1
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Pascariu M, Bernasconi L, Krzystyniak M, Taylor J, Rudić S. Comprehensive Analysis of Methyl-β-D-ribofuranoside: A Multifaceted Spectroscopic and Theoretical Approach. J Phys Chem A 2024; 128:2111-2120. [PMID: 38469744 PMCID: PMC10961842 DOI: 10.1021/acs.jpca.4c00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
This study presents a comprehensive analysis of the vibrational spectra of methyl-β-D-ribofuranoside. Employing a combination of inelastic neutron scattering, Raman, and infrared spectroscopy allows for the observation of all modes regardless of the selection rules. The experimental techniques were complemented by density functional theory computational methods using both gas-phase (Gaussian) and solid-state (CRYSTAL, CASTEP) approaches to provide an unambiguous assignment of the defining vibrational features. Two distinct structures of the molecule were identified in the unit cell, differentiated mainly by the orientation of the furanose ring O-H bonds. The low-energy region of the spectrum (<400 cm-1) is dominated by lattice vibrations and functional group rotation, while the midenergy region is dominated by out-of-plane bending motions of the furanose ring (400-900 cm-1) and by C-H bending in the methyl and methylene groups (1400-1600 cm-1). The high-energy region (>2800 cm-1) encompasses the C-H and O-H stretching modes and offers convincing evidence of at least one H-bonding interaction between the two structures of methyl-β-D-ribofuranoside.
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Affiliation(s)
- Matei Pascariu
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Leonardo Bernasconi
- Center
for Research Computing & Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Matthew Krzystyniak
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| | - James Taylor
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| | - Svemir Rudić
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
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2
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Konieczna J, Wrońska K, Kalińska M, Liberek B, Nowacki A. Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies. Carbohydr Res 2024; 537:109055. [PMID: 38373388 DOI: 10.1016/j.carres.2024.109055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/22/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).
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Affiliation(s)
- Justyna Konieczna
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Karolina Wrońska
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Marta Kalińska
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Andrzej Nowacki
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland.
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3
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Meredith RJ, McGurn M, Euell C, Rutkowski P, Cook E, Carmichael I, Serianni AS. MA'AT Analysis of Aldofuranosyl Rings: Unbiased Modeling of Conformational Equilibria and Dynamics in Solution. Biochemistry 2022; 61:239-251. [PMID: 35104120 DOI: 10.1021/acs.biochem.1c00630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MA'AT analysis has been applied to methyl β-d-ribofuranoside (3) and methyl 2-deoxy-β-d-erythro-pentofuranoside (4) to demonstrate the ability of this new experimental method to determine multi-state conformational equilibria in solution. Density functional theory (DFT) was used to obtain parameterized equations for >20 NMR spin-coupling constants sensitive to furanose ring conformation in 3 and 4, and these equations were used in conjunction with experimental spin-couplings to produce unbiased MA'AT models of ring pseudorotation. These models describe two-state north-south conformational exchange consistent with results obtained from traditional treatments of more limited sets of NMR spin-couplings (e.g., PSEUROT). While PSEUROT, MA'AT, and aqueous molecular dynamics models yielded similar two-state models, MA'AT analysis gives more reliable results since significantly more experimental observables are employed compared to PSEUROT, and no assumptions are needed to render the fitting tractable. MA'AT models indicate a roughly equal distribution of north and south ring conformers of 4 in aqueous (2H2O) solution compared to ∼80% north forms for 3. Librational motion about the mean pseudorotation phase angles P of the preferred north and south conformers of 3 in solution is more constrained than that for 4. The greater rigidity of the β-ribo ring may be caused by synergistic stereoelectronic effects and/or noncovalent (e.g., hydrogen-bonding) interactions in solution that preferentially stabilize north forms of 3. MA'AT analysis of oligonucleotides and other furanose ring-containing biomolecules promises to improve current experimental models of sugar ring behavior in solution and help reveal context effects on ring conformation in more complex biologically important systems.
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Affiliation(s)
- Reagan J Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Margaret McGurn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Christopher Euell
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Peter Rutkowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Evan Cook
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
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4
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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.
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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.
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5
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Alabugin IV, Kuhn L, Krivoshchapov NV, Mehaffy P, Medvedev MG. Anomeric effect, hyperconjugation and electrostatics: lessons from complexity in a classic stereoelectronic phenomenon. Chem Soc Rev 2021; 50:10212-10252. [PMID: 34542133 DOI: 10.1039/d1cs00564b] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interplay of multiple components (steric, electrostatic, stereoelectronic, dispersive, etc.) that define the overall energy, structure, and reactivity of organic molecules can be a daunting task. The task becomes even more difficult when multiple approaches based on different physical premises disagree in their analysis of a multicomponent molecular system. Herein, we will use a classic conformational "oddity", the anomeric effect, to discuss the value of identifying the key contributors to reactivity that can guide chemical predictions. After providing the background related to the relevant types of hyperconjugation and a brief historic outline of the origins of the anomeric effect, we outline variations of its patterns and provide illustrative examples for the role of the anomeric effect in structure, stability, and spectroscopic properties. We show that the complete hyperconjugative model remains superior in explaining the interplay between structure and reactivity. We will use recent controversies regarding the origin of the anomeric effect to start a deeper discussion relevant to any electronic effect. Why are such questions inherently controversial? How to describe a complex quantum system using a model that is "as simple as possible, but no simpler"? What is a fair test for such a model? Perhaps, instead of asking "who is right and who is wrong?" one should ask "why do we disagree?". Stereoelectronic thinking can reconcile quantum complexity with chemical intuition and build the conceptual bridge between structure and reactivity. Even when many factors contribute to the observed structural and conformational trends, electron delocalization is a dominating force when the electronic demand is high (i.e., bonds are breaking as molecules distort from their equilibrium geometries). In these situations, the role of orbital interactions increases to the extent where they can define reactivity. For example, negative hyperconjugation can unleash the "underutilized" stereoelectronic power of unshared electrons (i.e., the lone pairs) to stabilize a developing positive charge at an anomeric carbon. This analysis paves the way for the broader discussion of the omnipresent importance of negative hyperconjugation in oxygen-containing functional groups. From that point of view, the stereoelectronic component of the anomeric effect plays a unique role in guiding reaction design.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation. .,Lomonosov Moscow State University, Leninskie Gory 1 (3), Moscow, 119991, Russian Federation
| | - Patricia Mehaffy
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation. .,A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova St., 119991 Moscow, Russian Federation
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6
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Dong Y, Ding W, Sun C, Ji X, Ling C, Zhou Z, Chen Z, Chen X, Ju J. Julichrome Monomers from Marine Gastropod Mollusk‐Associated
Streptomyces
and Stereochemical Revision of Julichromes Q
3 ⋅ 5
and Q
3 ⋅ 3. Chem Biodivers 2020; 17:e2000057. [PMID: 32091654 DOI: 10.1002/cbdv.202000057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yuliang Dong
- School of Basic MedicineQingdao University Qingdao 266071 P. R. China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
| | - Wenjuan Ding
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
- College of OceanographyUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Changli Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
| | - Xiaoqi Ji
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
- College of OceanographyUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Chunyao Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
| | - Zhenbin Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
- College of OceanographyUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zhiyun Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
| | - Xuehong Chen
- School of Basic MedicineQingdao University Qingdao 266071 P. R. China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
- College of OceanographyUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
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7
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Calabrese C, Uriarte I, Insausti A, Vallejo-López M, Basterretxea FJ, Cochrane SA, Davis BG, Corzana F, Cocinero EJ. Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars. ACS CENTRAL SCIENCE 2020; 6:293-303. [PMID: 32123748 PMCID: PMC7047431 DOI: 10.1021/acscentsci.9b01277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 06/10/2023]
Abstract
The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.
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Affiliation(s)
- Camilla Calabrese
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Iciar Uriarte
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Aran Insausti
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Montserrat Vallejo-López
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Francisco J. Basterretxea
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Stephen A. Cochrane
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
- The
Rosalind Franklin Institute, Oxfordshire, OX11 0FA, United Kingdom
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La
Rioja, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
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8
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Stortz CA, Sarotti AM. Exhaustive exploration of the conformational landscape of mono- and disubstituted five-membered rings by DFT and MP2 calculations. RSC Adv 2019; 9:24134-24145. [PMID: 35527879 PMCID: PMC9069843 DOI: 10.1039/c9ra03524a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set. Our results showed that the conformational preference of these compounds was governed mainly by the specific characteristics of the substituents, with a minor influence of the level of theory employed. After a detailed analysis of the computational data, we found an interesting preference of the electronegative substituents to take pseudo-axial positions, whereas alkyl groups preferred adopting the pseudo-equatorial locations. Such preferences were pronounced with MP2 and M06-2X and underestimated by B3LYP. Despite each level of theory affording different landscapes in many cases, as a general trend, we noticed that M06-2X afforded much higher correlation with the MP2 results than B3LYP.
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Affiliation(s)
- Carlos A Stortz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas, Departamento de Química Orgánica, Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR) Ciudad Universitaria, Pab. 2 1428 Buenos Aires Argentina
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Suipacha 531 Rosario 2000 Argentina
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9
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Hövelmann Y, Lewin L, Hübner F, Humpf HU. Large-Scale Screening of Foods for Glucose-Derived β-Carboline Alkaloids by Stable Isotope Dilution LC-MS/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3890-3899. [PMID: 30875225 DOI: 10.1021/acs.jafc.8b07150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The occurrence of glucose-derived β-carboline alkaloids tangutorid E (Tan E) and tangutorid F (Tan F) as well as their dehydroxy-derivatives (DH-Tan E/F) was investigated in a broad variety of foodstuffs by LC-MS/MS-based stable isotope dilution analysis (SIDA). For that purpose, the target compounds and their 13C6-stable isotope-labeled analogues were synthesized from l-tryptophan and (13C6-)d-glucose and used to develop a rapid LC-MS/MS-SIDA method. After validation for several food matrices, the method was applied to the analysis of these β-carbolines in 80 food items. Quantitative amounts were detected in 46.3, 50.0, and 42.5% of the samples regarding Tan E, Tan F, and DH-Tan E/F, respectively, with corresponding ranges of 0.01-6.75, 0.01-5.07, and 0.01-0.75 mg/kg; the highest amounts were found in processed tomato products. A combination of the obtained occurrence data in foods with average food consumption data led to the calculation of rough estimates for the chronic daily intake of those alkaloids, yielding values of 0.44, 0.36, and 0.13 μg/kg body weight/day for Tan E, Tan F, and DH-Tan E/F, respectively. Evidently, the consumption of processed tomato-based products accounts for the majority of the total daily intake of the investigated β-carbolines; the potential bioactivities of Tan E, Tan F, and DH-Tan E/F have yet to be investigated.
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Affiliation(s)
- Yannick Hövelmann
- Institute of Food Chemistry , Westfälische Wilhelms-Universität Münster , 48149 Münster , Germany
| | - Lea Lewin
- Institute of Food Chemistry , Westfälische Wilhelms-Universität Münster , 48149 Münster , Germany
| | - Florian Hübner
- Institute of Food Chemistry , Westfälische Wilhelms-Universität Münster , 48149 Münster , Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry , Westfälische Wilhelms-Universität Münster , 48149 Münster , Germany
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10
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Nester K, Gaweda K, Plazinski W. A GROMOS Force Field for Furanose-Based Carbohydrates. J Chem Theory Comput 2019; 15:1168-1186. [DOI: 10.1021/acs.jctc.8b00838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
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11
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Alabugin IV, dos Passos Gomes G, Abdo MA. Hyperconjugation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1389] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Zhang W, Turney T, Surjancev I, Serianni AS. Enzymatic synthesis of ribo- and 2'-deoxyribonucleosides from glycofuranosyl phosphates: An approach to facilitate isotopic labeling. Carbohydr Res 2017; 449:125-133. [PMID: 28780317 DOI: 10.1016/j.carres.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/25/2023]
Abstract
Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by 1H and 13C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 °C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate. This methodology is attractive for the preparation of stable isotopically labeled ribo- and 2'-deoxyribonucleosides because of the ease of product purification and convenient use and recycling of nitrogen bases. The approach eliminates the need for separate reactions to prepare individual furanose-labeled ribonucleosides, since only one ribonucleoside (inosine) needs to be labeled, if desired, in the furanose ring, the latter achieved by a high-yield chemical N-glycosylation. 2'-Deoxyribonucleosides were prepared from 2'-deoxyinosine using the same methodology with minor modifications.
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Affiliation(s)
- Wenhui Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670 USA.
| | - Toby Turney
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670 USA
| | - Ivana Surjancev
- Department of Chemistry and Biochemistry, 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.
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13
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Wang X, Woods RJ. Insights into furanose solution conformations: beyond the two-state model. JOURNAL OF BIOMOLECULAR NMR 2016; 64:291-305. [PMID: 26968894 PMCID: PMC5115177 DOI: 10.1007/s10858-016-0028-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/08/2016] [Indexed: 05/15/2023]
Abstract
A two-state model is commonly used for interpreting ring conformations of furanoses based on NMR scalar (3) J-coupling constants, with the ring populating relatively narrow distributions in the North and the South of the pseudorotation itinerary. The validity of this simple approach has been questioned, and is examined here in detail employing molecular dynamics (MD) simulations with a new GLYCAM force field parameter set for furanoses. Theoretical (3) J-coupling constants derived from unrestrained MD simulations with the new furanose-specific parameters agreed with the experimental coupling constants to within 1 Hz on average. The results confirm that a two state model is a reasonable description for the ring conformation in the majority of methyl furanosides. However, in the case of methyl α-D-arabinofuranoside the ring populates a continuum of states from North to South via the eastern side of the pseudorotational itinerary. Two key properties are responsible for these differences. Firstly, East and West regions in β- and α-anomers, respectively, are destabilized by the absence of the anomeric effect. And, secondly, East or West conformations can be further destabilized by repulsive interactions among vicinal hydroxyl groups and ring oxygen atoms when the vicinal hydroxyl groups are in syn-configurations (such as in ribose and lyxose) more so than when in anti (arabinose, xylose).
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Affiliation(s)
- Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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14
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Sun JF, Wu Y, Yang B, Liu Y. Chemical Constituents of Marine Sponge Halichondria sp. from South China Sea. Chem Nat Compd 2015. [DOI: 10.1007/s10600-015-1467-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Yuan Y, Tian JM, Xiao J, Shao Q, Gao JM. Bioactive metabolites isolated from Penicillium sp. YY-20, the endophytic fungus from Ginkgo biloba. Nat Prod Res 2013; 28:278-81. [PMID: 24144081 DOI: 10.1080/14786419.2013.850686] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Six known metabolites, adenosine (1), methyl β-D-ribofuranoside (2), adenine (3), 2'-deoxyadenosine (4), 3-methylpiperazine-2,5-dione (5) and 2'-deoxyuridine (6), were isolated from the extracts of the endophytic fungus Penicillium sp. YY-20 isolated from the root of Ginkgo biloba, and their structures were elucidated by spectroscopic methods. The antioxidant and growth-promoting activities of these compounds were first evaluated. The results indicated that compounds 1, 3 and 4 exhibited potential DPPH-scavenging activities compared with positive control. In addition, all the compounds (except 5) stimulated seed germination of Raphanus sativus, Brassica napus and Brassica chinensis but had weak stimulating effect on their root and hypocotyl growth.
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Affiliation(s)
- Yuan Yuan
- a College of Science, Northwest A&F University , Yangling , Shaanxi 712100 , P.R. China
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16
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Richards MR, Bai Y, Lowary TL. Comparison between DFT- and NMR-based conformational analysis of methyl galactofuranosides. Carbohydr Res 2013; 374:103-14. [PMID: 23660004 DOI: 10.1016/j.carres.2013.03.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 11/26/2022]
Abstract
Galactofuranose (Galf) residues are found in a number of microbial polysaccharides, and knowledge of their conformation is key for developing a molecular-level understanding of their biological roles. To this end, we studied 180 conformations of methyl α- and β-Galf in aqueous solution (COSMO solvation model) using density functional theory (DFT). We compare the calculated low energy conformations to those determined from the program PSEUROT using (1)H NMR data. The lowest energy ring conformation for methyl α-Galf is (2)E, and this conformer is also the major solution conformation obtained by NMR spectroscopy. For methyl β-Galf, (4)E is the lowest energy ring conformation; however, DFT results do not agree with the solution NMR spectroscopic results. Additionally, we developed Galf-specific Karplus-like equations from these conformations.
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Affiliation(s)
- Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada
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17
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Rusakov YY, Krivdin LB. Modern quantum chemical methods for calculating spin–spin coupling constants: theoretical basis and structural applications in chemistry. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n02abeh004350] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013; 42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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19
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Zhang W, Hu X, Carmichael I, Serianni AS. Methyl [13C]Glucopyranosiduronic Acids: Effect of COOH Ionization and Exocyclic Structure on NMR Spin-Couplings. J Org Chem 2012; 77:9521-34. [DOI: 10.1021/jo3011182] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenhui Zhang
- Department of Chemistry and Biochemistry and §The Radiation Laboratory, University of Notre Dame, Notre Dame,
Indiana 46556-5670, United States
| | - Xiaosong Hu
- Department of Chemistry and Biochemistry and §The Radiation Laboratory, University of Notre Dame, Notre Dame,
Indiana 46556-5670, United States
| | - Ian Carmichael
- Department of Chemistry and Biochemistry and §The Radiation Laboratory, University of Notre Dame, Notre Dame,
Indiana 46556-5670, United States
| | - Anthony S. Serianni
- Department of Chemistry and Biochemistry and §The Radiation Laboratory, University of Notre Dame, Notre Dame,
Indiana 46556-5670, United States
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20
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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21
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Dynamic stereochemistry of Topiramate (anticonvulsant drug) in solution: theoretical approaches and experimental validation. Carbohydr Res 2012; 348:47-54. [DOI: 10.1016/j.carres.2011.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/10/2011] [Accepted: 11/11/2011] [Indexed: 11/23/2022]
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22
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Anizelli PR, Favaro DC, Contreras RH, Tormena CF. Effect of Electronic Interactions on NMR 1JCF and 2JCF Couplings in cis- and trans-4-t-Butyl-2-fluorocyclohexanones and Their Alcohol Derivatives. J Phys Chem A 2011; 115:5684-92. [DOI: 10.1021/jp202592c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Pedro R. Anizelli
- Chemistry Institute, University of Campinas, Post Office Box 6154, 13084-971 Campinas, SP, Brazil
| | - Denize C. Favaro
- Chemistry Institute, University of Campinas, Post Office Box 6154, 13084-971 Campinas, SP, Brazil
| | - Rubén H. Contreras
- Department of Physics, FCEyN, University of Buenos Aires and IFIBA-CONICET, Buenos Aires, Argentina
| | - Cláudio F. Tormena
- Chemistry Institute, University of Campinas, Post Office Box 6154, 13084-971 Campinas, SP, Brazil
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23
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Napolitano JG, Gavín JA, García C, Norte M, Fernández JJ, Daranas AH. On the configuration of five-membered rings: a spin-spin coupling constant approach. Chemistry 2011; 17:6338-47. [PMID: 21547972 DOI: 10.1002/chem.201100412] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Indexed: 11/06/2022]
Abstract
Five-membered rings are clearly among the most common structural motifs found in chemistry and biology. Nevertheless, the configuration of conformationally mobile five-membered rings is often difficult to assign from nuclear magnetic resonance (NMR) data. A simple, reliable, and efficient approach for the stereochemical analysis of five-membered rings based on the measurement of NMR coupling constants is presented. Density functional theory calculations using representative conformations of the full conformational space available to rings with different substitution patterns were used to identify differences between the accessible coupling constant values for cis and trans relative orientations of the substituents. The calculations were assessed experimentally using NMR data obtained from a number of models. This approach can be easily used to analyze different five-membered rings, such as oxolanes, cyclopentanes, furanosides and pyrrolidines, and their relative configuration can be determined without the need for making further conformational considerations.
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Affiliation(s)
- José G Napolitano
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
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24
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Alabugin IV, Gilmore KM, Peterson PW. Hyperconjugation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.6] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Igor V. Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Kerry M. Gilmore
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Paul W. Peterson
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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25
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Hendrickx PMS, Corzana F, Depraetere S, Tourwé DA, Augustyns K, Martins JC. The use of time-averaged 3JHH restrained molecular dynamics (tar-MD) simulations for the conformational analysis of five-membered ring systems: methodology and applications. J Comput Chem 2010; 31:561-72. [PMID: 19530112 DOI: 10.1002/jcc.21345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Because of its presence in many molecules of biological relevance, the conformational analysis of five-membered rings using (3)J(HH) scalar coupling data from NMR is a topic of considerable interest. Typically, conformational analysis involves the use of a well-established mathematical procedure, originally developed by de Leeuw et al., that fits two rigid conformations to the available experimental data. This so-called pseudorotation analysis approach is not without problems, however, as chemically unrealistic conformations are sometimes generated from the data. Here, we present our investigations in the use of time-averaged restrained molecular dynamics simulations as a generic tool to determine the conformations that agree with experimental (3)J(HH) scalar coupling data. For this purpose, a set of six ribose-based molecules has been used as model compounds. The influence of several modeling parameters is assessed and optimized values are proposed. The results obtained with the tar-MD approach are compared to those obtained from the two conformer fitting procedure. Interpretation of the latter is facilitated by the introduction of a fitting error analysis that allows mapping the solution space of the fitting procedure. The relative merits of both methods and the advantages that result from the use of a force field and a time-averaged restraint potential for the experimental data are discussed. When combined, both techniques allow an enhanced understanding of the molecules' conformational behavior and prevent possible overinterpretation. In view of the very reasonable computational burden of a tar-MD simulation for the systems investigated here, the approach should be generally applicable.
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Affiliation(s)
- Pieter M S Hendrickx
- NMR and Structure Analysis Unit, University of Ghent, Krijgslaan 281 S4, Ghent B-9000, Belgium
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26
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Rhoad JS, Cagg BA, Carver PW. Scanning the Potential Energy Surface of Furanosyl Oxocarbenium Ions: Models for Reactive Intermediates in Glycosylation Reactions. J Phys Chem A 2010; 114:5180-6. [DOI: 10.1021/jp9100448] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jonathan S. Rhoad
- Department of Chemistry, Missouri Western State University, 4525 Downs Drive, St. Joseph, Missouri 64507
| | - Brett A. Cagg
- Department of Chemistry, Missouri Western State University, 4525 Downs Drive, St. Joseph, Missouri 64507
| | - Patrick W. Carver
- Department of Chemistry, Missouri Western State University, 4525 Downs Drive, St. Joseph, Missouri 64507
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27
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Contreras RH, Provasi PF, dos Santos FP, Tormena CF. Stereochemical dependence of NMR geminal spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:113-120. [PMID: 18991325 DOI: 10.1002/mrc.2359] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work it was sought to explore the versatility of geminal spin-spin coupling constants, (2)J(XY) SSCCs, as probes for stereochemical studies. A set of compounds, where their experimental (2)J(XY) SSCCs through the X-C-Y molecular fragment are predicted to be sensitive to hyperconjugative interactions involving either bonding or antibonding orbitals containing the C carbon atom ('coupling pathway'), were analyzed. SSCC calculations were performed for some selected examples using the second order polarization propagator approximation (SOPPA) method or within the DFT-B3LYP framework. Hyperconjugative interactions were calculated within the Natural Bond Orbital (NBO) approach. Results are condensed in two qualitative rules: Rule I(M)-hyperconjugative interactions transferring charge into the coupling pathway yield a positive increase to the Fermi contact (FC), contribution to (2)K(XY) reduced spin-spin coupling constants (RSSCC), and Rule II(M)-hyperconjugative interactions transferring charge from the coupling pathway yield a negative increase to the FC contribution to (2)K(XY) RSSCC.
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Affiliation(s)
- Rubén H Contreras
- Department of Physics, FCEyN, University of Buenos Aires and CONICET, Buenos Aires, Argentina
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28
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Dowd MK, French AD, Reilly PJ. MM3 Modeling of Ribose and 2-Deoxyribose Ring Puckering. J Carbohydr Chem 2008. [DOI: 10.1080/07328300008544137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Michael K. Dowd
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
| | - Alfred D. French
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
| | - Peter J. Reilly
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
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Soriano E, Marco-Contelles J, Tomassi C, Nguyen Van Nhien A, Postel D. Computational Analysis of Aza Analogues of [2‘,5‘-Bis-O-(tert-butyldimethylsilyl)-β-d-ribofuranose]-3‘-spiro-5‘ ‘- (4‘ ‘-amino-1‘ ‘,2‘ ‘-oxathiole-2‘ ‘,2‘ ‘-dioxide) (TSAO) as HIV-1 Reverse Transcriptase Inhibitors: Relevance of Conformational Properties on the Inhibitory Activity. J Chem Inf Model 2006; 46:1666-77. [PMID: 16859298 DOI: 10.1021/ci0600410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have carried out a theoretical analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) by a variety of computational tools, aimed to account for the effect of the endocyclic amino moiety N-2" on the inhibitory activity against HIV-1. Docking studies suggest that compounds substituted at the N-3 and N-2' ' positions present the same binding mode to the [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide)thymine prototype, where the endocyclic amino group remains mostly exposed to the solvent. A careful conformational analysis performed through different theoretical levels, from molecular mechanics to high-level quantum mechanical calculations, provides a rationalization based on conformational preferences, which appears as strongly determined by the substitution at N-2", and on electrostatic effects from the bulk water.
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Affiliation(s)
- Elena Soriano
- Laboratorio de Resonancia Magnética, Instituto de Investigaciones Biomédicas (CSIC), C/ Arturo Duperier 4, 28029 Madrid, Spain.
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Suzuki T, Kawashima H, Kotoku H, Sota T. Structural Fluctuation and Dynamics of Ribose Puckering in Aqueous Solution from First Principles. J Phys Chem B 2005; 109:12997-3005. [PMID: 16852613 DOI: 10.1021/jp050475i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of beta-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm(-1). Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of beta-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of beta-ribofuranose puckering between two hydroxymethyl rotamers.
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Affiliation(s)
- Teppei Suzuki
- Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.
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32
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Suzuki T, Sota T. Circular Hydrogen Bond Networks on the Surface of β-Ribofuranose in Aqueous Solution. J Phys Chem B 2005; 109:12603-11. [PMID: 16852559 DOI: 10.1021/jp050100x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper examines the hydration structure on the surface of beta-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of beta-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of beta-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.
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Affiliation(s)
- Teppei Suzuki
- Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.
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33
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Topological analysis of the electronic charge density in nucleoside analogues derivatives of the AZT. Effects of X–H⋯O and X–H⋯F intramolecular H-bonds. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.12.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Thibaudeau C, Stenutz R, Hertz B, Klepach T, Zhao S, Wu Q, Carmichael I, Serianni AS. Correlated C-C and C-O bond conformations in saccharide hydroxymethyl groups: parametrization and application of redundant 1H-1H, 13C-1H, and 13C-13C NMR J-couplings. J Am Chem Soc 2005; 126:15668-85. [PMID: 15571389 DOI: 10.1021/ja0306718] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methyl alpha- and beta-pyranosides of d-glucose and d-galactose 1-4 were prepared containing single sites of (13)C-enrichment at C4, C5, and C6 (12 compounds), and (1)H and (13)C[(1)H] NMR spectra were obtained to determine a complete set of J-couplings ((1)J, (2)J, and (3)J) involving the labeled carbon and nearby protons and carbons within the exocyclic hydroxymethyl group (CH(2)OH) of each compound. In parallel theoretical studies, the dependencies of (1)J, (2)J, and (3)J involving (1)H and (13)C on the C5-C6 (omega) and C6-O6 (theta;) torsion angles in aldohexopyranoside model compounds were computed using density functional theory (DFT) and a special basis set designed to reliably recover the Fermi contact contribution to the coupling. Complete hypersurfaces for (1)J(C5,C6), (2)J(C5,H6)(R), (2)J(C5,H6)(S), (2)J(C6,H5), (2)J(C4,C6), (3)J(C4,H6)(R), (3)J(C4,H6)(S), and (3)J(C6,H4), as well as (2)J(H6)(R)(,H6)(S), (3)J(H5,H6)(R), and (3)J(H5,H6)(S), were obtained and used to parametrize new equations correlating these couplings to omega and/or theta;. DFT-computed couplings were also tested for accuracy by measuring J-couplings in (13)C-labeled 4,6-O-ethylidene derivatives of d-glucose and d-galactose in which values of omega and theta; were constrained. Using a new computer program, Chymesa, designed to utilize multiple J-couplings sensitive to exocyclic CH(2)OH conformation, the ensemble of experimental couplings observed in 1-4 were analyzed to yield preferred rotamer populations about omega and theta;. Importantly, due to the sensitivity of some couplings, most notably (2)J(H6)(R)(,H6)(S), (2)J(C5,H6)(R), and (2)J(C5,H6)(S), to both omega and theta;, unique information on correlated conformation about both torsion angles was obtained. The latter treatment represents a means of evaluating correlated conformation in 1,6-linked oligosaccharides, since psi and theta; are redundant in these linkages. In the latter regard, multiple, redundant scalar couplings originating from both sides of the glycosidic linkage can be used collectively to evaluate conformational correlations between psi/theta; and C5-C6 bond rotamers.
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Affiliation(s)
- Christophe Thibaudeau
- Department of Chemistry and Biochemistry and Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
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35
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Souto ML, Fernández JJ, Franco JM, Paz B, Gil LV, Norte M. Glycoyessotoxin a, a new yessotoxin derivative from cultures of Protoceratium reticulatum. JOURNAL OF NATURAL PRODUCTS 2005; 68:420-422. [PMID: 15787449 DOI: 10.1021/np040164j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The dinoflagellate Protoceratium reticulatum produces toxins of the yessotoxin group currently included in the diarrhetic shellfish poisoning class. In this paper we report on the isolation and structural elucidation of a 32-arabinoside of yessotoxin, G-YTXA (2), obtained from laboratory cultures of P. reticulatum (strain GG1AM) that possesses a pentose unit, beta-arabinofuranose, as a side chain.
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Affiliation(s)
- María L Souto
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Astrofísico Francisco Sanchez 2, 38206 La Laguna, Spain
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36
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The properties of DNA C4′-centered sugar radicals: the importance of the computational model. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.03.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Kövér KE, Forgó P. J-modulated ADEQUATE (JM-ADEQUATE) experiment for accurate measurement of carbon-carbon coupling constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 166:47-52. [PMID: 14675819 DOI: 10.1016/j.jmr.2003.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new method for the accurate determination of carbon-carbon coupling constants is described. The method is based on a modified ADEQUATE experiment, where a J-modulated spin-echo sequence precedes the ADEQUATE pulse scheme. The J-modulation and scaling of carbon-carbon couplings is based on simultaneous incrementation of 13C chemical shift and coupling evolution periods. The time increment for the homonuclear carbon-carbon coupling evolution can be suitably scaled with respect to the corresponding increment for the chemical shift evolution. Typically a scaling factor of 2 to 3 is employed for the measurement of one-bond coupling constants, while multiplication by a factor of 10 to 15 is applied when small long-range couplings are determined. The same pulse scheme with coupling evolution period optimized for one-bond or long-range couplings allows the determination of the corresponding carbon-carbon coupling constants. The splittings of the ADEQUATE crosspeaks in the F1 dimension yield the appropriately multiplied coupling constants.
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Affiliation(s)
- Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary.
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Affiliation(s)
- Alessandro Bagno
- Dipartimento di Scienze Chimiche, Università di Padova, and Istituto per la Tecnologia delle Membrane del CNR, Sezione di Padova, via Marzolo, 1-35131 Padova, Italy
| | - Federico Rastrelli
- Dipartimento di Scienze Chimiche, Università di Padova, and Istituto per la Tecnologia delle Membrane del CNR, Sezione di Padova, via Marzolo, 1-35131 Padova, Italy
| | - Giacomo Saielli
- Dipartimento di Scienze Chimiche, Università di Padova, and Istituto per la Tecnologia delle Membrane del CNR, Sezione di Padova, via Marzolo, 1-35131 Padova, Italy
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39
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Alabugin IV, Manoharan M, Zeidan TA. Homoanomeric Effects in Six-Membered Heterocycles. J Am Chem Soc 2003; 125:14014-31. [PMID: 14611238 DOI: 10.1021/ja037304g] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural and energetic consequences of homoanomeric n(X) --> beta-sigma(C-Y) interactions in saturated six-membered heterocycles where X = O, N, S, Se and Y = H, Cl were studied computationally using a combination of density functional theory (B3LYP) and Natural Bond Orbital (NBO) analysis. Unlike the classic anomeric effect where the interacting donor and acceptor orbitals are parallel and overlap sidewise in a pi-fashion, orbital interactions responsible for homoanomeric effects can follow different patterns imposed by the geometric restraints of the respective cyclic moieties. For the equatorial beta-C-Y bonds in oxa-, thia- and selena-cyclohexanes, only the homoanomeric n(X)(ax) --> sigma(C-Y)(eq) interaction (the Plough effect) with the axial lone pair of X is important, whereas the n(X)(eq) --> sigma(C-Y)(eq) interaction (the W-effect) is negligible. On the other hand, the W-effect is noticeably larger than the n(X)(ax) --> sigma(C-Y)(eq) interaction in azacyclohexanes. Hyperconjugation is a controlling factor which determines relative trends in the equatorial beta-C-H bonds in heterocycloxanes. In contrast, all homoanomeric interactions are weak for the respective axial bonds where relative lengths are determined by intramolecular electron transfer through exchange interactions and polarization-induced rehybridization. Although the homoanomeric effects are considerably weaker than the classic vicinal anomeric n(X)(ax)-->alpha-sigma(C-Y)(ax) interactions, their importance increases significantly when the acceptor ability of sigmaorbitals increases as a result of bond stretching and/or polarization. Depending on the number of electrons and the topology of interactions, homoconjugation interactions can be cooperative (enhance each other) or anticooperative (compete with each other). Such effects reflect symmetry of the wave function and can be considered as weak manifestations of sigma homoaromaticity or homoantiaromaticity.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA.
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Houseknecht JB, Lowary TL, Hadad CM. Gas- and Solution-Phase Energetics of the Methyl α- and β-d-Aldopentofuranosides. J Phys Chem A 2003. [DOI: 10.1021/jp027716w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Todd L. Lowary
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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41
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Extension of the Karplus Relationship for NMR Spin-Spin Coupling Constants to Nonplanar Ring Systems: Pseudorotation of Tetrahydrofuran. Int J Mol Sci 2003. [DOI: 10.3390/i4040158] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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42
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Houseknecht JB, Lowary TL, Hadad CM. Improved Karplus Equations for3JC1,H4in Aldopentofuranosides: Application to the Conformational Preferences of the Methyl Aldopentofuranosides. J Phys Chem A 2003. [DOI: 10.1021/jp026610y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Houseknecht JB, Lowary TL. Oligofuranosides containing conformationally restricted residues: synthesis and conformational analysis. J Org Chem 2002; 67:4150-64. [PMID: 12054950 DOI: 10.1021/jo011127p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of a panel of arabinofuranosyl oligosaccharide analogues (5-13) in which one ring is locked into either the E(3) or OE conformation is described. The E(3)-locked scaffolds 15 and 16 required for the synthesis of 5-10 were prepared in one step from known 1,5-anhydroalditols. A number of routes were explored for the preparation of the OE-locked monosaccharide derivative 17 needed for the preparation of 11-13. The successful synthesis of 17 was achieved in 17 steps from D-arabinose. Subsequent analysis of 5-13 by 1H NMR spectroscopy demonstrated that the locked residue does not exert any detectable influence upon the conformers populated by adjacent conformationally unrestricted furanose rings.
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Stenutz R, Carmichael I, Widmalm G, Serianni AS. Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants. J Org Chem 2002; 67:949-58. [PMID: 11856043 DOI: 10.1021/jo010985i] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental and theoretical methods have been used to correlate (2)J(HH) and (3)J(HH) values within the exocyclic hydroxymethyl groups (CH(2)OH) of saccharides with specific molecular parameters, and new equations are proposed to assist in the structural interpretation of these couplings. (3)J(HH) depends mainly on the C-C torsion angle (omega) as expected, and new Karplus equations derived from J-couplings computed from density functional theory (DFT) in a model aldopyranosyl ring are in excellent agreement with experimental values and with couplings predicted from a previously reported general Karplus equation. These results confirm the reliability of DFT-calculated (1)H-(1)H couplings in saccharides. (2)J(HH) values depend on both the C-C (omega) and C-O (theta) torsions. Knowledge of the former, which may be derived from other parameters (e.g., (3)J(HH)), allows theta to be evaluated indirectly from (2)J(HH). This latter approach complements more direct determinations of theta from (3)J(HCOH) and potentially extends these more conventional analyses to O-substituted systems lacking the hydroxyl proton. (1)J(CH) values within hydroxymethyl fragments were also examined and found to depend on r(CH), which is modulated by specific bond orientation and stereoelectronic factors. These latter factors could be largely, but not completely, accounted for by C-C and C-O torsional variables, leading to only semiquantitative treatments of these couplings (details discussed in the Supporting Information). New equations pertaining to (2)J(HH) and (3)J(HH) have been applied to the analysis of hydroxymethyl group J-couplings in several mono- and oligosaccharides, yielding information on C5-C6 and/or C6-O6 rotamer populations.
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Affiliation(s)
- Roland Stenutz
- Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
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45
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Callam CS, Lowary TL. Synthesis and conformational investigation of methyl 4a-carba-D-arabinofuranosides. J Org Chem 2001; 66:8961-72. [PMID: 11749629 DOI: 10.1021/jo010827r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The synthesis of carbasugar analogues of methyl alpha-D-arabinofuranoside and methyl beta-D-arabinofuranoside (3 and 4) is reported. The route developed involves the conversion of D-mannose into a suitably protected diene (13), which is then cyclized via olefin metathesis. The resulting cyclopentene (14) is stereoselectively hydrogenated to provide an intermediate that can be used for the synthesis of both targets. Through the use of NMR spectroscopy, we have probed the ring conformation of 3 and 4, as well as the rotamer populations about the C(4)-C(5) and C(1)-O(1) bonds. These studies have demonstrated that there are differences in ring conformation between these carbasugars and their glycoside parents (1 and 2). However, only minor differences are seen in the rotameric equilibrium about the C(4)-C(5) bond in 3 and 4 relative to 1 and 2. In regard to the C(1)-O(1) bond, NOE data from 3 and 4 suggest that the favored position about this bond is similar to that in the glycosides; that is, the methyl group is anti to C(2). However, confirmation of this preference through measurement of (3)J(C,C) between the methyl group and C(2) or C(4a) was not successful.
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Affiliation(s)
- C S Callam
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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46
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Zhu Y, Zajicek J, Serianni AS. Acyclic forms of [1-(13)C]aldohexoses in aqueous solution: quantitation by (13)C NMR and deuterium isotope effects on tautomeric equilibria. J Org Chem 2001; 66:6244-51. [PMID: 11559169 DOI: 10.1021/jo010541m] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-resolution (13)C NMR spectra (150 MHz) have been obtained on the complete series of D-aldohexoses (D-allose 1, D-altrose 2, D-galactose 3, D-glucose 4, D-gulose 5, D-idose 6, D-mannose 7, D-talose 8) selectively labeled with (13)C at C1 in order to detect and quantify the percentages of acyclic forms, and to measure and/or confirm percentages of furanoses and pyranoses, in aqueous solution. Aldehyde and hydrate signals were detected for all aldohexoses, and percentages of these forms at 30 degrees C ranged from 0.006 to 0.7% (hydrate) and 0.0032 to 0.09% (aldehyde). Aldehyde percentages are largest for the altro, ido, and talo configurations, ranging from 0.01 to 0.09%; the ido configuration yielded the most hydrate (0.74%). Hydrate/aldehyde ratios vary with aldohexose configuration, ranging from 1.5 to 13, with gluco exhibiting the smallest ratio and gulo the largest. (2)H Equilibrium isotope effects (EIEs) on aldohexose anomerization were measured in D-galactose 3 and D-talose 8 selectively (13)C- and (2)H-labeled at C1 and H1. The (2)H isotope effect on (13)C chemical shift, and broadband (1)H- and (2)H-decoupling, were exploited to permit simultaneous observation and quantitation of the protonated and deuterated molecules in NMR samples containing equimolar mixtures of D-[1-(13)C]aldose and D-[1-(13)C; 1-(2)H]aldose. Small (2)H EIEs were observed for 8, but were undetectable for 3. These results suggest that configuration at C2 influences the magnitude of the (2)H isotope effect at H1 and/or that the observed effect cannot be reliably interpreted due to complications arising from the involvement of acyclic aldehyde forms as intermediates in the interconversion of cyclic forms. The observed (2)H isotope effects on aldohexose tautomeric equilibria provide new insights into the important question of whether (2)H substitutions can alter aldofuranose ring conformation, and lead to the identification of an optimal (2)H- and (13)C-substituted 2-deoxyribofuranose isotopomer on which to investigate this potential effect.
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Affiliation(s)
- Y Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA
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47
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Malkina OL, Hricovíni M, Bízik F, Malkin VG. Chemical Shifts and Spin−Spin Coupling Constants in Me α-d-Xylopyranoside: A DFT Approach. J Phys Chem A 2001. [DOI: 10.1021/jp004530t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- O. L. Malkina
- Computing Center, Institute of Chemistry, Institute of Virology, Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - M. Hricovíni
- Computing Center, Institute of Chemistry, Institute of Virology, Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - F. Bízik
- Computing Center, Institute of Chemistry, Institute of Virology, Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
| | - V. G. Malkin
- Computing Center, Institute of Chemistry, Institute of Virology, Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
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48
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Houseknecht JB, McCarren PR, Lowary TL, Hadad CM. Conformational studies of methyl 3-O-methyl-alpha-D-arabinofuranoside: an approach for studying the conformation of furanose rings. J Am Chem Soc 2001; 123:8811-24. [PMID: 11535088 DOI: 10.1021/ja003768s] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A computational method for probing furanose conformation has been developed using a methylated monosaccharide derivative 1. First, a large library of conformers was generated by a systematic pseudo Monte Carlo search followed by optimization with the AMBER molecular mechanics force field. A subset of these conformers was then subjected to ab initio and density functional theory calculations in both the gas and aqueous phases. These calculations indicate that entropic contributions to the Gibbs free energy are important determinants of the Boltzmann distribution for the conformational preferences of 1 in the gas phase. The results obtained at each level of theory are discussed and compared with the experimentally determined conformer distribution from NMR studies in aqueous solution. In addition, the ability of each level of theory to reproduce the experimentally measured 1H-1H coupling constants in 1 is discussed. Empirical Karplus equations and density functional theory methods were used to determine average 3J(H1,H2), 3J(H2,H3), and 3J(H3,H4) for each level of theory. On the basis of this comparison, consideration of solvation with the MN-GSM model provided good agreement with the experimental data.
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Affiliation(s)
- J B Houseknecht
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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49
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Callam CS, Gadikota RR, Lowary TL. Sensitivity of (1)J[C(1)-H(1)] magnitudes to anomeric stereochemistry in 2,3-anhydro-O-furanosides. J Org Chem 2001; 66:4549-58. [PMID: 11421773 DOI: 10.1021/jo001747a] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The magnitude of the one-bond coupling constant between C(1) and H(1) in 2,3-anhydro-O-furanosides has been shown to be sensitive to the stereochemistry at the anomeric center. A panel of 24 compounds was studied and in cases where the anomeric hydrogen is trans to the epoxide moiety, (1)J[C(1)-H(1)] = 163-168 Hz; and when this hydrogen is cis to the oxirane ring, ((1)J[C(1)-H(1)] = 171-174 Hz. In contrast, for 2,3-anhydro-S-glycosides, the size of the (1)J[C(1)-H(1)] is not sensitive to C(1) stereochemistry. Computational studies on all four methyl 2,3-anhydro-O-furanosides (5-8) demonstrated that (1)J[C(1)-H(1)] was inversely proportional to the length of the C(1)-H(1) bond. A previously reported equation, which relates C(1)-H(1) bond distance and atomic charges to (1)J[C(1)-H(1)] magnitudes, could be used to accurately predict the J values in the alpha-lyxo (5) and beta-ribo (8) isomers. In contrast, with the beta-lyxo (6) and alpha-ribo isomers (7), this equation underestimated the size of these coupling constants by 10-20 Hz.
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Affiliation(s)
- C S Callam
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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50
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Cloran F, Carmichael I, Serianni AS. 2-Deoxy-beta-D-erythro-pentofuranose: hydroxymethyl group conformation and substituent effects on molecular structure, ring geometry, and NMR spin-spin coupling constants from quantum chemical calculations. J Am Chem Soc 2001; 123:4781-91. [PMID: 11457288 DOI: 10.1021/ja002525x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The effect of hydroxymethyl conformation (gg, gt, and tg rotamers about the C4-C5 bond) on the conformational energies and structural parameters (bond lengths, bond angles, bond torsions) of the 10 envelope forms of the biologically relevant aldopentofuranose, 2-deoxy-beta-D-erythro-pentofuranose (2-deoxy-D-ribofuranose) 2, has been investigated by ab initio molecular orbital calculations at the HF/6-31G level of theory. C4-C5 bond rotation induces significant changes in the conformational energy profile of 2 (2gt and 2tg exhibit one global energy minimum, whereas 2gg exhibits two nearly equivalent energy minima), and structural changes, especially those in bond lengths, are consistent with predictions based on previously reported vicinal, 1,3- and 1,4-oxygen lone pair effects. HF/6-31G-optimized envelope geometries of 2gg were re-optimized using density functional theory (DFT, B3LYP/6-31G), and the resulting structures were used in DFT calculations of NMR spin-spin coupling constants involving 13C (i.e., J(CH) and J(CC) over one, two, and three bonds) in 2gg according to methods described previously. The computed J-couplings were compared to those reported previously in 2gt to assess the effect of C4-C5 bond rotation on scalar couplings within the furanose ring and hydroxymethyl side chain. The results confirm prior predictions of correlations between 2J(CH), 3J(CH), 2J(CC) and 3J(CC), and ring conformation, and verify the usefulness of a concerted application of these couplings (both their magnitudes and signs) in assigning preferred ring and C4-C5 bond conformations in aldopentofuranosyl rings. The new calculated J-couplings in 2gg have particular relevance to related J-couplings in DNA (and RNA indirectly), where the gg rotamer, rather than the gt rotamer, is observed in most native structures. The effects of two additional structural perturbations on 2 were also studied, namely, deoxygenation at C5 (yielding 2,5-dideoxy-beta-D-erythro-pentofuranose 4) and methyl glycosidation at O1 (yielding methyl 2-deoxy-beta-D-erythro-pentofuranoside 5) at the HF/6-31G level. The conformational energy profile of 4 resembles that found for 2gt, not 2gg, indicating that 4 is an inappropriate structural mimic of the furanose ring in DNA. Glycosidation failed to induce differential stabilization of ring conformations containing an axial C1-O1 bond (anomeric effect), contrary to experimental data. The latter discrepancy indicates that either the magnitude of this differential stabilization depends on ring configuration or that solvent effects, which are neglected in these calculations, play a role in promoting this stabilization.
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Affiliation(s)
- F Cloran
- Department of Chemistry and Biochemistry, and the Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
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