On the Importance of σ–Hole Interactions in Crystal Structures

Elements from groups 14–18 and periods 3–6 commonly behave as Lewis acids, which are involved in directional noncovalent interactions (NCI) with electron-rich species (lone pair donors), π systems (aromatic rings, triple and double bonds) as well as nonnucleophilic anions (BF4−, PF6−, ClO4−, etc.). Moreover, elements of groups 15 to 17 are also able to act as Lewis bases (from one to three available lone pairs, respectively), thus presenting a dual character. These emerging NCIs where the main group element behaves as Lewis base, belong to the σ–hole family of interactions. Particularly (i) tetrel bonding for elements belonging to group 14, (ii) pnictogen bonding for group 15, (iii) chalcogen bonding for group 16, (iv) halogen bonding for group 17, and (v) noble gas bondings for group 18. In general, σ–hole interactions exhibit different features when moving along the same group (offering larger and more positive σ–holes) or the same row (presenting a different number of available σ–holes and directionality) of the periodic table. This is illustrated in this review by using several examples retrieved from the Cambridge Structural Database (CSD), especially focused on σ–hole interactions, complemented with molecular electrostatic potential surfaces of model systems.

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Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides

Molecules ◽

10.3390/molecules25153419 ◽

2020 ◽

Vol 25 (15) ◽

pp. 3419 ◽

Cited By ~ 4

Author(s):

Antonio Frontera

Keyword(s):

Crystal Engineering ◽

Lewis Acids ◽

Noncovalent Interactions ◽

Noble Gas ◽

Physical Nature ◽

Short Review ◽

Experimental Investigations ◽

Inorganic Crystal Structure Database ◽

Systematic Nomenclature ◽

Structural Database

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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Can lone pair-π and cation-π interactions coexist? A theoretical study

Open Chemistry ◽

10.2478/s11532-010-0127-7 ◽

2011 ◽

Vol 9 (1) ◽

pp. 25-34 ◽

Cited By ~ 13

Author(s):

Carolina Estarellas ◽

Antonio Frontera ◽

David Quiñonero ◽

Pere Deyà

Keyword(s):

Interaction Potential ◽

Theoretical Study ◽

Noncovalent Interactions ◽

Lone Pair ◽

Geometric Features ◽

Aromatic Rings ◽

Partition Scheme ◽

Π Interactions ◽

Cooperativity Effects ◽

Structural Database

AbstractThe interplay between two important noncovalent interactions involving different aromatic rings is studied by means of ab initio calculations (MP2/6-31++G**) computing the non-additivity energies. In this study we demonstrate the existence of cooperativity effects when cation-π and lone pair-π interactions coexist in the same system. These effects are studied theoretically using energetic and geometric features of the complexes. In addition we use Bader’s theory of atoms-in-molecules and Molecular Interaction Potential with polarization (MIPp) partition scheme to characterize the interactions. Experimental evidence for this combination of interactions has been obtained from the Cambridge Structural Database.

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Strong Tetrel Bonds: Theoretical Aspects and Experimental Evidence

Molecules ◽

10.3390/molecules23102642 ◽

2018 ◽

Vol 23 (10) ◽

pp. 2642 ◽

Cited By ~ 15

Author(s):

Mehdi Esrafili ◽

Parisasadat Mousavian

Keyword(s):

Experimental Evidence ◽

Noncovalent Interactions ◽

Lone Pair ◽

Lewis Base ◽

Orbital Interaction ◽

Bond Interaction ◽

Tetrel Bond ◽

Potential Applications ◽

Bonding Properties ◽

Bonded Complexes

In recent years, noncovalent interactions involving group-14 elements of the periodic table acting as a Lewis acid center (or tetrel-bonding interactions) have attracted considerable attention due to their potential applications in supramolecular chemistry, material science and so on. The aim of the present study is to characterize the geometry, strength and bonding properties of strong tetrel-bond interactions in some charge-assisted tetrel-bonded complexes. Ab initio calculations are performed, and the results are supported by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches. The interaction energies of the anionic tetrel-bonded complexes formed between XF3M molecule (X=F, CN; M=Si, Ge and Sn) and A− anions (A−=F−, Cl−, Br−, CN−, NC− and N3−) vary between −16.35 and −96.30 kcal/mol. The M atom in these complexes is generally characterized by pentavalency, i.e., is hypervalent. Moreover, the QTAIM analysis confirms that the anionic tetrel-bonding interaction in these systems could be classified as a strong interaction with some covalent character. On the other hand, it is found that the tetrel-bond interactions in cationic tetrel-bonded [p-NH3(C6H4)MH3]+···Z and [p-NH3(C6F4)MH3]+···Z complexes (M=Si, Ge, Sn and Z=NH3, NH2CH3, NH2OH and NH2NH2) are characterized by a strong orbital interaction between the filled lone-pair orbital of the Lewis base and empty BD*M-C orbital of the Lewis base. The substitution of the F atoms in the benzene ring provides a strong orbital interaction, and hence improved tetrel-bond interaction. For all charge-assisted tetrel-bonded complexes, it is seen that the formation of tetrel-bond interaction is accompanied bysignificant electron density redistribution over the interacting subunits. Finally, we provide some experimental evidence for the existence of such charge-assisted tetrel-bond interactions in crystalline phase.

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σ-Hole interactions in small-molecule compounds containing divalent sulfur groups R 1—S—R 2

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520620008598 ◽

2020 ◽

Vol 76 (4) ◽

pp. 707-718

Author(s):

Albert S. Lundemba ◽

Dikima D. Bibelayi ◽

Peter A. Wood ◽

Juliette Pradon ◽

Zéphyrin G. Yav

Keyword(s):

Small Molecule ◽

Crystal Engineering ◽

Noncovalent Interactions ◽

Interaction Strength ◽

Lone Pair ◽

Structural Data ◽

Data Bank ◽

Nbo Analysis ◽

Model Systems ◽

Divalent Sulfur

Hydrogen bonds, aromatic stacking contacts and σ-hole interactions are all noncovalent interactions commonly observed in biological systems. Structural data derived from the Protein Data Bank showed that methionine residues can interact with oxygen atoms through directional S...O contacts in the protein core. In the present work, the Cambridge Structural Database (CSD) was used in conjunction with ab initio calculations to explore the σ-hole interaction properties of small-molecule compounds containing divalent sulfur. CSD surveys showed that 7095 structures contained R 1—S—R 2 groups that interact with electronegative atoms like N, O, S and Cl. Frequencies of occurrence and geometries of the interaction were dependent on the nature of R 1 and R 2, and the hybridization of carbon atoms in C,C—S, and C,S—S fragments. The most common interactions in terms of frequency of occurrence were C,C—S...O, C,C—S...N and C,C—S...S with predominance of Csp 2. The strength of the chalcogen interaction increased when enhancing the electron-withdrawing character of the substituents. The most positive electrostatic potentials (V S,max; illustrating positive σ-holes) calculated on R 1—S—R 2 groups were located on the S atom, in the S—R 1 and S—R 2 extensions, and increased with electron-withdrawing R 1 and R 2 substituents like the interaction strength did. As with geometric data derived from the CSD, interaction geometries calculated for some model systems and representative CSD compounds suggested that the interactions were directed in the extensions of S—R 1 and S—R 2 bonds. The values of complexation energies supported attractive interactions between σ-hole bond donors and acceptors, enhanced by dispersion. The interactions of R 1—S—R 2 with large V S,max and nucleophiles with large negative V S,min coherently provided more negative energies. According to NBO analysis, chalcogen interactions consisted of charge transfer from a nucleophile lone pair to an S—R 1 or S—R 2 antibonding orbital. The directional σ-hole interactions at R 1—S—R 2 can be useful in crystal engineering and the area of supramolecular biochemistry.

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Halogen-bond geometry: a crystallographic database investigation of dihalogen complexes

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768103011510 ◽

2003 ◽

Vol 59 (4) ◽

pp. 512-526 ◽

Cited By ~ 102

Author(s):

Carole Ouvrard ◽

Jean-Yves Le Questel ◽

Michel Berthelot ◽

Christian Laurence

Keyword(s):

Solid State ◽

Lewis Acids ◽

Halogen Bond ◽

Lone Pair ◽

Halogen Bonding ◽

Lewis Acidity ◽

Lewis Bases ◽

Significant Relationships ◽

Geometrical Features ◽

Bonded Complexes

X-ray crystal structures of 141 halogen-bonded complexes Y—X...B formed between homo- and heteronuclear dihalogens Cl2, Br2, I2, IBr and ICl with O, S, Se, N, P and As Lewis bases show remarkable and constant geometrical features. The metrics of the halogen bond found in the gas phase for simple complexes [Legon (1999a). Angew Chem. Int. Ed. Eng. 38, 2686–2714] is supported (i) in the solid state, (ii) for new Lewis acids (I2 and IBr), (iii) for new basic centers (Se, As and =N—) and (iv) for more complicated bases. The Y—X...B arrangement is more linear than the corresponding Y—H...B hydrogen bond and the axis of the Y—X molecule lies in the plane of the B lone pair(s), with a preference for the putative lone-pair direction within that plane. However, exceptions to this lone-pair rule are found for sterically hindered thiocarbonyl and selenocarbonyl bases. A bond-order model of the halogen bond correctly predicts the observed correlation between the shortening of the X...B distance and the lengthening, Δd(Y—X), of the Y—X bond. The expectation that the solid-state geometric parameters d(X...B) and Δd(Y—X) reflect the strength of the interaction is supported by their significant relationships with the solution thermodynamic parameters of Lewis acidity and basicity strength, such as the Gibbs energy of 1:1 complexation of Lewis bases with diiodine. This analysis of halogen-bonded complexes in the solid state reinforces the similarities already known to exist between hydrogen and halogen bonding.

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The X40x10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation

10.26434/chemrxiv.5580007.v1 ◽

2017 ◽

Author(s):

Manoj Kumar Kesharwani ◽

Nitai Sylvetsky ◽

Debashree Manna ◽

Jan M.L. Martin

Keyword(s):

Dissociation Energy ◽

Noncovalent Interactions ◽

Halogen Bonding ◽

Coupled Cluster ◽

Dissociation Energies ◽

Iodine Species ◽

Explicitly Correlated ◽

High Level ◽

Cluster Methods ◽

Small Separation

<p>We have re-evaluated the X40x10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)–MP2 “high-level corrections” (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies, and turns out to be more important for noncovalent interactions than is generally realized. As in previous studies, we find that the most efficient way to obtain HLCs is to combine (T) from conventional CCSD(T) calculations with explicitly correlated CCSD-F12–MP2-F12 differences.</p>

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An insight to the noncovalent interactions in two triamine based mononuclear iron(III) Schiff base complexes with special emphasis on the formation of Br•••π halogen bonding

CrystEngComm ◽

10.1039/d0ce01534b ◽

2021 ◽

Author(s):

Shouvik Chattopadhyay ◽

Tanmoy Basak ◽

Antonio Frontera

Keyword(s):

Schiff Base ◽

Solid State ◽

Noncovalent Interactions ◽

Halogen Bonding ◽

Schiff Base Complexes ◽

X Ray ◽

Mononuclear Iron

Two mononuclear iron(III) complexes, [FeL1Cl]∙CH3CN (1) and [FeL2(N3)] (2) {H2L1= N,N′-bis(5-chlorosalicylidene)diethylenetriamine and H2L2= N,N′-bis(5-bromosalicylidene)diethylenetriamine}, have been synthesized and characterized by X-ray crystallographic studies. In the solid state, there are strong...

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The Affinity of Carboplatin to B-Vitamins and Nucleobases

International Journal of Molecular Sciences ◽

10.3390/ijms22073634 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3634

Author(s):

Beata Szefler ◽

Przemysław Czeleń ◽

Przemysław Krawczyk

Keyword(s):

Vitamin B6 ◽

Pyridoxal Phosphate ◽

Antitumor Agents ◽

Lone Pair ◽

Chemical Compounds ◽

Free Energies ◽

Aromatic Rings ◽

Anti Cancer ◽

Potential Impact ◽

Reactive Molecule

Platinum compounds have found wide application in the treatment of various types of cancer and carboplatin is one of the main platinum-based drugs used as antitumor agents. The anticancer activity of carboplatin arises from interacting with DNA and inducing programmed cell death. However, such interactions may occur with other chemical compounds, such as vitamins containing aromatic rings with lone-pair orbitals, which reduces the anti-cancer effect of carboplatin. The most important aspect of the conducted research was related to the evaluation of carboplatin affinity to vitamins from the B group and the potential impact of such interactions on the reduction of therapeutic capabilities of carboplatin in anticancer therapy. Realized computations, including estimation of Gibbs Free Energies, allowed for the identification of the most reactive molecule, namely vitamin B6 (pyridoxal phosphate). In this case, the computational estimations indicating carboplatin reactivity were confirmed by spectrophotometric measurements.

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