1
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Georges T, Ovens JS, Bryce DL. Electrostatic Surface Potentials and Chalcogen-Bonding Motifs of Substituted 2,1,3-Benzoselenadiazoles Probed via 77Se Solid-State NMR Spectroscopy. Chemistry 2024; 30:e202402254. [PMID: 38958873 DOI: 10.1002/chem.202402254] [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: 06/11/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/04/2024]
Abstract
Chalcogen bonds (ChB) are moderately strong, directional, and specific non-covalent interactions that have garnered substantial interest over the last decades. Specifically, the presence of two σ-holes offers great potential for crystal engineering, catalysis, biochemistry, and molecular sensing. However, ChB applications are currently hampered by a lack of methods to characterize and control chalcogen bonds. Here, we report on the influence of various substituents (halogens, cyano, and methyl groups) on the observed self-complementary ChB networks of 2,1,3-benzoselenadiazoles. From molecular electrostatic potential calculations, we show that the electrostatic surface potentials (ESP) of the σ-holes on selenium are largely influenced by the electron-withdrawing character of these substituents. Structural analyses via X-ray diffraction reveal a variety of ChB geometries and binding modes that are rationalized via the computed ESP maps, although the structure of 5,6-dimethyl-2,1,3-benzoselenadiazole also demonstrates the influence of steric interactions. 77Se solid-state magic-angle spinning NMR spectroscopy, in particular the analysis of the selenium chemical shift tensors, is found to be an effective probe able to characterize both structural and electrostatic features of these self-complementary ChB systems. We find a positive correlation between the value of the ESP maxima at the σ-holes and the experimentally measured 77Se isotropic chemical shift, while the skew of the chemical shift tensor is established as a metric which is reflective of the ChB binding motif.
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Affiliation(s)
- Tristan Georges
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private Ottawa, K1N 6N5, Ontario, Canada
| | - Jeffrey S Ovens
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private Ottawa, K1N 6N5, Ontario, Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private Ottawa, K1N 6N5, Ontario, Canada
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2
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Camilli L, Hogan C, Romito D, Persichetti L, Caporale A, Palummo M, Di Giovannantonio M, Bonifazi D. On-Surface Molecular Recognition Driven by Chalcogen Bonding. JACS AU 2024; 4:2115-2121. [PMID: 38938818 PMCID: PMC11200221 DOI: 10.1021/jacsau.4c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024]
Abstract
Chalcogen bonding interactions (ChBIs) have been widely employed to create ordered noncovalent assemblies in solids and liquids. Yet, their ability to engineer molecular self-assembly on surfaces has not been demonstrated. Here, we report the first demonstration of on-surface molecular recognition solely governed by ChBIs. Scanning tunneling microscopy and ab initio calculations reveal that a pyrenyl derivative can undergo noncovalent chiral dimerization on the Au(111) surface through double Ch···N interactions involving Te- or Se-containing chalcogenazolo pyridine motifs. In contrast, reference chalcogenazole counterparts lacking the pyridyl moiety fail to form regular self-assemblies on Au, resulting in disordered assemblies.
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Affiliation(s)
- Luca Camilli
- Department
of Physics, University of Rome “Tor
Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy
| | - Conor Hogan
- Department
of Physics, University of Rome “Tor
Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy
- CNR-Istituto
di Struttura della Materia (CNR-ISM), 00133 Roma, Italy
| | - Deborah Romito
- Department
of Organic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Luca Persichetti
- Department
of Physics, University of Rome “Tor
Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy
| | - Antonio Caporale
- Department
of Physics, University of Rome “Tor
Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy
| | - Maurizia Palummo
- INFN,
Department of Physics, University of Rome
“Tor Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy
| | | | - Davide Bonifazi
- Department
of Organic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
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3
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Eckstein BJ, Martin HR, Moghadasnia MP, Halder A, Melville MJ, Buzinski TN, Balaich GJ, McGuirk CM. Influence of donor point modifications on the assembly of chalcogen-bonded organic frameworks. Chem Commun (Camb) 2024; 60:758-761. [PMID: 38126447 DOI: 10.1039/d3cc05162e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Incremental, single-atom substitutions of Se-based chalcogen bond (Ch-bond) donors with stronger donating Te centers were implemented in two new triptycene tris(1,2,5-chalcogenadiazole) tectons. The appreciably more favorable Ch-bonding ability of the Te-based donors promotes assembly of low-density networks and more stable Ch-bonded organic frameworks (ChOFs).
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Affiliation(s)
- Brian J Eckstein
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Hannah R Martin
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | | | - Arijit Halder
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Michael J Melville
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Tara N Buzinski
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Gary J Balaich
- Department of Chemistry & Chemistry Research Center, Laboratories for Advanced Materials, United States Airforce Academy, Colorado Springs, Colorado, 80840, USA
| | - C Michael McGuirk
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
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4
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Radiush EA, Wang H, Chulanova EA, Ponomareva YA, Li B, Wei QY, Salnikov GE, Petrakova SY, Semenov NA, Zibarev AV. Halide Complexes of 5,6-Dicyano-2,1,3-Benzoselenadiazole with 1 : 4 Stoichiometry: Cooperativity between Chalcogen and Hydrogen Bonding. Chempluschem 2023; 88:e202300523. [PMID: 37750466 DOI: 10.1002/cplu.202300523] [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: 09/19/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
The [M4 -Hal]- (M=the title compound; Hal=Cl, Br, and I) complexes were isolated in the form of salts of [Et4 N]+ cation and characterized by XRD, NMR, UV-Vis, DFT, QTAIM, EDD, and EDA. Their stoichiometry is caused by a cooperative interplay of σ-hole-driven chalcogen (ChB) and hydrogen (HB) bondings. In the crystal, [M4 -Hal]- are connected by the π-hole-driven ChB; overall, each [Hal]- is six-coordinated. In the ChB, the electrostatic interaction dominates over orbital and dispersion interactions. In UV-Vis spectra of the M+[Hal]- solutions, ChB-typical and [Hal]- -dependent charge-transfer bands are present; they reflect orbital interactions and allow identification of the individual [Hal]- . However, the structural situation in the solutions is not entirely clear. Particularly, the UV-Vis spectra of the solutions are different from the solid-state spectra of the [Et4 N]+ [M4 -Hal]- ; very tentatively, species in the solutions are assigned [M-Hal]- . It is supposed that the formation of the [M4 -Hal]- proceeds during the crystallization of the [Et4 N]+ [M4 -Hal]- . Overall, M can be considered as a chromogenic receptor and prototype sensor of [Hal]- . The findings are also useful for crystal engineering and supramolecular chemistry.
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Affiliation(s)
- Ekaterina A Radiush
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Hui Wang
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Elena A Chulanova
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Institute for Applied Physics, University of Tübingen, 72076, Tübingen, Germany
| | - Yana A Ponomareva
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Natural Sciences, National Research University - Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Bin Li
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Qiao Yu Wei
- School of Physical Science and Technology, Southwest Jiaotong University, 610031, Chengdu, P. R. China
| | - Georgy E Salnikov
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Svetlana Yu Petrakova
- 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
| | - Andrey V Zibarev
- Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
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Scheiner S. Competition Between the Two σ-Holes in the Formation of a Chalcogen Bond. Chemphyschem 2023; 24:e202200936. [PMID: 36744997 DOI: 10.1002/cphc.202200936] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/07/2023]
Abstract
A chalcogen atom Y contains two separate σ-holes when in a R1 YR2 molecular bonding pattern. Quantum chemical calculations consider competition between these two σ-holes to engage in a chalcogen bond (ChB) with a NH3 base. R groups considered include F, Br, I, and tert-butyl (tBu). Also examined is the situation where the Y lies within a chalcogenazole ring, where its neighbors are C and N. Both electron-withdrawing substituents R1 and R2 act cooperatively to deepen the two σ-holes, but the deeper of the two holes consistently lies opposite to the more electron-withdrawing group, and is also favored to form a stronger ChB. The formation of two simultaneous ChBs in a triad requires the Y atom to act as double electron acceptor, and so anti-cooperativity weakens each bond relative to the simple dyad. This effect is such that some of the shallower σ-holes are unable to form a ChB at all when a base occupies the other site.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, 84322-0300, Logan, Utah, USA
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6
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Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives. Molecules 2022; 27:molecules27248847. [PMID: 36557978 PMCID: PMC9783803 DOI: 10.3390/molecules27248847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car-Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.
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Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic. Int J Mol Sci 2022; 23:ijms232213701. [PMID: 36430173 PMCID: PMC9691181 DOI: 10.3390/ijms232213701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/24/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum-chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree-Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM-binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.
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8
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Scheiner S. On the reliability of atoms in molecules, noncovalent index, and natural bond orbital to identify and quantify noncovalent bonds. J Comput Chem 2022; 43:1814-1824. [DOI: 10.1002/jcc.26983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan Utah USA
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9
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Zhang L, Zeng Y, Li X, Zhang X. Noncovalent interactions between benzochalcogenadiazoles and nitrogen bases. J Mol Model 2022; 28:248. [PMID: 35932432 DOI: 10.1007/s00894-022-05247-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
A theoretical study has been carried out on the intermolecular interactions between tetrafluoro-benzochalcogenadiazoles (chalcogen = S, Se, Te) and a series of nitrogen bases (FCN, ClCN, NP, trans-N2H2, pyridine, pyrazole, imidazole) at the B97-D3/def2-TZVP level, to obtain a better insight into the nature and strength of Ch···N chalcogen bond and secondary interaction in the binary and 1:2 ternary complexes. The dispersion force plays a prominent role on the stability of the sulfur complexes, and the electrostatic effect enhanced for the heavier chalcogen complexes. Most of intermolecular bonds display the characters of closed-shell and noncovalent interaction. For the complexes involving pyridine and imidazole, chalcogen bond is stronger than hydrogen bond, while the strength of chalcogen bond is equivalent to the secondary interaction for other complexes. With the addition of nitrogen base in the 1:2 complexes, chalcogen bond is weakened, while the secondary interaction remains unchanged. In the 1:2 complexes formed by pyridine and imidazole, stronger chalcogen bond results in larger negative cooperativity than that of other complexes.
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Affiliation(s)
- Lili Zhang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
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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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