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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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Darren Johnson. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Darren Johnson. Angew Chem Int Ed Engl 2020; 59:17330. [DOI: 10.1002/anie.202004305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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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Bauzá A, Frontera A. On the Importance of Nonbonding Donor-Acceptor Interactions Involving PO2.Radicals: An ab Initio Study. Chemphyschem 2017; 18:2191-2196. [DOI: 10.1002/cphc.201700399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/24/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Antonio Bauzá
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
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Bauzá A, Frontera A. On the Importance of π-Hole Beryllium Bonds: Theoretical Study and Biological Implications. Chemistry 2017; 23:5375-5380. [DOI: 10.1002/chem.201700682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Antonio Bauzá
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Antonio Frontera
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
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Bauzá A, Frontera A. On the Versatility of BH 2 X (X=F, Cl, Br, and I) Compounds as Halogen-, Hydrogen-, and Triel-Bond Donors: An Ab Initio Study. Chemphyschem 2016; 17:3181-3186. [PMID: 27428897 DOI: 10.1002/cphc.201600683] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 11/08/2022]
Abstract
In this manuscript, the ability of BH2 X compounds (X=F, Cl, Br, and I) to establish halogen-, hydrogen-, and triel-bonding interactions was studied at the RI-MP2/aug-cc-pVQZ level of theory. Several homodimers were taken into account, highlighting the versatility of these compounds to act as both electron donors and electron acceptors. Natural bond orbital analysis showed that orbital effects were important contributors to the global stabilization of the σ- and π-hole bonded complexes studied. Finally, some X-ray solid-state structures retrieved from the Cambridge structural database were described to demonstrate the importance of these interactions involving boron derivatives in the solid state.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain.
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Bauzá A, Mooibroek TJ, Frontera A. σ-Hole Opposite to a Lone Pair: Unconventional Pnicogen Bonding Interactions between ZF3(Z=N, P, As, and Sb) Compounds and Several Donors. Chemphyschem 2016; 17:1608-14. [DOI: 10.1002/cphc.201600073] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/24/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Antonio Bauzá
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Tiddo J. Mooibroek
- School of Chemistry of the; University of Bristol; Cantock's Close BS8 1TS Bristol UK
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
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Bauzá A, Frontera A. Theoretical Study on the Dual Behavior of XeO3and XeF4toward Aromatic Rings: Lone Pair-π versus Aerogen-π Interactions. Chemphyschem 2015; 16:3625-30. [DOI: 10.1002/cphc.201500757] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Antonio Bauzá
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca, Baleares Spain
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca, Baleares Spain
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Bauzá A, Frontera A. Competition between Halogen Bonding and π-Hole Interactions Involving Various Donors: The Role of Dispersion Effects. Chemphyschem 2015; 16:3108-13. [DOI: 10.1002/cphc.201500542] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/11/2022]
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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Zampella G, Neupane KP, De Gioia L, Pecoraro VL. The importance of stereochemically active lone pairs for influencing Pb(II) and As(III) protein binding. Chemistry 2012; 18:2040-50. [PMID: 22231489 PMCID: PMC3357087 DOI: 10.1002/chem.201102786] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Indexed: 10/14/2022]
Abstract
The toxicity of heavy metals, which is associated with the high affinity of the metals for thiolate rich proteins, constitutes a problem worldwide. However, despite this tremendous toxicity concern, the binding mode of As(III) and Pb(II) to proteins is poorly understood. To clarify the requirements for toxic metal binding to metalloregulatory sensor proteins such as As(III) in ArsR/ArsD and Pb(II) in PbrR or replacing Zn(II) in δ-aminolevulinc acid dehydratase (ALAD), we have employed computational and experimental methods examining the binding of these heavy metals to designed peptide models. The computational results show that the mode of coordination of As(III) and Pb(II) is greatly influenced by the steric bulk within the second coordination environment of the metal. The proposed basis of this selectivity is the large size of the ion and, most important, the influence of the stereochemically active lone pair in hemidirected complexes of the metal ion as being crucial. The experimental data show that switching a bulky leucine layer above the metal binding site by a smaller alanine residue enhances the Pb(II) binding affinity by a factor of five, thus supporting experimentally the hypothesis of lone pair steric hindrance. These complementary approaches demonstrate the potential importance of a stereochemically active lone pair as a metal recognition mode in proteins and, specifically, how the second coordination sphere environment affects the affinity and selectivity of protein targets by certain toxic ions.
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Affiliation(s)
- Giuseppe Zampella
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy), Tel: + 39 02 64483416, Fax: +39 02 64483478,
| | - Kosh P. Neupane
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA), Tel.: +1 734 763 1519, Fax: +1 734 936 7628,
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy), Tel: + 39 02 64483416, Fax: +39 02 64483478,
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA), Tel.: +1 734 763 1519, Fax: +1 734 936 7628,
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Cangelosi V, Zakharov L, Johnson D. Supramolecular “Transmetalation” Leads to an Unusual Self-Assembled P2L3Cryptand. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906460] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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14
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Cangelosi V, Zakharov L, Johnson D. Supramolecular “Transmetalation” Leads to an Unusual Self-Assembled P2L3 Cryptand. Angew Chem Int Ed Engl 2010; 49:1248-51. [DOI: 10.1002/anie.200906460] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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