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Crystals
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σ- and π-Hole Interactions
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σ- and π-Hole Interactions

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 52004

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Prof. Dr. Antonio Frontera

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Guest Editor
Department de Química, Universitat de les Illes Balears, Palma de Mallorca, 07122 Baleares, Spain
Interests: noncovalent interactions; theoretical chemistry; DFT calculations; σ- and π-hole interactions; crystallography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Noncovalent interactions are very important in many disciplines, especially in crystal growth and crystal engineering. Nowadays, we know, mostly from theoreticians, that the distribution of the electron density around covalently bonded atoms is anisotropic. Therefore, a single atom exhibits areas of higher and lower electron density, where the electrostatic potential can be negative and positive, respectively. Consequently, the positive area (σ- or π-hole) is able to form attractive interactions with any electron-rich site. After the emergence of the halogen bond (HaB), the interest in the similar behaviour of the elements of groups 13–16 and 18 from the periodic table to form analogous attractive interactions with nucleophiles, is growing exponentially. It is now well recognized that HaB and chalcogen bonds (ChB) form supramolecular synthons in their solid state. However, more experimental information is likely needed in order to extend such a statement to the elements of groups, 13, 14, and 15 acting as Lewis acids, and to be able to develop some general heuristic principles.

We invite researchers to contribute to the Special Issue on σ- and π-hole interactions, which is intended to serve as a unique multidisciplinary forum covering all aspects of noncovalent interactions involving π-block elements as electron acceptors in crystalline materials.

The potential topics include, but are not limited to, the following:

  • Synthesis and growth crystals exhibiting σ- and π-hole interactions
  • Crystal engineering based on σ- and π-hole interactions
  • Description, analysis, and theoretical studies of supramolecular assemblies
  • Structure and properties of new materials based on σ- and π-hole interactions

Prof. Dr. Antonio Frontera
Guest Editor

Manuscript Submission Information

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Keywords

  • halogen bonding
  • chalcogen bonding
  • pnicogen bonding
  • tetrel bonding
  • triel bonding
  • σ- and π-hole interactions

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

4 pages, 184 KiB  
Editorial
σ- and π-Hole Interactions
by Antonio Frontera
Crystals 2020, 10(9), 721; https://doi.org/10.3390/cryst10090721 - 19 Aug 2020
Cited by 12 | Viewed by 2103
Abstract
Supramolecular chemistry is a very active research field that was initiated in the last century [...] Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)

Research

Jump to: Editorial, Review

23 pages, 5946 KiB  
Article
N/N Bridge Type and Substituent Effects on Chemical and Crystallographic Properties of Schiff-Base (Salen/Salphen) Niii Complexes
by Cynthia S. Novoa-Ramírez, Areli Silva-Becerril, Fiorella L. Olivera-Venturo, Juan Carlos García-Ramos, Marcos Flores-Alamo and Lena Ruiz-Azuara
Crystals 2020, 10(7), 616; https://doi.org/10.3390/cryst10070616 - 15 Jul 2020
Cited by 11 | Viewed by 6268
Abstract
In total, 13 ligands R-salen (N,N’-bis(5-R-salicylidene)ethylenediamine (where R = MeO, Me, OH, H, Cl, Br, NO2) and R-salphen (N,N’-bis(5-R-salicylidene)-1,2-phenylenediamine (where R = MeO, Me, OH, H, Cl, Br) and their 13 nickel complexes NiRsalen and NiRsalphen were [...] Read more.
In total, 13 ligands R-salen (N,N’-bis(5-R-salicylidene)ethylenediamine (where R = MeO, Me, OH, H, Cl, Br, NO2) and R-salphen (N,N’-bis(5-R-salicylidene)-1,2-phenylenediamine (where R = MeO, Me, OH, H, Cl, Br) and their 13 nickel complexes NiRsalen and NiRsalphen were synthesized and characterized using IR (infrared) spectroscopy, mass spectrometry, elemental analysis, magnetic susceptibility, NMR (nuclear magnetic resonance), UV-vis (ultraviolet-visible) spectroscopy, cyclic voltammetry, and X-ray crystal diffraction. Previous studies have shown that all complexes have presented a square planar geometry in a solid state and as a solution (DMSO). In electrochemical studies, it was observed that in N/N aliphatic bridge complexes, the NiII underwent two redox reactions, which were quasi-reversible process, and the half-wave potential followed a trend depending on the ligand substituent in the 5,5’-R position. The electron-donor substituent—as -OH, and -CH3 decreased the E1/2 potential—favored the reductor ability of nickel. The crystals of the complexes NiMesalen, NiMeOsalen, NiMeOsalphen, and Nisalphen were obtained. It was shown that the crystal packaging corresponded to monoclinic systems in the first three cases, as well as the triclinic for Nisalphen. The Hirshfeld surface analysis showed that the packaging was favored by H∙∙∙H and C∙∙∙H/H∙∙∙C interactions, and C-H∙∙∙O hydrogen bridges when the substituent was -MeO and π-stacking was added to an aromatic bridge. Replacing the N/N bridge with an aromatic ring decreased distortion in square-planar geometry where the angles O-Ni-N formed a perfect square-planar. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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25 pages, 1115 KiB  
Article
Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors
by Seth Yannacone, Marek Freindorf, Yunwen Tao, Wenli Zou and Elfi Kraka
Crystals 2020, 10(7), 556; https://doi.org/10.3390/cryst10070556 - 30 Jun 2020
Cited by 20 | Viewed by 2667
Abstract
11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction [...] Read more.
11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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10 pages, 2198 KiB  
Article
Unexpected Sandwiched-Layer Structure of the Cocrystal Formed by Hexamethylbenzene with 1,3-Diiodotetrafluorobenzene: A Combined Theoretical and Crystallographic Study
by Yu Zhang, Jian-Ge Wang and Weizhou Wang
Crystals 2020, 10(5), 379; https://doi.org/10.3390/cryst10050379 - 7 May 2020
Cited by 5 | Viewed by 2277
Abstract
The cocrystal formed by hexamethylbenzene (HMB) with 1,3-diiodotetrafluorobenzene (1,3-DITFB) was first synthesized and found to have an unexpected sandwiched-layer structure with alternating HMB layers and 1,3-DITFB layers. To better understand the formation of this special structure, all the noncovalent interactions between these molecules [...] Read more.
The cocrystal formed by hexamethylbenzene (HMB) with 1,3-diiodotetrafluorobenzene (1,3-DITFB) was first synthesized and found to have an unexpected sandwiched-layer structure with alternating HMB layers and 1,3-DITFB layers. To better understand the formation of this special structure, all the noncovalent interactions between these molecules in the gas phase and the cocrystal structure have been investigated in detail by using the dispersion-corrected density functional theory calculations. In the cocrystal structure, the theoretically predicted π···π stacking interactions between HMB and the 1,3-DITFB molecules in the gas phase can be clearly seen, whereas there are no π···π stacking interactions between HMB molecules or between 1,3-DITFB molecules. The attractive interactions between HMB molecules in the corrugated HMB layers originate mainly in the dispersion forces. The 1,3-DITFB molecules form a 2D sheet structure via relatively weak C–I···F halogen bonds. The theoretically predicted much stronger C–I···π halogen bonds between HMB and 1,3-DITFB molecules in the gas phase are not found in the cocrystal structure. We concluded that it is the special geometry of 1,3-DITFB that leads to the formation of the sandwiched-layer structure of the cocrystal. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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14 pages, 5746 KiB  
Article
Intramolecular sp2-sp3 Disequalization of Chemically Identical Sulfonamide Nitrogen Atoms: Single Crystal X-Ray Diffraction Characterization, Hirshfeld Surface Analysis and DFT Calculations of N-Substituted Hexahydro-1,3,5-Triazines
by Alexey V. Kletskov, Diego M. Gil, Antonio Frontera, Vladimir P. Zaytsev, Natalia L. Merkulova, Ksenia R. Beltsova, Anna A. Sinelshchikova, Mikhail S. Grigoriev, Mariya V. Grudova and Fedor I. Zubkov
Crystals 2020, 10(5), 369; https://doi.org/10.3390/cryst10050369 - 4 May 2020
Cited by 5 | Viewed by 3571
Abstract
In this manuscript, the synthesis and single crystal X-ray diffraction characterization of four N-substituted 1,3,5-triazinanes are reported along with a detailed analysis of the noncovalent interactions observed in the solid state architecture to these compounds, focusing on C–H···π and C–H···O H-bonding interactions. These [...] Read more.
In this manuscript, the synthesis and single crystal X-ray diffraction characterization of four N-substituted 1,3,5-triazinanes are reported along with a detailed analysis of the noncovalent interactions observed in the solid state architecture to these compounds, focusing on C–H···π and C–H···O H-bonding interactions. These noncovalent contacts have been characterized energetically by using DFT calculations and also by Hirshfeld surface analysis. In addition, the supramolecular assemblies have been characterized using the quantum theory of “atoms-in-molecules” (QTAIM) and molecular electrostatic potential (MEP) calculations. The XRD analysis revealed a never before observed feature of the crystalline structure of some molecules: symmetrically substituted 1,3,5-triazacyclohexanes possess two chemically identical sulfonamide nitrogen atoms in different sp2 and sp3-hybridizations. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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15 pages, 3748 KiB  
Article
Anion–Cation Recognition Pattern, Thermal Stability and DFT-Calculations in the Crystal Structure of H2dap[Cd(HEDTA)(H2O)] Salt (H2dap = H2(N3,N7)-2,6-Diaminopurinium Cation)
by Jeannette Carolina Belmont-Sánchez, Noelia Ruiz-González, Antonio Frontera, Antonio Matilla-Hernández, Alfonso Castiñeiras and Juan Niclós-Gutiérrez
Crystals 2020, 10(4), 304; https://doi.org/10.3390/cryst10040304 - 15 Apr 2020
Cited by 4 | Viewed by 3846
Abstract
The proton transfer between equimolar amounts of [Cd(H2EDTA)(H2O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H2(N3,N7)dap[Cd(HEDTA)(H2O)]·H2O (1) that was studied by single-crystal X-ray diffraction, thermogravimetry, FT-IR spectroscopy, density functional theory [...] Read more.
The proton transfer between equimolar amounts of [Cd(H2EDTA)(H2O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H2(N3,N7)dap[Cd(HEDTA)(H2O)]·H2O (1) that was studied by single-crystal X-ray diffraction, thermogravimetry, FT-IR spectroscopy, density functional theory (DFT) and quantum theory of “atoms-in-molecules” (QTAIM) methods. The crystal was mainly dominated by H-bonds, favored by the observed tautomer of the 2,6-diaminopurinium(1+) cation. Each chelate anion was H-bonded to three neighboring cations; two of them were also connected by a symmetry-related anti-parallel π,π-staking interaction. Our results are in clear contrast with that previously reported for H2(N1,N9)ade [Cu(HEDTA)(H2O)]·2H2O (EGOWIG in Cambridge Structural Database (CSD), Hade = adenine), in which H-bonds and π,π-stacking played relevant roles in the anion–cation interaction and the recognition between two pairs of ions, respectively. Factors contributing in such remarkable differences are discussed on the basis of the additional presence of the exocyclic 2-amino group in 2,6-diaminopurinium(1+) ion. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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Graphical abstract

18 pages, 3237 KiB  
Article
Does Chlorine in CH3Cl Behave as a Genuine Halogen Bond Donor?
by Pradeep R. Varadwaj, Arpita Varadwaj and Helder M. Marques
Crystals 2020, 10(3), 146; https://doi.org/10.3390/cryst10030146 - 26 Feb 2020
Cited by 21 | Viewed by 5766
Abstract
The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base [...] Read more.
The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH2). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H3C–Cl···O=CH2 complex. By examining the nature of the chlorine’s surface in CH3Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH3Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH3Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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16 pages, 2029 KiB  
Article
Regium Bonds between Silver(I) Pyrazolates Dinuclear Complexes and Lewis Bases (N2, OH2, NCH, SH2, NH3, PH3, CO and CNH)
by Ibon Alkorta, Cristina Trujillo, Goar Sánchez-Sanz and José Elguero
Crystals 2020, 10(2), 137; https://doi.org/10.3390/cryst10020137 - 24 Feb 2020
Cited by 16 | Viewed by 3823
Abstract
A theoretical study and Cambridge Structural Database (CSD) search of dinuclear Ag(I) pyrazolates interactions with Lewis bases were carried out and the effect of the substituents and ligands on the structure and on the aromaticity were analyzed. A relationship between the intramolecular Ag–Ag [...] Read more.
A theoretical study and Cambridge Structural Database (CSD) search of dinuclear Ag(I) pyrazolates interactions with Lewis bases were carried out and the effect of the substituents and ligands on the structure and on the aromaticity were analyzed. A relationship between the intramolecular Ag–Ag distance and stability was found in the unsubstituted system, which indicates a destabilization at longer distances compensated by ligands upon complexation. It was also observed that the asymmetrical interaction with phosphines as ligands increases the Ag–Ag distance. This increase is dramatically higher when two simultaneous PH3 ligands are taken into account. The calculated 109Ag chemical shielding shows variation up to 1200 ppm due to the complexation. Calculations showed that six-membered rings possessed non-aromatic character while pyrazole rings do not change their aromatic character significantly upon complexation. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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Review

Jump to: Editorial, Research

24 pages, 17726 KiB  
Review
Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy
by Yi Wang, Xinrui Miao and Wenli Deng
Crystals 2020, 10(11), 1057; https://doi.org/10.3390/cryst10111057 - 20 Nov 2020
Cited by 17 | Viewed by 3661
Abstract
Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) [...] Read more.
Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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Graphical abstract

18 pages, 6431 KiB  
Review
A Survey of Supramolecular Aggregation Based on Main Group Element⋯Selenium Secondary Bonding Interactions—A Survey of the Crystallographic Literature
by Edward R. T. Tiekink
Crystals 2020, 10(6), 503; https://doi.org/10.3390/cryst10060503 - 12 Jun 2020
Cited by 12 | Viewed by 2769
Abstract
The results of a survey of the crystal structures of main group element compounds (M = tin, lead, arsenic, antimony, bismuth, and tellurium) for intermolecular M⋯Se secondary bonding interactions is presented. The identified M⋯Se interactions in 58 crystals can operate independent of conventional [...] Read more.
The results of a survey of the crystal structures of main group element compounds (M = tin, lead, arsenic, antimony, bismuth, and tellurium) for intermolecular M⋯Se secondary bonding interactions is presented. The identified M⋯Se interactions in 58 crystals can operate independent of conventional supramolecular synthons and can sustain zero-, one-, two, and, rarely, three-dimensional supramolecular architectures, which are shown to adopt a wide variety of topologies. The most popular architecture found in the crystals stabilized by M⋯Se interactions are one-dimensional chains, found in 50% of the structures, followed by zero-dimensional (38%). In the majority of structures, the metal center forms a single M⋯Se contact; however, examples having up to three M⋯Se contacts are evident. Up to about 25% of lead(II)-/selenium-containing crystals exhibit Pb⋯Se tetrel bonding, a percentage falling off to about 15% in bismuth analogs (that is, pnictogen bonding) and 10% or lower for the other cited elements. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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29 pages, 5431 KiB  
Review
Not Only Hydrogen Bonds: Other Noncovalent Interactions
by Ibon Alkorta, José Elguero and Antonio Frontera
Crystals 2020, 10(3), 180; https://doi.org/10.3390/cryst10030180 - 6 Mar 2020
Cited by 335 | Viewed by 14035
Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving [...] Read more.
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed. Full article
(This article belongs to the Special Issue σ- and π-Hole Interactions)
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