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Zachmann AKZ, Drappeau JA, Liu S, Alexanian EJ. C(sp 3)-H (N-Phenyltetrazole)thiolation as an Enabling Tool for Molecular Diversification. Angew Chem Int Ed Engl 2024; 63:e202404879. [PMID: 38657161 DOI: 10.1002/anie.202404879] [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: 03/11/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
Methods enabling the broad diversification of C(sp3)-H bonds from a common intermediate are especially valuable in chemical synthesis. Herein, we report a site-selective (N-phenyltetrazole)thiolation of aliphatic and (hetero)benzylic C(sp3)-H bonds using a commercially available disulfide to access N-phenyltetrazole thioethers. The thioether products are readily elaborated in diverse fragment couplings for C-C, C-O, or C-N construction. The C-H functionalization proceeds via a radical-chain pathway involving hydrogen atom transfer by the electron-poor N-phenyltetrazolethiyl radical. Hexafluoroisopropanol was found to be essential to reactions involving aliphatic C(sp3)-H thiolation, with computational analysis consistent with dual hydrogen bonding of the N-phenyltetrazolethiyl radical imparting increased radical electrophilicity to facilitate the hydrogen atom transfer. Substrate is limiting reagent in all cases, and the reaction displays an exceptional functional group tolerance well suited to applications in late-stage diversification.
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Affiliation(s)
- Ashley K Z Zachmann
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Justine A Drappeau
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shubin Liu
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Research Computing Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erik J Alexanian
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Lu T, Chen R, Liu Q, Zhong Y, Lei F, Zeng Z. Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO 2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations. Int J Mol Sci 2024; 25:5609. [PMID: 38891796 PMCID: PMC11171880 DOI: 10.3390/ijms25115609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/11/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Among various non-covalent interactions, selenium-centered chalcogen bonds (SeChBs) have garnered considerable attention in recent years as a result of their important contributions to crystal engineering, organocatalysis, molecular recognition, materials science, and biological systems. Herein, we systematically investigated π-hole-type Se∙∙∙O/S ChBs in the binary complexes of SeO2 with a series of O-/S-containing Lewis bases by means of high-level ab initio computations. The results demonstrate that there exists an attractive interaction between the Se atom of SeO2 and the O/S atom of Lewis bases. The interaction energies computed at the MP2/aug-cc-pVTZ level range from -4.68 kcal/mol to -10.83 kcal/mol for the Se∙∙∙O chalcogen-bonded complexes and vary between -3.53 kcal/mol and -13.77 kcal/mol for the Se∙∙∙S chalcogen-bonded complexes. The Se∙∙∙O/S ChBs exhibit a relatively short binding distance in comparison to the sum of the van der Waals radii of two chalcogen atoms. The Se∙∙∙O/S ChBs in all of the studied complexes show significant strength and a closed-shell nature, with a partially covalent character in most cases. Furthermore, the strength of these Se∙∙∙O/S ChBs generally surpasses that of the C/O-H∙∙∙O hydrogen bonds within the same complex. It should be noted that additional C/O-H∙∙∙O interactions have a large effect on the geometric structures and strength of Se∙∙∙O/S ChBs. Two subunits are connected together mainly via the orbital interaction between the lone pair of O/S atoms in the Lewis bases and the BD*(OSe) anti-bonding orbital of SeO2, except for the SeO2∙∙∙HCSOH complex. The electrostatic component emerges as the largest attractive contributor for stabilizing the examined complexes, with significant contributions from induction and dispersion components as well.
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Affiliation(s)
| | | | | | | | - Fengying Lei
- School of Basic Medical Sciences/School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China; (T.L.); (R.C.); (Q.L.); (Y.Z.)
| | - Zhu Zeng
- School of Basic Medical Sciences/School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China; (T.L.); (R.C.); (Q.L.); (Y.Z.)
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3
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Scheiner S, Amonov A. Types of noncovalent bonds within complexes of thiazole with CF 4 and SiF 4. Phys Chem Chem Phys 2024; 26:6127-6137. [PMID: 38299682 DOI: 10.1039/d4cp00057a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah 84322-0300, USA.
| | - Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University 140104, University blv. 15, Samarkand, Uzbekistan
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4
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Ishigaki Y, Harimoto T, Shimajiri T, Suzuki T. Carbon-based Biradicals: Structural and Magnetic Switching. Chem Rev 2023; 123:13952-13965. [PMID: 37948658 DOI: 10.1021/acs.chemrev.3c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Sterically hindered C═C double bonds often deform into a bent or twisted geometry. Thus, many overcrowded ethylenes or anthraquinodimethanes can adopt multiple conformations, such as a folded form or a twisted form, which are interconvertible under the application of external stimuli. A perpendicular form with biradical character can also be adopted when designed to incorporate a stable carbon-based radical unit, which is involved in stimuli-responsive magnetic switching accompanied by a structural change. This review focuses on recent advances in the development of such strained π-electron systems and reveals the factors that affect the mutual interconversion and switching behavior. The energy barrier for the interconversion of conformational isomers is affected by the tricyclic skeleton or bulky substituents on the C═C double bonds, whereas the relative stability of the perpendicular biradical form increases with the additional insertion of 9,10-anthrylene units into the C═C double bonds.
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Affiliation(s)
- Yusuke Ishigaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takashi Harimoto
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takuya Shimajiri
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Creative Research Institution, Hokkaido University, Sapporo 001-0021, Japan
| | - Takanori Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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5
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Carugo OI. Chalcogen bonds formed by protein sulfur atoms in proteins. A survey of high-resolution structures deposited in the protein data bank. J Biomol Struct Dyn 2023; 41:9576-9582. [PMID: 36342326 DOI: 10.1080/07391102.2022.2143427] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
The presence of chalcogen bonds in native proteins was investigated on a non-redundant and high-resolution (≤ 1 Angstrom) set of protein crystal structures deposited in the Protein Data Bank. It was observed that about one half of the sulfur atoms of methionines and disulfide bridges from chalcogen bonds with nucleophiles (oxygen and sulfur atoms, and aromatic rings). This suggests that chalcogen bonds are a non-bonding interaction important for protein stability. Quite numerous chalcogen bonds involve water molecules. Interestingly, in the case of disulfide bridges, chalcogen bonds have a marked tendency to occur along the S-S bond extension rather than along the C-S bond extension. Additionally, it has been observed that closer residues have a higher probability of being connected by a chalcogen bonds, while the secondary structure of the two residues connected by a chalcogen bond do not correlate with its formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oliviero Italo Carugo
- Department of Chemistry, University of Pavia, Pavia, Italy
- Department of Structural and Computational Biology, Max Perutz Labs University of Vienna, Vienna, Austria
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6
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Amonov A, Scheiner S. Heavy pnicogen atoms as electron donors in sigma-hole bonds. Phys Chem Chem Phys 2023; 25:23530-23537. [PMID: 37656119 DOI: 10.1039/d3cp03479h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
DFT calculations evaluate the strength of σ-hole bonds formed by ZH3 and ZMe3 (Z = N, P, As, Sb) acting as electron donor. Bond types considered include H-bond, halogen, chalcogen, pnicogen, and tetrel bond to perfluorinated Lewis acids FH, FBr, F2Se F3As, F4Ge, respectively, as well as their monofluorinated analogues. All of the Z atoms can engage in bonds of at least moderate strength, varying from 3 to more than 40 kcal mol-1. In most cases, N forms the strongest bonds, but the falloff from P to Sb is quite mild. However, this pattern is not characteristic of all cases, as for example in the halogen bonds, where the heavier Z atoms are comparable to, or even stronger than N. Most of the bonds are strengthened by replacing the three H atoms of ZH3 by methyl groups, better simulating the situation that would be generally encountered. Structural and NMR shielding data ought to facilitate the identification of these bonds within crystals or in solution.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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7
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Abstract
While a good deal of information has accumulated concerning the manner in which an intramolecular noncovalent bond can affect the relative energies of various conformers, less is known about how such bonds might affect the dynamics of interconversion between them. A series of molecules are constructed in which symmetrically equivalent conformers containing a noncovalent bond can be interconverted by a bond rotation, the energy barrier to which is computed by quantum chemical methods. The rotation of a CF3 group attached to a phenyl ring is speeded up if a Se··F chalcogen bond can be formed with a SeH or SeF group placed in an ortho position, a bond that is present in and stabilizes the rotational transition state. The analogous SnF3 group can, on the other hand, engage in a Sn··Se tetrel bond in its global minimum. The energetic cost of breakage of this bond is not fully compensated by the appearance of a Se··F chalcogen bond in the rotational transition state. Other systems were designed by placing two phenyl rings on opposite ends of an octahedrally disposed SeF4 group. A high barrier inhibits their rotation with bulky Br atoms in ortho positions, but this barrier is lowered if Br is replaced by groups that can engage in either chalcogen (SeH or SeF) or pnicogen (AsH2) bonds with the F atoms in the rotational transition state. The barrier reduction is closely related to the strength of these noncovalent bonds.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Brammer L, Peuronen A, Roseveare TM. Halogen bonds, chalcogen bonds, pnictogen bonds, tetrel bonds and other σ-hole interactions: a snapshot of current progress. Acta Crystallogr C Struct Chem 2023; 79:204-216. [PMID: 37212787 PMCID: PMC10240169 DOI: 10.1107/s2053229623004072] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023] Open
Abstract
We report here on the status of research on halogen bonds and other σ-hole interactions involving p-block elements in Lewis acidic roles, such as chalcogen bonds, pnictogen bonds and tetrel bonds. A brief overview of the available literature in this area is provided via a survey of the many review articles that address this field. Our focus has been to collect together most review articles published since 2013 to provide an easy entry into the extensive literature in this area. A snapshot of current research in the area is provided by an introduction to the virtual special issue compiled in this journal, comprising 11 articles and entitled `Halogen, chalcogen, pnictogen and tetrel bonds: structural chemistry and beyond.'
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Affiliation(s)
- Lee Brammer
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
| | - Anssi Peuronen
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Thomas M. Roseveare
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
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9
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Wang Z, Wang W, Li HB. Tuning of the Electrostatic Potentials on the Surface of the Sulfur Atom in Organic Molecules: Theoretical Design and Experimental Assessment. Molecules 2023; 28:molecules28093919. [PMID: 37175329 PMCID: PMC10180200 DOI: 10.3390/molecules28093919] [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: 03/29/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Noncovalent sulfur interactions are ubiquitous and play important roles in medicinal chemistry and organic optoelectronic materials. Quantum chemical calculations predicted that the electrostatic potentials on the surface of the sulfur atom in organic molecules could be tuned through the through-space effects of suitable substituents. This makes it possible to design different types of noncovalent sulfur interactions. The theoretical design was further confirmed by X-ray crystallographic experiments. The sulfur atom acts as the halogen atom acceptor to form the halogen bond in the cocrystal between 2,5-bis(2-pyridyl)-1,3,4-thiadiazole and 1,4-diiodotetrafluorobenzene, whereas it acts as the chalcogen atom donor to form the chalcogen bond in the cocrystal between 2,5-bis(3-pyridyl)-1,3,4-thiadiazole and 1,3,5-trifluoro-2,4,6-triiodobenzene.
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Affiliation(s)
- Ziyu Wang
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China
| | - Hai-Bei Li
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China
- Marine College, Shandong University, Weihai 264209, China
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10
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Aragoni MC, Arca M, Lippolis V, Pintus A, Torubaev Y, Podda E. A Structural Approach to the Strength Evaluation of Linear Chalcogen Bonds. Molecules 2023; 28:molecules28073133. [PMID: 37049895 PMCID: PMC10096081 DOI: 10.3390/molecules28073133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The experimental structural features of chalcogen bonding (ChB) interactions in over 34,000 linear fragments R–Ch⋯A (Ch = S, Se, Te; R = C, N, O, S, Se, Te; A = N, O, S, Se, Te, F, Cl, Br, I) were analyzed. The bond distances dR–Ch and the interaction distances dCh⋯A were investigated, and the functions δR–Ch and δCh⋯A were introduced to compare the structural data of R–Ch⋯A fragments involving different Ch atoms. The functions δR−Ch and δCh⋯A were calculated by normalizing the differences between the relevant bond dR–Ch and ChB interaction dCh⋯A distances with respect to the sum of the relevant covalent (rcovR + rcovCh) and the van der Waals (vdW) radii (rvdWCh + rvdWA), respectively. A systematic comparison is presented, highlighting the role of the chalcogen involved, the role of the R atoms covalently bonded to the Ch, and the role of the A species playing the role of chalcogen bond acceptor. Based on the results obtained, an innovative approach is proposed for the evaluation and categorization of the ChB strength based on structural data.
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11
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Carugo O. Interplay between hydrogen and chalcogen bonds in cysteine. Proteins 2023; 91:395-399. [PMID: 36250971 PMCID: PMC10092013 DOI: 10.1002/prot.26437] [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: 06/28/2022] [Revised: 10/04/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Abstract
Protein structures are stabilized by several types of chemical interactions between amino acids, which can compete with each other. This is the case of chalcogen and hydrogen bonds formed by the thiol group of cysteine, which can form three hydrogen bonds with one hydrogen acceptor and two hydrogen donors and a chalcogen bond with a nucleophile along the extension of the CS bond. A survey of the Protein Data Bank shows that hydrogen bonds are about 40-50 more common than chalcogen bonds, suggesting that they are stronger and, consequently, prevail, though not always. It is also observed that frequently a thiol group that forms a chalcogen bond is also involved, as a hydrogen donor, in a hydrogen bond.
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Affiliation(s)
- Oliviero Carugo
- Department of Chemistry, University of Pavia, Pavia, Italy.,Department of Structural and Computational Biology, University of Vienna, Vienna, Austria
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12
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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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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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15
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Jena S, Routray C, Dutta J, Biswal HS. Hydrogen Bonding Directed Reversal of
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C NMR Chemical Shielding. Angew Chem Int Ed Engl 2022; 61:e202207521. [DOI: 10.1002/anie.202207521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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16
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Definition of the Pnictogen Bond: A Perspective. INORGANICS 2022. [DOI: 10.3390/inorganics10100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This article proposes a definition for the term “pnictogen bond” and lists its donors, acceptors, and characteristic features. These may be invoked to identify this specific subset of the inter- and intramolecular interactions formed by elements of Group 15 which possess an electrophilic site in a molecular entity.
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17
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Jena S, Routray C, Dutta J, Biswal HS. Hydrogen‐Bonding Directed Reversal of 13C NMR Chemical Shielding. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Subhrakant Jena
- National Institute of Science Education and Research School of Chemical Sciences INDIA
| | - Chinmay Routray
- National Institute of Science Education and Research School of Chemical Sciences INDIA
| | - Juhi Dutta
- National Institute of Science Education and Research School of Chemical Sciences INDIA
| | - Himansu Sekhar Biswal
- National Institute of Science Education and Research School of Chemical Sciences Jatani 752050 Bhubaneswar INDIA
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19
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Abstract
The chalcogen Y atom in the aromatic ring of thiophene and its derivatives YC4H4 (Y = S, Se, Te) can engage in a number of different interactions with another such unit within the homodimer. Quantum calculations show that the two rings can be oriented perpendicular to one another in a T-shaped dimer in which the Y atom accepts electron density from the π-system of the other unit in a Y···π chalcogen bond (ChB). This geometry best takes advantage of attractions between the electrostatic potentials surrounding the two monomers. There are two other geometries in which the two Y atoms engage in a ChB with one another. However, instead of a simple interaction between a σ-hole on one Y and the lone pair of its neighbor, the interaction is better described as a pair of symmetrically equivalent Y···Y interactions, in which charge is transferred in both directions simultaneously, thereby effectively doubling the strength of the bond. These geometries differ from what might be expected based simply on the juxtaposition of the electrostatic potentials of the two monomers.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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20
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Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, 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, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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21
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Scheiner S. Principles Guiding the Square Bonding Motif Containing a Pair of Chalcogen Bonds between Chalcogenadiazoles. J Phys Chem A 2022; 126:1194-1203. [PMID: 35143197 DOI: 10.1021/acs.jpca.1c10818] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bonding motif adopted by a dimer of chalcogenadiazole molecules is characterized by a pair of equivalent Ch···N chalcogen bonds. Quantum calculations show that the interaction energy is substantial, varying between 4 kcal/mol for Ch = S and 17 kcal/mol for Te. The interaction is cooperative in that the total bond strength is greater than either chalcogen bond individually. Neither the addition of a phenyl ring nor the addition of a pair of cyano substituents to the diazole ring has much influence on this binding. Removal of one N from the diazole weakens the binding, and addition of two nitrogens has little effect. The largest perturbation arises with three N atoms in each ring, for which the binding energy increases by some 25%. The ring size plays a minor role in most cases, although a near doubling of bond strength occurs if there are two N atoms present on a four-membered ring.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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22
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Tulsiyan KD, Jena S, Dutta J, Biswal HS. Hydrogen Bonding with Polonium. Phys Chem Chem Phys 2022; 24:17185-17194. [DOI: 10.1039/d2cp01852g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonding (H-bonding) with heavier chalcogens such as polonium and tellurium is almost unexplored owing to their lower electronegativities, providing us an opportunity to delve into the uncharted territory of...
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Torubaev YV, Rozhkov AV, Skabitsky IV, Gomila RM, Frontera A, Kukushkin VY. Heterovalent chalcogen bonding: supramolecular assembly driven by the occurrence of a tellurium( ii)⋯Ch( i) (Ch = S, Se, Te) linkage. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01420c] [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
The revealed heterovalent TeII⋯ChI (Ch = S, Se, Te) chalcogen bonding was used for targeted noncovalent integration of two Ch centers in different oxidation states.
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Affiliation(s)
- Yury V. Torubaev
- N. S. Kurnakov Institute of General and Inorganic Chemistry of Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anton V. Rozhkov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Ivan V. Skabitsky
- N. S. Kurnakov Institute of General and Inorganic Chemistry of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Rosa M. Gomila
- Department of Chemistry, Universitat de les Illes Balears, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, 07122 Palma de Mallorca, Baleares, Spain
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russian Federation
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