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Azide⋅⋅⋅Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Sureshan KM, Madhusudhanan MC, Balan H, Werz DB. Azide···Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021; 60:22797-22803. [PMID: 34399025 DOI: 10.1002/anie.202106614] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/15/2021] [Indexed: 11/09/2022]
Abstract
We have designed, synthesized and crystallized 36 compounds, each containing an azide group and an oxygen atom separated by three bonds. Crystal structure analysis revealed that each of these molecules adopts a conformation in which the azide and oxygen groups orient syn to each other with a short O ··· N b contact. Geometry-optimized structures [using M06-2X/6-311G(d,p) level of theory ] also showed the syn conformation in all 36 of these cases, suggesting that this not merely a crystal packing effect. Quantum topological analysis using Bader's Atoms in Molecules (AIM) theory revealed bond paths and bond critical points (BCP) in these structures suggesting its nature and energetics to be similar to weak hydrogen bonding. The NCI-RDG plot clearly revealed the attractive interaction consisting of electrostatic or dispersive components in all the 36 systems. NBO analysis suggested a weak orbital-relaxation (charge-transfer) contribution of energy for a few (sp2) O-donor systems. Natural population analysis (NPA) and molecular electrostatic potential mapping (MESP) of these crystal structures further revealed the existence of favorable azide-oxygen interaction. A CSD search indicated the frequent and consistent occurrence of this interaction and its role dictating the syn conformation of azide and oxygen in molecules where these groups are separated by 2-4 bonds.
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Affiliation(s)
- Kana M Sureshan
- Indian Institute of Science Education and Research, School of Chemistry, Thiruvananthapuram, Maruthamala, 695551, Thiruvananthapuram, INDIA
| | - Mithun C Madhusudhanan
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram, School of Chemistry, Maruthamala, Vithura, 795551, Thiruvananthapuram, INDIA
| | - Haripriya Balan
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram, School of Chemistry, Maruthamala, Vithura, 695551, Thiruvananthapuram, INDIA
| | - Daniel B Werz
- TU Braunschweig: Technische Universitat Braunschweig, Institute fur Organic Chemie, Hagenring 30, Braunschweig, 38106, Braunschweig, GERMANY
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Poonia T, Silva WG, van Wijngaarden J. Derivation of an accurate geometry of 2-fluoroaniline from rotational spectroscopy and computational chemistry. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lomas JS. Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H … OH and C─H … OH bonding interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:666-684. [PMID: 32201981 DOI: 10.1002/mrc.5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Université de Paris, Paris, France
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Pnictogen, chalcogen, and halogen bonds in catalytic systems: theoretical study and detailed comparison. J Mol Model 2019; 26:16. [DOI: 10.1007/s00894-019-4275-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022]
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Martins F, Freitas MP. Revisiting the Case of an Intramolecular Hydrogen Bond Network Forming Four- and Five-Membered Rings in d-Glucose. ACS OMEGA 2018; 3:10250-10254. [PMID: 31459154 PMCID: PMC6645413 DOI: 10.1021/acsomega.8b01455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/20/2018] [Indexed: 05/11/2023]
Abstract
The conformational behavior of cyclic monosaccharides has been widely studied over the past years, but there is no general agreement about which effects are in fact responsible for the observed conformational preferences. A recent microwave spectroscopy study determined the conformational equilibrium of d-glucose in the gas phase with a preference for a counterclockwise arrangement of the hydroxyl groups. Nevertheless, the effects that control this orientation are still uncertain because the role of intramolecular hydrogen bonds (IHBs), electrostatic and steric repulsions is not clear. This work reports a density functional theory approach based on the conformational energies of d-glucose and of some derivatives in which the anomeric hydroxyl is replaced with hydrogen (H, small and not prone to participate in proton transfer), fluorine (F, small, electronegative, and as capable as OH of forming hydrogen bonds as a proton acceptor), and chlorine (Cl, big and not anticipated to be involved in effective hydrogen bond formation) to obtain insights into the effects of the substituent at the anomeric carbon on the arrangement of the hydroxyl groups in d-glucose. The nature of the substituents at this position is crucial to determine the orientation of the remaining hydroxyl groups. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses, in addition to NMR chemical shift calculations, have been provided to support the conformational energy outcomes. Overall, the results agree with the lack of IHBs forming four- and five-membered rings in d-glucose and emphasize that steric and electrostatic repulsions involving the hydroxyl groups in the clockwise orientation are driving forces of the conformational behavior.
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Holcomb M, Adhikary R, Zimmermann J, Romesberg FE. Topological Evidence of Previously Overlooked Ni+1–H···Ni H-Bonds and Their Contribution to Protein Structure and Stability. J Phys Chem A 2017; 122:446-450. [DOI: 10.1021/acs.jpca.7b11013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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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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Baggioli A, Cavallotti CA, Famulari A. Exploring short intramolecular interactions in alkylaromatic substrates. Phys Chem Chem Phys 2016; 18:29616-29628. [PMID: 27753437 DOI: 10.1039/c6cp03323g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.
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Affiliation(s)
- Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Carlo A Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Antonino Famulari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
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Tormena CF. Conformational analysis of small molecules: NMR and quantum mechanics calculations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:73-88. [PMID: 27573182 DOI: 10.1016/j.pnmrs.2016.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/14/2016] [Indexed: 06/06/2023]
Abstract
This review deals with conformational analysis in small organic molecules, and describes the stereoelectronic interactions responsible for conformational stability. Conformational analysis is usually performed using NMR spectroscopy through measurement of coupling constants at room or low temperature in different solvents to determine the populations of conformers in solution. Quantum mechanical calculations are used to address the interactions responsible for conformer stability. The conformational analysis of a large number of small molecules is described, using coupling constant measurements in different solvents and at low temperature, as well as recent applications of through-space and through-hydrogen bond coupling constants JFH as tools for the conformational analysis of fluorinated molecules. Besides NMR parameters, stereoelectronic interactions such as conjugative, hyperconjugative, steric and intramolecular hydrogen bond interactions involved in conformational preferences are discussed.
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Affiliation(s)
- Cláudio F Tormena
- Institute of Chemistry, University of Campinas, PO Box 6154, 13083-970 Campinas, Sao Paulo, Brazil.
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Zhang S, Wang G, Lu Y, Zhu W, Peng C, Liu H. The Interactions between Imidazolium-Based Ionic Liquids and Stable Nitroxide Radical Species: A Theoretical Study. J Phys Chem A 2016; 120:6089-102. [DOI: 10.1021/acs.jpca.6b05770] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shaoze Zhang
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guimin Wang
- Drug
Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yunxiang Lu
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Changjun Peng
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Honglai Liu
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
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The role of nonbonding interactions and the presence of fluoride on the conformational isomerism of 1,2-ethanediol. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Determination of the molecular structure of gaseous proline by electron diffraction, supported by microwave and quantum chemical data. Struct Chem 2015. [DOI: 10.1007/s11224-015-0589-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhang Y, Lu Y, Xu Z, Ding H, Wu W, Liu H. Intramolecular halogen bonds in 1,2-aryldiyne molecules: a theoretical study. Struct Chem 2015. [DOI: 10.1007/s11224-015-0671-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Bogdan E, Compain G, Mtashobya L, Le Questel JY, Besseau F, Galland N, Linclau B, Graton J. Influence of Fluorination on the Conformational Properties and Hydrogen-Bond Acidity of Benzyl Alcohol Derivatives. Chemistry 2015; 21:11462-74. [PMID: 26130594 PMCID: PMC4531824 DOI: 10.1002/chem.201501171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Indexed: 01/10/2023]
Abstract
The effect of fluorination on the conformational and hydrogen-bond (HB)-donating properties of a series of benzyl alcohols has been investigated experimentally by IR spectroscopy and theoretically with quantum chemical methods (ab initio (MP2) and DFT (MPWB1K)). It was found that o-fluorination generally resulted in an increase in the HB acidity of the hydroxyl group, whereas a decrease was observed upon o,o′-difluorination. Computational analysis showed that the conformational landscapes of the title compounds are strongly influenced by the presence of o-fluorine atoms. Intramolecular interaction descriptors based on AIM, NCI and NBO analyses reveal that, in addition to an intramolecular OH⋅⋅⋅F interaction, secondary CH⋅⋅⋅F and/or CH⋅⋅⋅O interactions also occur, contributing to the stabilisation of the various conformations, and influencing the overall HB properties of the alcohol group. The benzyl alcohol HB-donating capacity trends are properly described by an electrostatic potential based descriptor calculated at the MPWB1K/6-31+G(d,p) level of theory, provided solvation effects are taken into account for these flexible HB donors.
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Affiliation(s)
- Elena Bogdan
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - Guillaume Compain
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Lewis Mtashobya
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - François Besseau
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - Nicolas Galland
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - Bruno Linclau
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805.
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02.
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Braga CB, Ducati LC, Rittner R. Experimental and theoretical evaluation on the conformational behavior of l-aspartic acid dimethyl ester and its N-acetylated derivative. RSC Adv 2015. [DOI: 10.1039/c4ra14480e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The AspOMe and AcAspOMe conformational preferences and their corresponding intramolecular interactions were studied through spectroscopic and theoretical methodologies.
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Affiliation(s)
- Carolyne B. Braga
- Physical Organic Chemistry Laboratory
- Chemistry Institute
- University of Campinas
- Campinas
- Brazil
| | | | - Roberto Rittner
- Physical Organic Chemistry Laboratory
- Chemistry Institute
- University of Campinas
- Campinas
- Brazil
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