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Zuo S, Liu T, Li L, Xu H, Guo J, Wang Q, Yang Y, He Z, Sun J, Sun B. Tetrasulfide bond boosts the anti-tumor efficacy of dimeric prodrug nanoassemblies. Cell Rep Med 2024; 5:101432. [PMID: 38387464 PMCID: PMC10982979 DOI: 10.1016/j.xcrm.2024.101432] [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: 12/11/2023] [Accepted: 01/25/2024] [Indexed: 02/24/2024]
Abstract
Dimeric prodrug nanoassemblies (DPNAs) stand out as promising strategies for improving the efficiency and safety of chemotherapeutic drugs. The success of trisulfide bonds (-SSS-) in DPNAs makes polysulfide bonds a worthwhile focus. Here, we explore the comprehensive role of tetrasulfide bonds (-SSSS-) in constructing superior DPNAs. Compared to trisulfide and disulfide bonds, tetrasulfide bonds endow DPNAs with superlative self-assembly stability, prolonged blood circulation, and high tumor accumulation. Notably, the ultra-high reduction responsivity of tetrasulfide bonds make DPNAs a highly selective "tumor bomb" that can be ignited by endogenous reducing agents in tumor cells. Furthermore, we present an "add fuel to the flames" strategy to intensify the reductive stress at tumor sites by replenishing exogenous reducing agents, making considerable progress in selective tumor inhibition. This work elucidates the crucial role of tetrasulfide bonds in establishing intelligent DPNAs, alongside the combination methodology, propelling DPNAs to new heights in potent cancer therapy.
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Affiliation(s)
- Shiyi Zuo
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Tian Liu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Lingxiao Li
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Hezhen Xu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Jiayu Guo
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Qing Wang
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Yinxian Yang
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Zhonggui He
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Jin Sun
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China.
| | - Bingjun Sun
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China.
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2
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Islam AS, Pramanik S, Mondal S, Ghosh R, Ghosh P. Selective recognition and extraction of iodide from pure water by a tripodal selenoimidazol(ium)-based chalcogen bonding receptor. iScience 2024; 27:108917. [PMID: 38327780 PMCID: PMC10847689 DOI: 10.1016/j.isci.2024.108917] [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: 09/22/2023] [Revised: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024] Open
Abstract
A selenium-based tripodal chalcogen bond (ChB) donor TPI-3Se is demonstrated for the recognition and extraction of I- from 100% water medium. NMR and ITC studies with the halides reveal that the ChB donor selectively binds with the large, weakly hydrated I-. Interestingly, I- crystallizes out selectively in the presence of other halides supporting the superiority of the selective recognition of I-. The X-ray structure of the ChB-iodide complex manifests both the μ1 and μ2 coordinated interactions, which is rare in the C-Se···I chalcogen bonding. Furthermore, to validate the selective I- binding potency of TPI-3Se in pure water, comparisons are made with its hydrogen and halogen bond donor analogs. The computational analysis also provides the mode of I- recognition by TPI-3Se. Importantly, this receptor is capable of extracting I- from pure water through selenium sigma-hole and I- interaction with a high degree of efficiency (∼70%).
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Affiliation(s)
- Abu S.M. Islam
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sourav Pramanik
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sahidul Mondal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Rajib Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pradyut Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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3
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Scheiner S, Michalczyk M, Zierkiewicz W. Influence of Internal Angular Arrangement on Pnicogen Bond Strength. Inorg Chem 2023. [PMID: 38016913 DOI: 10.1021/acs.inorgchem.3c03141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The three Z-X covalent bonds of a ZX3 unit (Z = P, As, Sb, Bi) are normally arranged in a pyramidal structure. Quantum chemical calculations show that pnicogen bonds (ZBs) to the central Z are weakened if ZX3 is flattened, as in the opening of an umbrella. The partial closing of the umbrella has the opposite effect of substantially strengthening these ZBs, even amounting to a 2- or 3-fold magnification in certain cases. The strongest such bonds, wherein Sb and Bi are in a strained configuration within a ZO3CH model system, have interaction energies of 20 kcal/mol with an NH3 base. Most of these systems, whether flattened or more pyramidal, are capable of engaging in three ZBs simultaneously, despite a certain amount of negative cooperativity.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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4
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Abstract
The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.
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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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5
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Amonov A, Scheiner S. Relation between Halogen Bond Strength and IR and NMR Spectroscopic Markers. Molecules 2023; 28:7520. [PMID: 38005241 PMCID: PMC10673387 DOI: 10.3390/molecules28227520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/04/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C-X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded to X and the coupling constants involving the C-X bond and the C-H/F bond that lies ortho to the X substituent, but these correlations are not accurate enough for the quantitative assessment of energy. These correlations tend to improve as the Lewis acid becomes more potent, which makes for a wider range of XB strengths.
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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, UT 84322-0300, USA
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6
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Ghinato S, Giordana A, Diana E, Gomila RM, Priola E, Frontera A. Synthesis, X-ray characterization and DFT analysis of dicyanidoaurate telluronium salts: on the importance of charge assisted chalcogen bonds. Dalton Trans 2023; 52:15688-15696. [PMID: 37854010 DOI: 10.1039/d3dt02787b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
In this manuscript we report the synthesis and X-ray characterization of two cyanidoaurate telluronium salts, namely (3-fluorophenyl)(methyl)(phenyl)telluronium dicyanidoaurate [(3-F-Ph)(Me)(Ph)Te][Au(CN)2] (1) and methyldiphenyltelluronium dicyanidoaurate [(Me)(Ph)2Te][Au(CN)2] (2). In the solid state, the tellurium atom establishes three concurrent and directional chalcogen bonds (ChBs) with the adjacent anions, in both compounds. These charge-assisted ChBs (CAChBs) have been analyzed using DFT calculations and several computational tools. The MEP surface analysis discloses the existence of three σ-holes at the Te-atoms capable of establishing strong CAChBs with the counter-ions. In addition, significant charge transfer from the lone pair orbital at the N-atom of the anion to the antibonding σ*(Te-C) orbital of the cation is observed in some cases.
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Affiliation(s)
- Simone Ghinato
- Università degli Studi di Torino, Department of Chemistry, Via Pietro Giuria 7, 10125 Torino, Italy.
| | - Alessia Giordana
- Università degli Studi di Torino, Department of Chemistry, Via Pietro Giuria 7, 10125 Torino, Italy.
| | - Eliano Diana
- Università degli Studi di Torino, Department of Chemistry, Via Pietro Giuria 7, 10125 Torino, Italy.
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Emanuele Priola
- Università degli Studi di Torino, Department of Chemistry, Via Pietro Giuria 7, 10125 Torino, Italy.
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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7
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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: 12] [Impact Index Per Article: 12.0] [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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8
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Amonov A, Scheiner S. Competition between Binding to Various Sites of Substituted Imidazoliums. J Phys Chem A 2023. [PMID: 37490696 DOI: 10.1021/acs.jpca.3c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH3 base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.
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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, United States
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9
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Scheiner S. Does a halogen bond require positive potential on the acid and negative potential on the base? Phys Chem Chem Phys 2023; 25:7184-7194. [PMID: 36815530 DOI: 10.1039/d3cp00379e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
It is usually expected that formation of a halogen bond (XB) requires that a region of positive electrostatic potential associated with a σ or π-hole on the Lewis acid will interact with the negative potential of the base, either a lone pair or π-bond region. Quantum calculations of model systems suggest this not to be necessary. The placement of electron-withdrawing substituents on the base can reverse the sign of the potential in its lone pair or π-bond region to positive, and this base can nonetheless engage in a XB with the positive σ-hole of a Lewis acid. The reverse scenario is also possible in certain circumstances, as a negatively charged σ-hole can form a XB with the negative lone pair region of a base. Despite these classical Coulombic repulsions, the overall electrostatic interaction is attractive in these XBs, albeit only weakly so. The strengths of these bonds are surprisingly insensitive to changes in the partner molecule. For example, even a wide range in the depth of the σ-hole of the approaching acid yields only a minimal change in the strength of the XB to a base with a positive potential.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah, USA, 84322-0300.
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10
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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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11
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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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12
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Li L, Zou Z, Xue B, Pang B, Yang Y, Guan Q, Li B, Zhang W. Chalcogen bond-assisted syn-locked scaffolds: DFT analysis and biological implications of novel tubulin inhibitors. Biochem Biophys Res Commun 2023; 638:134-139. [PMID: 36455359 DOI: 10.1016/j.bbrc.2022.11.027] [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: 10/31/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
A series of new tubulin inhibitors containing chalcogen bonds have been discovered. Density functional theory (DFT) analysis of the O-C-C-S torsion profile shows a preference of 0.8 kcal/mol for the syn-conformer over the anti-conformer. Besides, the O-S natural bond orbital (NBO) analysis reveals that the OLP ∼ C-SBD∗ energy potential is 0.62 kcal/mol. Further pharmacochemical screening of several series of (4-arylthiophen-2-yl)(3,4,5-trimethoxyphenyl)methanones identified IPO-10 as a highly effective tubulin inhibitor with an IC50 of 23 nm for MCF-7.
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Affiliation(s)
- Long Li
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Zheng Zou
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Baoyu Xue
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Bokai Pang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Yukun Yang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Qi Guan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China.
| | - Bo Li
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Street, Heping District, Shenyang, 110002, China.
| | - Weige Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China.
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13
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Liu T, Li L, Wang S, Dong F, Zuo S, Song J, Wang X, Lu Q, Wang H, Zhang H, Cheng M, Liu X, He Z, Sun B, Sun J. Hybrid chalcogen bonds in prodrug nanoassemblies provides dual redox-responsivity in the tumor microenvironment. Nat Commun 2022; 13:7228. [PMID: 36434014 PMCID: PMC9700694 DOI: 10.1038/s41467-022-35033-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
Sulfur bonds, especially trisulfide bond, have been found to ameliorate the self-assembly stability of homodimeric prodrug nanoassemblies and could trigger the sensitive reduction-responsive release of active drugs. However, the antitumor efficacy of homodimeric prodrug nanoassemblies with single reduction-responsivity may be restricted due to the heterogeneous tumor redox microenvironment. Herein, we replace the middle sulfur atom of trisulfide bond with an oxidizing tellurium atom or selenium atom to construct redox dual-responsive sulfur-tellurium-sulfur and sulfur-selenium-sulfur hybrid chalcogen bonds. The hybrid chalcogen bonds, especially the sulfur-tellurium-sulfur bond, exhibit ultrahigh dual-responsivity to both oxidation and reduction conditions, which could effectively address the heterogeneous tumor microenvironment. Moreover, the hybrid sulfur-tellurium-sulfur bond promotes the self-assembly of homodimeric prodrugs by providing strong intermolecular forces and sufficient steric hindrance. The above advantages of sulfur-tellurium-sulfur bridged homodimeric prodrug nanoassemblies result in the improved antitumor efficacy of docetaxel with satisfactory safety. The exploration of hybrid chalcogen bonds in drug delivery deepened insight into the development of prodrug-based chemotherapy to address tumor redox heterogeneity, thus enriching the design theory of prodrug-based nanomedicines.
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Affiliation(s)
- Tian Liu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Lingxiao Li
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Shuo Wang
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Fudan Dong
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Shiyi Zuo
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Jiaxuan Song
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Xin Wang
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Qi Lu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Helin Wang
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Haotian Zhang
- Department of Pharmacology, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Xiaohong Liu
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Zhonggui He
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China
| | - Bingjun Sun
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China.
| | - Jin Sun
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Shenyang, People's Republic of China.
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15
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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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16
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Li J, Wan H, Zhang H, Wang XL, Liu G, Wu G, He X, Deng Z, Zhao YL. Molecular recognition between bacterial phosphorothioate DNA and sulfur-binding domain (SBD): competition between the water cage and chalcogen-hydrophobic packet. Phys Chem Chem Phys 2022; 24:9176-9187. [PMID: 35383346 DOI: 10.1039/d2cp00291d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial DNA phosphorothioation (PT) physiologically and stereo-specifically replaces a non-bridging oxygen in a phosphate link with a sulfur atom, which can be recognized by a highly conserved sulfur-binding domain (SBD). Here we conducted thermodynamic integration (TI), molecular dynamics simulation, and quantum chemical calculations to decipher the specific molecular interactions between PT-DNA and SBD in Streptomyces coelicolor type IV restriction enzyme ScoMcrA. The TI-calculated binding affinity of (5'-CCGRp-PSGCCGG-3')2 is larger than that of (5'-CCGGCCGG-3')2 by about 7.4-7.7 kcal mol-1. The binding difference dominantly stems from hydration energy of non-phosphorothioate DNA (9.8-10.6 kcal mol-1) in aqueous solution, despite the persistent preference of 2.6-3.2 kcal mol-1 in the DNA-SBD MD simulations. Furthermore, the quantum chemical calculations reveal an unusual non-covalent interaction in the phosphorothioate-binding scenario, where the PS⋯NP165 chalcogen bond prevails the PS⋯HCβ vdW interactions from the adjacent residues H116-R117-Y164-P165-A168. Thus, the chalcogen-hydrophobic interaction pulls PT-DNA into the SBD binding pocket while the water cage pulls a normal DNA molecule out. The synergetic mechanism suggests the special roles of the proline pyrrolidine group in the SBD proteins, consistent with the experimental observations in the X-ray crystallography and structural bioinformatics analysis.
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Affiliation(s)
- Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Haibo Wan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Haoqing Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Xiao-Lei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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17
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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
![]()
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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18
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Carugo O, Resnati G, Metrangolo P. Chalcogen Bonds Involving Selenium in Protein Structures. ACS Chem Biol 2021; 16:1622-1627. [PMID: 34477364 PMCID: PMC8453483 DOI: 10.1021/acschembio.1c00441] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/11/2022]
Abstract
Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18 266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.
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Affiliation(s)
- Oliviero Carugo
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Giuseppe Resnati
- Department
of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| | - Pierangelo Metrangolo
- Department
of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
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19
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study. J Comput Chem 2021; 42:688-698. [PMID: 33543482 PMCID: PMC7986859 DOI: 10.1002/jcc.26489] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/27/2022]
Abstract
We have performed a hierarchical ab initio benchmark and DFT performance study of D2 Ch•••A- chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all-electron relativistically contracted variants of Karlsruhe basis sets (ZORA-def2-SVP, ZORA-def2-TZVPP, ZORA-def2-QZVPP) with and without diffuse functions. The highest-level ZORA-CCSD(T)/ma-ZORA-def2-QZVPP counterpoise-corrected complexation energies (ΔECPC ) are converged within 1.1-3.4 kcal mol-1 and 1.5-3.1 kcal mol-1 with respect to the method and basis set, respectively. Next, we used the ZORA-CCSD(T)/ma-ZORA-def2-QZVPP (ΔECPC ) as reference data for analyzing the performance of 13 different ZORA-relativistic DFT approaches in combination with the Slater-type QZ4P basis set. We find that the three-best performing functionals are M06-2X, B3LYP, and M06, with mean absolute errors (MAE) of 4.1, 4.2, and 4.3 kcal mol-1 , respectively. The MAE for BLYP-D3(BJ) and PBE amount to 8.5 and 9.3 kcal mol-1 , respectively.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Institute for Molecules and MaterialsRadboud University NijmegenNijmegenNetherlands
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20
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de Azevedo Santos L, van der Lubbe SCC, Hamlin TA, Ramalho TC, Matthias Bickelhaupt F. A Quantitative Molecular Orbital Perspective of the Chalcogen Bond. ChemistryOpen 2021; 10:391-401. [PMID: 33594829 PMCID: PMC8015733 DOI: 10.1002/open.202000323] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-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). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.
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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 AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
| | - Stephanie C. C. van der Lubbe
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Teodorico C. Ramalho
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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21
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Tiekink ERT. Zero-, one-, two- and three-dimensional supramolecular architectures sustained by Se …O chalcogen bonding: A crystallographic survey. Coord Chem Rev 2021; 427:213586. [PMID: 33100367 PMCID: PMC7568495 DOI: 10.1016/j.ccr.2020.213586] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
The Cambridge Structural Database was evaluated for crystals containing Se…O chalcogen bonding interactions. These secondary bonding interactions are found to operate independently of complementary intermolecular interactions in about 13% of the structures they can potentially form. This number rises significantly when more specific interactions are considered, e.g. Se…O(carbonyl) interactions occur in 50% of cases where they can potentially form. In about 55% of cases, the supramolecular assemblies sustained by Se…O(oxygen) interactions are one-dimensional architectures, with the next most prominent being zero-dimensional assemblies, at 30%.
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Affiliation(s)
- Edward R T Tiekink
- Research Centre for Crystalline Materials, School of Science and Technology, 5 Jalan Universiti, Sunway University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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22
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Michalczyk M, Malik M, Zierkiewicz W, Scheiner S. Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond. J Phys Chem A 2021; 125:657-668. [PMID: 33423496 DOI: 10.1021/acs.jpca.0c10814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structure of the 5,6-dichloro-2,1,3-benzoselenadiazole homodimer, obtained by adding the ligand, 4,5-dichloro-o-phenylenediamine, to the methanolic solution of SeCl4, was determined by X-ray crystallography, augmented by Fourier transform infrared, Raman, and NMR spectroscopy. The binding motif involves a pair of Se···N chalcogen bonds, with a supplementary N···N pnicogen bond. Quantum calculations provide assessments of the strengths of the individual interactions as well as their contributing factors. All together, these three bonds compose a total interaction energy between 5.4 and 16.8 kcal/mol, with the larger chalcogen atom associated with the strongest interactions. Replacement of the Se atoms by S and Te analogues allows analysis of the dependence of these forces on the nature of the chalcogen atom. Calculations also measure the importance to the binding of the presence of a second N atom on each diazole unit as well as the substituted phenyl ring to which it is fused.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Magdalena Malik
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, Utah 84322-0300, United States
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23
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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24
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Basak T, Gomila RM, Frontera A, Chattopadhyay S. Differentiating intramolecular spodium bonds from coordination bonds in two polynuclear zinc( ii) Schiff base complexes. CrystEngComm 2021. [DOI: 10.1039/d1ce00214g] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two new zinc(ii) complexes have been synthesized and characterized. Theoretical study is devoted to distinguish between conventional coordination bonds and spodium bonds between the zinc and oxygen centers.
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Affiliation(s)
- Tanmoy Basak
- Department of Chemistry
- Inorganic Section
- Jadavpur University
- Kolkata-700032
- India
| | - Rosa M. Gomila
- Serveis Cientificotècnics
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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25
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Kumar P, Frontera A, Pandey SK. Coordination versus spodium bonds in dinuclear Zn( ii) and Cd( ii) complexes with a dithiophosphate ligand. NEW J CHEM 2021. [DOI: 10.1039/d1nj03165a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two new d10-metal dithiophosphate complexes have been synthesized in purely aqueous media and characterized by elemental and spectral analyses. DFT calculations, QTAIM and NCI Plot index methods are preformed to differentiate the coordination and spodium bonds in the complexes.
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Affiliation(s)
- Pretam Kumar
- Post Graduate Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu Tawi-180006, J&K, India
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Sushil K. Pandey
- Post Graduate Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu Tawi-180006, J&K, India
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26
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Gurbanov AV, Kuznetsov ML, Mahmudov KT, Pombeiro AJL, Resnati G. Resonance Assisted Chalcogen Bonding as a New Synthon in the Design of Dyes. Chemistry 2020; 26:14833-14837. [PMID: 32567710 DOI: 10.1002/chem.202002518] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Indexed: 12/31/2022]
Abstract
Intramolecular chalcogen bonding in arylhydrazones of sulfamethizole is strengthened by conjugation in the π-system of a noncovalent five-membered ring. The S⋅⋅⋅O distance in the sulfamethizole moiety of these compounds ranges from 2.698(3) to 2.806(15) Å, which indicates its strong dependence on the attached arylhydrazone fragments. Information on the nature of the intramolecular chalcogen bond was afforded by DFT calculations.
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Affiliation(s)
- Atash V Gurbanov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.,Department of Chemistry, Baku State University, Z. Xalilov Str. 23, Az, 1148, Baku, Azerbaijan
| | - Maxim L Kuznetsov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Kamran T Mahmudov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.,Department of Chemistry, Baku State University, Z. Xalilov Str. 23, Az, 1148, Baku, Azerbaijan
| | - Armando J L Pombeiro
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Giuseppe Resnati
- Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
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27
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Intramolecular Spodium Bonds in Zn(II) Complexes: Insights from Theory and Experiment. Int J Mol Sci 2020; 21:ijms21197091. [PMID: 32993027 PMCID: PMC7582961 DOI: 10.3390/ijms21197091] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/04/2023] Open
Abstract
Two new dinuclear zinc(II) complexes, [Zn2(µ1,3-OAc)(L1)2]I·MeOH (1) and [Zn2(µ1,3-OAc)(L2)(NCS)] (2), (where HL1 = 2-(((3-(dimethylamino)propyl)amino)methyl)-6-methoxy-phenol and H2L2 = 2,2′-[(1-Methyl-1,2-ethanediyl)bis(iminomethylene)]bis[6-ethoxyphenol]) have been synthesized and characterized by elemental and spectral analysis. Their X-ray solid state structures have been determined, revealing the existence of intramolecular Zn···O spodium bonds in both complexes due to the presence of methoxy (1) or ethoxy (2) substituents adjacent to the coordinated phenolic O-atom. These noncovalent interactions have been studied using density functional theory (DFT) calculations, the quantum theory of “atoms-in-molecules” and the noncovalent interaction plot. Moreover, a search in the Cambridge structure database (CSD) has been conducted in order to investigate the prevalence of intramolecular spodium bonds in Zn complexes. To our knowledge this is the first investigation dealing with intramolecular spodium bonds.
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28
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Grabarz A, Michalczyk M, Zierkiewicz W, Scheiner S. Noncovalent Bonds between Tetrel Atoms. Chemphyschem 2020; 21:1934-1944. [DOI: 10.1002/cphc.202000444] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/07/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Anna Grabarz
- Faculty of Chemistry Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan Utah 84322-0300 United States
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29
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Galmés B, Adrover J, Terraneo G, Frontera A, Resnati G. Radicalradical chalcogen bonds: CSD analysis and DFT calculations. Phys Chem Chem Phys 2020; 22:12757-12765. [PMID: 32463046 DOI: 10.1039/d0cp01643h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This manuscript reports a combination of crystallographic analysis (Cambridge Structural Database) and theoretical DFT calculations in chalcogen bonding interactions involving radicals in both the Ch bond (ChB) donor and acceptor. As a radical ChB acceptor (nucleophile) we have used benzodithiazolyl radical (BDTA) and as Ch bond donors (electrophile) we have used dithiadiazolyl and diselenadiazolyl radicals of the general formula p-X-C6F4-CNChChN (Ch = S, and Se). We have evaluated how the para substituent (X) affects the interaction energy, spin density and charge/spin transfer from the electron rich BDTA radical to the electron poor dichalcogenadiazolyl ring. The ability of the latter rings to form ChBs in the solid state has been examined by a comprehensive search in the CSD; several cases are used to exemplify the preferred geometric features of the complexes and they are compared with the theory. The molecular surface electrostatic potentials calculated for these ChB donors allow for a very precise rationalization of the self-assembly motifs most frequently adopted in the crystalline state and of their relative robustness.
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Affiliation(s)
- Bartomeu Galmés
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Jaume Adrover
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Giancarlo Terraneo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy.
| | - Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Giuseppe Resnati
- Laboratory of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy.
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30
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Abstract
A central pnicogen Z atom (Z = Sb, As) is covalently attached to the O atom of three -O(CH2)nX chains where X represents either an aldehyde or amine group. The chain can fold around so that the basic X group can engage in a noncovalent pnicogen bond with the central Z. The formation of up to three pnicogen bonds is energetically favored. The amine appears to engage in stronger pnicogen bonds than does the aldehyde, and bonds to Sb are favored over As, but there is little dependence on the length of the chain. The formation of each successive pnicogen bond reduces the magnitude of the σ-holes surrounding the Z atom, which tends to weaken the attraction for the basic end of the chain.
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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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31
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Navarro-García E, Galmés B, Velasco MD, Frontera A, Caballero A. Anion Recognition by Neutral Chalcogen Bonding Receptors: Experimental and Theoretical Investigations. Chemistry 2020; 26:4706-4713. [PMID: 31957917 DOI: 10.1002/chem.201905786] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/19/2020] [Indexed: 12/14/2022]
Abstract
The utilization of neutral receptors for the molecular recognition of anions based on chalcogen bonding (ChB) is an undeveloped area of host-guest chemistry. In this manuscript, the synthesis of two new families of sulfur, selenium, and tellurium-based ChB binding motifs are reported. The stability of the thiophene, selenophene, and tellurophene binding motifs has enabled the determination of the association constants for ChB halide anion binding in the polar aprotic solvent THF by 1 H, 77 Se, and 125 Te NMR experiments. Two different aromatic cores are used and one or two Ch-binding motifs are incorporated with the purpose of encapsulating the anion, offering up to two concurrent chalcogen bonds. Theoretical calculations and NMR experiments reveal that, for S and Se receptors, hydrogen-bonding interactions involving the acidic H atom adjacent to the chalcogen atom are energetically favored over the ChB interaction. However, for the tellurophene binding motif, the σ-hole interaction is competitive and more favored than the hydrogen bond.
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Affiliation(s)
| | - Bartomeu Galmés
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma, de Mallorca, Spain
| | - María D Velasco
- Departamento de Química Orgánica, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma, de Mallorca, Spain
| | - Antonio Caballero
- Departamento de Química Orgánica, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
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32
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Gomila RM, Frontera A. Charge assisted halogen and pnictogen bonds: insights from the Cambridge Structural Database and DFT calculations. CrystEngComm 2020. [DOI: 10.1039/d0ce00220h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This manuscript combines a search in the Cambridge Structural Database and DFT calculations to analyse the existence and importance of charge assisted pnictogen and halogen bonds in halophosphonium salts.
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Affiliation(s)
- Rosa M. Gomila
- Serveis Cientificotècnics
- University of Balearic Islands
- Palma
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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