydrate-based therapeutics, as well as in rationally modifying the chemical and physical properties of drugs and materials based on sugars. Although monosaccharides are conventionally presumed to adopt the canonical 4C1 chair conformation, it is not well known how altering the substituent identity around the pyranose ring affects the favored conformational state. This work provides a comprehensive and systematic computational comparison of all eight aldohexose isomers in the gas phase with reduction and oxidation at the C-6 position using density functional theory (M05-2X/cc-pVTZ(-f)//B3LYP/6-31G**) to determine the conformational and anomeric preference for each sugar in the gas phase. All 6-deoxyhexose and aldohexose isomers favored the 4C1 chair conformation, while oxidation at C-6 showed a shift in equilibrium to favor the 1C4 chair for β-alluronic acid, β-guluronic acid, and β-iduronic acid. The anomeric preference was found to be significantly affected by a remote change in oxidation state, with the alternate anomer favored for several isomers. These findings provide a fundamental platform to empirically test steric and electronic effects of pyranose substituents, with the goal of formulating straightforward rules that govern carbohydrate reactivity and drive quicker, more efficient syntheses. Graphical abstract A systematic comparative conformational analysis of all eight aldohexose isomers using DFT methods (M05-2X/cc-pVTZ(-f)) reveals changes in anomeric and ring conformational preference upon reduction or oxidation at the C-6 position for several sugars.
Collapse
|
17
|
Ahmadi S, ManickamAchari V, Hussain Z, Hashim R. Epimeric and anomeric relationship of octyl- α - d -gluco/galactosides: Insight from density functional theory and atom in molecules studies. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Tan Y, Zhao N, Liu J, Li P, Stedwell CN, Yu L, Polfer NC. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:539-550. [PMID: 28050874 DOI: 10.1007/s13361-016-1575-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 05/14/2023]
Abstract
Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Yanglan Tan
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ning Zhao
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
| | - Pengfei Li
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Long Yu
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
| |
Collapse
|
19
|
Chen JL, Nguan HS, Hsu PJ, Tsai ST, Liew CY, Kuo JL, Hu WP, Ni CK. Collision-induced dissociation of sodiated glucose and identification of anomeric configuration. Phys Chem Chem Phys 2017; 19:15454-15462. [DOI: 10.1039/c7cp02393f] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Difference in dehydration barrier heights results in different branching ratio, a simple and fast method for anomeric configuration identification.
Collapse
Affiliation(s)
- 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
| | - Po-Jen Hsu
- 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
| | - Chia Yen Liew
- 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
| | - Wei-Ping Hu
- Department of Chemistry and Biochemistry
- National Chung Cheng University
- Chia-Yi 621
- Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry
| |
Collapse
|
20
|
Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | | |
Collapse
|
21
|
Marianski M, Supady A, Ingram T, Schneider M, Baldauf C. Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose. J Chem Theory Comput 2016; 12:6157-6168. [DOI: 10.1021/acs.jctc.6b00876] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Adriana Supady
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Teresa Ingram
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Markus Schneider
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| |
Collapse
|
22
|
Plazinski W, Lonardi A, Hünenberger PH. Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. J Comput Chem 2015; 37:354-65. [PMID: 26525424 DOI: 10.1002/jcc.24229] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023]
Abstract
This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.
Collapse
Affiliation(s)
- Wojciech Plazinski
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland.,J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, Cracow, 30-239, Poland
| | - Alice Lonardi
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland
| | | |
Collapse
|
23
|
Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
Collapse
Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
| |
Collapse
|
24
|
Murillo JD, Moffet M, Biernacki JJ, Northrup S. High-temperature molecular dynamics simulation of cellobiose and maltose. AIChE J 2015. [DOI: 10.1002/aic.14854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jessica D. Murillo
- Dept. of Chemistry; Tennessee Technological University; Cookeville TN
- College of Interdisciplinary Studies; Environmental Sciences; Tennessee Technological University; Cookeville TN
| | - Melissa Moffet
- Dept. of Civil and Environmental Engineering; Tennessee Technological University; Cookeville TN
| | - Joseph J. Biernacki
- Dept. of Chemical Engineering; Tennessee Technological University; Cookeville TN
| | - Scott Northrup
- Dept. of Chemistry; Tennessee Technological University; Cookeville TN
| |
Collapse
|
25
|
Peña I, Cabezas C, Alonso JL. Unveiling epimerization effects: a rotational study of α-d-galactose. Chem Commun (Camb) 2015; 51:10115-8. [DOI: 10.1039/c5cc01783a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four conformers of α-d-galactose have been detected in the gas phase by laser ablation coupled with broadband Fourier transform microwave spectroscopy.
Collapse
Affiliation(s)
- Isabel Peña
- Grupo de Espectroscopía Molecular (GEM)
- Edificio Quifima, Área de Química-Física
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - Carlos Cabezas
- Grupo de Espectroscopía Molecular (GEM)
- Edificio Quifima, Área de Química-Física
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM)
- Edificio Quifima, Área de Química-Física
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| |
Collapse
|
26
|
Glycosaminoglycan monosaccharide blocks analysis by quantum mechanics, molecular dynamics, and nuclear magnetic resonance. BIOMED RESEARCH INTERNATIONAL 2014; 2014:808071. [PMID: 24804247 PMCID: PMC3997902 DOI: 10.1155/2014/808071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/22/2014] [Indexed: 01/25/2023]
Abstract
Glycosaminoglycans (GAGs) play an important role in many biological processes in the extracellular matrix. In a theoretical approach, structures of monosaccharide building blocks of natural GAGs and their sulfated derivatives were optimized by a B3LYP6311ppdd//B3LYP/6-31+G(d) method. The dependence of the observed conformational properties on the applied methodology is described. NMR chemical shifts and proton-proton spin-spin coupling constants were calculated using the GIAO approach and analyzed in terms of the method's accuracy and sensitivity towards the influence of sulfation, O1-methylation, conformations of sugar ring, and ω dihedral angle. The net sulfation of the monosaccharides was found to be correlated with the 1H chemical shifts in the methyl group of the N-acetylated saccharides both theoretically and experimentally. The ω dihedral angle conformation populations of free monosaccharides and monosaccharide blocks within polymeric GAG molecules were calculated by a molecular dynamics approach using the GLYCAM06 force field and compared with the available NMR and quantum mechanical data. Qualitative trends for the impact of sulfation and ring conformation on the chemical shifts and proton-proton spin-spin coupling constants were obtained and discussed in terms of the potential and limitations of the computational methodology used to be complementary to NMR experiments and to assist in experimental data assignment.
Collapse
|
27
|
Bestaoui-Berrekhchi-Berrahma N, Derreumaux P, Sekkal-Rahal M, Springborg M, Sayede A, Yousfi N, Kadoun AED. Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water. J Mol Model 2012; 19:893-904. [PMID: 23086461 DOI: 10.1007/s00894-012-1621-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.
Collapse
|
28
|
Mosapour Kotena Z, Behjatmanesh-Ardakani R, Hashim R, Manickam Achari V. Hydrogen bonds in galactopyranoside and glucopyranoside: a density functional theory study. J Mol Model 2012; 19:589-99. [DOI: 10.1007/s00894-012-1576-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
|
29
|
Azofra LM, Alkorta I, Elguero J, Popelier PL. Conformational study of the open-chain and furanose structures of d-erythrose and d-threose. Carbohydr Res 2012; 358:96-105. [DOI: 10.1016/j.carres.2012.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
|
30
|
Xie HB, Jin L, Rudić S, Simons JP, Gerber RB. Computational Studies of Protonated β-d-Galactose and Its Hydrated Complex: Structures, Interactions, Proton Transfer Dynamics, and Spectroscopy. J Phys Chem B 2012; 116:4851-9. [DOI: 10.1021/jp3028325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong-bin Xie
- Key Laboratory of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Lin Jin
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Svemir Rudić
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
- Institute of Chemistry
and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| |
Collapse
|
31
|
Alkorta I, Popelier PLA. Computational study of mutarotation in erythrose and threose. Carbohydr Res 2011; 346:2933-9. [DOI: 10.1016/j.carres.2011.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 11/26/2022]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006-Madrid, Spain.
| | | |
Collapse
|
32
|
Assary RS, Redfern PC, Greeley J, Curtiss LA. Mechanistic Insights into the Decomposition of Fructose to Hydroxy Methyl Furfural in Neutral and Acidic Environments Using High-Level Quantum Chemical Methods. J Phys Chem B 2011; 115:4341-9. [DOI: 10.1021/jp1104278] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajeev S. Assary
- Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | | |
Collapse
|
33
|
Hricovíni M. Effect of Solvent and Counterions upon Structure and NMR Spin−Spin Coupling Constants in Heparin Disaccharide. J Phys Chem B 2011; 115:1503-11. [DOI: 10.1021/jp1098552] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
| |
Collapse
|
34
|
Ardèvol A, Biarnés X, Planas A, Rovira C. The Conformational Free-Energy Landscape of β-d-Mannopyranose: Evidence for a 1S5 → B2,5 → OS2 Catalytic Itinerary in β-Mannosidases. J Am Chem Soc 2010; 132:16058-65. [DOI: 10.1021/ja105520h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Albert Ardèvol
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| | - Xevi Biarnés
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| | - Antoni Planas
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| | - Carme Rovira
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| |
Collapse
|
35
|
Assary RS, Redfern PC, Hammond JR, Greeley J, Curtiss LA. Computational Studies of the Thermochemistry for Conversion of Glucose to Levulinic Acid. J Phys Chem B 2010; 114:9002-9. [DOI: 10.1021/jp101418f] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajeev S. Assary
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Paul C. Redfern
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Jeff R. Hammond
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Jeffrey Greeley
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Larry A. Curtiss
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| |
Collapse
|
36
|
Schnupf U, Willett JL, Momany FA. 27 ps DFT molecular dynamics simulation of α-maltose: A reduced basis set study. J Comput Chem 2010; 31:2087-97. [DOI: 10.1002/jcc.21495] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
37
|
Schnupf U, Willett J, Momany F. DFTMD studies of glucose and epimers: anomeric ratios, rotamer populations, and hydration energies. Carbohydr Res 2010; 345:503-11. [DOI: 10.1016/j.carres.2009.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/24/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
|
38
|
Spiwok V, Tvaroska I. Conformational free energy surface of alpha-N-acetylneuraminic acid: an interplay between hydrogen bonding and solvation. J Phys Chem B 2009; 113:9589-94. [PMID: 19374421 DOI: 10.1021/jp8113495] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational free energy surface of alpha-N-acetylneuraminic acid (Neu5Ac, sialic acid) in the space of ring-puckering coordinates was calculated using the metadynamics method. Free energy surfaces in vacuum and with an explicit solvent were calculated in GLYCAM 06 force field. In vacuum three structures are almost equivalently populated, namely, the (2)C(5) chair and the B(3,6)/(2)S(6) and (O)S(3) boat/skew-boat conformations. The B(3,6)/(2)S(6) structure is stabilized by an ionic hydrogen bond between the amide N-H bond and the carboxylic group. However, this structure is unfavorable in a water environment in which the experimentally observed (2)C(5) chair conformation is predicted to be more stable than the other structures. These results indicate that environment significantly influences conformation of Neu5Ac and that Neu5Ac-processing enzymes might modify a conformation of their substrates solely by a changing polarity of the environment. The structure of Neu5Ac bound in influenza neuraminidase ((4)S(2)/B(2,5)) belongs to conformations preferred in a water environment. The free energy penalty of this conformational change was calculated (relative to (2)C(5)) as 10.2 +/- 2.0 and 17.3 +/- 2.0 kJ/mol for (4,O)B/(O)S(3) and (4)S(2), respectively. This result indicates that mimicking of the enzyme-bound conformation is likely to be a viable strategy for the design of neuraminidase inhibitors.
Collapse
Affiliation(s)
- Vojtech Spiwok
- Department of Structure and Function of Saccharides, Centre for Glycomics, Slovak Academy of Sciences, 84538 Bratislava, Slovak Republic.
| | | |
Collapse
|
39
|
Bosma WB, Schnupf U, Willett J, Momany FA. Density functional study of the infrared spectrum of glucose and glucose monohydrates in the OH stretch region. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.03.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
40
|
Csonka GI, French AD, Johnson GP, Stortz CA. Evaluation of Density Functionals and Basis Sets for Carbohydrates. J Chem Theory Comput 2009; 5:679-92. [DOI: 10.1021/ct8004479] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Gábor I. Csonka
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Alfred D. French
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Glenn P. Johnson
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Carlos A. Stortz
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| |
Collapse
|
41
|
Schnupf U, Willett J, Momany FA. DFT conformation and energies of amylose fragments at atomic resolution. Part 2: ‘band-flip’ and ‘kink’ forms of α-maltotetraose. Carbohydr Res 2009; 344:374-83. [DOI: 10.1016/j.carres.2008.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/06/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
|
42
|
DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose. Carbohydr Res 2008; 344:362-73. [PMID: 19111747 DOI: 10.1016/j.carres.2008.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/14/2008] [Accepted: 11/19/2008] [Indexed: 11/21/2022]
Abstract
DFT optimization studies of 90 syn alpha-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a (1)C(4) conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were examined at different locations in the residue sequence, and their influence on the bridge conformations phi/psi values and conformer energy is described. Hydroxyl groups were considered to be homodromic, that is, they are either in the all clockwise, 'c', or all counterclockwise, 'r'. Energy differences between conformations are examined in order to assess the stability of the different conformations and to identify the sources of energy that dictate amylose polymer formation. A small nearly cyclic compact structure is of low energy as one would expect when these flexible molecules are studied in vacuo. Many conformations in which the only differences are a single hydroxymethyl variation in the residue sequence show similar energies and bridge conformations, with trends being a result of the hydroxymethyl as well as hydroxyl orientation. In general the 'c' structures are of lower energy than the 'r' structures, although this is only true for the in vacuo state. The solvent dependence on conformational preference of several low-energy DP-4 structures was investigated via the continuum solvation method COSMO. These results suggest that the 'r' structures may be favored for fully solvated molecules.
Collapse
|
43
|
Nowacki A, Liberek B. Methyl 3-Amino-2,3,6,-trideoxy-l-hexopyranosides in DFT Level Theory Conformational Studies. J Phys Chem A 2008; 112:7072-9. [DOI: 10.1021/jp802248d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrzej Nowacki
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, PL-80-952 Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, PL-80-952 Gdańsk, Poland
| |
Collapse
|
44
|
Karamat S, Fabian WMF. Interaction of Methyl β-d-Xylopyranoside with Metal Ions: Density Functional Theory Study of Cationic and Neutral Bridging and Pendant Complexes. J Phys Chem A 2008; 112:1823-31. [DOI: 10.1021/jp0773583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sajjad Karamat
- Institut für Chemie, Karl-Franzens Universität Graz, Graz A-8010, Austria
| | | |
Collapse
|
45
|
Schnupf U, Willett JL, Bosma WB, Momany FA. DFT conformational studies of α-maltotriose. J Comput Chem 2008; 29:1103-12. [DOI: 10.1002/jcc.20872] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
46
|
Schnupf U, Willett JL, Bosma WB, Momany FA. DFT studies of the disaccharide, α-maltose: relaxed isopotential maps. Carbohydr Res 2007; 342:2270-85. [PMID: 17669381 DOI: 10.1016/j.carres.2007.06.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 06/12/2007] [Accepted: 06/20/2007] [Indexed: 10/23/2022]
Abstract
The disaccharide, alpha-maltose, forms the molecular basis for the analysis of the structure of starch, and determining the conformational energy landscape as the molecule oscillates around the glycosidic bonds is of importance. Thus, it is of interest to determine, using density functionals and a medium size basis set, a relaxed isopotential contour map plotted as a function of the phi(H) and psi(H) dihedral angles. The technical aspects include the method of choosing the starting conformations, the choice of scanning step size, the method of constraining the specific dihedral angles, and the fitting of data to obtain well defined contour maps. Maps were calculated at the B3LYP/6-31+G( *) level of theory in 5 degrees intervals around the (phi(H),psi(H))=(0 degrees ,0 degrees ) position, out to approximately +/-30 degrees or greater, for gg-gg'-c, gg-gg'-r, gt-gt'-c, gt-gt'-r, tg-tg'-c, and tg-tg'-r conformers, as well as one-split gg(c)-gg'(r) conformer. The results show that the preferred conformation of alpha-maltose in vacuo depends strongly upon the hydroxyl group orientations ('c'/'r'), but the energy landscape moving away from the minimum-energy position is generally shallow and transitions between conformational positions can occur without the addition of significant energy. Mapped deviations of selected parameters such as the dipole moment; the C1-O1-C4', H1-C1-O1, and H4'-C4'-O1 bond angles; and deviations in hydroxymethyl rotamers, O5-C5-C6-O6, O5'-C5'-C6'-O6', C5-C6-O6-H, and C5'-C6'-O6'-H', are presented. These allow visualization of the structural and energetic changes that occur upon rotation about the glycosidic bonds. Interactions across the bridge are visualized by deviations in H(O2)...O3', H(O3')...O2, and H1...H4' distances and the H(O2)-O2-C2-C1 and H'(O3')-O3'-C3'-C4' hydroxyl dihedral angles.
Collapse
Affiliation(s)
- Udo Schnupf
- Plant Polymer Research, National Center for Agricultural Utilization Research, ARS, USDA, 1905 N. University St., Peoria, IL 61604, United States
| | | | | | | |
Collapse
|
47
|
Kräutler V, Müller M, Hünenberger PH. Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field. Carbohydr Res 2007; 342:2097-124. [PMID: 17573054 DOI: 10.1016/j.carres.2007.05.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 04/06/2007] [Accepted: 05/01/2007] [Indexed: 11/23/2022]
Abstract
The present article reports long timescale (200 ns) simulations of four beta-D-hexopyranoses (beta-D-glucose, beta-D-mannose, beta-D-galactose and beta-D-talose) using explicit-solvent (water) molecular dynamics and vacuum stochastic dynamics simulations together with the GROMOS 45A4 force field. Free-energy and solvation free-energy differences between the four compounds are also calculated using thermodynamic integration. Along with previous experimental findings, the present results suggest that the formation of intramolecular hydrogen-bonds in water is an 'opportunistic' consequence of the close proximity of hydrogen-bonding groups, rather than a major conformational driving force promoting this proximity. In particular, the conformational preferences of the hydroxymethyl group in aqueous environment appear to be dominated by 1,3-syn-diaxial repulsion, with gauche and solvation effects being secondary, and intramolecular hydrogen-bonding essentially negligible. The rotational dynamics of the exocyclic hydroxyl groups, which cannot be probed experimentally, is found to be rapid (10-100 ps timescale) and correlated (flip-flop hydrogen-bonds interconverting preferentially through an asynchronous disrotatory pathway). Structured solvent environments are observed between the ring and lactol oxygen atoms, as well as between the 4-OH and hydroxymethyl groups. The calculated stability differences between the four compounds are dominated by intramolecular effects, while the corresponding differences in solvation free energies are small. An inversion of the stereochemistry at either C(2) or C(4) from equatorial to axial is associated with a raise in free energy. Finally, the particularly low hydrophilicity of beta-D-talose appears to be caused by the formation of a high-occurrence hydrogen-bonded bridge between the 1,3-syn-diaxial 2-OH and 4-OH groups. Overall, good agreement is found with available experimental and theoretical data on the structural, dynamical, solvation and energetic properties of these compounds. However, this detailed comparison also reveals some discrepancies, suggesting the need (and providing a solid basis) for further refinement.
Collapse
Affiliation(s)
- Vincent Kräutler
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | | |
Collapse
|
48
|
Biarnés X, Ardèvol A, Planas A, Rovira C, Laio A, Parrinello M. The Conformational Free Energy Landscape of β-d-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases. J Am Chem Soc 2007; 129:10686-93. [PMID: 17696342 DOI: 10.1021/ja068411o] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using ab initio metadynamics we have computed the conformational free energy landscape of beta-D-glucopyranose as a function of the puckering coordinates. We show that the correspondence between the free energy and the Stoddard's pseudorotational itinerary for the system is rather poor. The number of free energy minima (9) is smaller than the number of ideal structures (13). Moreover, only six minima correspond to a canonical conformation. The structural features, the electronic properties, and the relative stability of the predicted conformers permit the rationalization of the occurrence of distorted sugar conformations in all the available X-ray structures of beta-glucoside hydrolase Michaelis complexes. We show that these enzymes recognize the most stable distorted conformers of the isolated substrate and at the same time the ones better prepared for catalysis in terms of bond elongation/shrinking and charge distribution. This suggests that the factors governing the distortions present in these complexes are largely dictated by the intrinsic properties of a single glucose unit.
Collapse
Affiliation(s)
- Xevi Biarnés
- Centre especial de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
49
|
Momany FA, Schnupf U, Willett JL, Bosma WB. DFT study of α-maltose: influence of hydroxyl orientations on the glycosidic bond. Struct Chem 2007. [DOI: 10.1007/s11224-007-9191-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
50
|
Altoè P, Stenta M, Bottoni A, Garavelli M. A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0275-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|