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Akbaba S, Steinke T, Vogel L, Engelage E, Erdelyi M, Huber SM. Elucidating the Binding Mode of Sulfur- and Selenium-Based Cationic Chalcogen-Bond Donors. Chemistry 2024; 30:e202400608. [PMID: 38604947 DOI: 10.1002/chem.202400608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/13/2024]
Abstract
For a comparison of the interaction modes of various chalcogen-bond donors, 2-chalcogeno-imidazolium salts have been designed, synthesized, and studied by single crystal X-ray diffraction, solution NMR and DFT as well as for their ability to act as activators in an SN1-type substitution reaction. Their interaction modes in solution were elucidated based on NMR diffusion and chemical shift perturbation experiments, which were supported by DFT-calculations. Our finding is that going from lighter to the heavier chalcogens, hydrogen bonding plays a less, while chalcogen bonding an increasingly important role for the coordination of anions. Anion-π interactions also show importance, especially for the sulfur and selenium derivatives.
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Affiliation(s)
- Sercan Akbaba
- Department of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Tim Steinke
- Department of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Lukas Vogel
- Department of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Elric Engelage
- Department of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Stefan M Huber
- Department of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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2
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Liu CZ, Zhang C, Li ZY, Chen J, Wang T, Zhang XK, Yan M, Zhai B. Multiple non-covalent-interaction-directed supramolecular double helices: the orthogonality of hydrogen, halogen and chalcogen bonding. Chem Commun (Camb) 2024; 60:6063-6066. [PMID: 38780308 DOI: 10.1039/d4cc01472c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
In this study, a benzoselenadiazole- and pyridine-bifunctionalized hydrogen-bonded arylamide foldamer was synthesized. A co-crystallization experiment with 1,4-diiodotetrafluorobenzene showed that a new type of supramolecular double helices, which were induced by three orthogonal interactions, namely, three-center hydrogen bonding (O⋯H⋯O), I⋯N halogen bonding and Se⋯N chalcogen bonding, have been constructed in the solid state. This work presents a novel instance of multiple non-covalent interactions that work together to construct supramolecular architectures.
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Affiliation(s)
- Chuan-Zhi Liu
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
| | - Chi Zhang
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
| | - Zhong-Yi Li
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
| | - Jiale Chen
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
| | - Tonglu Wang
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
| | - Xiang-Kun Zhang
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
| | - Meng Yan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Bin Zhai
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, China.
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3
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Andolpho GA, Ramalho TC. Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme. J Comput Chem 2024; 45:1303-1315. [PMID: 38363124 DOI: 10.1002/jcc.27328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
This study addresses a comprehensive assessment of the interaction between chemical warfare agents (CWA) and acetylcholinesterase (AChE) systems, focus on the intriguing pnictogen-bond interaction (PnB). Utilizing the crystallographic data from the Protein Data Bank pertaining to the AChE-CWA complex involving Sarin (GB), Cyclosarin (GF), 2-[fluoro(methyl)phosphoryl]oxy-1,1-dimethylcyclopentane (GP) and venomous agent X (VX) agents, the CWA is systematically displaced by increments of 0.1 Å along the PO bond axis, extending its distance by 4 Å from the original position. The AIM analysis was carried out and consistently revealed the presence of a significant interaction along the PO bond. Investigating the intrinsic nature of the PnB, the NBO and the EDA analysis unearthed the contribution of orbital factors to the overall energy of the system. Strikingly, this observation challenges the conventional σ-hole explanation commonly associated with such interactions. This finding adds a layer of complexity to understanding of PnB, encouraging further exploration into the underlying mechanisms governing these intriguing chemical phenomena.
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Affiliation(s)
- Gustavo A Andolpho
- Chemistry Department, Institute of Natural Sciences, Universidade Federal de Lavras, Lavras, Brazil
| | - Teodorico C Ramalho
- Chemistry Department, Institute of Natural Sciences, Universidade Federal de Lavras, Lavras, Brazil
- Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
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4
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Liu CZ, Zhang C, Li CG, Chen HB, Yang W, Li ZY, Hu ZY, Xu L, Zhai B, Li ZT. Benzoselenadiazole-Functionalized H-Bonded Arylamide Foldamers: Solvent-Responsive Properties and Helix Self-Assembly Directed by Chalcogen Bonding in Solid State. Chemistry 2024:e202401150. [PMID: 38639722 DOI: 10.1002/chem.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/20/2024]
Abstract
In this study, a series of H-bonded arylamide foldamers bearing benzoselenadiazole ends with solvent-responsive properties have been synthesized. In dichloromethane or dimethyl sulfoxide solvents, the molecules exhibit meniscus or linear structures, respectively, which can be attributed to the unique intramolecular hydrogen bonding behavior evidenced by 1D 1H NMR and 2D NOESY spectra. UV-vis spectroscopy experiments show that the absorption wavelength of H-bonded arylamide foldamers are significantly red-shifted due to the presence of benzoselenadiazole group. In addition, the crystal structures reveal that effective intermolecular dual Se ⋅ ⋅ ⋅ N interactions between benzoselenadiazole groups induce further assembly of the monomers. Remarkably, supramolecular linear and double helices structures are constructed under the synergistic induction of intramolecular hydrogen bonding and intermolecular chalcogen bonding. Additionally, 2D DOSY diffusion spectra and theoretical modelling based on density functional theory (DFT) are performed to explore the persistence of intermolecular Se ⋅ ⋅ ⋅ N interactions beyond the crystalline state.
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Affiliation(s)
- Chuan-Zhi Liu
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Chi Zhang
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Chang-Gen Li
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Hui-Bin Chen
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Wen Yang
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Zhong-Yi Li
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Zhi-Yuan Hu
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Liang Xu
- School of Chemistry and Chemical Engineering/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, 221 Beisi Road, Shihezi, 832003, China
| | - Bin Zhai
- Engineering Research Centre for Optoelectronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Shangqiu Normal University, 55 Pingyuan middle Road, Shangqiu, Henan, 476000, China
| | - Zhan-Ting Li
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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5
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Aragoni MC, Podda E, Chaudhary S, Bhasin AKK, Bhasin KK, Coles SJ, Orton JB, Isaia F, Lippolis V, Pintus A, Slawin AMZ, Woollins JD, Arca M. An Experimental and Theoretical Insight into I 2 /Br 2 Oxidation of Bis(pyridin-2-yl)Diselane and Ditellane. Chem Asian J 2023; 18:e202300836. [PMID: 37843415 DOI: 10.1002/asia.202300836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
The reactivity between bis(pyridin-2-yl)diselane o Py2 Se2 and ditellane o Py2 Te2 (L1 and L2, respectively; o Py=pyridyn-2-yl) and I2 /Br2 is discussed. Single-crystal structure analysis revealed that the reaction of L1 with I2 yielded [(HL1+ )(I- )⋅5/2I2 ]∞ (1) in which monoprotonated cations HL1+ template a self-assembled infinite pseudo-cubic polyiodide 3D-network, while the reaction with Br2 yielded the dibromide Ho PySeII Br2 (2). The oxidation of L2 with I2 and Br2 yielded the compounds Ho PyTeII I2 (3) and Ho PyTeIV Br4 (6), respectively, whose structures were elucidated by X-ray diffraction analysis. FT-Raman spectroscopy measurements are consistent with a 3c-4e description of all the X-Ch-X three-body systems (Ch=Se, Te; X=Br, I) in compounds 2, 3, Ho PyTeII Br2 (5), and 6. The structural and spectroscopic observations are supported by extensive theoretical calculations carried out at the DFT level that were employed to study the electronic structure of the investigated compounds, the thermodynamic aspects of their formation, and the role of noncovalent σ-hole halogen and chalcogen bonds in the X⋅⋅⋅X, X⋅⋅⋅Ch and Ch⋅⋅⋅Ch interactions evidenced structurally.
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Affiliation(s)
- M Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Enrico Podda
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
- Centro Servizi di Ateneo per la Ricerca (CeSAR), Università degli Studi di Cagliari, S.S. 554 bivio Sestu, 09042, Monserrato (Cagliari), Italy
| | - Savita Chaudhary
- Department of Chemistry, Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Aman K K Bhasin
- Department of Chemistry, Amity University, Sector 82 A, Mohali, Punjab-140306, India
| | - Kuldip K Bhasin
- Department of Chemistry, Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Simon J Coles
- UK National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James B Orton
- UK National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Francesco Isaia
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Anna Pintus
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Alexandra M Z Slawin
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, UK
| | - J Derek Woollins
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, UK
- Department of Chemistry, Khalifa University, Abu Dhabi, 127788, United Arab Emirates
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
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6
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Echeverría J, Alvarez S. The borderless world of chemical bonding across the van der Waals crust and the valence region. Chem Sci 2023; 14:11647-11688. [PMID: 37920358 PMCID: PMC10619631 DOI: 10.1039/d3sc02238b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 11/04/2023] Open
Abstract
The definition of the van der Waals crust as the spherical section between the atomic radius and the van der Waals radius of an element is discussed and a survey of the application of the penetration index between two interacting atoms in a wide variety of covalent, polar, coordinative or noncovalent bonding situations is presented. It is shown that this newly defined parameter permits the comparison of bonding between pairs of atoms in structural and computational studies independently of the atom sizes.
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Affiliation(s)
- Jorge Echeverría
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Santiago Alvarez
- Department de Química Inorgànica i Orgànica, Secció de Química Inorgànica, e Institut de Química Teòrica i Computacional, Universitat de Barcelona Martí i Franquès 1-11 08028 -Barcelona Spain
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7
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Nieuwland C, Vermeeren P, Bickelhaupt FM, Fonseca Guerra C. Understanding chemistry with the symmetry-decomposed Voronoi deformation density charge analysis. J Comput Chem 2023; 44:2108-2119. [PMID: 37403918 DOI: 10.1002/jcc.27184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
The symmetry-decomposed Voronoi deformation density (VDD) charge analysis is an insightful and robust computational tool to aid the understanding of chemical bonding throughout all fields of chemistry. This method quantifies the atomic charge flow associated with chemical-bond formation and enables decomposition of this charge flow into contributions of (1) orbital interaction types, that is, Pauli repulsive or bonding orbital interactions; (2) per irreducible representation (irrep) of any point-group symmetry of interacting closed-shell molecular fragments; and now also (3) interacting open-shell (i.e., radical) molecular fragments. The symmetry-decomposed VDD charge analysis augments the symmetry-decomposed energy decomposition analysis (EDA) so that the charge flow associated with Pauli repulsion and orbital interactions can be quantified both per atom and per irrep, for example, for σ, π, and δ electrons. This provides detailed insights into fundamental aspects of chemical bonding that are not accessible from EDA.
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Affiliation(s)
- Celine Nieuwland
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pascal Vermeeren
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute of Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg, Johannesburg, South Africa
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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8
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Pale P, Mamane V. Chalcogen Bonding Catalysis: Tellurium, the Last Frontier? Chemistry 2023:e202302755. [PMID: 37743816 DOI: 10.1002/chem.202302755] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
Chalcogen bonding (ChB) is the non-covalent interaction occurring between chalcogen atoms as Lewis acid sites and atoms or groups of atoms able to behave as Lewis bases through their lone pair or π electrons. Analogously to its sister halogen bonding, the high directionality of this interaction was implemented for precise structural organizations in the solid state and in solution. Regarding catalysis, ChB is now accepted as a new mode of activation as demonstrated by the increased number of examples in the last five years. In the family of ChB catalysts, those based on tellurium rapidly appeared to overcome their lighter sulfur and selenium counterparts. In this review, we highlight the Lewis acid properties of tellurium-based derivatives in solution and summarize the start-of-the-art of their applications in catalysis.
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Affiliation(s)
- Patrick Pale
- Institute of Chemistry of Strasbourg, UMR 7177-LASYROC, CNRS and Strasbourg University, 4 rue Blaise Pascal, 67000, Strasbourg, France
| | - Victor Mamane
- Institute of Chemistry of Strasbourg, UMR 7177-LASYROC, CNRS and Strasbourg University, 4 rue Blaise Pascal, 67000, Strasbourg, France
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9
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Intermolecular Covalent Interactions: Nature and Directionality. Chemistry 2023; 29:e202203791. [PMID: 36478415 DOI: 10.1002/chem.202203791] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Quantum chemical methods were employed to analyze the nature and the origin of the directionality of pnictogen (PnB), chalcogen (ChB), and halogen bonds (XB) in archetypal Fm Z⋅⋅⋅F- complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA-M06/QZ4P. Quantitative Kohn-Sham MO and energy decomposition analyses (EDA) show that all these intermolecular interactions have in common that covalence, that is, HOMO-LUMO interactions, provide a crucial contribution to the bond energy, besides electrostatic attraction. Strikingly, all these bonds are directional (i.e., F-Z⋅⋅⋅F- is approximately linear) despite, and not because of, the electrostatic interactions which, in fact, favor bending. This constitutes a breakdown of the σ-hole model. It was shown how the σ-hole model fails by neglecting both, the essential physics behind the electrostatic interaction and that behind the directionality of electron-rich intermolecular interactions. Our findings are general and extend to the neutral, weaker ClI⋅⋅⋅NH3 , HClTe⋅⋅⋅NH3 , and H2 ClSb⋅⋅⋅NH3 complexes.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras CEP, 37200-900, Lavras, MG, Brazil.,Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Chemical Sciences, University of Johannesburg Auckland Park, Johannesburg, 2006, South Africa
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10
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Pale P, Mamane V. Chalcogen Bonds: How to Characterize Them in Solution? Chemphyschem 2023; 24:e202200481. [PMID: 36205925 DOI: 10.1002/cphc.202200481] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/07/2022] [Indexed: 11/08/2022]
Abstract
Chalcogen bonds (ChBs) occur between molecules containing Lewis acidic chalcogen substituents and Lewis bases. Recently, ChB emerged as a pivotal interaction in solution-based applications such as anion recognition, anion transport and catalysis. However, before moving to applications, the involvement of ChB must be established in solution. In this Concept article, we provide a brief review of the currently available experimental investigations of ChB in solution.
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Affiliation(s)
- Patrick Pale
- UMR 7177, LASYROC, CNRS and Strasbourg University, 4 rue Blaise Pascal, 67000, Strasbourg, France
| | - Victor Mamane
- UMR 7177, LASYROC, CNRS and Strasbourg University, 4 rue Blaise Pascal, 67000, Strasbourg, France
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11
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Aragoni M, Arca M, Caltagirone C, Castellano C, Demartin F, Jones PG, Pivetta T, Podda E, Lippolis V, Murgia S, Picci G. Role of the Solvent in the Reactivity of Bis-4-imidazoline-2-selone Derivatives toward I 2: An Experimental and Theoretical Approach. J Org Chem 2022; 87:15448-15465. [DOI: 10.1021/acs.joc.2c01982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- M.Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
| | - Claudia Caltagirone
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
| | - Carlo Castellano
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, I-20133Milano, Italy
| | - Francesco Demartin
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, I-20133Milano, Italy
| | - Peter G. Jones
- Institut für Anorganische und Analytische Chemie der Technischen Universität Braunschweig, Hagenring 30, D-38106Braunschweig, Germany
| | - Tiziana Pivetta
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
| | - Enrico Podda
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
- Centro Servizi di Ateneo per la Ricerca-CeSAR, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, Cagliari, Italy
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
| | - Sergio Murgia
- Dipartimento di Scienze della Vita e dell’ambiente, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
| | - Giacomo Picci
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042 Monserrato, Cagliari, Italy
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12
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Scheiner S, Michalczyk M, Zierkiewicz W. Involvement of Arsenic Atom of AsF 3 in Five Pnicogen Bonds: Differences between X-ray Structure and Theoretical Models. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196486. [PMID: 36235021 PMCID: PMC9572024 DOI: 10.3390/molecules27196486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Bonding within the AsF3 crystal is analyzed via quantum chemical methods so as to identify and quantify the pnicogen bonds that are present. The structure of a finite crystal segment containing nine molecules is compared with that of a fully optimized cluster of the same size. The geometries are qualitatively different, with a much larger binding energy within the optimized nonamer. Although the total interaction energy of a central unit with the remaining peripheral molecules is comparable for the two structures, the binding of the peripherals with one another is far larger in the optimized cluster. This distinction of much stronger total binding within the optimized cluster is not limited to the nonamer but repeats itself for smaller aggregates as well. The average binding energy of the cluster rises quickly with size, asymptotically approaching a value nearly triple that of the dimer.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
- Correspondence: to: (S.S.); (M.M.); (W.Z.)
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: to: (S.S.); (M.M.); (W.Z.)
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: to: (S.S.); (M.M.); (W.Z.)
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13
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Romito D, Fresta E, Cavinato LM, Kählig H, Amenitsch H, Caputo L, Chen Y, Samorì P, Charlier J, Costa RD, Bonifazi D. Supramolecular Chalcogen‐Bonded Semiconducting Nanoribbons at Work in Lighting Devices. Angew Chem Int Ed Engl 2022; 61:e202202137. [PMID: 35274798 PMCID: PMC9544418 DOI: 10.1002/anie.202202137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 11/24/2022]
Abstract
This work describes the design and synthesis of a π‐conjugated telluro[3,2‐β][1]‐tellurophene‐based synthon that, embodying pyridyl and haloaryl chalcogen‐bonding acceptors, self‐assembles into nanoribbons through chalcogen bonds. The ribbons π‐stack in a multi‐layered architecture both in single crystals and thin films. Theoretical studies of the electronic states of chalcogen‐bonded material showed the presence of a local charge density between Te and N atoms. OTFT‐based charge transport measurements showed hole‐transport properties for this material. Its integration as a p‐type semiconductor in multi‐layered CuI‐based light‐emitting electrochemical cells (LECs) led to a 10‐fold increase in stability (38 h vs. 3 h) compared to single‐layered devices. Finally, using the reference tellurotellurophene congener bearing a C−H group instead of the pyridyl N atom, a herringbone solid‐state assembly is formed without charge transport features, resulting in LECs with poor stabilities (<1 h).
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Affiliation(s)
- Deborah Romito
- Department of Organic Chemistry Faculty of Chemistry University of Vienna Währinger Straße 38 1090 Vienna Austria
| | - Elisa Fresta
- Technical University of Munich Chair of Biogenic Functional Materials Schulgasse 22 94315 Straubing Germany
| | - Luca M. Cavinato
- Technical University of Munich Chair of Biogenic Functional Materials Schulgasse 22 94315 Straubing Germany
| | - Hanspeter Kählig
- Department of Organic Chemistry Faculty of Chemistry University of Vienna Währinger Straße 38 1090 Vienna Austria
| | - Heinz Amenitsch
- Graz University of Technology Institute for Inorganic Chemistry Stremayergasse 9/V 8010 Graz Austria
| | - Laura Caputo
- Institute of Condensed Matter and Nanosciences Université catholique de Louvain (UCLouvain) Chemin des étoiles 8 1348 Louvain-la-Neuve Belgium
| | - Yusheng Chen
- Université de Strasbourg, CNRS, ISIS 8 allée Gaspard Monge 67000 Strasbourg France
| | - Paolo Samorì
- Université de Strasbourg, CNRS, ISIS 8 allée Gaspard Monge 67000 Strasbourg France
| | - Jean‐Christophe Charlier
- Institute of Condensed Matter and Nanosciences Université catholique de Louvain (UCLouvain) Chemin des étoiles 8 1348 Louvain-la-Neuve Belgium
| | - Rubén D. Costa
- Technical University of Munich Chair of Biogenic Functional Materials Schulgasse 22 94315 Straubing Germany
| | - Davide Bonifazi
- Department of Organic Chemistry Faculty of Chemistry University of Vienna Währinger Straße 38 1090 Vienna Austria
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14
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor. Int J Mol Sci 2022; 23:ijms23094674. [PMID: 35563065 PMCID: PMC9099767 DOI: 10.3390/ijms23094674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence:
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
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15
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Extending NMR Quantum Computation Systems by Employing Compounds with Several Heavy Metals as Qubits. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nuclear magnetic resonance (NMR) is a spectroscopic method that can be applied to several areas. Currently, this technique is also being used as an experimental quantum simulator, where nuclear spins are employed as quantum bits or qubits. The present work is devoted to studying heavy metal complexes as possible candidates to act as qubit molecules. Nuclei such 113Cd, 199Hg, 125Te, and 77Se assembled with the most common employed nuclei in NMR-QIP implementations (1H, 13C, 19F, 29Si, and 31P) could potentially be used in heteronuclear systems for NMR-QIP implementations. Hence, aiming to contribute to the development of future scalable heteronuclear spin systems, we specially designed four complexes, based on the auspicious qubit systems proposed in our previous work, which will be explored by quantum chemical calculations of their NMR parameters and proposed as suitable qubit molecules. Chemical shifts and spin–spin coupling constants in four complexes were examined using the spin–orbit zeroth-order regular approximation (ZORA) at the density functional theory (DFT) level, as well as the relaxation parameters (T1 and T2). Examining the required spectral properties of NMR-QIP, all the designed complexes were found to be promising candidates for qubit molecules.
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16
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Miller DK, Chernyshov IY, Torubaev YV, Rosokha SV. From weak to strong interactions: structural and electron topology analysis of the continuum from the supramolecular chalcogen bonding to covalent bonds. Phys Chem Chem Phys 2022; 24:8251-8259. [PMID: 35320823 DOI: 10.1039/d1cp05441d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The relationship between covalent and supramolecular bonding, and the criteria of the assignments of different interactions were explored via the review of selenium and tellurium containing structures in the Cambridge Structural Database and their computational analysis using Quantum Theory of Atoms in Molecules (QTAIM). This combined study revealed continuums of the interatomic Se⋯Br and Te⋯I distances, dCh⋯X, in the series of associations from the sums of the van der Waals radii of these atoms (rCh + rX) to their covalent bond lengths. The electron densities, ρ(r), at Bond Critical Points (BCPs) along the chalcogen bond paths increased gradually from about 0.01 a.u. common for the non-covalent interactions to about 0.1 a.u. typical for the covalent bonds. The log ρ(r) values fell on the same linear trend line when plotted against normalized interatomic distances, RXY = dCh⋯X/(rCh + rX). The transition from the positive to negative values of the energy densities, H(r), at the BCPs (related to a changeover of essentially non-covalent into partially covalent interactions) were observed at RXY ≈ 0.80. Synchronous changes of bonding characteristics with RXY (similar to that found earlier in the halogen-bonded systems) designated normalized interatomic separation as a critical factor determining the nature of these bondings. The uninterrupted continuums of Te⋯I and Se⋯Br bond lengths and BCPs' characteristics signified an intrinsic link between limiting types of bonding involving chalcogen atoms and between covalent and supramolecular bonding in general.
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Affiliation(s)
- Daniel K Miller
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
| | - Ivan Yu Chernyshov
- TheoMat group, ChemBio Cluster, ITMO University, Lomonosova 9, St. Petersburg, 191002, Russia
| | - Yury V Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, L eninsky prospect, 31, Moscow, 119991, Russia
| | - Sergiy V Rosokha
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
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17
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Romito D, Fresta E, Cavinato LM, Kählig H, Amenitsch H, Caputo L, Chen Y, Samorì P, Charlier JC, Costa R, Bonifazi D. Supramolecular Chalcogen‐Bonded Semiconducting Nanoribbons at work in Lighting Devices. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Deborah Romito
- University of Vienna Faculty of Chemistry: Universitat Wien Fakultat fur Chemie Organic Chemistry Währinger Straße 38 1090 Vienna AUSTRIA
| | - Elisa Fresta
- Technical University Munich: Technische Universitat Munchen Chair of Biogenic Functional Materials Schulgasse 22 94315 Straubing GERMANY
| | - Luca Maria Cavinato
- Technical University of Munich: Technische Universitat Munchen Chair of Biogenic Functional Materials Schulgasse 22 94315 Straubing GERMANY
| | - Hanspeter Kählig
- University of Vienna Faculty of Chemistry: Universitat Wien Fakultat fur Chemie Organic Chemistry Währinger Straße 38 1090 vienna AUSTRIA
| | - Heinz Amenitsch
- Graz University of Technology: Technische Universitat Graz Institute for Inorganic Chemistry Stremayergasse 9/V 8010 Graz AUSTRIA
| | - Laura Caputo
- UCLouvain Saint-Louis Bruxelles: Universite Saint-Louis - Bruxelles Institute of Condensed Matter and Nanosciences Chemin des étoiles 8 B-1348 Louvain-la-Neuve BELGIUM
| | - Yusheng Chen
- Universite de Strasbourg CNRS, ISIS 8 allée Gaspard Monge 67000 Strasbourg FRANCE
| | - Paolo Samorì
- Universite de Strasbourg CNRS, ISIS 8 allée Gaspard Monge 67000 Strasbourg FRANCE
| | - Jean-Christophe Charlier
- UCLouvain Saint-Louis Bruxelles: Universite Saint-Louis - Bruxelles Institute of Condensed Matter and Nanosciences Chemin des étoiles 8 B-1348 Louvain-la-Neuve BELGIUM
| | - Rubén Costa
- Technical University of Munich: Technische Universitat Munchen Chair of Biogenic Functional Materials Schulgasse 22 94315 Straubing GERMANY
| | - Davide Bonifazi
- University of Vienna Faculty of Chemistry: Universitat Wien Fakultat fur Chemie Institute of Organic Chemistry Währinger Strasse 38 1090 Vienna AUSTRIA
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18
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Fellowes T, White JM. Simulating chalcogen bonding using molecular mechanics: a pseudoatom approach to model ebselen. J Mol Model 2022; 28:66. [PMID: 35201444 PMCID: PMC8867462 DOI: 10.1007/s00894-021-05023-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19; however, efforts to model ebselen in silico have been hampered by the lack of an efficient and accurate method to assess its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to simulate the σ-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach is justified using an energy decomposition analysis of a number of density functional theory–optimized structures, which shows that the σ-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting molecular dynamics simulations on a number of simple complexes, as well as the clinically relevant enzyme SOD1 (superoxide dismutase), which is known to bind to ebselen. Ebselen is an organoselenium drug that has shown promise for the treatment of a number of conditions. Computational modelling of drug-target complexes is commonly performed to determine the likely mechanism of action, however this is difficult in the case of ebselen, as an important mode of interaction is not simulated using current techniques. We present here an extension to common methods, which accurately captures this interaction. ![]()
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Affiliation(s)
- Thomas Fellowes
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, Australia.
| | - Jonathan M White
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, Australia
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19
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. The Phosphorus Bond, or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor. Molecules 2022; 27:molecules27051487. [PMID: 35268588 PMCID: PMC8911988 DOI: 10.3390/molecules27051487] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence:
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
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20
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Chalcogen···Chalcogen Bonding in Molybdenum Disulfide, Molybdenum Diselenide and Molybdenum Ditelluride Dimers as Prototypes for a Basic Understanding of the Local Interfacial Chemical Bonding Environment in 2D Layered Transition Metal Dichalcogenides. INORGANICS 2022. [DOI: 10.3390/inorganics10010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some ability to reproduce the intermolecular geometries and binding energies. The intermolecular geometries and binding energies of all nine dimers are discussed, together with the charge density topological aspects of the chemical bonding interactions that emerge from the application of the quantum theory of atoms in molecules (QTAIM), the isosurface topology of the reduced density gradient noncovalent index, interaction region indicator and independent gradient model (IGM) approaches. While the electrostatic surface potential model fails to explain the origin of the S···S interaction in the (MoS2)2 dimer, we show that the intermolecular bonding interactions in all nine dimers examined are a result of hyperconjugative charge transfer delocalizations between the lone-pair on (Ch/Ch′) and/or the π-orbitals of a Mo–Ch/Ch′ bond of one monomer and the dπ* anti-bonding orbitals of the same Mo–Ch/Ch′ bond in the second monomer during dimer formation, and vice versa. The HOMO–LUMO gaps calculated with the MN12-L functional were 0.9, 1.0, and 1.1 eV for MoTe2, MoSe2 and MoS2, respectively, which match very well with the solid-state theoretical (SCAN-rVV10)/experimental band gaps of 0.75/0.88, 0.90/1.09 and 0.93/1.23 eV of the corresponding systems, respectively. We observed that the gas phase dimers examined are perhaps prototypical for a basic understanding of the interfacial/inter-layer interactions in molybdenum-based dichalcogenides and their derivatives.
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21
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Jia S, Ye H, You L. Interplay between chalcogen bonds and dynamic covalent bonds. Org Chem Front 2022. [DOI: 10.1039/d2qo00684g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of chalcogen bonds, one type of emerging non-covalent bonding force, and imine bonds, allow the control of the dynamic covalent chemistry with orbital interactions and the reversal of kinetic and thermodynamic selectivity.
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Affiliation(s)
- Shuaipeng Jia
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
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22
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Radiush EA, Pritchina EA, Chulanova EA, Dmitriev AA, Bagryanskaya IY, Slawin AMZ, Woollins JD, Gritsan NP, Zibarev AV, Semenov NA. Chalcogen-bonded donor–acceptor complexes of 5,6-dicyano[1,2,5]selenadiazolo[3,4- b]pyrazine with halide ions. NEW J CHEM 2022. [DOI: 10.1039/d2nj02345h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With halides X− (X = Cl, Br, I) 5,6-dicyano-[1,2,5]selenadiazolo[3,4-b]pyrazine 1 forms chalcogen-bonded complexes [1–X]− structurally defined by XRD. UV/Vis spectra of [1–X]− feature red-shifted charge-transfer bands in the Vis part.
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Affiliation(s)
- Ekaterina A. Radiush
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena A. Pritchina
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, National Research University – Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena A. Chulanova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey A. Dmitriev
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, National Research University – Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | | | - J. Derek Woollins
- School of Chemistry, University of St. Andrews, St Andrews, Fife KY16 9ST, UK
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Nina P. Gritsan
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zibarev
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nikolay A. Semenov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
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23
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Holthoff JM, Weiss R, Rosokha SV, Huber SM. "Anti-electrostatic" Halogen Bonding between Ions of Like Charge. Chemistry 2021; 27:16530-16542. [PMID: 34409662 PMCID: PMC9293363 DOI: 10.1002/chem.202102549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 12/15/2022]
Abstract
Halogen bonding occurs between molecules featuring Lewis acidic halogen substituents and Lewis bases. It is often rationalized as a predominantly electrostatic interaction and thus interactions between ions of like charge (e. g., of anionic halogen bond donors with halides) seem counter-intuitive. Herein, we provide an overview on such complexes. First, theoretical studies are described and their findings are compared. Next, experimental evidences are presented in the form of crystal structure database analyses, recent examples of strong "anti-electrostatic" halogen bonding in crystals, and the observation of such interactions also in solution. We then compare these complexes to select examples of "counter-intuitive" adducts formed by other interactions, like hydrogen bonding. Finally, we comment on key differences between charge-transfer and electrostatic polarization.
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Affiliation(s)
- Jana M. Holthoff
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
| | - Robert Weiss
- Institut für Organische ChemieFriedrich-Alexander-Universität Erlangen-NürnbergHenkestraße 4291054ErlangenGermany
| | | | - Stefan M. Huber
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
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24
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Biswal HS, Sahu AK, Galmés B, Frontera A, Chopra D. Se⋅⋅⋅O/S and S⋅⋅⋅O Chalcogen Bonds in Small Molecules and Proteins: A Combined CSD and PDB Study. Chembiochem 2021; 23:e202100498. [PMID: 34693623 PMCID: PMC9298333 DOI: 10.1002/cbic.202100498] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/23/2021] [Indexed: 12/13/2022]
Abstract
The importance of selenium-centered noncovalent chalcogen bonds represented as Se⋅⋅⋅A (A=O/S) has been explored for short directional contacts in small molecules and proteins. In addition, S⋅⋅⋅O centered contacts have been analyzed. Computational analyses involving the quantitative assessment of the associated energetics, the molecular electrostatic potentials (MEP), and electron density derived topological parameters, namely, quantum theory of atom in molecules (QTAIM) analyses, and NBO (natural bond orbital) based calculations, have been performed to unequivocally establish the strength, stability, and attractive role of chalcogen bonds in the solid-state. This investigation has been performed in molecules from both the Cambridge Structural Database (CSD) and Protein Data Bank (PDB). Thus futuristic materials may be designed keeping in mind the significance of these interactions, including their relevance in biology.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Bartomeu Galmés
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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Piña MDLN, Frontera A, Bauza A. Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study. ACS Chem Biol 2021; 16:1701-1708. [PMID: 34427431 PMCID: PMC8525861 DOI: 10.1021/acschembio.1c00417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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In this study, we provide experimental
(Protein Data Bank (PDB)
inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence
of the involvement of charge assisted chalcogen bonding (ChB) interactions
in the recognition and folding mechanisms of S-adenosylmethionine
(SAM) riboswitches. Concretely, an initial PDB search revealed several
examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine
(EEM) molecules and uracil (U) bases belonging to RNA take place.
While these interactions are usually described as a merely Coulombic
attraction between the positively charged S/Se group and RNA, theoretical
calculations indicated that the σ holes of S and Se are involved.
Moreover, computational models shed light on the strength and directionality
properties of the interaction, which was also further characterized
from a charge-density perspective using Bader’s “Atoms
in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot)
visual index, and Natural Bonding Orbital (NBO) analyses. As far as
our knowledge extends, this is the first time that ChBs in SAM–RNA
complexes have been systematically analyzed, and we believe the results
might be useful for scientists working in the field of RNA engineering
and chemical biology as well as to increase the visibility of the
interaction among the biological community.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauza
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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de Azevedo Santos L, Hamlin TA, Ramalho TC, Bickelhaupt FM. The pnictogen bond: a quantitative molecular orbital picture. Phys Chem Chem Phys 2021; 23:13842-13852. [PMID: 34155488 PMCID: PMC8297534 DOI: 10.1039/d1cp01571k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
We have analyzed the structure and stability of archetypal pnictogen-bonded model complexes D3PnA- (Pn = N, P, As, Sb; D, A = F, Cl, Br) using state-of-the-art relativistic density functional calculations at the ZORA-M06/QZ4P level. We have accomplished two tasks: (i) to compute accurate trends in pnictogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. We have found that pnictogen bonds have a significant covalent character stemming from strong HOMO-LUMO interactions between the lone pair of A- and σ* of D3Pn. As such, the underlying mechanism of the pnictogen bond is similar to that of hydrogen, halogen, and chalcogen bonds.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and Department of Chemistry, Institute of Natural Sciences, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil and Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Tarannam N, Voelkel MHH, Huber SM, Kozuch S. Chalcogen vs Halogen Bonding Catalysis in a Water-Bridge-Cocatalyzed Nitro-Michael Reaction. J Org Chem 2021; 87:1661-1668. [PMID: 34181414 DOI: 10.1021/acs.joc.1c00894] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, a tellurium-based chalcogen-bond-catalyzed nitro-Michael reaction was reported ( Angew. Chem. Int. Ed. 2019, 58, 16923), taking advantage of the strong Lewis acidity of the catalyst. This species was found to be more effective than an analogous iodine-based halogen bond organocatalyst. Herein, we present a detailed mechanistic and kinetic analysis of these catalytic cycles including the influence of the solvent (and the performance of different intrinsic solvation models). While the chalcogen bonding interaction is fundamental to activate the C-C bond formation, we found that the presence of a two-water molecular bridge is critical to allow the following, otherwise high-energy proton transfer step. Even though the iodine-based halogen bonding interaction is stronger than the tellurium-based chalcogen bonding one, which makes the former a stronger Lewis acid and hence in principle a more efficient catalyst, solvation effects explain the smaller energy span of the latter.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Martin H H Voelkel
- Faculty for Chemistry and Biochemistry, Organic Chemistry I, Ruhr-Universitat Bochum, Bochum 44801, Germany
| | - Stefan M Huber
- Faculty for Chemistry and Biochemistry, Organic Chemistry I, Ruhr-Universitat Bochum, Bochum 44801, Germany
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Inscoe B, Rathnayake H, Mo Y. Role of Charge Transfer in Halogen Bonding. J Phys Chem A 2021; 125:2944-2953. [PMID: 33797922 DOI: 10.1021/acs.jpca.1c01412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer interaction. Here, we visited a series of prominent halogen bonded complexes of the types Y3C-X···Z (X = Br, I; Y = F, Cl, Br; Z = F-, Cl-, Br-, I-, NMe3) with the block-localized wave function (BLW) method at the M06-2X-D3/6-311+G(d,p) (def2-SVP for iodine) level of theory. As the simplest variant of ab initio valence bond (VB) theory, the BLW method is unique in the strict localization of electrons within interacting moieties, allowing for quantitative evaluation of the charge transfer effect on geometries, spectral properties, and energetics in halogen bonding complexes. By comparing the halogen bonding complexes with and without the charge transfer interaction, we proved that the charge transfer interaction significantly shortens the X···Z bonding distance and stretches the C-X bonds. But the shortening of the halogen bonding results in the less favorable steric effect, which is composed of Pauli repulsion, electrostatics, and electron correlation. There are approximate linear correlations between the charge transfer effect and binding energy and between bonding distance and binding energy. These correlations may lead to the illusion that the charge transfer interaction is unimportant or irrelevant, but further analyses showed that the inclusion of charge transfer is critical for the proper description of the halogen bonding, as considering only electrostatics and polarization leads to only about 45-60% of the binding strengths and much elongated bonding distances.
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Affiliation(s)
- Brandon Inscoe
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Hemali Rathnayake
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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Zierkiewicz W, Michalczyk M, Scheiner S. Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons. Molecules 2021; 26:molecules26061740. [PMID: 33804617 PMCID: PMC8003638 DOI: 10.3390/molecules26061740] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA;
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