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Ibrahim MA, Mahmoud AM, Shehata MN, Saeed RR, Moussa NA, Sayed SR, Abd El-Rahman MK, Shoeib T. σ-Hole Site-Based Interactions within Hypervalent Pnicogen, Halogen, and Aerogen-Bearing Molecules with Lewis Bases: A Comparative Study. ACS OMEGA 2024; 9:10391-10399. [PMID: 38463322 PMCID: PMC10918780 DOI: 10.1021/acsomega.3c08178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 03/12/2024]
Abstract
σ-Hole site-based interactions in the trigonal bipyramidal geometrical structure of hypervalent pnicogen, halogen, and aerogen-bearing molecules with pyridine and NCH Lewis bases (LBs) were comparatively examined. In this respect, the ZF5···, XF3O2···, and AeF2O3···LB complexes (where Z = As, Sb; X = Br, I; Ae = Kr, Xe; and LB = pyridine and NCH) were investigated. The electrostatic potential (EP) analysis affirmations outlined the occurrence of σ-holes on the systems under consideration with disparate magnitudes that increased according to the following order: AeF2O3 < XF3O2 < ZF5. In line with EP outcomes, the proficiency of σ-hole site-based interactions increased as the atomic size of the central atom increased with a higher favorability for the pyridine-based complexes over NCH-based ones. The interaction energy showed the most favorable negative values of -35.97, -44.53, and -56.06 kcal/mol for the XeF2O3···, IF3O2···, and SbF5···pyridine complexes, respectively. The preferentiality pattern of the studied interactions could be explained as a consequence of (i) the dramatic rearrangement of ZF5 molecules from the trigonal bipyramid geometry to the square pyramidal one, (ii) the significant and tiny deformation energy in the case of the interaction of XF3O2 molecules with pyridine and NCH, respectively, and (iii) the absence of geometrical deformation within the AeF2O3···pyridine and ···NCH complexes other than the XeF2O3···pyridine one. Quantum theory of atoms in molecules and noncovalent interaction index findings reveal the partially covalent nature of most of the investigated interactions. Symmetry-adapted perturbation theory affirmations declared that the electrostatic component was the driving force beyond the occurrence of the considered interactions. The obtained findings will help in improving our understanding of the effect of geometrical deformation on intermolecular interactions.
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Affiliation(s)
- Mahmoud A.A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal,
Westville Campus, Durban 4000, South Africa
| | - Asmaa M.M. Mahmoud
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohammed N.I. Shehata
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Rehab R.A. Saeed
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A.M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Shaban R.M. Sayed
- Department
of Botany and Microbiology, College of Science,
King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed Khaled Abd El-Rahman
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Tamer Shoeib
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
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Ibrahim MAA, Saeed RRA, Shehata MNI, Moussa NAM, Tawfeek AM, Ahmed MN, Abd El-Rahman MK, Shoeib T. Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases. ACS OMEGA 2023; 8:32828-32837. [PMID: 37720791 PMCID: PMC10500585 DOI: 10.1021/acsomega.3c03981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
Abstract
For the first time, sigma (σ)- and lone-pair (lp)-hole site-based interactions of SF4 and SeF4 molecules in seesaw geometry with NH3 and FH Lewis bases were herein comparatively investigated. The obtained findings from the electrostatic potential analysis outlined the emergence of sundry holes on the molecular entity of the SF4 and SeF4 molecules, dubbed the σ- and lp-holes. The energetic viewpoint announced splendid negative binding energy values for σ-hole site-based interactions succeeded by lp-hole analogues, which were found to be -9.21 and -0.50 kcal/mol, respectively, for SeF4···NH3 complex as a case study. Conspicuously, a proper concurrence between the strength of chalcogen σ-hole site-based interactions and the chalcogen's atomic size was obtained, whereas a reverse pattern was proclaimed for the lp-hole counterparts. Further, a higher preference for the YF4···NH3 complexes with elevated negative binding energy was promulgated over the YF4···FH ones, indicating the eminent role of Lewis basicity. The indications of the quantum theory of atoms in molecules generally asserted the closed-shell nature of all the considered interactions. The observation of symmetry-adapted perturbation theory revealed the substantial contributing role of the electrostatic forces beyond the occurrence of σ-hole site-based interactions. In comparison, the dispersion forces were specified to govern the lp-hole counterparts. Such emerging findings would be a gate for the fruitful forthcoming applications of chalcogen bonding interactions in crystal engineering and biological systems.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Rehab R. A. Saeed
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohammed N. I. Shehata
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ahmed M. Tawfeek
- Chemistry
Department, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Mohamed K. Abd El-Rahman
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Tamer Shoeib
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
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Novikov AS, Bolotin DS. Xenon Derivatives as Aerogen Bond-Donating Catalysts for Organic Transformations: A Theoretical Study on the Metaphorical "Spherical Cow in a Vacuum" Provides Insights into Noncovalent Organocatalysis. J Org Chem 2023; 88:1936-1944. [PMID: 35679603 DOI: 10.1021/acs.joc.2c00680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Computations indicate that cationic and noncharged xenon derivatives should exhibit higher catalytic activity than their iodine-based noncovalent organocatalytic congeners. Perfluorophenyl xenonium(II) is expected to demonstrate the best balance between catalytic activity and chemical stability for use in organocatalysis. Comparing its catalytic activity with that of isoelectronic perfluoroiodobenzene indicates that the high catalytic activity of cationic noncovalent organocatalysts is predominantly attributed to the electrostatic interactions with the reaction substrates, which cause the polarization of ligated species during the reaction progress. In contrast, the electron transfer and covalent contributions to the bonding between the catalyst and substrate have negligible effects. The dominant effect of electrostatic interactions results in a strong negative correlation between the calculated Gibbs free energies of activation for the modeled reactions and the highest potentials of the σ-holes on the central atoms of the catalysts. No such correlation is observed for noncharged catalysts.
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Affiliation(s)
- Alexander S Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation.,Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russian Federation
| | - Dmitrii S Bolotin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
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Oliveira BGD. Why much of Chemistry may be indisputably non-bonded? SEMINA: CIÊNCIAS EXATAS E TECNOLÓGICAS 2023. [DOI: 10.5433/1679-0375.2022v43n2p211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In this compendium, the wide scope of all intermolecular interactions ever known has been revisited, in particular giving emphasis the capability of much of the elements of the periodic table to form non-covalent contacts. Either hydrogen bonds, dihydrogen bonds, halogen bonds, pnictogen bonds, chalcogen bonds, triel bonds, tetrel bonds, regium bonds, spodium bonds or even the aerogen bond interactions may be cited. Obviously that experimental techniques have been used in some works, but it was through the theoretical methods that these interactions were validate, wherein the QTAIM integrations and SAPT energy partitions have been useful in this regard. Therefore, the great goal concerns to elucidate the interaction strength and if the intermolecular system shall be total, partial or non-covalently bonded, wherein this last one encompasses the most majority of the intermolecular interactions what leading to affirm that chemistry is debatably non-bonded.
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-Comparison of σ/ π-hole aerogen-bonding interactions based on C 2H 4···NgOX 2 (Ng = Kr, Xe; X = F, Cl, Br) complexes. J Mol Model 2022; 28:339. [PMID: 36190570 DOI: 10.1007/s00894-022-05290-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 10/10/2022]
Abstract
The geometric structure, energy properties, and electronic properties of the aerogen-bonding interaction formed by C2H4 and NgOX2 (Ng = Kr, Xe; X = F, Cl, Br) have been studied at the B2PLYP-D3(BJ)/ aug-cc-pVTZ (PP) level. Two kinds of aerogen-bonding interactions were observed among the title systems: the σ-hole and the π-hole complexes. The σ-hole aerogen-bonding complex has a binding energy in the range of - 6.29 ~ - 8.17 kcal/mol, which is the most stable. The binding energies of C2H4···NgOX2 increased as X = F < Cl < Br and Ng = KrOX2 < XeOX2 for the σ/π-hole aerogen-bonding complexes. The atoms in molecules (AIM), the non-covalent interaction (NCI) index, and the LMO-EDA energy decomposition analysis were adopted to study the nature of the σ/π-hole aerogen-bonding interaction. The results show that the electrostatic term contributes the most to the total interaction energy for the σ/π-hole aerogen-bonding complexes.
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Bhandary S, Pathigoolla A, Madhusudhanan MC, Sureshan KM. Azide–Alkyne Interactions: A Crucial Attractive Force for Their Preorganization for Topochemical Cycloaddition Reaction. Chemistry 2022; 28:e202200820. [DOI: 10.1002/chem.202200820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Subhrajyoti Bhandary
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Atchutarao Pathigoolla
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Mithun C. Madhusudhanan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Kana M. Sureshan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
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Nemec V, Lisac K, Bedeković N, Fotović L, Stilinović V, Cinčić D. Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals. CrystEngComm 2021. [DOI: 10.1039/d1ce00158b] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This highlight presents an overview of the current advances in the preparation of halogen bonded metal–organic multi-component solids, including salts and cocrystals comprising neutral and ionic constituents.
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Affiliation(s)
- Vinko Nemec
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Katarina Lisac
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Nikola Bedeković
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Luka Fotović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Dominik Cinčić
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
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Wang R, Wang Z, Yu X, Li Q. Synergistic and Diminutive Effects between Regium and Aerogen Bonds. Chemphyschem 2020; 21:2426-2431. [PMID: 32889745 DOI: 10.1002/cphc.202000720] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/03/2020] [Indexed: 11/07/2022]
Abstract
The aerogen bond is formed in complexes of HCN-XeF2 O and C2 H4 -XeF2 O. The lone pair on the N atom of HCN is a better electron donor in the aerogen bond than the π electron on the C=C bond of C2 H4 . The coinage substitution strengthens the aerogen bond in MCN-XeF2 O (M=Cu, Ag, and Au) and its enhancing effect becomes larger in the Au<Cu<Ag pattern. The aerogen bond is further enhanced by the regium bond in C2 H2 -MCN-XeF2 O and C2 H4 -MCN-XeF2 O, but is weakened by the regium bond in MCN-C2 H4 -XeF2 O and C2 (CN)4 -MCN-XeF2 O. Simultaneously, the regium bond is also strengthened or weakened in these triads. The synergistic and diminutive effects between regium and aerogen bonds have been explained by means of charge transfer and electrostatic potentials.
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Affiliation(s)
- Ruijing Wang
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Zheng Wang
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Xuefang Yu
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry, and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
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Yang Q, Yao X, Yang X. Influence of N-Base and O-Base Hybridization on Triel Bonds. ACS OMEGA 2020; 5:21300-21308. [PMID: 32875266 PMCID: PMC7450710 DOI: 10.1021/acsomega.0c03394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
The complexes of TrR3 (Tr = B and Al; R = H, F, Cl, and Br) with three N-bases (NH3, CH2NH, and HCN) and three O-bases (CH3OH, H2CO, and CO) are utilized to explore the hybridization effect of N and O atoms on the strength, properties, and nature of the triel bond. The sp-hybridized O and N atoms form the weakest triel bond, followed by the sp2-hybridized O atom or the sp3-hybridized N atom, and the sp3-hybridized O atom or the sp2-hybridized N atom engages in the strongest triel bond. The hybridization effect is also related to the substituent of TrR3. Most complexes are dominated by electrostatic, with increasing polarization contribution from sp to sp2 to sp3. Although the CO oxygen engages in a weaker triel bond, its carbon atom is a better electron donor and the interaction energy even amounts to -37 kcal/mol in the BH3 complex.
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Frontera A. Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides. Molecules 2020; 25:molecules25153419. [PMID: 32731517 PMCID: PMC7435756 DOI: 10.3390/molecules25153419] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Noble gas (or aerogen) bond (NgB) can be outlined as the attractive interaction between an electron-rich atom or group of atoms and any element of Group-18 acting as an electron acceptor. The IUPAC already recommended systematic nomenclature for the interactions of groups 17 and 16 (halogen and chalcogen bonds, respectively). Investigations dealing with noncovalent interactions involving main group elements (acting as Lewis acids) have rapidly grown in recent years. They are becoming acting players in essential fields such as crystal engineering, supramolecular chemistry, and catalysis. For obvious reasons, the works devoted to the study of noncovalent Ng-bonding interactions are significantly less abundant than halogen, chalcogen, pnictogen, and tetrel bonding. Nevertheless, in this short review, relevant theoretical and experimental investigations on noncovalent interactions involving Xenon are emphasized. Several theoretical works have described the physical nature of NgB and their interplay with other noncovalent interactions, which are discussed herein. Moreover, exploring the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD), it is demonstrated that NgB interactions are crucial in governing the X-ray packing of xenon derivatives. Concretely, special attention is given to xenon fluorides and xenon oxides, since they exhibit a strong tendency to establish NgBs.
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Affiliation(s)
- 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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