151
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Michalczyk M, Zierkiewicz W, Scheiner S. Triel-Bonded Complexes between TrR3
(Tr=B, Al, Ga; R=H, F, Cl, Br, CH3
) and Pyrazine. Chemphyschem 2018; 19:3122-3133. [DOI: 10.1002/cphc.201800774] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Wiktor Zierkiewicz
- 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 United States
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152
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Naseer MM, Hussain M, Bauzá A, Lo KM, Frontera A. Intramolecular Noncovalent Carbon Bonding Interaction Stabilizes the cis Conformation in Acylhydrazones. Chempluschem 2018; 83:881-885. [PMID: 31950685 DOI: 10.1002/cplu.201800329] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/14/2022]
Abstract
Noncovalent carbon bonding, a recently explored σ-hole interaction, was hitherto supposed to be a weak and structure-guided interaction. Here, its role in the intramolecular stabilization of the cis conformation of the amide moiety in acylhydrazones is described. The calculations reveal an electron donation from the lone pair of the nitrogen atom to the empty antibonding C-N orbital [LP(N)→BD*(C-N)] with a concomitant stabilization energy of E(2) =1.2 kcal mol-1 .
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Affiliation(s)
| | - Majid Hussain
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Kong Mun Lo
- Research Centre for Crystalline Materials School of Science and Technology, Sunway University, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
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153
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Zierkiewicz W, Michalczyk M, Scheiner S. Regium bonds between M n clusters (M = Cu, Ag, Au and n = 2-6) and nucleophiles NH 3 and HCN. Phys Chem Chem Phys 2018; 20:22498-22509. [PMID: 30140798 DOI: 10.1039/c8cp03883j] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The most stable geometries of the coinage metal (or regium) atom (Cu, Ag, Au) clusters Mn for n up to 6 are all planar, and adopt the lowest possible spin multiplicity. Clusters with even numbers of M atoms are thus singlets, while those with odd n are open-shell doublets. Examination of the molecular electrostatic potential (MEP) of each cluster provides strong indications of the most likely site of attack by an approaching nucleophile, generally one of two positions. A nucleophile (NH3 or HCN) most favorably approaches one particular M atom of each cluster, rather than a bond midpoint or face. In the closed-shell clusters, the interaction energies are highly dependent upon the intensity of the MEP, but this correlation fades for the open-shell systems studied in this work. The strength of the interaction is also closely related to the basicity of the nucleophile. Regium bond energies can be more than 30 kcal mol-1 and tend to follow the Au > Cu > Ag order. These interaction energies are in large part derived from Coulombic attraction, with a smaller orbital interaction contribution.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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154
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Escudero-Adán EC, Bauzá A, Lecomte C, Frontera A, Ballester P. Boron triel bonding: a weak electrostatic interaction lacking electron-density descriptors. Phys Chem Chem Phys 2018; 20:24192-24200. [PMID: 30209451 DOI: 10.1039/c8cp04401e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In an effort to describe π-hole interactions, we undertook accurate high-resolution X-ray diffraction analyses of single crystals of 1,4-dinitrobenzene, a co-crystal of cis-tartaric acid and bis-pyridine N-oxide and the hydrochloride of B-4-pyridinylboronic acid. We selected these three compounds owing to the π-hole accessibility features that the sp2 hybridized B, C and N atoms provide, thus allowing us to compare the fundamental characteristics of π-hole interactions using Bader's Atom in Molecules (AIM) theory. This particular study required extremely accurate experimental diffraction data, because the interaction of interest is weak. As shown by the experimental charge density maps of the -YO2 (Y = B, C, N) units, we assign the depletion of electron-density present in the central boron, carbon and nitrogen atoms (electrophilic π-holes) as the main origin for the establishment of intermolecular Lewis acid-Lewis base attractive interaction with complementary electron-rich regions. Unexpectedly, the Bader's analyses of both experimentally and theoretically calculated charge distribution maps for the solid involving the - BO2H2 group do not show the presence of bond paths, neither of the bond critical points, between the interacting electron rich sites and the boron or carbon atoms featuring the electron hole. In contrast, these topological descriptors of chemical interactions for the AIM theory were easily located in the solid-state structures of the compounds involving the carboxylic and the nitro groups.
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Affiliation(s)
- Eduardo C Escudero-Adán
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Paısos Catalans, 16, 43007, Tarragona, Spain.
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155
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Lim JYC, Liew JY, Beer PD. Thermodynamics of Anion Binding by Chalcogen Bonding Receptors. Chemistry 2018; 24:14560-14566. [PMID: 30063097 DOI: 10.1002/chem.201803393] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/30/2018] [Indexed: 01/16/2023]
Abstract
The application of chalcogen bonding (ChB) to anion recognition is an underdeveloped area of host-guest supramolecular chemistry. The chemical instability of heavier chalcogen derivatives may in part be responsible for the lack of progress. Herein, the synthesis of a new structurally simple, tellurium-based ChB binding motif is reported, the robust stability of which has enabled the thermodynamic properties for ChB halide anion binding in polar aprotic and wet protic organic solvent media to be elucidated. The thermodynamic data reveals how the subtle interplay between ChB host, anion guest and solvent dictates halide binding selectivity and affinity trends. These findings help to provide a deeper insight into the nature of the ChB-anion interaction.
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Affiliation(s)
- Jason Y C Lim
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jane Y Liew
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Paul D Beer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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156
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Bauzá A, Frontera A. Tetrel Bonding Interactions in Perchlorinated Cyclopenta- and Cyclohexatetrelanes: A Combined DFT and CSD Study. Molecules 2018; 23:molecules23071770. [PMID: 30029469 PMCID: PMC6100242 DOI: 10.3390/molecules23071770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/15/2018] [Accepted: 07/15/2018] [Indexed: 11/23/2022] Open
Abstract
In this manuscript, we combined DFT calculations (PBE0-D3/def2-TZVP level of theory) and a Cambridge Structural Database (CSD) survey to evaluate the ability of perchlorinated cyclopenta- and cyclohexatetrelanes in establishing tetrel bonding interactions. For this purpose, we used Tr5Cl10 and Tr6Cl12 (Tr = Si and Ge) and HCN, HF, OH− and Cl− as electron donor entities. Furthermore, we performed an Atoms in Molecules (AIM) analysis to further describe and characterize the interactions studied herein. A survey of crystal structures in the CSD reveals that close contacts between Si and lone-pair-possessing atoms are quite common and oriented along the extension of the covalent bond formed by the silicon with the halogen atom.
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Affiliation(s)
- Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - 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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157
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Kříž K, Fanfrlík J, Lepšík M. Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations. Chemphyschem 2018; 19:2540-2548. [PMID: 30003638 DOI: 10.1002/cphc.201800409] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 11/10/2022]
Abstract
A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the Protein Data Bank (PDB). We have found that a large fraction (23 %) of complexes with a S/Se-containing ligand feature close S/Se⋅⋅⋅O/N/S contacts. Eleven non-redundant representative potential S/Se⋅⋅⋅O chalcogen-bond motifs were selected and truncated to model systems and seven more model systems were prepared by S-to-Se substitution. These systems were then subjected to analysis by quantum chemical (QM) methods-electrostatic potential, geometry optimisation or interaction energy calculations, including solvent effects. The QM calculations indicate that chalcogen bonding does indeed play a dominant role in stabilising some of the interaction motifs studied. We thus advocate further exploration of chalcogen bonding with the aim of potential future use in structure-based drug design.
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Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry Faculty of Science, Charles University, Hlavova 8, 128 40, Praha 2, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
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158
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Esrafili MD, Mousavian P, Mohammadian-Sabet F. Tuning of pnicogen and chalcogen bonds by an aerogen-bonding interaction: a comparative ab initio study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1492746] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Parisasadat Mousavian
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Fariba Mohammadian-Sabet
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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159
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Regium-π vs Cation-π Interactions in M2 and MCl (M = Cu, Ag and Au) Complexes with Small Aromatic Systems: An ab Initio Study. INORGANICS 2018. [DOI: 10.3390/inorganics6030064] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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160
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Comparison between Tetrel Bonded Complexes Stabilized by σ and π Hole Interactions. Molecules 2018; 23:molecules23061416. [PMID: 29891824 PMCID: PMC6100375 DOI: 10.3390/molecules23061416] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 01/22/2023] Open
Abstract
The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH₄, TH₃F, and TH₂F₂ (T = Si, Ge, Sn) and the latter by TH₂=CH₂, THF=CH₂, and TF₂=CH₂, all paired with NH₃ as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of the tetrel bond, whether σ or π. The magnitudes of the maxima of the molecular electrostatic potential in the two types of systems are not good indicators of either the interaction energy or even the full Coulombic energy. The geometry of the Lewis acid is significantly distorted by the formation of the dimer, more so in the case of the σ-bonded complexes, and this deformation intensifies the σ and π holes.
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161
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Zhang Y, Wang JG, Sun X, Liu Q, Wang W, Wang YB. Supramolecular Interactions of Fullerene C 60
with 1,3,5-Trifluoro-2,4,6-triiodobenzene: A Combined Theoretical and Experimental Study. Chempluschem 2018; 83:470-477. [DOI: 10.1002/cplu.201800174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/01/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Zhang
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Jian-Ge Wang
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Xiaotian Sun
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Qiaohong Liu
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Yi-Bo Wang
- Department of Chemistry; Key Laboratory of Guizhou High Performance Computational Chemistry; Guizhou University; Guiyang 550025 P. R. China
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162
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Grabowski SJ. Coordination of Be and Mg Centres by HCN Ligands - Be…N and Mg…N Interactions. Chemphyschem 2018; 19:1830-1840. [PMID: 29709103 DOI: 10.1002/cphc.201800274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 11/06/2022]
Abstract
ωB97XD/aug-cc-pVTZ calculations were performed for clusters of Z2+ cations (Z=Be and Mg) and HCN molecules (up to six molecules). The clusters of Be(CH3 )2 and Mg(CH3 )2 with HCN species were also calculated to analyse the influence of the Be/Mg-C formally covalent bonds on interactions of Be or Mg centre with ligands. The beryllium and magnesium centres possess different areas of a positive electrostatic potential that depend on a number of HCN ligands in the cluster considered. Numerous correlations between geometrical, energetic and topological parameters of the clusters considered are discussed since various theoretical approaches are applied; Quantum Theory of 'Atoms in Molecules', Natural Bond Orbital method and decomposition of the energy of interaction. The Be/Mg…N interactions classified as beryllium and magnesium bonds possess numerous characteristics which are known for the hydrogen bonds. Different types of coordination of Be and Mg centres analysed here exist also in crystal structures.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia, International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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163
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Frontera A, Bauzá A. Regium-π bonds: An Unexplored Link between Noble Metal Nanoparticles and Aromatic Surfaces. Chemistry 2018. [PMID: 29521478 DOI: 10.1002/chem.201800820] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The ability of metal clusters involving elements from group 11 (Ag, Cu, Au) to favorably interact with π systems of different size and electronic nature was evaluated at the PBE0-D3/def2-TZVPP//PBE0-D3/def2-TZVP level of theory. The M9 clusters (M=Cu, Ag, Au) were used as σ-hole and σ-lump donors, and benzene, trifluorobenzene, and hexafluorobenzene as aromatic rings. In addition, the study was expanded to the analysis of extended π systems by using naphthalene and anthracene as well as their corresponding perfluorinated derivatives. Furthermore, Bader's theory of Atoms in Molecules as well as natural bonding orbital and spin-density calculations were used to further investigate and characterize the regium-π and σ-lump complexes described herein. Apparently, regium-π bonds have not previously been described in the literature and may be of great importance in the understanding of organocatalytic processes involving aromatic substrates as well as in the design of new materials based on this novel subclass of σ-hole bonding.
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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, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
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164
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165
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Esrafili MD, Sadr-Mousavi A. A computational study on the strength and nature of bifurcated aerogen bonds. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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166
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Grabowski SJ. Magnesium Bonds: From Divalent Mg Centres to Trigonal and Tetrahedral Coordination. ChemistrySelect 2018. [DOI: 10.1002/slct.201703137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sławomir J. Grabowski
- Faculty of Chemistry; University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072; 20080 San Sebastian Spain
- IKERBASQUE; Basque Foundation for Science; 48011 Bilbao Spain
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167
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Bauzá A, Frontera A. Chalcogen 'like-like' Interactions Involving Trisulphide and Triselenide Compounds: A Combined CSD and Ab Initio Study. Molecules 2018; 23:molecules23030699. [PMID: 29562728 PMCID: PMC6017106 DOI: 10.3390/molecules23030699] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 11/30/2022] Open
Abstract
In this manuscript, we combined a search in the Cambridge Structural Database (CSD) and ab initio calculations (RI-MP2/def2-TZVPD level of theory) to analyze the ability of trisulphide and triselenide moieties to establish chalcogen ‘like-like’ interactions. A preliminary CSD inspection revealed two predominant structural patterns, depending on the anti or syn conformation adopted by the substituents of the S3/Se3 bridge, leading to bifurcated or double chalcogen bonding interactions, respectively. In order to analyze these two relevant structural motifs we have used a series of S and Se derivatives Ch3X2 (Ch = S and Se and X = H, F, CN, and CF3) which act as both electron donor (using the lone pairs) and acceptor (using the σ-holes) entities. Besides, we have carried out “atoms in molecules” (AIM) and natural bonding orbital (NBO) analyses to further describe and characterize the chalcogen bonding interactions described herein. As far as we know, chalcogen···chalcogen interactions involving trichalconides (S3/Se3) have not been previously described in literature a may be of great importance in the preparation and characterization of new solids based on this subclass of σ-hole bonding.
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Affiliation(s)
- Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - 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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168
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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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169
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Dong W, Yang X, Cheng J, Li W, Li Q. Comparison for σ-hole and π-hole tetrel-bonded complexes involving F 2 C CFTF 3 (T C, Si, and Ge): Substitution, hybridization, and solvation effects. J Fluor Chem 2018. [DOI: 10.1016/j.jfluchem.2018.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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170
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Niyas MA, Ramakrishnan R, Vijay V, Hariharan M. Structure-Packing-Property Correlation of Self-Sorted Versus Interdigitated Assembly in TTF⋅TCNQ-Based Charge-Transport Materials. Chemistry 2018; 24:12318-12329. [DOI: 10.1002/chem.201705537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Indexed: 11/09/2022]
Affiliation(s)
- M. A. Niyas
- School of Chemistry; Indian Institute of, Science Education and Research Thiruvananthapuram, Vithura; Thiruvananthapuram 695551 Kerala India
| | - Remya Ramakrishnan
- School of Chemistry; Indian Institute of, Science Education and Research Thiruvananthapuram, Vithura; Thiruvananthapuram 695551 Kerala India
| | - Vishnu Vijay
- School of Chemistry; Indian Institute of, Science Education and Research Thiruvananthapuram, Vithura; Thiruvananthapuram 695551 Kerala India
| | - Mahesh Hariharan
- School of Chemistry; Indian Institute of, Science Education and Research Thiruvananthapuram, Vithura; Thiruvananthapuram 695551 Kerala India
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171
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Zierkiewicz W, Michalczyk M, Scheiner S. Aerogen bonds formed between AeOF 2 (Ae = Kr, Xe) and diazines: comparisons between σ-hole and π-hole complexes. Phys Chem Chem Phys 2018; 20:4676-4687. [PMID: 29345698 DOI: 10.1039/c7cp08048d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between KrOF2 or XeOF2 and the 1,2, 1,3, and 1,4 diazines is characterized chiefly by a Kr/XeN aerogen bond, as deduced from ab initio calculations. The most stable dimers take advantage of the σ-hole on the aerogen atom, wherein the two molecules lie in the same plane. The interaction is quite strong, as much as 18 kcal mol-1. A second class of dimer geometry utilizes the π-hole above the aerogen atom in an approximate perpendicular arrangement of the two monomers; these structures are not as strongly bound: 6-8 kcal mol-1. Both sorts of dimers contain auxiliary CHF H-bonds which contribute to their stability, but even with their removal, the aerogen bond energy remains as high as 14 kcal mol-1. The nature and strength of each specific interaction is confirmed and quantified by AIM, NCI, NBO, and electron density shift patterns. There is not a great deal of sensitivity to the identity of either the aerogen atom or the position of the two N atoms in the diazine.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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172
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Frontera A, Bauzá A. Concurrent aerogen bonding and lone pair/anion-π interactions in the stability of organoxenon derivatives: a combined CSD and ab initio study. Phys Chem Chem Phys 2018; 19:30063-30068. [PMID: 29095452 DOI: 10.1039/c7cp06685f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this manuscript the ability of organoxenon fluorides to establish concurrent π-hole aerogen bonding and lone pair/anion-π interactions has been studied at the RI-MP2/def2-TZVP level of theory. The presence of both an aromatic system (benzene, trifluorobenzene and pentafluorobenzene) and a xenon atom makes these molecules suitable for simultaneously establishing both interactions. In this regard, we have used CH3CN, NH3, O(CH3)2, Cl-, CN- and BF4- as neutral and charged electron donors, respectively. Moreover, the NBO analysis showed that orbital effects contribute to the global stabilization of the complexes studied. Furthermore, we have used Bader's theory of "atoms in molecules" to analyse and characterize the noncovalent interactions described herein from a charge-density perspective. Finally, several examples retrieved from the CSD are also included, highlighting the impact of these interactions in the solid state chemistry of Xe.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain.
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173
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Quiñonero D. Sigma-hole carbon-bonding interactions in carbon-carbon double bonds: an unnoticed contact. Phys Chem Chem Phys 2018; 19:15530-15540. [PMID: 28581553 DOI: 10.1039/c7cp01780d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this manuscript, we combine high-level ab initio calculations on some small complexes and a CSD survey to analyze the existence of unprecedented noncovalent carbon bonds in X2C[double bond, length as m-dash]CH2Y systems (Y = electron-rich atom or group). The methylene group is usually seen as a weak hydrogen bond donor when interacting with an electron-rich atom. However, we demonstrate that when the electron-rich atom is located equidistant from the two H atoms and along the C[double bond, length as m-dash]C bond a σ-hole noncovalent carbon-bonding interaction is established, instead of a bifurcated hydrogen bond, as derived from Atoms-in-Molecules (AIM) and Natural bond orbital (NBO) analyses. The physical nature of the interaction has been analyzed using the Symmetry Adapted Perturbation Theory (SAPT) method. The results indicate that electrostatics is very important followed by either the induction or dispersion terms in anionic and neutral complexes, respectively. In addition the CSD analysis reveals the existence of such interactions, giving reliability to our calculations, which are much more numerous for neutral than for anionic Y systems.
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Affiliation(s)
- D Quiñonero
- Department de Química, Universitat de les Illes Balears, Crta. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain.
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174
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Grabowski SJ. Hydrogen bonds and other interactions as a response to protect doublet/octet electron structure. J Mol Model 2018; 24:38. [PMID: 29313158 DOI: 10.1007/s00894-017-3569-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/14/2017] [Indexed: 11/29/2022]
Abstract
MP2/aug-cc-pVTZ calculations were performed for complexes linked by hydrogen bonds. Three types of proton donating species were taken into account: H2O, CCl3H, and H3O+. These calculations are supported by the natural bond orbital (NBO) method and the quantum theory of atoms in molecules (QTAIM) approach. Numerous correlations between parameters of H-bonded systems were found. The most important are those which show the response of the system on the H-bond formation; for example, the increase of polarization of the A-H bond correlates with the strength of the hydrogen bond. Similar relationships were found for the σ-hole bonds while the π-hole bonds do not follow the trends known for the hydrogen bonds. Graphical abstract Hydrogen bonds and other interactions as a response to protect doublet/octet electron structureᅟ.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Spain. .,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain.
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175
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176
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Zierkiewicz W, Michalczyk M, Scheiner S. Implications of monomer deformation for tetrel and pnicogen bonds. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00430g] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Monomer rearrangement raises the interaction energy by up to 20 kcal mol−1and intensifies its σ-hole by a factor of 1.5–2.9.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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177
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Wang H, Liu J, Wang W. Intermolecular and very strong intramolecular C–Se⋯O/N chalcogen bonds in nitrophenyl selenocyanate crystals. Phys Chem Chem Phys 2018; 20:5227-5234. [DOI: 10.1039/c7cp08215k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Different bonding strengths of C–Se⋯O/N chalcogen bonds involved in polymorphic o-NSC (1a/1b) and monomorphic p-NSC (2) result in different thermal properties.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, College of Chemistry & Material Science, Shanxi Normal University
- Linfen
- People's Republic of China
| | - Ju Liu
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, College of Chemistry & Material Science, Shanxi Normal University
- Linfen
- People's Republic of China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University
- Luoyang 471934
- People's Republic of China
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178
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Hussain M, Bauzá A, Frontera A, Lo KM, Naseer MM. Structure guided or structure guiding? Mixed carbon/hydrogen bonding in a bis-Schiff base of N-allyl isatin. CrystEngComm 2018. [DOI: 10.1039/c7ce01697b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A supramolecular motif listed as ‘carbon bonded’ or ‘hydrogen bonded’ may have the character of both. We highlight the hybrid character of the non-covalent interaction in a bis-Schiff base of N-allyl isatin by combining theory and experiment.
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Affiliation(s)
- Majid Hussain
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad 45320
- Pakistan
| | - Antonio Bauzá
- Departament de Quimica
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Antonio Frontera
- Departament de Quimica
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Kong Mun Lo
- Research Centre for Crystalline Materials
- School of Science and Technology
- Sunway University
- Selangor Darul Ehsan
- Malaysia
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179
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Roy S, Drew MGB, Bauzá A, Frontera A, Chattopadhyay S. Non-covalent tetrel bonding interactions in hemidirectional lead(ii) complexes with nickel(ii)-salen type metalloligands. NEW J CHEM 2018. [DOI: 10.1039/c7nj05148d] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tetrel bonding interactions have been investigated in hetero-dinuclear nickel(ii)/lead(ii) complexes using MEP and DFT calculations.
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Affiliation(s)
- Sourav Roy
- Department of Chemistry
- Inorganic Section
- Jadavpur University
- Kolkata-700032
- India
| | | | - Antonio Bauzá
- Department of Chemistry
- Universitat de les Illes Balears
- Crta de Valldemossa km 7.5
- 07122 Palma de Mallorca (Baleares)
- Spain
| | - 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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180
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Abstract
With molecular orbital theory it is possible to distinguish and design σ, π and the elusive δ electrostatic holes.
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Affiliation(s)
- V. Angarov
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 841051
- Israel
| | - S. Kozuch
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 841051
- Israel
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181
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Seth SK, Bauzá A, Mahmoudi G, Stilinović V, López-Torres E, Zaragoza G, Keramidas AD, Frontera A. On the importance of Pb⋯X (X = O, N, S, Br) tetrel bonding interactions in a series of tetra- and hexa-coordinated Pb(ii) compounds. CrystEngComm 2018. [DOI: 10.1039/c8ce00919h] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We study Pb⋯X (X = N, S, Br) tetrel bonding interactions in a series of tetra- and hexa-coordinated Pb(ii) compounds that exhibit hemidirectional coordination.
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Affiliation(s)
- Saikat Kumar Seth
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
- Departament de Química
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Ghodrat Mahmoudi
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Elena López-Torres
- Departamento de Química Inorgánica
- Facultad de Ciencias
- Módulo 07
- Universidad Autónoma de Madrid
- 28049 Madrid
| | | | | | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
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182
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Mahmoudi G, Seth SK, Bauzá A, Zubkov FI, Gurbanov AV, White J, Stilinović V, Doert T, Frontera A. Pb⋯X (X = N, S, I) tetrel bonding interactions in Pb(ii) complexes: X-ray characterization, Hirshfeld surfaces and DFT calculations. CrystEngComm 2018. [DOI: 10.1039/c8ce00110c] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis and X-ray characterization of four new Pb(ii) complexes of nicotinoylhydrazone and picolinoylhydrazone-based ligands and three different anionic co-ligands (acetate, thiocyanate and iodide) exhibiting relevant tetrel bonding interactions.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Saikat Kumar Seth
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
- Departament de Química
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
| | - Fedor I. Zubkov
- Organic Chemistry Department
- Faculty of Science
- Peoples' Friendship University of Russia (RUDN University)
- Moscow
- Russian Federation
| | - Atash V. Gurbanov
- Department of Organic Chemistry
- Baku State University
- Baku
- Azerbaijan
- Centro de Química Estrutural
| | - Jonathan White
- BIO-21 Molecular Science and Biotechnology
- University of Melbourne
- Parkville
- Australia
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- 10000 Zagreb
- Croatia
| | - Thomas Doert
- Department of Chemistry and Food Chemistry
- Dresden University of Technology
- 01069 Dresden
- Germany
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
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183
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New Type of Halogen Bond: Multivalent Halogen Interacting with π- and σ-Electrons. Molecules 2017; 22:molecules22122150. [PMID: 29206144 PMCID: PMC6149982 DOI: 10.3390/molecules22122150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 12/05/2022] Open
Abstract
MP2/aug-cc-pVTZ calculations were performed for complexes of BrF3 and BrF5 acting as Lewis acids through the bromine centre, with species playing a role of Lewis base: dihydrogen, acetylene, ethylene, and benzene. The molecular hydrogen donates electrons by its σ-bond, while in remaining moieties—in complexes of hydrocarbons; such an electron transfer follows from π-electrons. The complexes are linked by a kind of the halogen bond that is analyzed for the first time in this study, i.e., it is the link between the multivalent halogen and π or σ-electrons. The nature of such a halogen bond is discussed, as well as various dependencies and correlations are presented. Different approaches are applied here, the Quantum Theory of Atoms in Molecules, Natural Bond Orbital method, the decomposition of the energy of interaction, the analysis of electrostatic potentials, etc.
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184
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Oliveira V, Kraka E. Systematic Coupled Cluster Study of Noncovalent Interactions Involving Halogens, Chalcogens, and Pnicogens. J Phys Chem A 2017; 121:9544-9556. [PMID: 29154546 DOI: 10.1021/acs.jpca.7b10196] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The noncovalent interactions of 32 complexes involving pnicogens, chalcogens, and halogens atoms were investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Two different types of complexes could be distinguished on the basis of geometric parameters, electron difference densities, and the charge transfer mechanisms associated with each type. In the type I conformation, the monomers adopt a skewed orientation allowing charge to be transfer between both monomers, whereas in the type II conformation the monomers adopt a linear arrangement, maximizing charge transfer in only one direction. Type I complexes involving the interaction between pnicogens and chalcogens cannot be unambiguously defined as chalcogen or pnicogen bonds, they are an admixture of both. The charge transfer dependence on the conformation adopted by the complexes described in this work can serve as a novel conformationally driven design concept for materials.
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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
| | - 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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185
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Scilabra P, Terraneo G, Resnati G. Fluorinated elements of Group 15 as pnictogen bond donor sites. J Fluor Chem 2017. [DOI: 10.1016/j.jfluchem.2017.10.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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186
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Tetrel, Chalcogen, and Charge-Assisted Hydrogen Bonds in 2-((2-Carboxy-1-(substituted)-2-hydroxyethyl)thio) Pyridin-1-ium Chlorides. CRYSTALS 2017. [DOI: 10.3390/cryst7110327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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187
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Pinto de Magalhães H, Togni A, Lüthi HP. Importance of Nonclassical σ-Hole Interactions for the Reactivity of λ3-Iodane Complexes. J Org Chem 2017; 82:11799-11805. [DOI: 10.1021/acs.joc.7b01716] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Halua Pinto de Magalhães
- Departement of Chemistry
and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Antonio Togni
- Departement of Chemistry
and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Hans Peter Lüthi
- Departement of Chemistry
and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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188
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Pascoe DJ, Ling KB, Cockroft SL. The Origin of Chalcogen-Bonding Interactions. J Am Chem Soc 2017; 139:15160-15167. [PMID: 28985065 DOI: 10.1021/jacs.7b08511] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Favorable molecular interactions between group 16 elements have been implicated in catalysis, biological processes, and materials and medicinal chemistry. Such interactions have since become known as chalcogen bonds by analogy to hydrogen and halogen bonds. Although the prevalence and applications of chalcogen-bonding interactions continues to develop, debate still surrounds the energetic significance and physicochemical origins of this class of σ-hole interaction. Here, synthetic molecular balances were used to perform a quantitative experimental investigation of chalcogen-bonding interactions. Over 160 experimental conformational free energies were measured in 13 different solvents to examine the energetics of O···S, O···Se, S···S, O···HC, and S···HC contacts and the associated substituent and solvent effects. The strongest chalcogen-bonding interactions were found to be at least as strong as conventional H-bonds, but unlike H-bonds, surprisingly independent of the solvent. The independence of the conformational free energies on solvent polarity, polarizability, and H-bonding characteristics showed that electrostatic, solvophobic, and van der Waals dispersion forces did not account for the observed experimental trends. Instead, a quantitative relationship between the experimental conformational free energies and computed molecular orbital energies was consistent with the chalcogen-bonding interactions being dominated by n → σ* orbital delocalization between a lone pair (n) of a (thio)amide donor and the antibonding σ* orbital of an acceptor thiophene or selenophene. Interestingly, stabilization was manifested through the same acceptor molecular orbital irrespective of whether a direct chalcogen···chalcogen or chalcogen···H-C contact was made. Our results underline the importance of often-overlooked orbital delocalization effects in conformational control and molecular recognition phenomena.
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Affiliation(s)
- Dominic J Pascoe
- EaStCHEM School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Kenneth B Ling
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
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189
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The σ and π Holes. The Halogen and Tetrel Bondings: Their Nature, Importance and Chemical, Biological and Medicinal Implications. ChemistrySelect 2017. [DOI: 10.1002/slct.201701676] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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190
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Bagheri S, Masoodi HR, Akrami-Mohajeri AR. A theoretical survey of substituent effects on the properties of pnicogen and hydrogen bonds in cationic complexes of PH 4 + with substituted benzonitrile. J Mol Graph Model 2017; 77:64-71. [DOI: 10.1016/j.jmgm.2017.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 11/27/2022]
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191
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Esrafili MD, Mousavian P. The Key Role of Orbital Interaction in Cooperativity between B⋅⋅⋅N and Hydrogen/Lithium Bonding: An ab initio Study. ChemistrySelect 2017. [DOI: 10.1002/slct.201701309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry; Department of Chemistry; University of Maragheh, P.O. Box: 5513864596; Maragheh Iran
| | - Parisasadat Mousavian
- Laboratory of Theoretical Chemistry; Department of Chemistry; University of Maragheh, P.O. Box: 5513864596; Maragheh Iran
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192
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Grabowski SJ. Two faces of triel bonds in boron trihalide complexes. J Comput Chem 2017; 39:472-480. [PMID: 28857264 DOI: 10.1002/jcc.25056] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/02/2017] [Accepted: 08/13/2017] [Indexed: 01/15/2023]
Abstract
The N⋅⋅⋅B triel bonds in complexes of boron trihalides, BX3 (X = F, Cl, Br, and I), with species acting as Lewis bases through the nitrogen center, NH3 , N2 , and HCN, are analyzed theoretically (MP2/aug-cc-pVTZ calculations). It is confirmed that stronger Lewis acid properties of the boron center are observed for the BCl3 moiety than for the BF3 one in complexes with the strong Lewis base (NH3 ); while the opposite order is observed for complexes with the weak Lewis base (N2 ). The BX3 NCH complexes (for X = Cl, Br, and I) are characterized by two tautomeric forms and by two corresponding N⋅⋅⋅B distances, the shorter one possesses characteristics of the covalent bond. In a case of the BF3 NCH complex one energetic minimum is observed. Ab initio calculations are supported by an analysis of molecular electrostatic potentials (EPs) and electron density distributions. The quantum theory of 'atoms in molecules' and the decomposition of the energy of interaction are applied. The aforementioned acidity orders as well as the existence of two tautomers for some of complexes result partly from the electrostatic interactions' balance; the EP distribution is different for the BF3 species than for the other BX3 species where X = Cl, Br, and I. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, Polymer Science and Technology Department, University of the Basque Country and Donostia, International Physics Center (DIPC), P.K. 1072, Donostia, 20080, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Spain
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193
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194
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Mahmoudi G, Dey L, Chowdhury H, Bauzá A, Ghosh BK, Kirillov AM, Seth SK, Gurbanov AV, Frontera A. Synthesis and crystal structures of three new lead(II) isonicotinoylhydrazone derivatives: Anion controlled nuclearity and dimensionality. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.02.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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195
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Esrafili MD, Kiani H. Cooperativity between the hydrogen bonding and σ-hole interaction in linear NCX···(NCH)n=2–5 and O3Z···(NCH)n=2–5 complexes (X = Cl, Br; Z = Ar, Kr): a comparative study. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantum chemical calculations are performed to investigate the cooperativity of hydrogen bonding with halogen or aerogen bonding interactions in linear NCX···(NCH)n=2–5 and O3Z···(NCH)n=2–5 clusters, where X = Cl, Br and Z = Ar, Kr. To understand the cooperativity mechanism in these systems, the corresponding binary NCX···NCH and O3Z···NCH complexes are also considered. The binding distances, interaction energies, and bonding properties of the NCX···(NCH)n=2–5 and O3Z···(NCH)n=2–5 clusters are analyzed in detail. It is found that the cooperative effects in the hydrogen bonding tend to strengthen X···N and Z···N interactions. For both NCX···(NCH)n and O3Z···(NCH)n clusters, a small bond shrinkage is observed from n = 4 to n = 5, which suggests that the cooperativity effects are almost saturated in the larger clusters (n > 5). As the size of the X or Z atom is increased, the magnitude of the cooperative energy in these systems is also increased, which is mainly ascribed to changes in electrostatic potentials and orbital interactions. Our results indicate that the cooperative effects lead to a substantial change in the 14N nuclear quadrupole coupling constants of the NCH molecule.
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Hossein Kiani
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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196
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Grabowski SJ, Sokalski WA. Are Various σ-Hole Bonds Steered by the Same Mechanisms? Chemphyschem 2017; 18:1569-1577. [DOI: 10.1002/cphc.201700224] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Sławomir J. Grabowski
- Faculty of Chemistry; University of the Basque Country and Donostia, International Physics Center (DIPC); P.K. 1072 20080 Donostia Spain
- IKERBASQUE, Basque Foundation for Science; 48011 Bilbao Spain
| | - W. Andrzej Sokalski
- Department of Chemistry K1/W1; Wrocław University of Science and Technology; Wyb. Wyspiańskiego 27 50-370 Wrocław Poland
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197
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198
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Affiliation(s)
- Mehdi D. Esrafili
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
| | - Ayda Sabouri
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
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199
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Characterization of non-classical C Br⋯π interactions in (E)-1,3-dibromo-5-(2-(ferrocenyl)vinyl)benzene and related derivatives of ferrocene. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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200
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Stilinović V, Horvat G, Hrenar T, Nemec V, Cinčić D. Halogen and Hydrogen Bonding between (N-Halogeno)-succinimides and Pyridine Derivatives in Solution, the Solid State and In Silico. Chemistry 2017; 23:5244-5257. [PMID: 28111817 DOI: 10.1002/chem.201605686] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Indexed: 01/18/2023]
Abstract
A study of strong halogen bonding within three series of halogen-bonded complexes, derived from seven para-substituted pyridine derivatives and three N-halosuccinimides (iodo, bromo and chloro), has been undertaken with the aid of single-crystal diffraction, solution complexation and computational methods. The halogen bond was compared with the hydrogen bond in an equivalent series based on succinimide. The halogen-bond energies are in the range -60 to -20 kJ mol-1 and change regularly with pyridine basicity and the Lewis acidity of the halogen. The halogen-bond energies correlate linearly with the product of charges on the contact atoms, which indicates a predominantly electrostatic interaction. The binding enthalpies in solution are around 19 kJ mol-1 less negative due to solvation effects. The optimised geometries of the complexes in the gas phase are comparable to those of the solid-state structures, and the effects of the supramolecular surroundings in the latter are discussed. The bond energies for the hydrogen-bonded series are intermediate between the halogen-bond energies of iodine and bromine, although there are specific differences in the geometries of the halogen- and hydrogen-bonded complexes.
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Affiliation(s)
- Vladimir Stilinović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Tomica Hrenar
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Vinko Nemec
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Dominik Cinčić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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