Close contacts and noncovalent interactions in crystals

Murray, Jane S.; Resnati, Giuseppe; Politzer, Peter

doi:10.1039/c7fd00062f

Cited by 66 publications

(60 citation statements)

References 71 publications

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“…This is consistent with theoretical calculations which show that the region of most positive electrostatic potential opposite to a covalent bond deviates from the extension of the bond to the greatest extent in pnictogen derivatives and to the least extent in tetrel derivatives [134,135]. The greater linearity of TBs may be related to the fact that the electronic asymmetry generated around germanium and tin atoms by the four residues bonded to them is usually smaller than the electronic asymmetry generated around pnictogen and chalcogen atoms by the residues bonded to them and their lone pair(s) [136].…”

Section: Discussionsupporting

confidence: 91%

Close contacts involving germanium and tin in crystal structures: experimental evidence of tetrel bonds

et al. 2018

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Modeling indicates the presence of a region of low electronic density (a Bσ-hole^) on group 14 elements, and this offers an explanation for the ability of these elements to act as electrophilic sites and to form attractive interactions with nucleophiles. While many papers have described theoretical investigations of interactions involving carbon and silicon, such investigations of the heavier group 14 elements are relatively scarce. The purpose of this review is to rectify, to some extent, the current lack of experimental data on interactions formed by germanium and tin with nucleophiles. A survey of crystal structures in the Cambridge Structural Database is reported. This survey reveals that close contacts between Ge or Sn and lone-pair-possessing atoms are quite common, they can be either intra-or intermolecular contacts, and they are usually oriented along the extension of the covalent bond formed by the tetrel with the most electron-withdrawing substituent. Several examples are discussed in which germanium and tin atoms bear four carbon residues or in which halogen, oxygen, sulfur, or nitrogen substituents replace one, two, or three of those carbon residues. These close contacts are assumed to be the result of attractive interactions between the involved atoms and afford experimental evidence of the ability of germanium and tin to act as electrophilic sites, namely tetrel bond (TB) donors. This ability can govern the conformations and the packing of organic derivatives in the solid state. TBs can therefore be considered a promising and robust tool for crystal engineering.

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Section: Discussionsupporting

confidence: 91%

Close contacts involving germanium and tin in crystal structures: experimental evidence of tetrel bonds

et al. 2018

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“…Analogous situations have been found, both computationally and crystallographically, for a number of other four-and five-membered heterocyclic rings [53,54,59,73]. In each case, the negative site is in close contacts with two neighboring atoms of the ring but the interaction is in reality with the strong positive potential located between the extensions of the bonds to these atoms.…”

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confidence: 69%

“…On the other hand, it is not unusual to find that the most positive (or most negative) potential in a molecular region cannot be associated with a particular atom [53,54,59,[73][74][75]. A good example of this is hexafluorothiacyclobutane 5.…”

Section: Van Der Waals Radii and Close Contactsmentioning

confidence: 99%

“…However, this assumes that the interaction can be attributed to those specific atoms. This is indeed very often the case; crystallography shows numerous examples of close contacts that do indicate noncovalent interactions [12,73]. Similarly, in the complexes 4, 7 and 8 the interactions are specifically between the positive σ-hole potentials of the bromine or arsenic and the negative lone pair of the nitrogen, and their separations (3.22 Å in 4, 2.82 Å in 7 and 3.19 Å in 8) are well below the sums of the respective van der Waals radii (3.52 Å for Br-N and 3.54 Å for As-N [70]).…”

Section: Van Der Waals Radii and Close Contactsmentioning

confidence: 99%

“…The ureas, 11, are a good example of this. Instead of each N-H hydrogen having a σ-hole VS,max, as would be expected, there is just a single one approximately midway between them [73,74]. Thus intermolecular interactions, e.g., in their crystal lattices, that have customarily been described as bifurcated hydrogen bonds, 12 [76,77], are more realistically viewed as in 13.…”

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σ-Hole Interactions: Perspectives and Misconceptions

2017

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After a brief discussion of the σ-hole concept and the significance of molecular electrostatic potentials in noncovalent interactions, we draw attention to some common misconceptions that are encountered in that context: (1) Since the electrostatic potential reflects the contributions of both the nuclei and the electrons, it cannot be assumed that negative potentials correspond to "electron-rich" regions and positive potentials to "electron-poor" ones; (2) The electrostatic potential in a given region is determined not only by the electrons and nuclei in that region, but also by those in other portions of the molecule, especially neighboring ones; (3) A σ-hole is a region of lower electronic density on the extension of a covalent bond, not an electrostatic potential; (4) Noncovalent interactions are between positive and negative regions, which are not necessarily associated with specific atoms, so that "close contacts" between atoms do not always indicate the actual interactions.Keywords: σ-holes; noncovalent interactions; electrostatic potential; close contacts A Brief History of the σ-HoleThe σ-hole concept was introduced by Clark in the context of halogen bonding, at a conference in 2005 [1], although it did not appear in the chemical literature until 2007 [2]. Halogen bonding involves a favorable noncovalent interaction between a covalently-bonded halogen and a negative site, such as a lone pair. Such interactions were already known to experimentalists in the 19th century [3,4], and were studied extensively in the 20th [5][6][7][8][9][10], with crystallography playing a major role [10][11][12][13]. Nevertheless the basis for halogen bonding was not really understood. It was frequently rationalized as "charge transfer" from an electron "donor" (e.g., the lone pair) to an "acceptor" (the halogen), invoking the valence bond formalism of Mulliken [14] (which was later put in molecular orbital terms by Flurry [15,16]).However, the halogen is the most electronegative atom in each row of the periodic table, and a singly-bonded halogen atom is generally viewed as being negative in character. So why should it interact attractively with a donor of electronic charge? It was in fact pointed out long ago [7,17] that Mulliken's charge-transfer formalism was not intended to be an elucidation of the bonding in a ground-state noncovalent complex; it was purely a mathematical modeling of the transition of the ground-state complex to a low-lying excited state. The existence of halogen bonding was thus viewed by many as an enigma.The key to resolving the enigma was the molecular electrostatic potential. This is the potential V(r) that is created at any point r in the space of a molecule by its nuclei and electrons, given rigorously by Equation (1):Z A is the charge on nucleus A, located at R A , and ρ(r) is the molecule's electronic density. Regions in which V(r) is positive, indicating the dominance of the nuclear contribution, are attractive to

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Molecular Electrostatic Potentials: Significance and Applications

Politzer

Murray

2021

Chemical Reactivity in Confined Systems

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Close contacts and noncovalent interactions in crystals

Cited by 66 publications

References 71 publications

Close contacts involving germanium and tin in crystal structures: experimental evidence of tetrel bonds

Close contacts involving germanium and tin in crystal structures: experimental evidence of tetrel bonds

σ-Hole Interactions: Perspectives and Misconceptions

Molecular Electrostatic Potentials: Significance and Applications

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