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Synthesis and Spectroscopic Characterization of Selected Phenothiazines and Phenazines Rationalized Based on DFT Calculation. Molecules 2022; 27:molecules27217519. [PMID: 36364378 PMCID: PMC9653876 DOI: 10.3390/molecules27217519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Two unique structures were isolated from the phosphorylation reaction of 10H-phenothiazine. The 5,5-dimethyl-2-(10H-phenothiazin-10-yl)-1,3,2-dioxaphosphinane 2-oxide (2a) illustrates the product of N-phosphorylation of phenothiazine. Moreover, a potential product of 2a instability, a thiophosphoric acid 2b, was successfully isolated and structurally characterized. Molecule 2a, similarly to sulfoxide derivative 3, possesses interesting phosphorescence properties due to the presence of d-pπ bonds. The X-ray, NMR, and DFT computational studies indicate that compound 2a exhibits an anomeric effect. Additionally, the syntheses of selected symmetrical and unsymmetrical pyridine-embedded phenazines were elaborated. To compare the influence of phosphorus and sulfur atoms on the structural characteristics of 10H-phenothiazine derivatives, the high-quality crystals of (4a,12a-dihydro-12H-benzo[5,6][1,4]thiazino[2,3-b]quinoxalin-12-yl)(phenyl)methanone (1) and selected phenazines 5,12-diisopropyl-3,10-dimethyldipyrido[3,2-a:3′,2′-h]phenazine (5) and 5-isopropyl-N,N,3-trimethylpyrido[3,2-a]phenazin-10-amine (6a) were obtained. The structures of molecules 1, 2a, 2-mercapto-5,5-dimethyl-1,3,2-dioxaphosphinane 2-oxide (2b), 3,7-dinitro-10H-phenothiazine 5-oxide (3), 5 and 6a were determined by single-crystal X-ray diffraction measurements.
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2
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3
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Nguan HS, Tsai ST, Ni CK. Collision-Induced Dissociation of Cellobiose and Maltose. J Phys Chem A 2022; 126:1486-1495. [PMID: 35212541 DOI: 10.1021/acs.jpca.1c10046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure determination is a longstanding bottleneck of carbohydrate research. Tandem mass spectrometry (MS/MS) is one of the most widely used methods for carbohydrate structure determination. However, the effectiveness of MS/MS depends on how the precursor structures are derived from the observed fragments. Understanding the dissociation mechanisms is crucial for MS/MS-based structure determination. Herein, we investigate the collision-induced dissociation mechanism of β-cellobiose and β-maltose sodium adducts using quantum chemical calculations and experimental measurements. Four dissociation channels are studied. Dehydration mainly occurs through the transfer of an H atom to O1 of the sugar at the reducing end, followed by a C1-O1 bond cleavage; cross-ring dissociation starts with a ring-opening reaction, which occurs through the transfer of an H atom from O1 to O5 of the sugar at the reducing end. These two dissociation channels are analogous to that of glucose monosaccharide. The third channel, generation of B1 and Y1 ions, occurs through the transfer of an H atom from O3 (cellobiose) or O2 (maltose) to O1 of the sugar at the nonreducing end, followed by a glycosidic bond cleavage. The fourth channel, C1-Z1 fragmentation, has two mechanisms: (1) the transfer of an H atom from O3 or O2 to O4 of the sugar at the reducing end to generate C ions in the ring form and (2) the transfer of an H atom from O3 of the sugar at the reducing end to O5 of the sugar at the nonreducing end to produce C ions in the linear form. The results of calculations are supported by experimental collision-induced dissociation spectral measurements.
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Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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4
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Weldu WD, Wang CC. Rationalizing the Stereoelectronic Influence of Interglycosidic Bond Conformations on the Reactivity of 1,4- O-Linked Disaccharide Donors. J Org Chem 2021; 86:17906-17917. [PMID: 34818891 DOI: 10.1021/acs.joc.1c02207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Disaccharide donors are key precursors in convergent glycan synthesis strategies. Unexpectedly, we observed that disaccharide thioglycosyl donors containing 1,4-O-linked α-glycosidic bonds are much more reactive than their β-analogues with the same protecting group pattern. Herein, we rationalized that such a difference in their reactivity is attributed to the conformation of the 1,4-O-interglycosidic bond which is controlled by anomeric and exo-anomeric effects. Moreover, the conformational preferences of these donors are dictated by the dihedral angles ϕ and ψ of their interglycosidic linkages and the torsional angle ω of their side chain along the C5-C6 bond. This fundamental research clarifies how the long-range stereoelectronic effects from the nonreducing end sugar can influence the reactivity of the leaving group at the reducing end and the behavior of disaccharide donors thereof.
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Affiliation(s)
- Welday Desta Weldu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Sustainable Chemical Science and Technology (SCST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 115, Taiwan.,Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Cheng-Chung Wang
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Sustainable Chemical Science and Technology (SCST), Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 115, Taiwan
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5
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Khani F, Atabaki H. Exploring the Origin of the Axial-Conformation Preferences in the 3-Halopiperidinium Cations: the Importance of the Coulombic Potential Energies. ACS OMEGA 2020; 5:24311-24317. [PMID: 33015447 PMCID: PMC7528170 DOI: 10.1021/acsomega.0c02506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Although there are some published conclusions in the literature concerning the origin of the axial-conformation preference in 3-fluoropiperidinium cations (charge-dipole orientation effect), the origin of the axial-conformation preferences in the 3-halopiperidinium cations [halogen = F (1), Cl (2), Br (3)] has remained an open question. To explore the origin of the axial-conformation preferences in compounds 1-3, we assessed the roles and contributions of the hyperconjugative interactions, the Coulombic electrostatic interactions, the electrostatic model associated with dipole-dipole interactions, and the steric effects associated with the Pauli exchange-type repulsions on the conformational properties of compounds 1-3 utilizing the G3MP2, LC-ωPBE, and B3LYP methods and natural bond orbital (NBO) interpretations. Natural Coulombic potential energies are in favor of the axial conformations of compounds 1-3, and justify their corresponding total energy differences. The through-space hyperconjugative interactions between the donor lone pairs of halogen atoms (LP3X) and the acceptor antibonding orbitals of H-N bonds [σ*(H-N) ⊕], LP3X → σ*(H-N) ⊕, increase from compound 1 to compound 3. The inspection of the dipole moments of the parallel C-X and H-N bonds in the axial conformations of compounds 1-3 revealed that the variations of their corresponding four-center dipole-dipole interactions correlate well with their corresponding conformational behaviors. The steric effects associated with the Pauli exchange-type repulsions are strongly in favor of the equatorial conformations of compounds 1-3. Accordingly, the charge-dipole orienting effect associated with the four-center dipole-dipole interactions is a dominant factor in the conformational behaviors of compounds 1-3.
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Affiliation(s)
- Farnousha Khani
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
| | - Hooshang Atabaki
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
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6
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Zhu F, Walczak MA. Stereochemistry of Transition Metal Complexes Controlled by the Metallo-Anomeric Effect. J Am Chem Soc 2020; 142:15127-15136. [PMID: 32786781 DOI: 10.1021/jacs.0c06882] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The use of stereoelectronic interactions to control reactivity and selectivity has a long history in chemistry. The anomeric effect, one of the fundamental concepts in organic chemistry, describes the preferences of a substituent at the anomeric carbon in glycosides to adopt axial configuration when the anomeric group is an electronegative element such as oxygen or a halogen. The origin of the anomeric effect has been the subject of intense debate. Explanations capitalizing on either the delocalization of the endocyclic oxygen lone pair into the antibonding σ*(C-X) orbital or the minimization of the dipole-dipole interactions are currently the two leading theoretical models. Although the majority of experimental and theoretical studies have focused on the elements from groups 6 and 7, little is known about conformational preferences of tetrahydropyran rings substituted with a transition metal at the anomeric carbon and the role of these interactions in stereoselective synthesis. Here, we report studies on conformational and configurational preferences of organometallic complexes stabilized by vicinal heteroatoms. We provide computational evidence that late transition metals adopt the axial position in heterocycles or synclinal geometry in acyclic systems. Furthermore, the anomeric preferences of late transition metals correlate with the oxidation state of the metal and can be explained by hyperconjugative interactions between endocyclic heteroatom and the σ* acceptor orbitals of the C-M bond. In a broader context, this discovery provides insight into the role of previously unanticipated stereoelectronic effects that can be harnessed in the design of stereoselective reactions, including chemical glycosylation and enantioselective catalysis.
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Affiliation(s)
- Feng Zhu
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Maciej A Walczak
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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Khalilov LM, Mescheryakova ES, Bikmukhametov KS, Makhmudiyarova NN, Shangaraev KR, Tulyabaev AR. Twist-chair conformation of the tetraoxepane ring remains unchanged in tetraoxaspirododecane diamines. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:276-286. [PMID: 32132286 DOI: 10.1107/s2053229620001382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/31/2020] [Indexed: 11/10/2022]
Abstract
A detailed structural analysis has been performed for N,N'-bis(4-chlorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22Cl2N2O4, (I), N,N'-bis(2-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (II), and N,N'-bis(4-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (III). The seven-membered ring with two peroxide groups adopts a twist-chair conformation in all three compounds. The lengths of the C-N and O-O bonds are slightly shorter than the average statistical values found in the literature for azepanes and 1,2,4,5-tetraoxepanes. The geometry analysis of compounds (I)-(III), the topological analysis of the electron density at the (3, -1) bond critical points within Bader's quantum theory of `Atoms in molecules' (QTAIM) and NBO (natural bond orbital) analysis at the B3LYP/6-31G(d,2p) level of theory showed that there are nO→σ*(C-O), nN→σ*(C-O) and nO→σ*(C-N) stereoelectronic effects. The molecules of compounds (I) and (III) are packed in the crystals as zigzag chains due to strong N-H...O and C-H...O hydrogen-bond interactions, whereas the molecules of compound (II) form chains in the crystals bound by N-H...O, C-H...π and C-H...O contacts. All these data show that halogen atoms and their positions have a minimal effect on the geometric parameters, stereoelectronic effects and crystal packing of compounds (I)-(III), so that the twist-chair conformation of the tetraoxepane ring remains unchanged.
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Affiliation(s)
- Leonard M Khalilov
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Ekaterina S Mescheryakova
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Kamil Sh Bikmukhametov
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Natalia N Makhmudiyarova
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Kamil R Shangaraev
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Arthur R Tulyabaev
- Institute of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
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Haouache S, Karam A, Chave T, Clarhaut J, Amaniampong PN, Garcia Fernandez JM, De Oliveira Vigier K, Capron I, Jérôme F. Selective radical depolymerization of cellulose to glucose induced by high frequency ultrasound. Chem Sci 2020; 11:2664-2669. [PMID: 34084325 PMCID: PMC8157487 DOI: 10.1039/d0sc00020e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The depolymerization of cellulose to glucose is a challenging reaction and often constitutes a scientific obstacle in the synthesis of downstream bio-based products. Here, we show that cellulose can be selectively depolymerized to glucose by ultrasonic irradiation in water at a high frequency (525 kHz). The concept of this work is based on the generation of H˙ and ˙OH radicals, formed by homolytic dissociation of water inside the cavitation bubbles, which induce the cleavage of the glycosidic bonds. The transfer of radicals on the cellulose particle surfaces prevents the side degradation of released glucose into the bulk solution, allowing maintaining the selectivity to glucose close to 100%. This work is distinguished from previous technologies in that (i) no catalyst is needed, (ii) no external source of heating is required, and (iii) the complete depolymerization of cellulose is achieved in a selective fashion. The addition of specific radical scavengers coupled to different gaseous atmospheres and ˙OH radical dosimetry experiments suggested that H˙ radicals are more likely to be responsible for the depolymerisation of cellulose.
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Affiliation(s)
- Somia Haouache
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers-CNRS 1 Rue Marcel Doré 86073 Poitiers France .,INRA, Site de la Géraudière 44316 Nantes France
| | - Ayman Karam
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers-CNRS 1 Rue Marcel Doré 86073 Poitiers France
| | - Tony Chave
- ICSM, Univ Montpellier, CNRS, CEA, ENSCM Bagnols-sur-Cèze France
| | - Jonathan Clarhaut
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers-CNRS 1 Rue Marcel Doré 86073 Poitiers France
| | - Prince Nana Amaniampong
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers-CNRS 1 Rue Marcel Doré 86073 Poitiers France
| | - José M Garcia Fernandez
- Institute for Chemical Research, CSIC and University of Sevilla Americo Vespucio 49, Isla de la Cartuja 41092 Sevilla Spain
| | - Karine De Oliveira Vigier
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers-CNRS 1 Rue Marcel Doré 86073 Poitiers France
| | | | - François Jérôme
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers-CNRS 1 Rue Marcel Doré 86073 Poitiers France
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9
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Donnelly DP, Agar J, Lopez SA. Nucleophilic substitution reactions of cyclic thiosulfinates are accelerated by hyperconjugative interactions. Chem Sci 2019. [DOI: 10.1039/c9sc01098j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cyclic thiosulfinates are a class of biocompatible molecules, currently expanding our in vivo toolkit.
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Affiliation(s)
- Daniel P. Donnelly
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
- Barnett Institute of Chemical and Biological Analysis
| | - Jeffrey N. Agar
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
- Barnett Institute of Chemical and Biological Analysis
| | - Steven A. Lopez
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
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10
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Vickman AE, Pohl NLB. Probing deoxysugar conformational preference: A comprehensive computational study investigating the effects of deoxygenation. Carbohydr Res 2018; 475:17-26. [PMID: 30771703 DOI: 10.1016/j.carres.2018.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Deoxysugars are intrinsic components in a number of antibiotics, antimicrobials, and therapeutic agents that often dictate receptor binding, improve efficacy, and provide a diverse toolbox in modifying glycoconjugate function due to an extensive number of unique isomers and inherent conformational flexibility. Hence, this work provides a comprehensive examination of the conformational effects associated with deoxygenation of the pyranose ring. Both the location and degree of deoxygenation were evaluated by interrogating the energetic landscape for a number of mono- and dideoxyhexopyranose derivatives using DFT methods (M05-2X/cc-pVTZ(-f)). Both anomeric forms and in some cases, the alternate chair form, have been investigated in the gas phase. As was documented in a preceding study, variation of the C-6 oxidation state has been shown to affect the anomeric preference of select glucose stereoisomers. Similar results were also observed for several deoxysugar isomers in this work, wherein the alternate anomer was favored upon reduction to the 6-deoxyhexose derivative or oxidation to the hexonic acid. Additionally, comparison of relative Gibbs free energies revealed C-3 deoxygenation imparts greater instability compared to C-2 or C-4 deoxygenation, as indicated by an increase in free energy for 3-deoxysugars. A polarizable continuum solvation model was also applied to empirically validate theoretical results for several deoxysugars, wherein good agreement with both carbon (σ = 1.6 ppm) and proton (σ = 0.20 ppm) NMR shifts was observed for the majority of isomers. Solvated and gas phase anomeric ratios were also calculated and compared favorably to reported literature values, although some discrepancies are noted.
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Affiliation(s)
- Alison E Vickman
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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11
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Suenaga M, Nakata K, Abboud JLM, Mishima M. A natural bond orbital analysis of aryl-substituted polyfluorinated carbanions: negative hyperconjugation. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Masahiko Suenaga
- Department of Chemistry, Graduate School of Science; Kyushu University; Fukuoka Japan
| | | | - José-Luis M. Abboud
- Institute for Materials Chemistry and Engineering; Kyushu University; Fukuoka Japan
| | - Masaaki Mishima
- Institute for Materials Chemistry and Engineering; Kyushu University; Fukuoka Japan
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Voss JM, Kregel SJ, Fischer KC, Garand E. IR-IR Conformation Specific Spectroscopy of Na +(Glucose) Adducts. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:42-50. [PMID: 28956282 DOI: 10.1007/s13361-017-1813-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 05/14/2023]
Abstract
We report an IR-IR double resonance study of the structural landscape present in the Na+(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na+(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctive Na+ coordination. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan M Voss
- Department of Chemistry, University of Wisconsin, 1101 University Ave., Madison, WI, 53706, USA
| | - Steven J Kregel
- Department of Chemistry, University of Wisconsin, 1101 University Ave., Madison, WI, 53706, USA
| | - Kaitlyn C Fischer
- Department of Chemistry, University of Wisconsin, 1101 University Ave., Madison, WI, 53706, USA
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin, 1101 University Ave., Madison, WI, 53706, USA.
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Suenaga M, Nakata K, Abboud JLM, Mishima M. Negative Hyperconjugation in Acidity of Polyfluorinated Alkanes. A Natural Bond Orbital Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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14
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Atabaki H, Nori-Shargh D, Momen-Heravi M. Assessing the effective factors affecting the conformational preferences and the early and late transition states of the unimolecular retro-ene decomposition reactions of ethyl cyanate, ethyl thiocyanate and ethyl selenocyanate. RSC Adv 2017. [DOI: 10.1039/c7ra00520b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The variations of Δ[(HCGAE(X3–C4weakening) – HCGAE(X3–C4strengthening)] parameters correlate well with the variations of the retro-ene decomposition reactions barrier heights going from compound1to compound3.
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Affiliation(s)
- Hooshang Atabaki
- Department of Chemistry
- College of Science
- Islamic Azad University
- Mashhad
- Iran
| | - Davood Nori-Shargh
- Department of Chemistry
- College of Science
- Islamic Azad University
- Arak
- Iran
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15
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Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
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16
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Satoh H, Oda T, Nakakoji K, Uno T, Tanaka H, Iwata S, Ohno K. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers. J Chem Theory Comput 2016; 12:5293-5308. [PMID: 27673598 DOI: 10.1021/acs.jctc.6b00439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4 and 4C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1 conformations; that is, the potential energy of the global minimum of 4C1 is lower than that of 1C4 (thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from 4C1 to 1C4 is lower than that of 1C4 to 4C1 (kinetic predominance).
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Affiliation(s)
- Hiroko Satoh
- Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan.,Department of Chemistry, University of Zurich , 8057 Zurich, Switzerland.,National Institute of Informatics (NII), Tokyo 101-8430, Japan.,Institute for Quantum Chemical Exploration (IQCE), Tokyo 108-0022, Japan
| | - Tomohiro Oda
- Software Research Associates Inc., Tokyo 171-8513, Japan
| | - Kumiyo Nakakoji
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University , Kyoto 606-8501, Japan
| | - Takeaki Uno
- National Institute of Informatics (NII), Tokyo 101-8430, Japan
| | - Hiroaki Tanaka
- Department of Mathematical Informatics, University of Tokyo , Tokyo 113-8654, Japan
| | - Satoru Iwata
- Department of Mathematical Informatics, University of Tokyo , Tokyo 113-8654, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration (IQCE), Tokyo 108-0022, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
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17
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Delaux J, Ortiz Mellet C, Canaff C, Fourré E, Gaillard C, Barakat A, García Fernández JM, Tatibouët JM, Jérôme F. Impact of Nonthermal Atmospheric Plasma on the Structure of Cellulose: Access to Soluble Branched Glucans. Chemistry 2016; 22:16522-16530. [DOI: 10.1002/chem.201603214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Joakim Delaux
- Institut de Chimie des Milieux et Matériaux de Poitiers; CNRS/Université de Poitiers, ENSIP; 1 rue Marcel Doré, Bat 1, TSA 41105 86073 Poitiers Cedex 9 France
- UMR IATE, CIRAD; Montpellier SupAgro, INRA; Université de Montpelier; 34060 Montpellier France
| | - Carmen Ortiz Mellet
- Dpto. Química Orgánica; Faculty of Chemistry; University of Sevilla; c/Profesor García González 1 41012 Sevilla Spain
| | - Christine Canaff
- Institut de Chimie des Milieux et Matériaux de Poitiers; CNRS/Université de Poitiers, ENSIP; 1 rue Marcel Doré, Bat 1, TSA 41105 86073 Poitiers Cedex 9 France
| | - Elodie Fourré
- Institut de Chimie des Milieux et Matériaux de Poitiers; CNRS/Université de Poitiers, ENSIP; 1 rue Marcel Doré, Bat 1, TSA 41105 86073 Poitiers Cedex 9 France
| | - Cédric Gaillard
- INRA, UR 1268 Biopolymers Interaction Assemblies (BIA); Centre Angers-Nantes; Rue de la Géraudière 44000 Nantes France
| | - Abdellatif Barakat
- UMR IATE, CIRAD; Montpellier SupAgro, INRA; Université de Montpelier; 34060 Montpellier France
| | - José M. García Fernández
- Instituto de Investigaciones Químicas (IIQ); CSIC - University of Sevilla; Avda. Americo Vespucio 49 41092 Sevilla Spain
| | - Jean-Michel Tatibouët
- Institut de Chimie des Milieux et Matériaux de Poitiers; CNRS/Université de Poitiers, ENSIP; 1 rue Marcel Doré, Bat 1, TSA 41105 86073 Poitiers Cedex 9 France
| | - François Jérôme
- Institut de Chimie des Milieux et Matériaux de Poitiers; CNRS/Université de Poitiers, ENSIP; 1 rue Marcel Doré, Bat 1, TSA 41105 86073 Poitiers Cedex 9 France
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18
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Nori-Shargh D, Mousavi SN, Tale R, Yahyaei H. Hyperconjugative interactions are the main responsible for the anomeric effect: a direct relationship between the hyperconjugative anomeric effect, global hardness and zero-point energy. Struct Chem 2016. [DOI: 10.1007/s11224-016-0791-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Ghanbarpour P, Nori-Shargh D. Exploring the origin of the anomeric relationships in 2-cyanooxane, 2-cyanothiane, 2-cyanoselenane and their corresponding isocyano isomers. Correlations between hyper-conjugative anomeric effect, hardness and electrostatic interactions. RSC Adv 2016. [DOI: 10.1039/c6ra06080c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The impacts of the HCAE, hardness, PETR and electrostatic interactions on the anomeric relationships in 2-cyanooxane, -thiane, -selenane and their iso-cyano isomers have been explored.
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Affiliation(s)
- Peyvand Ghanbarpour
- Department of Chemistry
- College of Science
- Arak Branch
- Islamic Azad University
- Arak
| | - Davood Nori-Shargh
- Department of Chemistry
- College of Science
- Arak Branch
- Islamic Azad University
- Arak
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20
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Szczepaniak M, Moc J. Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study. J Phys Chem A 2015; 119:10946-58. [DOI: 10.1021/acs.jpca.5b07720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek Szczepaniak
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
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21
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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22
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Hasanzadeh N, Nori-Shargh D. Correlations between hardness, electronegativity, anomeric effect associated with electron delocalizations and electrostatic interactions in 1,4,5,8-tetraoxadecalin and its analogs containing S and Se atoms. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Hasanzadeh N, Nori-Shargh D, Farzipour M, Ahmadi B. The origin of the anomeric effect: probing the impacts of stereoelectronic interactions. Org Biomol Chem 2015; 13:6965-76. [DOI: 10.1039/c5ob00585j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To gain further insight on the origin of the anomeric effect, the correlations between SE, EM, PETR, bond-orders, donor and acceptor orbital energies and occupancies, structural parameters and configurational behavior of dihalo-1,4-oxathianes were investigated.
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Affiliation(s)
- Neda Hasanzadeh
- Department of Chemistry
- Ahvaz Branch
- Islamic Azad University
- Ahvaz
- Iran
| | | | | | - Bahareh Ahmadi
- Department of Chemistry
- Arak Branch
- Islamic Azad University
- Arak
- Iran
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24
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Sladek V, Holka F, Tvaroška I. Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE. Phys Chem Chem Phys 2015; 17:18501-13. [DOI: 10.1039/c5cp02191j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxygen substitution in 2-methoxytetrahydropyran by sulphur in 2-methoxythiane approximately doubles the anomeric effect, which slows down enzymatic processing of 2-methoxythiane.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Filip Holka
- Faculty of Materials Science and Technology in Trnava
- Slovak University of Technology in Bratislava
- SK-917 24 Trnava
- Slovakia
| | - Igor Tvaroška
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
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25
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Szczepaniak M, Moc J. Cyclic and Acyclic Fructose Conformers in the Gas Phase: A Large-Scale Second-Order Perturbation Theory Study. J Phys Chem A 2014; 118:7925-38. [DOI: 10.1021/jp505719m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Marek Szczepaniak
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
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26
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Nori-Shargh D, Mousavi SN, Kayi H. Conformational behaviors of trans-2,3- and trans-2,5-dihalo-1,4-diselenanes. A complete basis set, hybrid-density functional theory study and natural bond orbital interpretations. J Mol Model 2014; 20:2249. [PMID: 24817665 DOI: 10.1007/s00894-014-2249-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/10/2014] [Indexed: 10/25/2022]
Abstract
Complete basis set CBS-4, hybrid-density functional theory (hybrid-DFT: B3LYP/6-311+G**) based methods and natural bond orbital (NBO) interpretations have been used to examine the contributions of the hyperconjugative, electrostatic, and steric effects on the conformational behaviors of trans-2,3-dihalo-1,4-diselenane [halo = F (1), Cl (2), Br (3)] and trans-2,5-dihalo-1,4-diselenane [halo = F (4), Cl (5), Br (6)]. Both levels of theory showed that the axial conformation stability, compared to its corresponding equatorial conformation, decreases from compounds 1 → 3 and 4 → 6. Based on the results obtained from the NBO analysis, there are significant anomeric effects for compounds 1-6. The anomeric effect associated with the electron delocalization is in favor of the axial conformation and increases from compounds 1 → 3 and 4 → 6. On the other hand, dipole moment differences between the axial and equatorial conformations [Δ(μ(eq)-μ(ax)] decrease from compounds 1 → 3. Although Δ(μ(eq)-μ(ax)) parameter decreases from compound 1 to compound 3, the dipole moment values of the axial conformations are smaller than those of their corresponding equatorial conformations. Therefore, the anomeric effect associated with the electron delocalizations (for halogen-C-Se segments) and the electrostatic model associated with the dipole-dipole interactions fail to account for the increase of the equatorial conformations stability on going from compound 1 to compound 3. Since there is no dipole moment for the axial and equatorial conformations of compounds 4-6, consequently, the conformational preferences in compounds 1-6 is in general dictated by the steric hindrance factor associated with the 1,3-syn-axial repulsions. Importantly, the CBS-4 results show that the entropy difference (∆S) between the equatorial axial conformations increases from compounds 1 → 3 and 4 → 6. This fact can be explained by the anomeric effect associated with the electron delocalization which affects the C₂-Se bond orders and increase the rigidity of the corresponding rings. The Gibbs free energy difference values between the axial and equatorial conformations (i.e. ΔG(ax-ax) and ΔG(eq-eq)) of compounds 1 and 4, 2 and 5 and also 3 and 6 have been calculated. The correlations between the anomeric effect, electrostatic model, ΔG(eq-ax), ΔG(ax-ax), ΔG(eq-eq), bond orders, dipole-dipole interactions, structural parameters and conformational behaviors of compounds 1-6 have been investigated.
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Affiliation(s)
- Davood Nori-Shargh
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran,
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27
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Mayes HB, Tian J, Nolte MW, Shanks BH, Beckham GT, Gnanakaran S, Broadbelt LJ. Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment. J Phys Chem B 2013; 118:1990-2000. [PMID: 24308866 DOI: 10.1021/jp409481f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering, Northwestern University , Evanston, Illinois 60208, United States
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28
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Lin X, Qu Y, Lv Y, Xi Y, Phillips DL, Liu C. The first dehydration and the competing reaction pathways of glucose homogeneously and heterogeneously catalyzed by acids. Phys Chem Chem Phys 2013; 15:2967-82. [DOI: 10.1039/c2cp43644b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Freitas MP. The anomeric effect on the basis of natural bond orbital analysis. Org Biomol Chem 2013; 11:2885-90. [DOI: 10.1039/c3ob40187a] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Wu M, Nerinckx W, Piens K, Ishida T, Hansson H, Sandgren M, Ståhlberg J. Rational design, synthesis, evaluation and enzyme-substrate structures of improved fluorogenic substrates for family 6 glycoside hydrolases. FEBS J 2012; 280:184-98. [DOI: 10.1111/febs.12060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/31/2012] [Accepted: 11/05/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Miao Wu
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Wim Nerinckx
- Laboratory for Protein Biochemistry and Biomolecular Engineering; Department of Biochemistry and Microbiology; University of Gent; Gent; Belgium
| | | | - Takuya Ishida
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Henrik Hansson
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Mats Sandgren
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Jerry Ståhlberg
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
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31
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Kasaei GA, Nori-Shargh D, Yahyaei H, Mousavi SN, Pourdavoodi E. Complete basis set, hybrid-DFT study and NBO interpretation of conformational analysis of 2-methoxytetrahydropyran and its thiopyran and selenopyran analogues in relation to the anomeric effect. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.683527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Mayato C, Dorta RL, Palazón JM, Vázquez JT. Comparison of the conformational properties of carbasugars and glycosides: the role of the endocyclic oxygen. Carbohydr Res 2012; 352:101-8. [DOI: 10.1016/j.carres.2012.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/18/2012] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
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33
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Beck JM, Miller SM, Peczuh MW, Hadad CM. C2 Hydroxyl Group Governs the Difference in Hydrolysis Rates of Methyl-α-d-glycero-d-guloseptanoside and Methyl-β-d-glycero-d-guloseptanoside. J Org Chem 2012; 77:4242-51. [DOI: 10.1021/jo202639g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jeremy M. Beck
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Shawn M. Miller
- Department of Chemistry, The University of Connecticut, 55 North Eagleville
Road, Storrs, Connecticut 06269, United States
| | - Mark W. Peczuh
- Department of Chemistry, The University of Connecticut, 55 North Eagleville
Road, Storrs, Connecticut 06269, United States
| | - Christopher M. Hadad
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
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34
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Juaristi E, Bandala Y. Anomeric Effect in Saturated Heterocyclic Ring Systems. ADVANCES IN HETEROCYCLIC CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396530-1.00002-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Sensing the anomeric effect in a solvent-free environment. Nature 2011; 469:76-9. [DOI: 10.1038/nature09693] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/23/2010] [Indexed: 11/08/2022]
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36
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Liang H, MacKay M, Grindley TB, Robertson KN, Cameron TS. Configurations and conformations of glycosyl sulfoxides. CAN J CHEM 2010. [DOI: 10.1139/v10-091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.
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Affiliation(s)
- Hong Liang
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
| | - Micheline MacKay
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
| | - T. Bruce Grindley
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
| | | | - T. Stanley Cameron
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
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37
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Nunes SCC, Jesus AJL, Moreno MJ, Eusébio MES. Conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution. Carbohydr Res 2010; 345:2048-59. [PMID: 20709315 DOI: 10.1016/j.carres.2010.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 06/30/2010] [Accepted: 07/06/2010] [Indexed: 10/19/2022]
Abstract
This work presents an investigation on the conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution. Eighty-one systematically selected structures were studied at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level, giving rise to 40 unique conformers. The 19 lower energy structures and some selected other were further re-optimized at the B3LYP/6-311++G(d,p) level. The main factors accounting for the conformer's stability were pointed out and discussed. NBO and QTAIM analyses were performed in some selected conformers in order to address the anomeric and exo-anomeric effects as well as intramolecular hydrogen bonding. The effect of solvent water on the relative stability of the conformers was accounted for by applying the conductor-like polarizable continuum model, CPCM.
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Affiliation(s)
- Sandra C C Nunes
- Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
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38
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Cantú D, Nerinckx W, Reilly PJ. Theory and computation show that Asp463 is the catalytic proton donor in human endoplasmic reticulum α-(1→2)-mannosidase I. Carbohydr Res 2008; 343:2235-42. [DOI: 10.1016/j.carres.2008.05.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 05/07/2008] [Accepted: 05/13/2008] [Indexed: 11/25/2022]
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39
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Nimlos MR, Qian X, Davis M, Himmel ME, Johnson DK. Energetics of xylose decomposition as determined using quantum mechanics modeling. J Phys Chem A 2007; 110:11824-38. [PMID: 17048814 DOI: 10.1021/jp0626770] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The decomposition of xylose has been studied using quantum mechanical calculations supported by NMR data. Proposed mechanisms for the decomposition of xylose have been investigated by obtaining the structures and energies of transition states and products. The intent of this study was to understand the experimentally observed formation of furfural and formic acid that occurs during the decomposition of xylose in mildly hot acidic solutions. A mechanism of furfural formation involving the opening of the pyranose ring and subsequent dehydration of the aldose was compared to a direct intramolecular rearrangement of the protonated pyranose. Energies were determined using CBS-QB3, and it was shown that the barriers for dehydration of the aldose were high compared to intramolecular rearrangement. This result suggests that the latter mechanism is a more likely mechanism for furfural formation. The intramolecular rearrangement step results from protonation of xylose at the O2 hydroxyl group. In addition, it has been shown that formic acid formation is a likely result of the protonation of xylose at the O3 hydroxyl group. Finally, solvation of xylose decomposition was studied by calculating energy barriers for xylose in selected water clusters. The mechanisms proposed here were supported in part by 13C-labeling studies using NMR.
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Affiliation(s)
- Mark R Nimlos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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40
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Woodcock HL, Moran D, Pastor RW, MacKerell AD, Brooks BR. Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran. Biophys J 2007; 93:1-10. [PMID: 17554075 PMCID: PMC1914444 DOI: 10.1529/biophysj.106.099986] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A range of ab initio calculations were carried out on the axial and equatorial anomers of the model carbohydrate 2-ethoxy tetrahydropyran to evaluate the level of theory required to accurately evaluate the glycosyl dihedral angle and the anomeric ratio. Vacuum CCSD(T)/CBS extrapolations at the global minimum yield DeltaE = E(equatorial) - E(axial) = 1.42 kcal/mol. When corrected for solvent (by the IEFPCM model), zero-point vibrations and entropy, DeltaG(298) = 0.49 kcal/mol, in excellent agreement with the experimental value of 0.47 +/- 0.3 kcal/mol. A new additivity scheme, the layered composite method (LCM), yields DeltaE to within 0.1 kcal/mol of the CCSD(T)/CBS result at a fraction of the computer requirements. Anomeric ratios and one-dimensional torsional surfaces generated by LCM and the even more efficient MP2/cc-pVTZ level of theory are in excellent agreement, indicating that the latter is suitable for force-field parameterization of carbohydrates. Hartree-Fock and density functional theory differ from CCSD(T)/CBS for DeltaE by approximately 1 kcal/mol; they show similar deviations in torsional surfaces evaluated from LCM. A comparison of vacuum and solvent-corrected one- and two-dimensional torsional surfaces indicates the equatorial form of 2-ethoxy tetrahydropyran is more sensitive to solvent than the axial.
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Affiliation(s)
- H Lee Woodcock
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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41
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Mayato C, Dorta RL, Vázquez JT. The exo-deoxoanomeric effect in the conformational preferences of C-glycosides. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Kavitha V, Viswanathan KS. Conformations of dimethoxydimethylsilane: matrix isolation infrared and ab initio studies. J Phys Chem A 2007; 111:1879-86. [PMID: 17388276 DOI: 10.1021/jp066837j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Conformations of dimethoxydimethylsilane (DMDMS) were studied using matrix isolation infrared spectroscopy, by trapping the silane in argon and nitrogen matrixes. The matrix was deposited using both an effusive and a supersonic jet source. The effusive source was maintained at two different temperatures, viz. 298 and 433 K, during deposition to alter the conformational population of the silane. The experimental results were supported by computations performed at both the HF and B3LYP levels, using 6-31++G** basis set. Vibrational frequency calculations were carried out to assign the experimental features and also to ensure that the computed structures did indeed correspond to minima. A conformer with a G+/-G-/+ structure was found to be the ground state, while G+/-T and G+/-G+/- structures were the next higher energy conformers with energies of 1.32 and 1.48 kcal/mol, respectively. Natural bond orbital analysis was carried out at both HF/6-31++G** and B3LYP/6-31++G** level which indicated that the charge-transfer hyperconjugative interactions largely determine the conformational preferences in this molecule. This interaction appears to be smaller in DMDMS than in the corresponding carbon analogue, dimethoxypropane (DMP).
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Affiliation(s)
- V Kavitha
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
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43
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Aguirre‐Valderrama A, Dobado JA. Conformational Analysis of Thiosugars: Theoretical NMR Chemical Shifts and3JH,HCoupling Constants of 5‐Thio‐Pyranose Monosaccharides. J Carbohydr Chem 2007. [DOI: 10.1080/07328300600966471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Alonso Aguirre‐Valderrama
- a Grupo de Modelización y Diseño Molecular, Departamento de Química Orgánica , Facultad de Ciencias, Universidad de Granada , Granada, Spain
| | - José A. Dobado
- a Grupo de Modelización y Diseño Molecular, Departamento de Química Orgánica , Facultad de Ciencias, Universidad de Granada , Granada, Spain
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44
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Gerbst AG, Grachev AA, Shashkov AS, Nifantiev NE. Computation techniques in the conformational analysis of carbohydrates. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2007. [DOI: 10.1134/s1068162007010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Silva AM, da Silva EC, da Silva CO. A theoretical study of glucose mutarotation in aqueous solution. Carbohydr Res 2006; 341:1029-40. [PMID: 16584715 DOI: 10.1016/j.carres.2006.02.035] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Accepted: 02/16/2006] [Indexed: 11/27/2022]
Abstract
In this work the mechanism of glucose mutarotation is investigated in aqueous solution considering the most likely pathways proposed from experimental work. Two mechanisms are studied. The first involves an intramolecular proton transfer as proposed by textbooks of organic chemistry, and the second uses one solvent water molecule to assist proton transfer. Both mechanisms are studied in the gas phase and in aqueous solution with the help of a polarizable continuum model, which is adopted to introduce the electrostatic nonspecific influence of bulk solvent. The structures are fully characterized through the calculation of the corresponding vibrational frequencies. The rate coefficients for each mechanism are calculated following transition-state theory in both the gas phase and in aqueous solution. Values computed for the water-assisted pathway in the continuum solvent agree best with the experimental results.
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Affiliation(s)
- Alexander M Silva
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, BR 465 km 7, Seropédica, RJ 23890-000, Brazil
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46
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47
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Bitzer RS, Barbosa AGH, da Silva CO, Nascimento MAC. On the generalized valence bond description of the anomeric and exo-anomeric effects: an ab initio conformational study of 2-methoxytetrahydropyran. Carbohydr Res 2005; 340:2171-84. [PMID: 16054606 DOI: 10.1016/j.carres.2005.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Revised: 06/22/2005] [Accepted: 07/06/2005] [Indexed: 10/25/2022]
Abstract
An ab initio conformational study of the alpha- and beta-glycosidic C1-O1 bonds has been carried out on the axial and equatorial forms of 2-methoxytetrahydropyran (2-MTHP) at the HF/6-31G(d,p) and GVB-PP/6-31G(d,p) levels of calculation. Six conformers of 2-MTHP were fully optimized at both levels. The calculations have shown that the conformer containing the (+sc) orientation around the axial C1-O1 bond is the most stable one and is favored over that bearing the (-sc) arrangement about the equatorial C1-O1 bond by 1.39 (HF) and 1.52 (GVB-PP)kcal/mol. The potential energy surfaces for rotating about the axial and equatorial C1-O1 bonds were constructed at the HF and GVB-PP levels. For each form of 2-MTHP the HF and GVB-PP potential curves exhibit similar profiles. This shows that both methods provide similar descriptions for the position of the conformational minima and for the values and location of the rotational barriers. In addition to the conformational study, a discussion concerning the nature of the chemical bond in acetal fragments and the origin of the anomeric and exo-anomeric effects is presented in terms of optimized non-orthogonal GVB orbitals of 2-MTHP. The intramolecular factors that respond for the order of stability and conformational changes in bond lengths of the conformers of 2-MTHP are examined in light of the GVB description. The problems associated with the use of the NBOs (natural bond orbitals) to analyze chemical bonding in the acetal fragments are discussed, and the choice for the GVB-PP description is justified.
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Affiliation(s)
- Rodrigo S Bitzer
- Departamento de Físico-Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Brazil
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48
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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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49
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Jaud S, Tobias DJ, Brant DA. Molecular Dynamics Simulations of Aqueous Pullulan Oligomers. Biomacromolecules 2005; 6:1239-51. [PMID: 15877338 DOI: 10.1021/bm049463d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulations have been used to model small-angle X-ray scattering (SAXS) data on aqueous solutions of four oligomeric segments of the glucan pullulan: the trimer G(3) (comprising one polymer repeating unit), the hexamer (G(3))(2), the nonamer (G(3))(3), and the dodecamer (G(3))(4). The AMBER force field was used in conjunction with the GB/SA continuum solvation model to calculate both the mean global dimensions of the oligomers from the limiting small angle scattering behavior and the shorter range structural information implicit in the Debye scattering function at larger scattering angles. This same force field and solvation treatment were employed earlier by Liu et al. (Macromolecules 1999, 32, 8611-8620) with apparent success in a rotational isomeric state (RIS) treatment of the same experimental data. The present work discloses that, despite numerical success in modeling the SAXS data, the RIS treatment, which includes only the interactions within dimeric segments of the polymer chain, fails to account accurately for excluded volume effects at the range of 3-12 sugar residues in the polymer backbone. It is suggested that MD simulations using continuum solvation models can be used to circumvent errors inherent in the computationally efficient RIS treatments of polymer nano- and picosecond dynamics while at the same time avoiding the heavy computational requirements of all-atom methods.
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Affiliation(s)
- Simon Jaud
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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50
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Stortz CA. Comparative performance of MM3(92) and two TINKER? MM3 versions for the modeling of carbohydrates. J Comput Chem 2005; 26:471-83. [PMID: 15690417 DOI: 10.1002/jcc.20185] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 1992 version of MM3 was largely used for modeling mono-, di-, and trisaccharides. In later versions of MM3 improvements were made in some parameters that may be important for carbohydrates. This corrected MM3 force field is part of the Tinker package, freely available (as its 4.1 version), and included in the Chem 3D Ultra 8.0 package (as the 3.7 version). The latter version lacks the corrections to the standard bond lengths produced by electronegativity and anomeric effects, whereas the Tinker 4.1 version only lacks the latter correction. The present work compares the performance of the three MM3 versions (and in some cases, DFT and/or HF/ab initio procedures) on several carbohydrate model problems as the chair and rotamer equilibria in 2-hydroxy- and 2-methoxytetrahydropyran, hydrogen bonding in cis-2,3-dihydroxytetrahydropyran, and the potential energy surfaces around the glycosidic bonds of two sulfated disaccharides and two trisaccharides. Tinker MM3 can be used accurately to estimate carbohydrate energies and geometries, and-with the help of some programming-to pursue studies on the potential energy surfaces of di- and trisaccharides. In most cases results obtained using the three MM3 versions are similar, although large energy differences are obtained when comparing a rotameric distribution around a O-C-O-H dihedral, which is almost forced to the exo-anomeric position by the Tinker versions. In other systems smaller energy differences are found, but they can nevertheless lead to a different global minimum when comparing conformers of similar energy. MM3(92) establishes better the differences between the bond lengths in both anomers, as an expected expression of the anomeric correction.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, UBA, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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