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García-Santos I, Krümpelmann J, Saa M, Burguera S, Frontera A, Castiñeiras A. Silver(I) Octanuclear Complexes Containing N'-(4-Oxotiazolidin-2-Iliden)picolinohydrazonamide and Nitrate as Bridge Ligands. An Example of Solvatomorphism? Inorg Chem 2024; 63:9221-9236. [PMID: 38713512 PMCID: PMC11110015 DOI: 10.1021/acs.inorgchem.4c00794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
The versatile coordination chemistry of (2Z,N'E)-N'-(4-oxothiazolidin-2-ylidene)picolinohydrazonamide (HAmDHotaz) facilitated the synthesis of new complexes with different silver(I) salts. This paper describes the synthesis and characterization, through elemental analysis and spectroscopic techniques (when solubility permits), of a series of compounds that illustrate the coordinative and structural diversity achievable with the HAmDHotaz ligand. Five silver clusters containing the [Ag8(AmDHotaz)4]4+ nucleus were structurally analyzed by single-crystal X-ray diffraction and were found to exhibit solvomorphism. The compositions of these are [Ag8(AmDHotaz)4(NO3)3(MeOH)(H2O)](NO3)·MeOH·7.5H2O (1), {[Ag8(AmDHotaz)4(NO3)3(H2O)2](NO3)·9.5(H2O)}n (2), {[Ag8(AmDHotaz)4(NO3)3(H2O)2](NO3)·11.5(H2O)}n (2a), {[Ag8(AmDHotaz)4(NO3)2(H2O)2](NO3)(OH)·6H2O}n (3), and {[Ag8(AmDHotaz)4(NO3)2(H2O)](NO3)(OH)·4.5H2O}n (3a). Argentophilic interactions are present in each of the octanuclear structures, where Ag···Ag distances range from 2.828(2) to 2.986(1) Å. These distances are influenced by crystal packing, determined by the counterion and solvent molecules in the structure. In the solvatomorphs, solvent molecules were observed to be disordered. Various hydrogen-bonding interactions, such as N-H···O-N, O-H···O, N-H···O═C, C-H···O-N, and π-π stacking interactions, contribute to the crystal packing. The influence of these weak interactions on the crystal packing was further analyzed using DFT calculations and Bader's theory of atoms-in-molecules, with a focus on argentophilic interactions and Ag···S interactions.
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Affiliation(s)
- Isabel García-Santos
- Department
of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Julia Krümpelmann
- Department
of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Manuel Saa
- Department
of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Sergi Burguera
- Department
de Química, Universitat de les Illes
Balears, Crta. de Valldemossa km 7.5, Palma de Mallorca 07122, Spain
| | - Antonio Frontera
- Department
de Química, Universitat de les Illes
Balears, Crta. de Valldemossa km 7.5, Palma de Mallorca 07122, Spain
| | - Alfonso Castiñeiras
- Department
of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
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2
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Onn CS, Hill AF, Ward JS. Spodium bonding in bis(alkynyl)mecurials. Chem Commun (Camb) 2024; 60:2552-2555. [PMID: 38343202 DOI: 10.1039/d3cc06027f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The new bis(alkynyl)mercurial Hg{CCSeCW(CO)2(Tp*)}2 (Tp* = tris(dimethylpyrazolyl)borate) forms adducts with fluoride and phenathroline, the structures of which are interpreted in the context of two-coordinate mercury presenting a σ-torroid for spodium bonding.
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Affiliation(s)
- Chee S Onn
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, ACT 2601, Australia.
| | - Anthony F Hill
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, ACT 2601, Australia.
| | - Jas S Ward
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, ACT 2601, Australia.
- Department of Chemistry, University of Jyväskylä, FI-40014, Jyväskylä, Finland
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3
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Majumdar D, Frontera A, Roy S, Sutradhar D. Experimental and Theoretical Survey of Intramolecular Spodium Bonds/σ/π-Holes and Noncovalent Interactions in Trinuclear Zn(II)-Salen Type Complex with OCN - Ions: A Holistic View in Crystal Engineering. ACS OMEGA 2024; 9:1786-1797. [PMID: 38222609 PMCID: PMC10785279 DOI: 10.1021/acsomega.3c08422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024]
Abstract
In this work, one new centrosymmetric trinuclear Zn(II) complex 1, [{(OCN)Zn(L)}2Zn], using a salen-type ligand (H2L) in the presence of OCN- was synthesized and characterized via elemental, spectral, SEM-EDX, and single-crystal X-ray diffraction (SCXRD) study. In 1, SCXRD reveals two different stereochemical environments of zinc metal ions; one terminal Zn(II) center adopts square pyramidal geometries with the Addison parameter (τ) 0.095, and the central Zn(II) is tetracoordinated tetrahedral geometry. This article provides evidence of the significance and presence of spodium bonds (SpBs) in solid-state crystal structures involving a pseudotetrahedral environment of the central Zn-atom. X-ray structures reveal intramolecular Zn···O SpBs caused by the methoxy (-OCH3) substituent O-atom adjacent to the coordinated phenoxy O-atom. These noncovalent interactions have been thoroughly studied using density functional theory calculations at the RI-BP86[2]-D3[3]/def2-TZVP level of theory that characterizes the nature of SpBs, including the Baders quantum theory of atoms-in-molecules "QTAIM", molecular electrostatic potential (MEP) surface, and noncovalent index plot (NCI). In addition, a unique complex-isomer-based theoretical model has been vividly employed to estimate the SpBs energy in the complex. Natural bond orbital (NBO) analysis also tries to establish the differentiation between σ-hole and π-hole SpBs' natures more authentically. The complex energy frameworks were used to investigate noncovalent interactions. To better understand the different intermolecular interactions, we conducted a Hirshfeld surface, which revealed N···H (15.4%) and O···H (9.1%) contacts and Zn···O (5.1%) (SpBs).
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Affiliation(s)
- Dhrubajyoti Majumdar
- Department
of Chemistry, Tamralipta Mahavidyalaya, Tamluk, West Bengal 721636, India
| | - Antonio Frontera
- Department
de Quimica, Universitat de les Illes Balears, Cra. de Valldemossa km 7.5, Palma de Mallorca (Baleares) 07122, Spain
| | - Sourav Roy
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bangalore 560012, India
| | - Dipankar Sutradhar
- School
of Advanced Sciences and Languages, VIT
Bhopal University, Kothrikalan, Sehore, Madhya Pradesh 466114, India
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4
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Alizadeh V, Mahmoudi G, Priola E, Kumar Seth S, White JM, Frontera A, Safin DA. Helical coordination complex of Hg(ClO4)2 with bulky hydrazone derivative: a Möbius-like discrete metal chelate. INORG CHEM COMMUN 2023. [DOI: 10.1016/j.inoche.2023.110393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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5
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Yang Q, Wu Q, Zhang X, Yang X, Li Q. Hydrogen and halogen bonds formed by MCO 3 (M = Zn, Cd) and their enhancement by a spodium bond. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Qingqing Yang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Qiaozhuo Wu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Xiaolong Zhang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Xin Yang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
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6
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Gao M, Zhao Q, Yu H, Fu M, Li Q. Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study. Molecules 2022; 27:molecules27092885. [PMID: 35566234 PMCID: PMC9101229 DOI: 10.3390/molecules27092885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023] Open
Abstract
The spodium–π bonding between MX2 (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C2H2/C2H4 acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX2⋯C2F2 complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.
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Affiliation(s)
- Meng Gao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
- Correspondence: (M.G.); (Q.L.)
| | - Qibo Zhao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Hao Yu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Min Fu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
- Correspondence: (M.G.); (Q.L.)
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8
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Sánchez-Férez F, Solans-Monfort X, Calvet T, Font-Bardia M, Pons J. Controlling the Formation of Two Concomitant Polymorphs in Hg(II) Coordination Polymers. Inorg Chem 2022; 61:4965-4979. [PMID: 35298147 PMCID: PMC8965880 DOI: 10.1021/acs.inorgchem.1c03762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Controlling the formation
of the desired product in the appropriate
crystalline form is the fundamental breakthrough of crystal engineering.
On that basis, the preferential formation between polymorphic forms,
which are referred to as different assemblies achieved by changing
the disposition or arrangement of the forming units within the crystalline
structure, is one of the most challenging topics still to be understood.
Herein, we have observed the formation of two concomitant polymorphs
with general formula {[Hg(Pip)2(4,4′-bipy)]·DMF}n (P1A, P1B; Pip = piperonylic acid;
4,4′-bipy = 4,4′-bipyridine). Besides, [Hg(Pip)2(4,4′-bipy)]n (2) has been achieved during the attempts to isolate these polymorphs.
The selective synthesis of P1A and P1B has
been successfully achieved by changing the synthetic conditions. The
formation of each polymorphic form has been ensured by unit cell measurements
and decomposition temperature. The elucidation of their crystal structure
revealed P1A and P1B as polymorphs, which
originates from the Hg(II) cores and intermolecular associations,
especially pinpointed by Hg···π and π···π
interactions. Density functional theory (DFT) calculations suggest
that P1B, which shows Hg(II) geometries that are further
from ideality, is more stable than P1A by 13 kJ·mol–1 per [Hg(Pip)2(4,4′-bipy)]·DMF
formula unit, and this larger stability of P1B arises
mainly from metal···π and π···π
interactions between chains. As a result, these structural modifications
lead to significant variations of their solid-state photoluminescence. We have successfully isolated two concomitant
polymorphs
with formula {[Hg(Pip)2(4,4′-bipy)]·DMF}n (P1A and P1B), as
well as their desolvated form 2. Then, both polymorphs
were selectively synthesized by temperature or anion-template formation.
Their crystal structures revealed distorted pentagonal pyramidal geometries
and show that differences arise from geometry and packing that led
to different solid-state photoluminescence emissions. According to
periodic-DFT calculations, distortions in P1B are counterbalanced
leading to a more stable form by Hg(II)···π and
π···π interactions.
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Affiliation(s)
- Francisco Sánchez-Férez
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Xavier Solans-Monfort
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Teresa Calvet
- Departament de Mineralogia, Petrologia i Geologia Aplicada, Universitat de Barcelona, Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Mercè Font-Bardia
- Unitat de Difracció de Raig-X, Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), Universitat de Barcelona, Solé i Sabarís, 1-3, 08028 Barcelona, Spain
| | - Josefina Pons
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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9
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Spodium bonds and metal–halogen···halogen–metal interactions in propagation of monomeric units to dimeric or polymeric architectures. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Majumdar D, Frontera A, Gomila RM, Das S, Bankura K. Synthesis, spectroscopic findings and crystal engineering of Pb(ii)-Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation. RSC Adv 2022; 12:6352-6363. [PMID: 35424552 PMCID: PMC8982041 DOI: 10.1039/d1ra09346k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), [(Cd)(Pb)(L)(η1-NCS)(η1-SCN)] n (1), using a compartmental Salen ligand (H3L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group P21/c with Z = 4. SCXRD reveals Cd(ii) and Pb(ii) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(ii) is placed in the inner N2O2 and heavier Pb(ii) in the outer O4 compartments of the de-protonated form of the ligand [L]2-. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(ii) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(ii) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.
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Affiliation(s)
- Dhrubajyoti Majumdar
- Department of Chemistry, Tamralipta Mahavidyalaya Tamluk 721636 West Bengal India .,Department of Chemistry, Indian Institute of Technology (Indian School of Mines) Dhanbad Jharkhand 826004 India
| | - A Frontera
- Department de Quimica, Universitat de les Illes Balears Cra. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Rosa M Gomila
- Department de Quimica, Universitat de les Illes Balears Cra. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Sourav Das
- Department of Basic Sciences, Chemistry Discipline, Institute of Infrastructure Technology Research and Management Near Khokhara Circle, Maninagar East Ahmedabad-380026 Gujarat India
| | - Kalipada Bankura
- Department of Chemistry, Tamralipta Mahavidyalaya Tamluk 721636 West Bengal India
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11
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García-Santos I, Castiñeiras A, Mahmoudi G, Babashkina MG, Zangrando E, Gomila RM, Frontera A, Safin DA. Lead(ii) supramolecular structures formed through a cooperative influence of the hydrazinecarbothioamide derived and ancillary ligands. CrystEngComm 2022. [DOI: 10.1039/d1ce01251g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on tetrel bonding and other noncovalent interactions in the lead(ii)-derived complexes with the hydrazinecarbothioamide derived and ancillary ligands, which predominantly drive the formation of extended architectures.
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Affiliation(s)
- Isabel García-Santos
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Alfonso Castiñeiras
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, P.O. Box 55181-83111, Maragheh, Iran
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Rosa M. Gomila
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km. 7.5, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km. 7.5, 07122 Palma de Mallorca, Baleares, Spain
| | - Damir A. Safin
- University of Tyumen, Volodarskogo Str. 6, 625003 Tyumen, Russian Federation
- “Advanced Materials for Industry and Biomedicine” Laboratory, Kurgan State University, Sovetskaya Str. 63/4, 640020 Kurgan, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B. N. Eltsin, Mira Str. 19, Ekaterinburg, 620002, Russian Federation
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Liu N, Li Q. Group 12 Carbonates and their Binary Complexes with Nitrogen Bases and FH 2 Z Molecules (Z=P, As, Sb): Synergism in Forming Ternary Complexes. Chemphyschem 2021; 22:1698-1705. [PMID: 34106509 DOI: 10.1002/cphc.202100348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/03/2021] [Indexed: 11/10/2022]
Abstract
MCO3 (M=Zn, Cd, Hg) forms a spodium bond with nitrogen-containing bases (HCN, NHCH2 , NH3 ) and a pnicogen bond with FH2 Z (Z=P, As, Sb). The spodium bond is very strong with the interaction energy ranging from -31 kcal/mol to -56 kcal/mol. Both NHCH2 and NH3 have an equal electrostatic potential on the N atom, but the corresponding interaction energy is differentiated by 1.5-4 kcal/mol due to the existence of spodium and hydrogen bonds in the complex with NHCH2 as the electron donor. The spodium bond is weakest in the HCN complex, which is not consistent with the change of the binding distance. The spodium bond becomes stronger in the CdCO3 <ZnCO3 <HgCO3 sequence although the positive electrostatic potential on the Hg atom is smallest. This is because the electrostatic interaction is dominant in the spodium-bonded complexes of CdCO3 and ZnCO3 but the polarization interaction in that of HgCO3 . The pnicogen bond is much weaker than the spodium bond and the former has a larger enhancement than the latter in the FH2 Z⋅⋅⋅OCO2 M⋅⋅⋅N-base ternary complexes.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, P. R. China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, P. R. China
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13
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Llull R, Montalbán G, Vidal I, Gomila RM, Bauzá A, Frontera A. Theoretical study of spodium bonding in the active site of three Zn-proteins and several model systems. Phys Chem Chem Phys 2021; 23:16888-16896. [PMID: 34328165 DOI: 10.1039/d1cp02150h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this manuscript, three examples retrieved from the PDB are selected to demonstrate the existence and relevance of spodium bonding (SpB) in biological systems. SpB is defined as an attractive noncovalent interaction between elements of group 12 of the periodic table acting as a Lewis acid and any atom or group of atoms acting as an electron donor. The utilization of this term (SpB) is convenient to differentiate classical coordination bonds from noncovalent interactions. In the latter, the distance between the electron rich and the spodium atoms is longer than the sum of the covalent radii but shorter than the sum of the van der Waals radii. In most Zn-dependent metalloenzymes, the spodium atom is bonded to three imidazole moieties belonging to the side chains of histidine amino-acids. Herein, in addition to the investigation of the SpB in the active site of three exemplifying enzymes, theoretical models where the Zn(ii) atom is bonded either to three imidazole or triazole ligands are used in order to investigate the strength of the SpB and its competition with hydrogen bonding. A series of Lewis bases and anions have been used as SpB acceptors combined with six SpB donors (receptors) of general formula [ZnY3X]+ (Y = imidazole and triazole and X = Cl, N3 and SCH3). In addition to the investigation of the energetic and geometric features of the complexes, the SpB interactions have been further characterized using the natural bond orbital (NBO) method, quantum theory of "atoms-in-molecules" and the noncovalent interaction plot (NCI plot).
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Affiliation(s)
- Rosa Llull
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
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14
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Biswal HS, Kumar Sahu A, Frontera A, Bauzá A. Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. J Chem Inf Model 2021; 61:3945-3954. [PMID: 34375103 PMCID: PMC8525862 DOI: 10.1021/acs.jcim.1c00594] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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15
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Evaluation of the antitumor activity of a series of the pincer-type metallocomplexes produced from isonicotinohydrazide derivative. J Inorg Biochem 2021; 223:111525. [PMID: 34237626 DOI: 10.1016/j.jinorgbio.2021.111525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 01/30/2023]
Abstract
In this work we report on the antitumor properties of a series of pincer-type metallocomplexes [Hg2(HL-keto)Cl4]n (1), [Hg(HL-keto)I2] (2) and [Mn(HL-zwitterion)Cl2]∙MeOH (3∙MeOH), derived from N'-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and corresponding metal salts. The Hg(II) and Mn(II) salts are chelated by the keto (HL-keto) or zwitterionic (HL-zwitterion) form of HL, respectively. The cytotoxic effects of these compounds have been accessed against lung adenocarcinoma (A549) and hepatocellular carcinoma (HepG2 and Huh7) cell lines. Complexes 1 and 2 were found to be most efficient against the cell line Huh7 with IC50 value of 2.56 and 9.90 μM, respectively, while they exhibit moderate activity towards cell lines A549 and HepG2, as evidenced from IC50 values in the range 27.98-56.99 μM. Complex 3∙MeOH is less efficient towards all the three cell lines with relatively high IC50 values. The mechanisms of the metallocomplexes killing the aforementioned cells were elucidated by flow cytometry, colony formation and polymerase chain reaction (PCR) analysis of apoptosis related expression of the genes. The results of the cytotoxic effects and antitumor activity on different cell lines are affected by the metal nature and the presence of the coordinated halide.
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16
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Gomila RM, Bauza A, Mooibroek TJ, Frontera A. π-Hole spodium bonding in tri-coordinated Hg(II) complexes. Dalton Trans 2021; 50:7545-7553. [PMID: 34037019 DOI: 10.1039/d1dt01235e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The important role of π-hole spodium bonding in tri-coordinated planar Hg(ii) complexes is highlighted in this feature article. Selected examples of Hg(ii)X3 structures (X = any atom) illustrate that this noncovalent interaction is relevant as a structural guiding force in crystal structures. For some examples, the interactions have been characterized using the quantum theory of "atoms in molecules" and the noncovalent interaction plot index. Finally, an analysis of the Cambridge structural database revealed that the HgX3 structures are predominantly T-shaped and that they are directional π-hole donors for electron rich atoms.
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Affiliation(s)
- Rosa M Gomila
- Universitat de les Illes Balears, Serveis Científico Tècnics, Crta. de Valldemossa km. 7.5, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Bauza
- Universitat de les Illes Balears, Department of Chemistry, Crta. de Valldemossa km. 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Tiddo J Mooibroek
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park A, 904, E1.26, 1098 XH Amsterdam, Netherlands
| | - Antonio Frontera
- Universitat de les Illes Balears, Department of Chemistry, Crta. de Valldemossa km. 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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17
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Ganguly S, Drew MG, Gomila RM, Frontera A, Ghosh A. Tri- and pentanuclear CuII–CdII complexes of N2O2 donor ligands with the variation of carboxylate coligands: Structural elucidation and theoretical study. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Wysokiński R, Zierkiewicz W, Michalczyk M, Scheiner S. Crystallographic and Theoretical Evidences of Anion⋅⋅⋅Anion Interaction. Chemphyschem 2021; 22:818-821. [PMID: 33719162 DOI: 10.1002/cphc.202100132] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Indexed: 11/10/2022]
Abstract
Planar (HgCl3 )- anions are stacked fairly closely together in a slipped parallel arrangement within several crystal structures. Quantum chemical analysis shows evidence of strong noncovalent spodium bonds between the Hg π-hole of one unit and the Cl atom of an adjacent unit. Anion⋅⋅⋅anion spodium bonds work in tandem with crystal packing forces.
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Affiliation(s)
- Rafał Wysokiński
- 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
| | - Mariusz Michalczyk
- 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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19
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Zierkiewicz W, Michalczyk M, Scheiner S. Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons. Molecules 2021; 26:molecules26061740. [PMID: 33804617 PMCID: PMC8003638 DOI: 10.3390/molecules26061740] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA;
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20
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Gomila RM, Bauzá A, Mooibroek TJ, Frontera A. Spodium bonding in five coordinated Zn(ii): a new player in crystal engineering? CrystEngComm 2021. [DOI: 10.1039/d1ce00221j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This highlight evidences the existence and importance of spodium bonds (SpB) in solid state structures involving five-coordinated square-pyramidal Zn(ii) spodium atom.
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Affiliation(s)
- Rosa M. Gomila
- Universitat de les Illes Balears
- Serveis Científico-Tècnics
- 07122 Palma de Mallorca
- Spain
| | - Antonio Bauzá
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- Netherlands
| | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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21
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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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22
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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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