1
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Ma W, Kirchhoff JL, Strohmann C, Grabe B, Loh CCJ. Cooperative Bifurcated Chalcogen Bonding and Hydrogen Bonding as Stereocontrolling Elements for Selective Strain-Release Septanosylation. J Am Chem Soc 2023; 145:26611-26622. [PMID: 38032866 PMCID: PMC10722516 DOI: 10.1021/jacs.3c06984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
The exploitation of noncovalent interactions (NCIs) is emerging as a vital handle in tackling broad stereoselectivity challenges in synthesis. In particular, there has been significant recent interest in the harnessing of unconventional NCIs to surmount difficult selectivity challenges in glycosylations. Herein, we disclose the exploitation of an unconventional bifurcated chalcogen bonding and hydrogen bonding (HB) network, which paves the way for a robust catalytic strategy into biologically useful seven-membered ring sugars. Through 13C nuclear magnetic resonance (NMR) in situ monitoring, NMR titration experiments, and density functional theory (DFT) modeling, we propose a remarkable contemporaneous activation of multiple functional groups consisting of a bifurcated chalcogen bonding mechanism working hand-in-hand with HB activation. Significantly, the ester moiety installed on the glycosyl donor is critical in the establishment of the postulated ternary complex for stereocontrol. Through the 13C kinetic isotopic effect and kinetic studies, our data corroborated that a dissociative SNi-type mechanism forms the stereocontrolling basis for the excellent α-selectivity.
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Affiliation(s)
- Wenpeng Ma
- Abteilung
Chemische Biologie, Max-Planck-Institut
für Molekulare Physiologie, Otto-Hahn-Straße 11, Dortmund 44227, Germany
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, Dortmund 44227, Germany
| | - Jan-Lukas Kirchhoff
- Fakultät
für Chemie und Chemische Biologie, Anorganische Chemie, Technische Universität Dortmund, Otto-Hahn-Straße 6, Dortmund 44227, Germany
| | - Carsten Strohmann
- Fakultät
für Chemie und Chemische Biologie, Anorganische Chemie, Technische Universität Dortmund, Otto-Hahn-Straße 6, Dortmund 44227, Germany
| | - Bastian Grabe
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, Dortmund 44227, Germany
| | - Charles C. J. Loh
- Abteilung
Chemische Biologie, Max-Planck-Institut
für Molekulare Physiologie, Otto-Hahn-Straße 11, Dortmund 44227, Germany
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, Dortmund 44227, Germany
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2
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Abstract
While a good deal of information has accumulated concerning the manner in which an intramolecular noncovalent bond can affect the relative energies of various conformers, less is known about how such bonds might affect the dynamics of interconversion between them. A series of molecules are constructed in which symmetrically equivalent conformers containing a noncovalent bond can be interconverted by a bond rotation, the energy barrier to which is computed by quantum chemical methods. The rotation of a CF3 group attached to a phenyl ring is speeded up if a Se··F chalcogen bond can be formed with a SeH or SeF group placed in an ortho position, a bond that is present in and stabilizes the rotational transition state. The analogous SnF3 group can, on the other hand, engage in a Sn··Se tetrel bond in its global minimum. The energetic cost of breakage of this bond is not fully compensated by the appearance of a Se··F chalcogen bond in the rotational transition state. Other systems were designed by placing two phenyl rings on opposite ends of an octahedrally disposed SeF4 group. A high barrier inhibits their rotation with bulky Br atoms in ortho positions, but this barrier is lowered if Br is replaced by groups that can engage in either chalcogen (SeH or SeF) or pnicogen (AsH2) bonds with the F atoms in the rotational transition state. The barrier reduction is closely related to the strength of these noncovalent bonds.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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3
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Scheiner S. Competition Between the Two σ-Holes in the Formation of a Chalcogen Bond. Chemphyschem 2023; 24:e202200936. [PMID: 36744997 DOI: 10.1002/cphc.202200936] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/07/2023]
Abstract
A chalcogen atom Y contains two separate σ-holes when in a R1 YR2 molecular bonding pattern. Quantum chemical calculations consider competition between these two σ-holes to engage in a chalcogen bond (ChB) with a NH3 base. R groups considered include F, Br, I, and tert-butyl (tBu). Also examined is the situation where the Y lies within a chalcogenazole ring, where its neighbors are C and N. Both electron-withdrawing substituents R1 and R2 act cooperatively to deepen the two σ-holes, but the deeper of the two holes consistently lies opposite to the more electron-withdrawing group, and is also favored to form a stronger ChB. The formation of two simultaneous ChBs in a triad requires the Y atom to act as double electron acceptor, and so anti-cooperativity weakens each bond relative to the simple dyad. This effect is such that some of the shallower σ-holes are unable to form a ChB at all when a base occupies the other site.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, 84322-0300, Logan, Utah, USA
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4
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Scheiner S. Properties and Stabilities of Cyclic and Open Chains of Halogen Bonds. J Phys Chem A 2022; 126:6443-6455. [PMID: 36084144 DOI: 10.1021/acs.jpca.2c04967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Open and cyclic chains from two to eight units of ICl and IF are constructed and examined by density functional theory (DFT) calculations. These chains contain either I···I or I···X halogen bonds (XBs) where X refers to Cl or F. The closed rings are more stable than the open chains due to the presence of an additional XB and enhanced cooperativity. This pattern is true even for most trimers where there is sizable geometric distortion in the rings. I···F rings are generally more stable than the corresponding I···I cycles as the I···F bond is stronger than I···I even in the simple dimer. However, I···I rings are comparable in energy to I···Cl. It is possible to construct I···I rings of at least as large as eight units, which are held together exclusively by XBs. On the other hand, the maximum possible size of I···X rings is 6. Red shifts are observed in the I-X stretching frequency bands, which magnify as the chain, both cyclic and open, grows longer. The NMR chemical shielding of the I atoms increases for I···I chains but diminishes when I···Cl bonds are present.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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5
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Liu N, Li Q, Scheiner S, Xie X. Resonance-assisted intramolecular triel bonds. Phys Chem Chem Phys 2022; 24:15015-15024. [PMID: 35695162 DOI: 10.1039/d2cp01244h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The possibility that the intramolecular Tr⋯S triel bond is strengthened by resonance is examined by quantum chemical calculations within the planar five-membered ring of TrH2-CRCR-CRS (Tr = Al, Ga, In; R = NO2, CH3). This internal bond is found to be rather short (2.4-2.7 Å) with a large bond energy between 12 and 21 kcal mol-1. The pattern of bond length alternation and atomic charges within the ring is consistent with resonance involving the conjugated double bonds. This resonance enhances the triel bond strength by some 25%. The electron-withdrawing NO2 group weakens the bond, but it is strengthened by the electron-donating CH3 substituent. NICS analysis suggests the presence of a certain degree of aromaticity within the ring.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P. R. China.
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P. R. China.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
| | - Xiaoying Xie
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P. R. China.
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6
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Iribarren I, Sánchez-Sanz G, Alkorta I, Elguero J, Trujillo C. Evaluation of Electron Density Shifts in Noncovalent Interactions. J Phys Chem A 2021; 125:4741-4749. [PMID: 34061527 PMCID: PMC8279648 DOI: 10.1021/acs.jpca.1c00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Indexed: 12/12/2022]
Abstract
In the present paper, we report the quantitative evaluation of the electron density shift (EDS) maps within different complexes. Values associated with the total EDS maps exhibited good correlation with different quantities such as interaction energies, Eint, intermolecular distances, bond critical points, and LMOEDA energy decomposition terms. Besides, EDS maps at different cutoffs were also evaluated and related with the interaction energies values. Finally, EDS maps and their corresponding values are found to correlate with Eint within systems with cooperative effects. To our knowledge, this is the first time that the EDS has been quanitatively evaluated.
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Affiliation(s)
- Iñigo Iribarren
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish
Centre For High-End Computing, 7 Floor, The Tower, Grand Canal Quay, Dublin 2 D02 HP83, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Cristina Trujillo
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
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7
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Wessig P, John L, Sperlich E, Kelling A. Sulfur Tuning of [1,3]‐Dioxolo[4.5‐
f
]benzodioxole (DBD) Fluorescent Dyes. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pablo Wessig
- Institut für Chemie Universität Potsdam Karl-Liebknecht-Str. 24–25 14476 Potsdam Germany E-mail: ag-wessig.chem.uni-potsdam.de
| | - Leonard John
- Institut für Chemie Universität Potsdam Karl-Liebknecht-Str. 24–25 14476 Potsdam Germany E-mail: ag-wessig.chem.uni-potsdam.de
| | - Eric Sperlich
- Institut für Chemie Universität Potsdam Karl-Liebknecht-Str. 24–25 14476 Potsdam Germany E-mail: ag-wessig.chem.uni-potsdam.de
| | - Alexandra Kelling
- Institut für Chemie Universität Potsdam Karl-Liebknecht-Str. 24–25 14476 Potsdam Germany E-mail: ag-wessig.chem.uni-potsdam.de
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8
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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9
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Liu N, Li Q, McDowell SAC. Reliable Comparison of Pnicogen, Chalcogen, and Halogen Bonds in Complexes of 6-OXF 2-Fulvene (X = As, Sb, Se, Te, Be, I) With Three Electron Donors. Front Chem 2020; 8:608486. [PMID: 33425859 PMCID: PMC7793776 DOI: 10.3389/fchem.2020.608486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/27/2020] [Indexed: 01/03/2023] Open
Abstract
The pnicogen, chalcogen, and halogen bonds between 6-OXF2-fulvene (X = As, Sb, Se, Te, Br, and I) and three nitrogen-containing bases (FCN, HCN, and NH3) are compared. For each nitrogen base, the halogen bond is strongest, followed by the pnicogen bond, and the chalcogen bond is weakest. For each type of bond, the binding increases in the FCN < HCN < NH3 pattern. Both FCN and HCN engage in a bond with comparable strengths and the interaction energies of most bonds are < -6 kcal/mol. However, the strongest base NH3 forms a much more stable complex, particularly for the halogen bond with the interaction energy going up to -18 kcal/mol. For the same type of interaction, its strength increases as the mass of the central X atom increases. These bonds are different in strength, but all of them are dominated by the electrostatic interaction, with the polarization contribution important for the stronger interaction. The presence of these bonds changes the geometries of 6-OXF2-fulvene, particularly for the halogen bond formed by NH3, where the F-X-F arrangement is almost vertical to the fulvene ring.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
| | - Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
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10
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Menon PK, Krishnaraj K, Anabha E, Devaky K, Thomas SP. Synthesis, crystal structure and electron density analysis of a sulfanyl 2-pyridone analogue: Tautomeric preference and conformation locking by S···O chalcogen bonding. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Frontera A. Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides. Molecules 2020; 25:molecules25153419. [PMID: 32731517 PMCID: PMC7435756 DOI: 10.3390/molecules25153419] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Noble gas (or aerogen) bond (NgB) can be outlined as the attractive interaction between an electron-rich atom or group of atoms and any element of Group-18 acting as an electron acceptor. The IUPAC already recommended systematic nomenclature for the interactions of groups 17 and 16 (halogen and chalcogen bonds, respectively). Investigations dealing with noncovalent interactions involving main group elements (acting as Lewis acids) have rapidly grown in recent years. They are becoming acting players in essential fields such as crystal engineering, supramolecular chemistry, and catalysis. For obvious reasons, the works devoted to the study of noncovalent Ng-bonding interactions are significantly less abundant than halogen, chalcogen, pnictogen, and tetrel bonding. Nevertheless, in this short review, relevant theoretical and experimental investigations on noncovalent interactions involving Xenon are emphasized. Several theoretical works have described the physical nature of NgB and their interplay with other noncovalent interactions, which are discussed herein. Moreover, exploring the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD), it is demonstrated that NgB interactions are crucial in governing the X-ray packing of xenon derivatives. Concretely, special attention is given to xenon fluorides and xenon oxides, since they exhibit a strong tendency to establish NgBs.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
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12
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Abstract
A central pnicogen Z atom (Z = Sb, As) is covalently attached to the O atom of three -O(CH2)nX chains where X represents either an aldehyde or amine group. The chain can fold around so that the basic X group can engage in a noncovalent pnicogen bond with the central Z. The formation of up to three pnicogen bonds is energetically favored. The amine appears to engage in stronger pnicogen bonds than does the aldehyde, and bonds to Sb are favored over As, but there is little dependence on the length of the chain. The formation of each successive pnicogen bond reduces the magnitude of the σ-holes surrounding the Z atom, which tends to weaken the attraction for the basic end of the chain.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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13
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14
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Bauzá A, Frontera A. σ/π-Hole noble gas bonding interactions: Insights from theory and experiment. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213112] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Dutta J, Sahoo DK, Jena S, Tulsiyan KD, Biswal HS. Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond? Phys Chem Chem Phys 2020; 22:8988-8997. [DOI: 10.1039/d0cp00330a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crystal structure analysis and quantum chemical calculations enabled us to discover a new non-covalent interaction, coined as carbo-hydrogen bond (CH-bond).
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Affiliation(s)
- Juhi Dutta
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Dipak Kumar Sahoo
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Subhrakant Jena
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Kiran Devi Tulsiyan
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Himansu S. Biswal
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
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16
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Channar PA, Saeed A, Larik FA, Flörke U, El-Seedi H, Rodríguez Pirani LS, Erben MF. An intramolecular 1,5-chalcogen bond on the conformational preference of carbonyl thiocarbamate species. NEW J CHEM 2020. [DOI: 10.1039/c9nj06417f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two closely related carbamothioates were prepared by the reaction of benzoyl isothiocyanates and methanol. The crystal structures show the occurrence of 1,5-O⋯O intramolecular short distance that determines the conformational preference.
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Affiliation(s)
| | - Aamer Saeed
- Department of Chemistry
- Quaid-I-Azam University
- Islamabad 45320
- Pakistan
| | - Fayaz Ali Larik
- Department of Chemistry
- Quaid-I-Azam University
- Islamabad 45320
- Pakistan
| | - Ulrich Flörke
- Department Chemie
- Fakultät für Naturwissenschaften
- Universität Paderborn
- D-33098 Paderborn
- Germany
| | - Hesham El-Seedi
- International Research Center for Food Nutrition and Safety
- Jiangsu University
- Zhenjiang 212013
- China
- Al-Rayan Research and Innovation Center
| | - Lucas S. Rodríguez Pirani
- CEQUINOR (UNLP, CONICET-CCT La Plata)
- Departamento de Química
- Facultad de Ciencias Exactas
- Universidad Nacional de La Plata
- La Plata
| | - Mauricio F. Erben
- CEQUINOR (UNLP, CONICET-CCT La Plata)
- Departamento de Química
- Facultad de Ciencias Exactas
- Universidad Nacional de La Plata
- La Plata
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17
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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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18
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19
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Viglianisi C, Menichetti S. Chain Breaking Antioxidant Activity of Heavy (S, Se, Te) Chalcogens Substituted Polyphenols. Antioxidants (Basel) 2019; 8:antiox8100487. [PMID: 31623080 PMCID: PMC6826409 DOI: 10.3390/antiox8100487] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022] Open
Abstract
Polyphenols are probably the most important family of natural and synthetic chain-breaking antioxidants. Since long ago, chemists have studied how structural (bioinspired) modifications can improve the antioxidant activity of these compounds in terms of reaction rate with radical reactive oxygen species (ROS), catalytic character, multi-defence action, hydrophilicity/lipophilicity, biodistribution etc. In this framework, we will discuss the effect played on the overall antioxidant profile by the insertion of heavy chalcogens (S, Se and Te) in the phenolic skeleton.
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Affiliation(s)
- Caterina Viglianisi
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy.
| | - Stefano Menichetti
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy.
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20
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Zierkiewicz W, Wysokiński R, Michalczyk M, Scheiner S. Chalcogen bonding of two ligands to hypervalent YF 4 (Y = S, Se, Te, Po). Phys Chem Chem Phys 2019; 21:20829-20839. [PMID: 31517347 DOI: 10.1039/c9cp04006d] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability of two NH3 ligands to engage in simultaneous chalcogen bonds to a hypervalent YF4 molecule, with Y = S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis structure places the two ligands adjacent to one another in a pseudo-octahedral geometry, held there by a pair of σ-hole chalcogen bonds. The bases can also lie nearly opposite one another, in a distorted octahedron containing one π-hole and one strained σ-hole bond. The cis geometry is favored for Y = S, while Te, and Po tend toward the trans structure; they are nearly equally stable for Se. In either case, the binding energy rises rapidly with the size of the Y atom, exceeding 30 kcal mol-1 for PoF4.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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21
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22
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Franconetti A, Frontera A. Theoretical and Crystallographic Study of Lead(IV) Tetrel Bonding Interactions. Chemistry 2019; 25:6007-6013. [DOI: 10.1002/chem.201900447] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Antonio Franconetti
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.7 07122 Palma de Mallorca Spain
| | - Antonio Frontera
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.7 07122 Palma de Mallorca Spain
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23
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Bauzá A, Seth SK, Frontera A. Tetrel bonding interactions at work: Impact on tin and lead coordination compounds. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.01.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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24
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Trujillo C, Rozas I, Elguero J, Alkorta I, Sánchez-Sanz G. Modulating intramolecular chalcogen bonds in aromatic (thio)(seleno)phene-based derivatives. Phys Chem Chem Phys 2019; 21:23645-23650. [DOI: 10.1039/c9cp03694f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intramolecular chalcogen interactions have been studied for four different derivatives of compounds within two different families, S or Se, to evaluate the effect of these IMChBs in the stability of the interacting and non-interacting systems.
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Affiliation(s)
- Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin 152-160 Pearse Street
- Dublin 2
- Ireland
| | - Isabel Rozas
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin 152-160 Pearse Street
- Dublin 2
- Ireland
| | - José Elguero
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- 3
- E-28006 Madrid
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- 3
- E-28006 Madrid
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25
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Unravelling syn- and anti- orientation in the regioselectivity of carbonyl groups of 5-fluorouracil an anticancer drug toward proton donors. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Nuzzo S, Twamley B, Platts JA, Baker RJ. Pseudohalide Tectons within the Coordination Sphere of the Uranyl Ion: Experimental and Theoretical Study of C-H···O, C-H···S, and Chalcogenide Noncovalent Interactions. Inorg Chem 2018. [PMID: 29542918 DOI: 10.1021/acs.inorgchem.7b02967] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A series of uranyl thiocyanate and selenocyanate of the type [R4N]3[UO2(NCS)5] (R4 = nBu4, Me3Bz, Et3Bz), [Ph4P][UO2(NCS)3(NO3)] and [R4N]3[UO2(NCSe)5] (R4 = Me4, nPr4, Et3Bz) have been prepared and structurally characterized. The resulting noncovalent interactions have been examined and compared to other examples in the literature. The nature of these interactions is determined by the cation so that when the alkyl groups are small, chalcogenide···chalcogenide interactions are present, but this "switches off" when R = nPr and charge assisted U═O···H-C and S(e)···H-C hydrogen bonding remain the dominant interaction. Increasing the size of the chain to nBu results in only S···H-C interactions. The spectroscopic implications of these chalcogenide interactions have been explored in the vibrational and photophysical properties of the series [R4N]3[UO2(NCS)5] (R4 = Me4, Et4, nPr4, nBu4, Me3Bz, Et3Bz), [R4N]3[UO2(NCSe)5] (R4 = Me4, nPr4, Et3Bz) and [Et4N]4[UO2(NCSe)5][NCSe]. The data suggest that U═O···H-C interactions are weak and do not perturb the uranyl moiety. While the chalcogenide interactions do not influence the photophysical properties, a coupling of the U═O and δ(NCS) or δ(NCSe) vibrational modes is observed in the 77 K solid state emission spectra. A theoretical examination of representative examples of Se···Se, C-H···Se, and C-H···O═U by molecular electrostatic potentials and NBO and AIM methodologies gives a deeper understanding of these weak interactions. C-H···Se are individually weak but C-H···O═U interactions are even weaker, supporting the idea that the -yl oxo's are weak Lewis bases. An Atoms in Molecules study suggests that the chalcogenide interaction is similar to lone pair···π or fluorine···fluorine interactions. An oxidation of the NCS ligands to form [(UO2)(SO4)2(H2O)4]·3H2O was also noted.
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Affiliation(s)
- Stefano Nuzzo
- School of Chemistry , University of Dublin, Trinity College , Dublin 2 , Ireland
| | - Brendan Twamley
- School of Chemistry , University of Dublin, Trinity College , Dublin 2 , Ireland
| | - James A Platts
- School of Chemistry, Main Building , Cardiff University , Park Place , Cardiff CF10 3AT , U.K
| | - Robert J Baker
- School of Chemistry , University of Dublin, Trinity College , Dublin 2 , Ireland
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27
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Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes. CRYSTALS 2018. [DOI: 10.3390/cryst8030112] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.
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28
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Gleiter R, Haberhauer G, Werz DB, Rominger F, Bleiholder C. From Noncovalent Chalcogen-Chalcogen Interactions to Supramolecular Aggregates: Experiments and Calculations. Chem Rev 2018; 118:2010-2041. [PMID: 29420879 DOI: 10.1021/acs.chemrev.7b00449] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review considers noncovalent bonds between divalent chalcogen centers. In the first part we present X-ray data taken from the solid state structures of dimethyl- and diphenyl-dichalcogenides as well as oligoalkynes kept by alkyl-sulfur, -selenium, and -tellurium groups. Furthermore, we analyzed the solid state structures of medium sized (12-24 ring size) selenium coronands and medium to large rings with alkyne and alkene units between two chalcogen centers. The crystal structures of the cyclic structures revealed columnar stacks with close contacts between neighboring rings via noncovalent interactions between the chalcogen centers. To get larger space within the cavities, rings with diyne units between the chalcogen centers were used. These molecules showed channel-like structures in the solid state. The flexibility of the rings permits inclusion of guest molecules such as five-membered heterocycles and aromatic six-membered rings. In the second part we discuss the results of quantum chemical calculations. To treat properly the noncovalent bonding between chalcogens, we use diffuse augmented split valence basis sets in combination with electron correlation methods. Our model substances were 16 dimers consisting of two Me-X-Me (X = O, S, Se, Te) pairs and dimers of Me-X-Me/Me-X-CN (X = O, S, Se, Te) pairs. The calculations show the anticipated increase of the interaction energy from (Me-O-Me)2 (-2.15 kcal/mol) to (Me-O-Me/Me-Te-CN) (-6.59 kcal/mol). An analysis by the NBO method reveals that in the case of the chalcogen centers O and S the hydrogen bridges between the molecules dominate. However, in the case of Se and Te the major bonding between the pairs originates from dispersion forces between the chalcogen centers. It varies between -1.7 and -4.0 kcal/mol.
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Affiliation(s)
- Rolf Gleiter
- Organisch-Chemisches Institut, Universität Heidelberg , Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
| | - Gebhard Haberhauer
- Institut für Organische Chemie, Universität Duisburg-Essen , Universitätsstraße 7, D-45117 Essen, Germany
| | - Daniel B Werz
- Institut für Organische Chemie, Technische Universität Braunschweig , Hagenring 30, D-38106 Braunschweig, Germany
| | - Frank Rominger
- Organisch-Chemisches Institut, Universität Heidelberg , Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry & Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306-4390, United States
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29
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Sánchez-Sanz G, Trujillo C. Improvement of Anion Transport Systems by Modulation of Chalcogen Interactions: The influence of solvent. J Phys Chem A 2018; 122:1369-1377. [DOI: 10.1021/acs.jpca.7b10920] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal
Quay, Dublin 2, Ireland
| | - Cristina Trujillo
- School
of Chemistry, Trinity Biomedical Sciences, Trinity College Dublin, 152−160 Pearse Street, Dublin 2, Ireland
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30
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Geboes Y, De Vos E, Herrebout WA. S⋯S and S⋯P chalcogen bonding in solution: a cryospectroscopic study of the complexes of 2,2,4,4-tetrafluoro-1,3-dithietane with dimethyl sulfide and trimethylphosphine. NEW J CHEM 2018. [DOI: 10.1039/c8nj01648h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental evidence on the formation of S⋯S and P⋯S chalcogen bonded complexes between 2,2,4,4-tetrafluoro-1,3-dithiethane and the Lewis bases dimethyl sulfide and trimethylphosphine is obtained using infrared spectroscopy of solutions in liquid krypton.
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Affiliation(s)
- Yannick Geboes
- Department of Chemistry
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - Elias De Vos
- Department of Chemistry
- University of Antwerp
- 2020 Antwerp
- Belgium
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31
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Wei Y, Li Q, Yang X, McDowell SAC. Intramolecular Si⋅⋅⋅O Tetrel Bonding: Tuning of Substituents and Cooperativity. ChemistrySelect 2017. [DOI: 10.1002/slct.201702280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yuanxin Wei
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering,; Yantai University,; Yantai 264005 China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering,; Yantai University,; Yantai 264005 China
| | - Xin Yang
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering,; Yantai University,; Yantai 264005 China
| | - Sean A. C. McDowell
- Department of Biological and Chemical Sciences; The University of the West Indies, Cave Hill Campus; Barbados
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32
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Enhancing Intramolecular Chalcogen Interactions in 1-Hydroxy-8-YH-naphthalene Derivatives. J Phys Chem A 2017; 121:8995-9003. [DOI: 10.1021/acs.jpca.7b09678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cristina Trujillo
- School
of Chemistry, Trinity Biomedical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica, Consejo Superior de Investigaciones Científicas, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica, Consejo Superior de Investigaciones Científicas, Juan de la Cierva, 3, E-28006 Madrid, Spain
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33
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Oliveira V, Cremer D, Kraka E. The Many Facets of Chalcogen Bonding: Described by Vibrational Spectroscopy. J Phys Chem A 2017; 121:6845-6862. [PMID: 28782954 DOI: 10.1021/acs.jpca.7b06479] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A diverse set of 100 chalcogen-bonded complexes comprising neutral, cationic, anionic, divalent, and double bonded chalcogens has been investigated using ωB97X-D/aug-cc-pVTZ to determine geometries, binding energies, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching force constants, and associated bond strength orders. The accuracy of ωB97X-D was accessed by CCSD(T)/aug-cc-pVTZ calculations of a subset of 12 complexes and by the CCSD(T)/aug-cc-pVTZ //ωB97X-D binding energies of 95 complexes. Most of the weak chalcogen bonds can be rationalized on the basis of electrostatic contributions, but as the bond becomes stronger, covalent contributions can assume a primary role in the strength and geometry of the complexes. Covalency in chalcogen bonds involves the charge transfer from a lone pair orbital of a Lewis base into the σ* orbital of a divalent chalcogen or a π* orbital of a double bonded chalcogen. We describe for the first time a symmetric chalcogen-bonded homodimer stabilized by a charge transfer from a lone pair orbital into a π* orbital. New polymeric materials based on chalcogen bonds should take advantage of the extra stabilization granted by multiple chalcogen bonds, as is shown for 1,2,5-telluradiazole dimers.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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34
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Pavan MS, Sarkar S, Row TNG. Exploring the rare S—H...S hydrogen bond using charge density analysis in isomers of mercaptobenzoic acid. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:626-633. [DOI: 10.1107/s2052520617008344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/06/2017] [Indexed: 11/10/2022]
Abstract
Experimental and theoretical charge density analyses on isomers of mercaptobenzoic acid have been carried out to quantify the hydrogen bonding of the hitherto less explored thiols, to assess the strength of the interactions using the topological features of the electron density. The electron density study offers interesting insights into the nature of the S—H...S interaction. The interaction energy is comparable with that of a weak hydrogen bond. The strength and directionality of the S—H...S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of the intramolecular S...O chalcogen bond in 2-mercaptobenzoic acid and is stronger than in 3-mercaptobenzoic acid, which lacks the intramolecular S...O bond. Thepara-substituted mercaptobenzoic acid depicts a type I S...S interaction.
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35
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Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds. Molecules 2017; 22:molecules22020227. [PMID: 28157170 PMCID: PMC6155622 DOI: 10.3390/molecules22020227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/26/2017] [Indexed: 01/19/2023] Open
Abstract
A theoretical study of the peri interactions, both intramolecular hydrogen (HB) and chalcogen bonds (YB), in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se) being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO) analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y–H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.
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36
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Goettel JT, Gerken M. Synthesis and Characterization of Adducts between SF 4 and Oxygen Bases: Examples of O···S(IV) Chalcogen Bonding. Inorg Chem 2016; 55:12441-12450. [PMID: 27934407 DOI: 10.1021/acs.inorgchem.6b02373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lewis acid-base adducts between SF4 and the oxygen bases tetrahydrofuran, cyclopentanone, and 1,2-dimethoxyethane were synthesized and characterized by Raman spectroscopy and X-ray crystallography. Crystal structures of (SF4·OC4H8)2, SF4·(OC4H8)2, SF4·CH3OC2H4OCH3, and SF4·(O═C5H8)2 show weak S···O chalcogen bonding interactions ranging from 2.662(2) to 2.8692(9) Å. Caffeine, which has three Lewis basic sites, was reacted with SF4 and one aliquot of HF forming C8H10N4O2·2SF4·HF, which was also characterized by X-ray crystallography. Density functional theory calculations aided in the assignment of the vibrational spectra of (SF4·OC4H8)2, SF4·(OC4H8)2, SF4·CH3OC2H4OCH3, and SF4·(O═C5H8)2. Bonding was studied by natural bond order and the quantum theory of atoms in molecules analyses.
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Affiliation(s)
- James T Goettel
- The Canadian Centre for Research in Advanced Fluorine Technologies and Department of Chemistry and Biochemistry, University of Lethbridge , Lethbridge, Alberta T1K 3M4, Canada
| | - Michael Gerken
- The Canadian Centre for Research in Advanced Fluorine Technologies and Department of Chemistry and Biochemistry, University of Lethbridge , Lethbridge, Alberta T1K 3M4, Canada
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37
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Menichetti S, Amorati R, Meoni V, Tofani L, Caminati G, Viglianisi C. Role of Noncovalent Sulfur···Oxygen Interactions in Phenoxyl Radical Stabilization: Synthesis of Super Tocopherol-like Antioxidants. Org Lett 2016; 18:5464-5467. [DOI: 10.1021/acs.orglett.6b02557] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Menichetti
- Department
of Chemistry “U. Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Riccardo Amorati
- Department
of Chemistry “Ciamician”, University of Bologna, Via San Giacomo 11, 40126 Bologna, Italy
| | - Valentina Meoni
- Department
of Chemistry “U. Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Lorenzo Tofani
- Department
of Chemistry “U. Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Gabriella Caminati
- Department
of Chemistry “U. Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
- CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Caterina Viglianisi
- Department
of Chemistry “U. Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
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38
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SHUKLA RAHUL, CHOPRA DEEPAK. Understanding the effect of substitution on the formation of S. . .F chalcogen bond. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1176-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Sánchez-Sanz G, Trujillo C, Alkorta I. Structure, binding energy and chiral discrimination in oxathiirane homodimers. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.06.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Scheiner S. Interpretation of Spectroscopic Markers of Hydrogen Bonds. Chemphyschem 2016; 17:2263-71. [DOI: 10.1002/cphc.201600326] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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41
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Ho PC, Szydlowski P, Sinclair J, Elder PJW, Kübel J, Gendy C, Lee LM, Jenkins H, Britten JF, Morim DR, Vargas-Baca I. Supramolecular macrocycles reversibly assembled by Te(…)O chalcogen bonding. Nat Commun 2016; 7:11299. [PMID: 27090355 PMCID: PMC4838886 DOI: 10.1038/ncomms11299] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 03/11/2016] [Indexed: 12/25/2022] Open
Abstract
Organic molecules with heavy main-group elements frequently form supramolecular links to electron-rich centres. One particular case of such interactions is halogen bonding. Most studies of this phenomenon have been concerned with either dimers or infinitely extended structures (polymers and lattices) but well-defined cyclic structures remain elusive. Here we present oligomeric aggregates of heterocycles that are linked by chalcogen-centered interactions and behave as genuine macrocyclic species. The molecules of 3-methyl-5-phenyl-1,2-tellurazole 2-oxide assemble a variety of supramolecular aggregates that includes cyclic tetramers and hexamers, as well as a helical polymer. In all these aggregates, the building blocks are connected by Te(…)O-N bridges. Nuclear magnetic resonance spectroscopic experiments demonstrate that the two types of annular aggregates are persistent in solution. These self-assembled structures form coordination complexes with transition-metal ions, act as fullerene receptors and host small molecules in a crystal.
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Affiliation(s)
- Peter C Ho
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Patrick Szydlowski
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Jocelyn Sinclair
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Philip J W Elder
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Joachim Kübel
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Chris Gendy
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Lucia Myongwon Lee
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Hilary Jenkins
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - James F Britten
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Derek R Morim
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Ignacio Vargas-Baca
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
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42
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Fick RJ, Kroner GM, Nepal B, Magnani R, Horowitz S, Houtz RL, Scheiner S, Trievel RC. Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9. ACS Chem Biol 2016; 11:748-54. [PMID: 26713889 DOI: 10.1021/acschembio.5b00852] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent studies have demonstrated that carbon-oxygen (CH···O) hydrogen bonds have important roles in S-adenosylmethionine (AdoMet) recognition and catalysis in methyltransferases. Here, we investigate noncovalent interactions that occur between the AdoMet sulfur cation and oxygen atoms in methyltransferase active sites. These interactions represent sulfur-oxygen (S···O) chalcogen bonds in which the oxygen atom donates a lone pair of electrons to the σ antibonding orbital of the AdoMet sulfur atom. Structural, biochemical, and computational analyses of an asparagine mutation in the lysine methyltransferase SET7/9 that abolishes AdoMet S···O chalcogen bonding reveal that this interaction enhances substrate binding affinity relative to the product S-adenosylhomocysteine. Corroborative quantum mechanical calculations demonstrate that sulfonium systems form strong S···O chalcogen bonds relative to their neutral thioether counterparts. An inspection of high-resolution crystal structures reveals the presence of AdoMet S···O chalcogen bonding in different classes of methyltransferases, illustrating that these interactions are not limited to SET domain methyltransferases. Together, these results demonstrate that S···O chalcogen bonds contribute to AdoMet recognition and can enable methyltransferases to distinguish between substrate and product.
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Affiliation(s)
| | | | - Binod Nepal
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Roberta Magnani
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Scott Horowitz
- Howard Hughes Medical Institute, Ann Arbor, Michigan 48109, United States
| | - Robert L. Houtz
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Steve Scheiner
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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43
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An ab initio study on cationic chalcogen bond interactions between F3−H S+ (n= 0–2) and nitrogen bases. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.12.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Nziko VDPN, Scheiner S. Comparison of π-hole tetrel bonding with σ-hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and NH3. Phys Chem Chem Phys 2016; 18:3581-90. [DOI: 10.1039/c5cp07545a] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In addition to the standard halogen bond formed when NH3approaches XCN (X = F, Cl, Br, I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X–C bond.
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Affiliation(s)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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45
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Nepal B, Scheiner S. Substituent Effects on the Binding of Halides by Neutral and Dicationic Bis(triazolium) Receptors. J Phys Chem A 2015; 119:13064-73. [DOI: 10.1021/acs.jpca.5b09738] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Binod Nepal
- Department of Chemistry and
Biochemistry, Utah State University Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University Logan, Utah 84322-0300, United States
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46
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Zins EL, Alikhani ME. Double π-hole tetrel-chalcogen interactions can lead to stable molecular heterodimer. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1118570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- E. L. Zins
- MONARIS, UMR, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
- CNRS, MONARIS, UMR, Université Pierre et Marie Curie, Paris, France
| | - M. E. Alikhani
- MONARIS, UMR, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
- CNRS, MONARIS, UMR, Université Pierre et Marie Curie, Paris, France
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47
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Nziko VDPN, Scheiner S. Interactions between Thiourea and Imines. Prelude to Catalysis. J Org Chem 2015; 80:10334-41. [DOI: 10.1021/acs.joc.5b01985] [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)
- Vincent de Paul N. Nziko
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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48
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Dissection of the Factors Affecting Formation of a CH∙∙∙O H-Bond. A Case Study. CRYSTALS 2015. [DOI: 10.3390/cryst5030327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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49
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Scheiner S. Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds. J Phys Chem A 2015; 119:9189-99. [DOI: 10.1021/acs.jpca.5b06831] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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50
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Esrafili MD, Mohammadian-Sabet F. Bifurcated chalcogen bonds: A theoretical study on the structure, strength and bonding properties. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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