1
|
Lin J, Meredith RJ, Oliver AG, Carmichael I, Serianni AS. Two-bond 13C- 13C spin-coupling constants in saccharides: dependencies on exocyclic hydroxyl group conformation. Phys Chem Chem Phys 2021; 23:22912-22922. [PMID: 34617529 DOI: 10.1039/d1cp03320d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Seven doubly 13C-labeled isotopomers of methyl β-D-glucopyranoside, methyl β-D-xylopyranoside, methyl β-D-galactopyranoside, methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside and methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside were prepared, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13C NMR spectroscopy to determine experimentally the dependence of 2JC1,C3 values in aldopyranosyl rings on the C1-C2-O2-H torsion angle, θ2, involving the C2 carbon of the C1-C2-C3 coupling pathway. Using X-ray crystal structures to determine θ2 in crystalline samples and by selecting compounds that exhibit a relatively wide range of θ2 values in the crystalline state, 2JC1,C3 values measured in crystalline samples were plotted against θ2 and the resulting plot compared to that obtained from density functional theory (DFT) calculations. For θ2 values ranging from ∼90° to ∼240°, very good agreement was observed between the experimental and theoretical plots, providing strong validation of DFT-calculated spin-coupling dependencies on exocyclic C-O bond conformation involving the central carbon of geminal C-C-C coupling pathways. These findings provide new experimental evidence supporting the use of 2JCCC values as non-conventional spin-coupling constraints in MA'AT conformational modeling of saccharides in solution, and the use of NMR spin-couplings not involving coupled hydroxyl hydrogens as indirect probes of C-O bond conformation. Solvomorphism was observed in crystalline βGal-(1→4)-βGlcOCH3 wherein the previously-reported methanol solvate form was found to spontaneously convert to a monohydrate upon air-drying, leading to small but discernible conformational changes in, and a new crystalline form of, this disaccharide.
Collapse
Affiliation(s)
- Jieye Lin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA.
| | - Reagan J Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA.
| | - Allen G Oliver
- Molecular Structure Facility, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Ian Carmichael
- The Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA.
| |
Collapse
|
2
|
Zhang W, Yoon MK, Meredith RJ, Zajicek J, Oliver AG, Hadad M, Frey MH, Carmichael I, Serianni AS. 13C- 13C spin-coupling constants in crystalline 13C-labeled saccharides: conformational effects interrogated by solid-state 13C NMR spectroscopy. Phys Chem Chem Phys 2019; 21:23576-23588. [PMID: 31621725 DOI: 10.1039/c9cp03228b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-state 13C NMR spectroscopy has been used in conjunction with selectively 13C-labeled mono- and disaccharides to measure 13C-13C spin-couplings (JCC) in crystalline samples. This experimental approach allows direct correlation of JCC values with specific molecular conformations since, in crystalline samples, molecular conformation is essentially static and can be determined by X-ray crystallography. JCC values measured in the solid-state in known molecular conformations can then be compared to corresponding JCC values calculated in the same conformations using density functional theory (DFT). The latter comparisons provide important validation of DFT-calculated J-couplings, which is not easily obtained by other approaches and is fundamental to obtaining reliable experiment-based conformational models from redundant J-couplings by MA'AT analysis. In this study, representative 1JCC, 2JCCC and 3JCOCC values were studied as either intra-residue couplings in the aldohexopyranosyl rings of monosaccharides or inter-residue (trans-glycoside) couplings in disaccharides. The results demonstrate that (a) accurate JCC values can be measured in crystalline saccharides that have been suitably labeled with 13C, and (b) DFT-calculated JCC values compare favorably with those determined by solid-state 13C NMR when molecular conformation is a constant in both determinations.
Collapse
Affiliation(s)
- Wenhui Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Zhang W, Turney T, Meredith R, Pan Q, Sernau L, Wang X, Hu X, Woods RJ, Carmichael I, Serianni AS. Conformational Populations of β-(1→4) O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics. J Phys Chem B 2017; 121:3042-3058. [PMID: 28296420 DOI: 10.1021/acs.jpcb.7b02252] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twelve disaccharides containing β-(1→4) linkages and displaying systematic structural variations in the vicinity of these linkages were selectively labeled with 13C to facilitate measurements of multiple NMR spin-spin (scalar; J) coupling constants (JCH and JCC values) across their O-glycosidic linkages. Ensembles of spin-couplings (2JCOC, 3JCOCH, 3JCOCC) sensitive to the two linkage torsion angles, phi (ϕ) and psi (ψ), were analyzed by using parametrized equations obtained from density functional theory (DFT) calculations, Fredholm theory, and circular statistics to calculate experiment-based rotamer populations for ϕ and ψ in each disaccharide. With the statistical program MA'AT, torsion angles ϕ and ψ were modeled as a single von Mises distribution, which yielded two parameters, the mean position and the circular standard deviation (CSD) for each angle. The NMR-derived rotamer populations were compared to those obtained from 1 μs aqueous molecular dynamics (MD) simulations and crystallographic database statistical analyses. Conformer populations obtained exclusively from the MA'AT treatment of redundant J-couplings were in very good agreement with those obtained from the MD simulations, providing evidence that conformational populations can be determined by NMR for mobile molecular elements such as O-glycosidic linkages with minimal input from theory. The approach also provides an experimental means to validate the conformational preferences predicted from MD simulations. The conformational behaviors of ϕ in the 12 disaccharides were very similar, but those of ψ varied significantly, allowing a classification of the 12 disaccharides based on preferred linkage conformation in solution.
Collapse
Affiliation(s)
- Wenhui Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Toby Turney
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Reagan Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Qingfeng Pan
- Omicron Biochemicals Inc. , South Bend, Indiana 46617-2701, United States
| | - Luke Sernau
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Xiaosong Hu
- Department of Chemistry, Wuhan University of Technology , Wuhan 430070, China
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| |
Collapse
|
4
|
Watkin DJ, Cooper RI. Why direct and post-refinement determinations of absolute structure may give different results. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:661-683. [PMID: 27698307 DOI: 10.1107/s2052520616012890] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Direct determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.
Collapse
Affiliation(s)
- David John Watkin
- Chemical Crystallography Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, Oxfordshire OX1 3TA, England
| | - Richard Ian Cooper
- Chemical Crystallography Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, Oxfordshire OX1 3TA, England
| |
Collapse
|
5
|
Klepach T, Zhao H, Hu X, Zhang W, Stenutz R, Hadad MJ, Carmichael I, Serianni AS. Informing saccharide structural NMR studies with density functional theory calculations. Methods Mol Biol 2015; 1273:289-331. [PMID: 25753718 DOI: 10.1007/978-1-4939-2343-4_20] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Density functional theory (DFT) is a powerful computational tool to enable structural interpretations of NMR spin-spin coupling constants ( J-couplings) in saccharides, including the abundant (1)H-(1)H ( JHH), (13)C-(1)H ( JCH), and (13)C-(13)C ( JCC) values that exist for coupling pathways comprised of 1-4 bonds. The multiple hydroxyl groups in saccharides, with their attendant lone-pair orbitals, exert significant effects on J-couplings that can be difficult to decipher and quantify without input from theory. Oxygen substituent effects are configurational and conformational in origin (e.g., axial/equatorial orientation of an OH group in an aldopyranosyl ring; C-O bond conformation involving an exocyclic OH group). DFT studies shed light on these effects, and if conducted properly, yield quantitative relationships between a specific J-coupling and one or more conformational elements in the target molecule. These relationships assist studies of saccharide structure and conformation in solution, which are often challenged by the presence of conformational averaging. Redundant J-couplings, defined as an ensemble of J-couplings sensitive to the same conformational element, are particularly helpful when the element is flexible in solution (i.e., samples multiple conformational states on the NMR time scale), provided that algorithms are available to convert redundant J-values into meaningful conformational models. If the latter conversion is achievable, the data can serve as a means of testing, validating, and refining theoretical methods like molecular dynamics (MD) simulations, which are currently relied upon heavily to assign conformational models of saccharides in solution despite a paucity of experimental data needed to independently validate the method.
Collapse
Affiliation(s)
- Thomas Klepach
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556-5670, USA
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Zhang W, Oliver AG, Vu HM, Duman JG, Serianni AS. Methyl 4-O-β-D-xylopyranosyl β-D-mannopyranoside, a core disaccharide of an antifreeze glycolipid. Acta Crystallogr C 2013; 69:1047-50. [DOI: 10.1107/s0108270113019021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/09/2013] [Indexed: 11/10/2022] Open
Abstract
Methyl β-D-xylopyranosyl-(1→4)-β-D-mannopyranoside, C12<!?tlsb=-0.02pt>H22O10, crystallized as colorless block-like needles from methanol–water solvent. Comparisons to the internal linkage conformations in the two crystallographic forms of the structurally related disaccharide methyl β-D-mannopyranosyl-(1→4)-β-D-xylopyranoside are discussed. Intramolecular inter-residue hydrogen bonding is observed between one mannopyranosyl hydroxy O atom and the ring O atom of the xylopyranosyl residue. Intermolecular hydrogen bonding yields a bilayered two-dimensional sheet of molecules that are located parallel to thebcplane.
Collapse
|
7
|
Flack HD. Absolute-structure reports. Acta Crystallogr C 2013; 69:803-7. [PMID: 23907862 DOI: 10.1107/s0108270113014789] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 05/29/2013] [Indexed: 11/10/2022] Open
Abstract
All the 139 noncentrosymmetric crystal structures published inActa Crystallographica Section Cbetween January 2011 and November 2012 inclusive have been used as the basis of a detailed study of the reporting of absolute structure. These structure determinations cover a wide range of space groups, chemical composition and resonant-scattering contribution. DefiningAandDas the average and difference of the intensities of Friedel opposites, their level of fit has been examined using 2ADand selected-Dplots. It was found, regardless of the expected resonant-scattering contribution to Friedel opposites, that the Friedel-difference intensities are often dominated by random uncertainty and systematic error. An analysis of data collection strategy is provided. It is found that crystal-structure determinations resulting in a Flack parameter close to 0.5 may not necessarily be from crystals twinned by inversion. Friedifstatis shown to be a robust estimator of the resonant-scattering contribution to Friedel opposites, very little affected by the particular space group of a structure nor by the occupation of special positions. There is considerable confusion in the text of papers presenting achiral noncentrosymmetric crystal structures. Recommendations are provided for the optimal way of treating noncentrosymmetric crystal structures for which the experimenter has no interest in determining the absolute structure.<!?tpb=25.7pt>
Collapse
|
8
|
Zhang W, Oliver AG, Vu HM, Duman JG, Serianni AS. Methyl 4-O-β-D-mannopyranosyl β-D-xylopyranoside. Acta Crystallogr C 2012; 68:o502-6. [DOI: 10.1107/s0108270112046689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/12/2012] [Indexed: 11/10/2022] Open
Abstract
Methyl β-D-mannopyranosyl-(1→4)-β-D-xylopyranoside, C12H22O10, (I), crystallizes as colorless needles from water, with two crystallographically independent molecules, (IA) and (IB), comprising the asymmetric unit. The internal glycosidic linkage conformation in molecule (IA) is characterized by a φ′ torsion angle (O5′Man—C1′Man—O1′Man—C4Xyl; Man is mannose and Xyl is xylose) of −88.38 (17)° and a ψ′ torsion angle (C1′Man—O1′Man—C4Xyl—C5Xyl) of −149.22 (15)°, whereas the corresponding torsion angles in molecule (IB) are −89.82 (17) and −159.98 (14)°, respectively. Ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (–CH2OH) C atom in the β-Xylpand β-Manpresidues, respectively. By comparison, the internal glycosidic linkage in the major disorder component of the structurally related disaccharide, methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside), (II) [Zhang, Oliver & Serriani (2012).Acta Cryst.C68, o7–o11], is characterized by φ′ = −85.7 (6)° and ψ′ = −141.6 (8)°. Inter-residue hydrogen bonding is observed between atoms O3Xyland O5′Manin both (IA) and (IB) [O3Xyl...O5′Maninternuclear distances = 2.7268 (16) and 2.6920 (17) Å, respectively], analogous to the inter-residue hydrogen bond detected between atoms O3Xyland O5′Galin (II). Exocyclic hydroxymethyl group conformation in the β-Manpresidue of (IA) isgauche–gauche, whereas that in the β-Manpresidue of (IB) isgauche–trans.
Collapse
|