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On-Surface Molecular Recognition Driven by Chalcogen Bonding
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Letter

On-Surface Molecular Recognition Driven by Chalcogen Bonding
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Cite this: JACS Au 2024, 4, 6, 2115–2121
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https://doi.org/10.1021/jacsau.4c00325
Published June 5, 2024

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Abstract

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Chalcogen bonding interactions (ChBIs) have been widely employed to create ordered noncovalent assemblies in solids and liquids. Yet, their ability to engineer molecular self-assembly on surfaces has not been demonstrated. Here, we report the first demonstration of on-surface molecular recognition solely governed by ChBIs. Scanning tunneling microscopy and ab initio calculations reveal that a pyrenyl derivative can undergo noncovalent chiral dimerization on the Au(111) surface through double Ch···N interactions involving Te- or Se-containing chalcogenazolo pyridine motifs. In contrast, reference chalcogenazole counterparts lacking the pyridyl moiety fail to form regular self-assemblies on Au, resulting in disordered assemblies.

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Introduction

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The manipulation of organic nanostructures on surfaces through the supramolecular approach has garnered substantial attention in recent decades. (1−7) Among the various supramolecular interactions, H-bonding interactions have been extensively harnessed to foster the formation of highly organized two-dimensional (2D) networks. (8−12) This has been followed by examples reporting coordination bonding (13−17) and dipole–dipole (18,19) interactions (Figure 1a–c). More recently, there has been a notable surge of interest in employing secondary bonding interactions (SBIs), (20) which have a dual nature. Notably, from an electrostatic point of view, (21,22) highly polarizable atoms are involved in effective SBIs through regions of depletion of electrons called σ-holes. (23) The second aspect that drives flourishing interest for SBIs relies on the orbital mixing, (24) described as n2(Y) → σ*(E–X) donation involving nonbonding electrons of the electron-rich Y atom, and the antibonding σE–X* on the E atom (with X being its covalent substituent). Within the category of SBIs, halogen bonding interactions (25−29) have demonstrated their efficacy in creating regular supramolecular networks on surfaces, (30,31) as revealed by scanning tunneling microscopy (STM) studies highlighting intermolecular Br···O, (32,33) Br···Br, (34,35) and Br···S (36) halogen bonds (Figure 1d) governing the self-assembly. However, chalcogen bonding interactions (ChBIs) (37) have not yet demonstrated comparable effectiveness on surfaces as they have in crystal engineering (38−42) for developing functional materials, (43) such as supramolecular semiconductors. (44,45) Intermolecular Ch···N ChBs acting as the driving force for self-assembling chalcogenazole derivatives on surfaces, have only been theoretically explored in two recent studies. (46,47) To the best of our knowledge, the role of ChB interactions in driving self-assembly on surfaces remained largely underinvestigated experimentally when compared to hydrogen bonds, (48) metal coordination bonds, (49) and dipole–dipole interactions, (50) with only two reports suggesting the presence of ChB interactions and other noncovalent contacts. (18,51)

Figure 1

Figure 1. Schematic representations of the first examples of noncovalent molecular self-assembly at surfaces, respectively driven by (A) hydrogen bonds, (48) (B) metal coordination bonds, (49) (C) dipole–dipole interactions, (50) (D) halogen bonds, (35) and (E) ChBIs investigated in this work.

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In this Letter, we combined bond-resolved STM (BRSTM) measurements with quantum chemistry calculations to elucidate the first example of ChB-driven molecular self-assembly on Au(111) using tailored recognition motifs that undergo self-assembly solely through ChB interactions. If one excludes the use of cationic heterocycles, one can note that outside a crystalline environment, the formation of such dimers is unprecedented. Indeed, even in solution, conclusive data demonstrating such self-assembly of neutral heterocycles have yet to be reported thus far. (52,53) Building on earlier studies at the solid state, in which we have shown that chalcogenazolo pyridine (CGP) moieties persistently undergo self-assembly into dimers through double Ch···N interactions, (54−59) we conjectured that the Se- and Te-bearing CGP motifs could also be exploited to govern molecular assemblies on surfaces (Figure 1e). (58) With this aim, we designed and prepared pyrene-based CGP modules that could undergo dimerization through ChB-driven molecular recognition. Reference benzochalcogenazole congeners have also been investigated in which a C–H moiety has substituted the N-pyridyl atom and is, thus, not expected to establish any ChBIs (Section S1).

Results

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A constant-current STM image of a Au(111) crystal after room temperature deposition of CGP-Te in vacuum is shown in Figure 2a. Isolated, straight structures with a length of 2.5 ± 0.1 nm, displaying 6-fold rotational symmetry as exemplified by the three white rectangles, are usually found on the face-centered cubic (fcc) regions of the reconstructed Au(111) surface. Given the inherent asymmetry of the molecules on surfaces, two enantiomers for each dimer were found (R and L, inset in Figure 2a) with a relative distribution of around 50% (see Section S4). A close-up view of one of these structures highlights the presence of two bright-contrast spots in the middle region 4.9 ± 0.2 Å from each other (Figure 2b). The simulated STM image (Figure 2c), obtained by density functional theory (DFT) calculations of the adsorbed dimer in its most stable geometry (see below), is in perfect agreement with the experimental images. Thus, it is reasonable to conclude that the observed structure is a dimer (CGP-Te)2, in which the two middle bright-contrast spots correspond to the Te atoms belonging to the CGP-Te moieties. Notably, the two monomers are oriented head-to-head with the Te atoms facing the N-pyridyl atom of the neighboring molecule, supporting the presence of the ChB-driven association. As observed in the STM images of CGP-Se (Figures 2d,e and S5), dimeric (CGP-Se)2 structures are also formed. Dimers are also observed when CGP-Te molecules are deposited on a Ag(110) held at room temperature, which generalizes our findings (Figure S4). On the other hand, when reference benzo-Te molecules are deposited on Au, only irregular aggregate-type species are observed (Figure 2f,g). This confirms our hypothesis that the absence of the N-pyridyl atoms prevents dimer formation since the double ChBIs can no longer be established. Similarly, reference benzo-Se modules do not undergo dimerization; only individual molecules are observed (Figure S2).

Figure 2

Figure 2. (A) STM image of (CGP-Te)2 dimers on Au(111). The herringbone reconstruction of the Au substrate is also visible. In the rectangles, the 3-fold equivalent dimer orientations are highlighted. Tunneling current (It) = 300 pA; tunneling bias (Vt) = 1.000 V; T = 11 K. The top-right-corner inset shows two enantiomers; It = 250 pA; Vt = 0.500 V. (B) Experimental (It = 300 pA; Vt= 0.630 V; T = 11 K) and (C) simulated (Vt = 0.630 V) STM image of an individual dimer. In the simulated image, the chemical structure of the monomer is also overlaid to display the strong Te-centered signal. (D) STM image of self-assembled (CGP-Se)2 dimers on Au(111). It = 300 pA; Vt = 0.800 V; T = 8.5 K. (E) STM image of an individual dimer. It = 150 pA; Vt = 0.100 V; T = 8.5 K. (F) STM image of the reference tellurazole molecules deposited on Au(111). Kinetic aggregates of various shapes and sizes can be observed. It = 400 pA; Vt = 1.000 V; T = 11 K. (G) Detail of a molecular assembly. It = 400 pA; Vt = 1.000 V; T = 11 K. Scale bars: 5 nm in (A), (D), and (F); 0.5 nm in (B), (C), (E), and (G); and 2 nm in the inset of (A).

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To unequivocally disclose the chemical structure of the self-assembled (CGP-Te)2 and (CGP-Se)2 dimers, constant-height STM experiments with a CO-functionalized tip were performed. Figure 3 reports so-called bond-resolved (BR)STM images of the individual dimers and the respective relaxed geometrical model computed by DFT. The pyrene and pyridyl moieties are distinguishable in the experimental images, while a robust electronic signal arises around the Ch atoms. The total length of the dimers can be measured as 2.49 and 2.41 nm for (CGP-Te)2 and (CGP-Se)2, respectively, while their width is 9.0 Å in both cases. DFT geometry optimizations reveal that the two Ch atoms in the dimer lie at on-top positions with respect to the underlying Au lattice and bind to second-nearest-neighbor (second NN) atoms (Figure 3). Indeed, the optimized Te···Te (Se···Se) distance of 4.94 Å (4.82 Å) in the gas-phase dimer matches well with the Au second nn distance of 5.05 Å (Table S1). The calculated Te···Te (Se···Se) distance of 5.01 Å (4.94 Å) in the adsorbed dimer is in notable agreement with the distance measured between the two bright-contrast spots observed in the STM image (Figure 2b,e).

Figure 3

Figure 3. From top to bottom: BRSTM image (constant height, Vt = 5 mV, T = 8.7 K) and DFT relaxed geometrical model of the individual (CGP-Te)2 and (CGP-Se)2 dimers.

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The formation of dimers (or lack thereof) is determined by the interaction energy, ΔEint, between the monomers. In the gas phase, ΔEint is defined as the energy gain in forming the dimer from its constituent fixed-geometry fragments (see Section S10). The computed values (Table S1) indicate exothermic processes of −9.2 and −6.2 kcal mol–1 for CGP-Te and CGP-Se, respectively. The corresponding geometry for (CGP-Te)2 is plotted in Figure 4a, showing alignment of the chalcogenazole rings Te···N distances of 3.0 Å (Table S1). For comparison, the ΔEint value for chalcogenadiazole dimers is about −17 and −7 kcal mol–1 for Te- and Se-containing congeners (Ch···N distances are 2.6 and 2.9 Å), respectively. (59,60) When adsorbed on Au(111), surface strain and relaxation effects must also be considered when computing the ΔEint. A derivation of the on-surface interaction energy is given in Sections S10 and S17. We calculated ΔEint values at −5.7 and −3.9 kcal mol–1 for (CGP-Te)2 and (CGP-Se)2, respectively, suggesting that the dimer formation remains favorable, albeit weaker, also on Au(111). It is worth pointing out that the interaction between CGP-Te or CGP-Se monomers in the dimer is, in fact, still strong enough to allow us to manipulate a dimer with the STM tip without breaking it apart (Figure S3). In contrast, the ΔEint value for dimers of reference benzo-Te is revealed to be +1.1 kcal mol–1 on the surface, consistent with the experimental observation that no dimers are formed. A deeper analysis of ΔEint is given in Section S17.

Figure 4

Figure 4. DFT analysis of ChBIs in a (CGP-Te)2 dimer. (A, B) Gas phase and adsorption geometries (side view). The tilt angle of the chalcogenazole moiety with respect to the pyrene unit is shown. (C, D) Electrostatic potential (in au) superimposed on a charge density isosurface (ρ = 0.025 au). Atomic charges Q are reported for Te and N. (E, F) Molecular graph showing bond paths (dotted lines), bond critical points in red, and ring critical points in green. For clarity, bond paths between the dimer and substrate are not shown, except for Te···Au and N···Au. (G, H) Reduced density gradient (on the 0.5 au isosurface) showing the noncovalent ChBIs; blue and red regions indicate attractive and repulsive interactions, respectively; the dashed circles highlight the attractive interaction at the bond critical point between Te and N atoms.

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DFT was then used to analyze the chemical nature of the ChBIs. Previous theoretical studies elucidating the character of ChBIs in homodimers (24,47,59−62) included molecular electrostatic potential maps, reduced density gradient (RDG) plots, (63) and quantum theory of atoms-in-molecules (AIM) (64) and natural bond order calculations. Moreover, energy decomposition analyses (59,61) reveal that electrostatic effects can contribute significantly (up to 58%) to ΔEint in chalcogenadiazole dimers, while the orbital mixing component can be as large as 41% in telluradiazoles. (62) A favorable ΔEint combined with the electrostatic potential map, RDG, and AIM analyses is sufficient to confirm the presence and the noncovalent nature of ChBIs in these systems. (37,47)
Figure 4c shows the molecular electrostatic potential for CGP-Te superimposed on a charge density isosurface. The blue maxima appearing at the extensions of the Te back-bonds indicate σ-holes. Their alignment with the red minima, corresponding to the N-lone-pairs, is a typical feature in ChBIs. (65) After Au adsorption (Figure 4d), the σ-hole character remains present, although it appears tilted toward the surface (see also Figures 4b and S7) due to the strong Te···Au (and N···Au) interaction. The subsequent misalignment of the σ-hole and N-lone-pair binding the two monomers is consistent with the reduction of the calculated ΔEint after adsorption. The AIM analysis (Figure 4e) reveals bond paths along both Te···N contacts containing bond critical points, constituting evidence of a ChBI. Notably, both features persist in the Au-adsorbed (CGP-Te)2 (Figure 4f) and (CGP-Se)2 (Figure S8) dimers. Finally, RDG plots (Figure 4g) explicitly identify the Te···N interaction as noncovalent. (63) The blue color of the RDG isosurface, centered at the Te···N bond, indicates that the Te···N interaction is attractive, as expected from the sign of ΔEint. The Te···N interaction persists in the adsorbed system (Figure 4h), although the less intense color indicates a weaker contact. The interaction appears weaker again in (CGP-Se)2 dimers (Figure S8), consistent with an expected smaller orbital contribution. (62) These conclusions are further supported by calculations of the charge density difference (Figure S9) and molecular projected density of states (Figure S13). In contrast, similar analyses for Benzo-Te reveal a fundamentally different, weaker interaction (Figure S10 and Table S2).
The total energy and charge density analyses support our hypothesis that the ChBIs govern the surface-confined dimerization of the pyrenyl derivatives and confirm the STM results. This occurs despite a considerable dimer···Au interaction which determines the adsorption site, flattened molecular geometry, and azimuthal orientation (Figure S6). Although a large van der Waals component anchors the molecule to the surface, a Te···Au bond is identifiable (Figures S7 and S9). The total charge transfer from (CGP-Te)2 to the Au(111) surface is 0.36e, mainly coming from the Te atom (ΔQTe = +0.08e, see Figure 4b). Such an increase might naively imply a larger electrostatic interaction after adsorption. However, the computed reduction in interaction energy suggests that the charge depletion is associated with the Te lone pair aligned toward the Au surface. It thus has little influence on the in-plane intermolecular ChBI.

Conclusions

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In conclusion, our study comprehensively explores nanostructure self-assembly on surfaces guided by ChBI molecular recognition. Specifically, we utilized chalcogenazolo pyridine (with Ch = Se and Te) moieties to create supramolecular chiral dimers through double ChBIs on Au(111). The combination of BRSTM measurements and quantum chemistry calculations clarified the formation of these dimers, characterized by distinct 6-fold rotational symmetry and upheld by nonbonding interactions between Ch atoms and adjacent pyridine moieties. On-surface ChBI was also demonstrated on other substrates (Figure S4) and for other moieties (Figure S10). (46,47) In contrast, reference chalcogenazole compounds lacking the N-pyridyl atom and thus incapable of establishing ChBIs do not form dimers but assemble into irregularly shaped kinetic aggregates. Charge density analysis of the (CGP-Te)2 dimer confirmed the attractive noncovalent nature of Te···N interactions, which persist when assembled on Au(111). The distinctive feature of ChBIs, characterized by their strong orbital contribution, leads us to anticipate that our findings will pave the way for designing and fabricating precise supramolecular nanostructures on surfaces with tailored semiconducting properties. (41) Ultimately, this study not only expands our comprehension of supramolecular interactions but also sheds light on a promising avenue for future research in the bottom-up engineering of two-dimensional (2D) monolayered supramolecular chalcogenide-type materials as we delve into the novel role of ChBIs in surface-based molecular recognition.

Methods

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Synthesis

The syntheses of CGP-Te, CGP-Se, and Benzo-Te were performed following previous literature reports. (54,56) For details on the protocols and structural characterization, please see the Supporting Information.

Surface Studies

All molecules studied here were sublimated in ultrahigh vacuum from a commercial evaporator (Kentax) onto an Au(111) single crystal that was previously cleaned following standard Ar+ sputter/anneal cleaning cycles. During sublimation, the Au(111) substrate was held at room temperature, with the pressure in the chamber being below 2 × 10–10 mbar. All STM measurements were performed using a commercial Infinity system from Scienta Omicron held at temperatures between 11 and 8 K (the exact temperature is specified in the text for each reported STM image). The STM images were calibrated so that the measured Au lattice constant would coincide with the one from the simulation after geometry optimization (lattice constant: 4.122 Å). A CO-functionalized W tip was used for BRSTM. BRSTM images were collected in constant height mode with a low tunneling bias (5 mV). All experimental images were analyzed using the Gwyddion software. (66)
Surface studies Calculations were performed using DFT in a planewave/pseudopotential framework implemented in the quantum-ESPRESSO (QE) code. (67) The Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional was used, (68) and van der Waals interactions were accounted for semiempirically via the Grimme-D3 method with Becke-Johnson damping. (69) Ultrasoft Rappe-Rabe-Joannopoulos-Kaxiras (RRJK) pseudopotentials were used (cutoff 45/360 Ry). Gas phase geometries were computed in a 45 × 35 × 25 Å3 cell. The optimal monomer geometry was determined by rotating the pyrene group about the bond to the azole unit until an energy minimum was reached and then free relaxation was performed. The substrate was modeled using a four-layer Au(111) slab (a0 = 4.12 Å), whose backmost two layers were fied. Monomer and dimer adsorption were modeled within supercells of size 46.6 Å × 20.2 Å, ensuring an intermolecular separation of at least 12 Å and a vacuum spacing between periodically repeating images of 20 Å. Gamma-point sampling with a Marzari-Vanderbilt smearing of 0.1 eV was used throughout. (70) Geometry optimizations were performed using a tight 5 meV Å–1 threshold. Several initial geometries for monomer adsorption were tested. The most stable geometry features the chalcogen atom at the on-top site. By testing the azimuthal energy dependence, we identified the optimal orientation of having the pyrene groups aligned along the Au atom rows. This configuration was then used to construct possible geometries for the dimer, including chalcogen atoms at the nearest and second nearest neighbor sites and for different lateral offsets and azimuthal orientations. The most stable geometries are the ones reported in the main text. The RDG (71) and electrostatic maps were also computed using QE. Analysis of atomic charges and quantum theory of AIM paths were performed with the critic2 code (72) using all-electron charge densities computed with the QE package. RDG and molecular electrostatic potential (MEP) maps were visualized using VESTA. (9) The MEP maps are plotted on a relatively high value of charge density isosurface (ρ = 0.025 au; Figure S5 for a comparison with the standard plot at ρ = 0.001 au) to reveal the σ-holes also in the dimer and the adsorbed systems. RDG isosurfaces are colorized using the product of the charge density and sign of the second eigenvalue of the electron density Hessian matrix in the range [−0.02:0.02] au. (73) STM images were computed using the Tersoff-Hamann approximation. (74) Atomic charges were computed using the Voronoi deformation density (VDD) method. (75)

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacsau.4c00325.

  • Experimental details and additional data (PDF)

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Author Information

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  • Corresponding Authors
  • Authors
    • Deborah Romito - Department of Organic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria;  Orcidhttps://orcid.org/0000-0003-2820-9896
    • Luca Persichetti - Department of Physics, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy;  Orcidhttps://orcid.org/0000-0001-6578-254X
    • Antonio Caporale - Department of Physics, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy
    • Maurizia Palummo - INFN, Department of Physics, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, 00133 Roma, Italy;  Orcidhttps://orcid.org/0000-0002-3097-8523
    • Marco Di Giovannantonio - CNR-Istituto di Struttura della Materia (CNR-ISM), 00133 Roma, Italy;  Orcidhttps://orcid.org/0000-0001-8658-9183
  • Author Contributions

    L.C., C.H., and D.R. contributed equally.

  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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D.B. gratefully acknowledges the EU through the funding scheme projects MSCA-RISE INFUSION (N° 734834), H2020-NMBP-2017 DECOCHROM (N° 760973), MSCA-RISE VIT (N° 101008237), and the University of Vienna. C.H. and M.P. acknowledge CINECA for supercomputing resources and support under the ISCRA initiative. L.C., M.D.G., L.P., and C.H. acknowledge financial support from the Italian Ministry of University and Research (MUR) under the PRIN 2022 program (project No. 2022JW8LHZ, ATYPICAL).

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    Chemical Society Reviews (2020), 49 (7), 2020-2038CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. Two-dimensional (2D) nanomaterials, such as graphene and single layer covalent org. frameworks (sCOFs) are being widely studied due to their unusual structure/property relationships. sCOFs typically feature at. thickness, intrinsic nanoscale porosity and a cryst. lattice. Compared to other org. 2D materials, sCOFs exhibit major advantages including topol. designation and constitutional tunability. This review describes the state of the art of surface-confined sCOFs, emphasizing reticular design, synthesis approaches, and key challenges related to improving quality and exploring applications.
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    Ariga, K.; Yamauchi, Y. Nanoarchitectonics from atom to life. Chem. Asian J. 2020, 15 (6), 718– 728,  DOI: 10.1002/asia.202000106
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    Ariga, K.; Jia, X.; Song, J.; Hill, J. P.; Leong, D. T.; Jia, Y.; Li, J. Nanoarchitectonics beyond self-assembly: challenges to create bio-like hierarchic organization. Angew. Chem., Int. Ed. 2020, 59 (36), 15424– 15446,  DOI: 10.1002/anie.202000802
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    Nanoarchitectonics beyond Self-Assembly: Challenges to Create Bio-Like Hierarchic Organization
    Ariga, Katsuhiko; Jia, Xiaofang; Song, Jingwen; Hill, Jonathan P.; Leong, David Tai; Jia, Yi; Li, Junbai
    Angewandte Chemie, International Edition (2020), 59 (36), 15424-15446CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. Incorporation of non-equil. actions in the sequence of self-assembly processes would be an effective means to establish bio-like high functionality hierarchical assemblies. As a novel methodol. beyond self-assembly, nanoarchitectonics, which has as its aim the fabrication of functional materials systems from nanoscopic units through the methodol. fusion of nanotechnol. with other scientific disciplines including org. synthesis, supramol. chem., microfabrication, and bio-process, has been applied to this strategy. The application of non-equil. factors to conventional self-assembly processes is discussed on the basis of examples of directed assembly, Langmuir-Blodgett assembly, and layer-by-layer assembly. In particular, examples of the fabrication of hierarchical functional structures using bio-active components such as proteins or by the combination of bio-components and two-dimensional nanomaterials, are described. Methodologies described in this review article highlight possible approaches using the nanoarchitectonics concept beyond self-assembly for creation of bio-like higher functionalities and hierarchical structural organization.
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    Bai, L.; Wang, N.; Li, Y. Controlled Growth and Self-Assembly of Multiscale Organic Semiconductor. Adv. Mater. 2022, 34 (22), 2102811,  DOI: 10.1002/adma.202270168
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    Zhang, S.; Chen, C.; Li, J.; Ma, C.; Li, X.; Ma, W.; Zhang, M.; Cheng, F.; Deng, K.; Zeng, Q. The self-assembly and pyridine regulation of a hydrogen-bonded dimeric building block formed by a low-symmetric aromatic carboxylic acid. Nanoscale 2022, 14 (6), 2419– 2426,  DOI: 10.1039/D1NR07840B
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    Barragán, A.; Lois, S.; Sarasola, A.; Vitali, L. Empowering non-covalent hydrogen, halogen, and [S-N] 2 bonds in synergistic molecular assemblies on Au (111). Nanoscale 2022, 14 (48), 17895– 17899,  DOI: 10.1039/D2NR05984C
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    Lei, P.; Luo, W.; Tu, B.; Xiao, X.; Fang, Q.; Wang, C.; Zeng, Q. Minor adjustments in the chemical structures of pyridine derivatives induced different co-assemblies by O-H··· N hydrogen bonds. Chem. Commun. 2022, 58 (71), 9914– 9917,  DOI: 10.1039/D2CC03859E
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    Tao, J.; Xiao, Y.; Sun, L.; Liu, J.; Zeng, Q.; Xu, H. Synthesis, optical properties and self-assemblies of three novel asymmetrical perylene diimides modified with functional hydrogen bonding groups at bay positions. New J. Chem. 2022, 46 (36), 17235– 17243,  DOI: 10.1039/D2NJ03624J
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    Xie, R.; Zeng, X.; Jiang, Z.-H.; Hu, Y.; Lee, S.-L. STM Study of the Self-Assembly of Biphenyl-3, 3′, 5, 5′-Tetracarboxylic Acid and Its Mixing Behavior with Coronene at the Liquid-Solid Interface. Langmuir 2023, 39 (10), 3637– 3644,  DOI: 10.1021/acs.langmuir.2c03199
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    Vijayaraghavan, S.; Ecija, D.; Auwärter, W.; Joshi, S.; Seufert, K.; Drach, M.; Nieckarz, D.; Szabelski, P.; Aurisicchio, C.; Bonifazi, D. Supramolecular Assembly of Interfacial Nanoporous Networks with Simultaneous Expression of Metal-Organic and Organic-Bonding Motifs. Chem. Eur. J. 2013, 19 (42), 14143– 14150,  DOI: 10.1002/chem.201301852
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    Sun, Q.; Cai, L.; Ma, H.; Yuan, C.; Xu, W. On-surface construction of a metal-organic Sierpiński triangle. Chem. Commun. 2015, 51 (75), 14164– 14166,  DOI: 10.1039/C5CC05554G
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    On-surface construction of a metal-organic Sierpi´nski triangle
    Sun, Qiang; Cai, Liangliang; Ma, Honghong; Yuan, Chunxue; Xu, Wei
    Chemical Communications (Cambridge, United Kingdom) (2015), 51 (75), 14164-14166CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    Through a careful design of the mol. precursor the authors have successfully constructed the metal-org. Sierpi´nski triangles on Au(111) via on-surface coordination chem., which is demonstrated by the interplay of high-resoln. STM imaging and DFT calcns. The coordination Sierpi´nski triangles show high stabilities as evidenced by room temp. STM imaging, and could withstand a thermal treatment up to 450 K.
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    Geng, Y.-f.; Li, P.; Li, J.-z.; Zhang, X.-m.; Zeng, Q.-d.; Wang, C. STM probing the supramolecular coordination chemistry on solid surface: Structure, dynamic, and reactivity. Coord. Chem. Rev. 2017, 337, 145– 177,  DOI: 10.1016/j.ccr.2017.01.014
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    STM probing the supramolecular coordination chemistry on solid surface: Structure, dynamic, and reactivity
    Geng, Yan-fang; Li, Ping; Li, Ji-zhen; Zhang, Xue-mei; Zeng, Qing-dao; Wang, Chen
    Coordination Chemistry Reviews (2017), 337 (), 145-177CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
    A review. Supramol. coordination chem. is currently a very popular topic in metalorg. chem. and has a very large impact on a broad field of applications. More importantly, the invention of STM has opened new doorways to study these concepts on surfaces. This review summarizes the recent progress on surface-confined metallosupramol. engineering based on the supramol. coordination chem., with the aid of STM. At the beginning, a discussion of metalloids, alkali metals, and alk. earth metal-based metallosupramol. engineering is conducted. Next, transition metal-based coordination chem. on surfaces is discussed. Then, polygonal, double- and triple-decker structures based on rare-earth-metal coordination chem. are presented. Based on these supramol. structures, the dynamics of coordination as well as the formed supramols. are discussed. In the end, the coordination chem., including stability of coordination bonds, org. mols., and gas mol. adsorption is described. Throughout this review, the coordination structures, dynamics and reactivity were emphasized, which are important current and future research themes.
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    Sun, X.; Yao, X.; Lafolet, F. d. r.; Lemercier, G.; Lacroix, J.-C. One-Dimensional Double Wires and Two-Dimensional Mobile Grids: Cobalt/Bipyridine Coordination Networks at the Solid/Liquid Interface. J. Phys. Chem. Lett. 2019, 10 (15), 4164– 4169,  DOI: 10.1021/acs.jpclett.9b01292
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    16
    One-Dimensional Double Wires and Two-Dimensional Mobile Grids: Cobalt/Bipyridine Coordination Networks at the Solid/Liquid Interface
    Sun, Xiaonan; Yao, Xinlei; Lafolet, Frederic; Lemercier, Gilles; Lacroix, Jean-Christophe
    Journal of Physical Chemistry Letters (2019), 10 (15), 4164-4169CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
    Various architectures have been generated and obsd. by STM at a solid/liq. interface resulting from an in situ chem. reaction between the bipyridine terminal groups of a ditopic ligand and Co(II) ions. Large monodomains of one-dimensional (1D) double wires are formed by Co(II)/ligand coordination, with polymer lengths as long as 150 nm. The polymers are organized as parallel wires 8 nm apart, and the voids between wires are occupied by solvent mols. Two-dimensional (2D) grids, showing high surface mobility, coexist with the wires. The wires are formed from linear chain motifs where each cobalt center is bonded to two bipyridines. 2D grids are generated from a bifurcation node where one cobalt bonds to three bipyridines. Surface reconstruction of the grids and of the 1D wires was obsd. under the STM tip. As an exciting result, anal. of these movements strongly indicates surface reactions at the solid/liq. interface.
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    Moreno, D.; Santos, J.; Parreiras, S. O.; Martín-Fuentes, C.; Lauwaet, K.; Urgel, J. I.; Miranda, R.; Martín, N.; Gallego, J. M.; Écija, D. Stoichiometry-Directed Two-Level Hierarchical Growth of Lanthanide-Based Supramolecular Nanoarchitectures. Chem. Eur. J. 2023, 29, e202300461  DOI: 10.1002/chem.202300461
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    Stöhr, M.; Boz, S.; Schär, M.; Nguyen, M. T.; Pignedoli, C. A.; Passerone, D.; Schweizer, W. B.; Thilgen, C.; Jung, T. A.; Diederich, F. Self-Assembly and Two-Dimensional Spontaneous Resolution of Cyano-Functionalized [7] Helicenes on Cu (111). Angew. Chem., Int. Ed. 2011, 50 (42), 9982– 9986,  DOI: 10.1002/anie.201102627
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    Politzer, P.; Murray, J. S.; Clark, T. Halogen bonding and other σ-hole interactions: A perspective. Phys. Chem. Chem. Phys. 2013, 15 (27), 11178– 11189,  DOI: 10.1039/c3cp00054k
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    Halogen bonding and other σ-hole interactions: a perspective
    Politzer, Peter; Murray, Jane S.; Clark, Timothy
    Physical Chemistry Chemical Physics (2013), 15 (27), 11178-11189CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    A review. A σ-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV-VII and a neg. site, e.g. a lone pair of a Lewis base or an anion. It involves a region of pos. electrostatic potential, labeled a σ-hole, on the extension of one of the covalent bonds to the atom. The σ-hole is due to the anisotropy of the atom's charge distribution. Halogen bonding is a subset of σ-hole interactions. Their features and properties can be fully explained in terms of electrostatics and polarization plus dispersion. The strengths of the interactions generally correlate well with the magnitudes of the pos. and neg. electrostatic potentials of the σ-hole and the neg. site. In certain instances, however, polarizabilities must be taken into account explicitly, as the polarization of the neg. site reaches a level that can be viewed as a degree of dative sharing (coordinate covalence). In the gas phase, σ-hole interactions with neutral bases are often thermodynamically unfavorable due to the relatively large entropy loss upon complex formation.
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    Lim, J. Y.; Beer, P. D. Sigma-hole interactions in anion recognition. Chem. 2018, 4 (4), 731– 783,  DOI: 10.1016/j.chempr.2018.02.022
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    Sigma-Hole Interactions in Anion Recognition
    Lim, Jason Y. C.; Beer, Paul D.
    Chem (2018), 4 (4), 731-783CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)
    A review. Sigma (σ)-holes are electron-deficient regions that arise from the anisotropic distribution of electron d. on the atom of group 14 (tetrels), 15 (pnictogens), 16 (chalcogens), and 17 (halogens) elements when covalently bonded to electron-withdrawing groups. Named after the donor atom's group, the σ-hole interactions, halogen bonding, and chalcogen bonding with anionic species have found ground-breaking applications in anion supramol. chem. within the last decade. In this review, we feature key recent discoveries and advances across the whole range of σ-hole interactions for anion recognition, from the familiar halogen bonding to the almost unknown pnictogen and tetrel bonding. In particular, the novel anion recognition properties and applications that result from the unique aspects of each σ-hole interaction, together with detailed design considerations of anion-binding receptor motifs, are highlighted.
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    Mallada, B.; Gallardo, A.; Lamanec, M.; De La Torre, B.; Špirko, V.; Hobza, P.; Jelinek, P. Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy. Science 2021, 374 (6569), 863– 867,  DOI: 10.1126/science.abk1479
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    23
    Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy
    Mallada, B.; Gallardo, A.; Lamanec, M.; de la Torre, B.; Spirko, V.; Hobza, P.; Jelinek, P.
    Science (Washington, DC, United States) (2021), 374 (6569), 863-867CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
    An anisotropic charge distribution on individual atoms, such as σ-holes, may strongly affect the material and structural properties of systems. However, the spatial resoln. of such anisotropic charge distributions on an atom represents a long-standing exptl. challenge. In particular, the existence of the σ-hole on halogen atoms has been demonstrated only indirectly through the detn. of the crystal structures of org. mols. contg. halogens or with theor. calcns., consequently calling for its direct exptl. visualization. We show that Kelvin probe force microscopy with a properly functionalized probe can image the anisotropic charge of the σ-hole and the quadrupolar charge of a carbon monoxide mol. This opens a new way to characterize biol. and chem. systems in which anisotropic at. charges play a decisive role.
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    Pascoe, D. J.; Ling, K. B.; Cockroft, S. L. The origin of chalcogen-bonding interactions. J. Am. Chem. Soc. 2017, 139 (42), 15160– 15167,  DOI: 10.1021/jacs.7b08511
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    The Origin of Chalcogen-Bonding Interactions
    Pascoe, Dominic J.; Ling, Kenneth B.; Cockroft, Scott L.
    Journal of the American Chemical Society (2017), 139 (42), 15160-15167CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Favorable mol. interactions between group 16 elements have been implicated in catalysis, biol. processes, and materials and medicinal chem. Such interactions have since become known as chalcogen bonds by analogy to hydrogen and halogen bonds. Although the prevalence and applications of chalcogen-bonding interactions continues to develop, debate still surrounds the energetic significance and physicochem. origins of this class of σ-hole interaction. Here, synthetic mol. balances were used to perform a quant. exptl. investigation of chalcogen-bonding interactions. Over 160 exptl. conformational free energies were measured in 13 different solvents to examine the energetics of O···S, O···Se, S···S, O···HC, and S···HC contacts and the assocd. substituent and solvent effects. The strongest chalcogen-bonding interactions were found to be at least as strong as conventional H-bonds, but unlike H-bonds, surprisingly independent of the solvent. The independence of the conformational free energies on solvent polarity, polarizability, and H-bonding characteristics showed that electrostatic, solvophobic, and van der Waals dispersion forces did not account for the obsd. exptl. trends. Instead, a quant. relationship between the exptl. conformational free energies and computed MO energies was consistent with the chalcogen-bonding interactions being dominated by n → σ* orbital delocalization between a lone pair (n) of a (thio)amide donor and the antibonding σ* orbital of an acceptor thiophene or selenophene. Interestingly, stabilization was manifested through the same acceptor MO irresp. of whether a direct chalcogen···chalcogen or chalcogen···H-C contact was made. Our results underline the importance of often-overlooked orbital delocalization effects in conformational control and mol. recognition phenomena.
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    Teyssandier, J.; Mali, K. S.; De Feyter, S. Halogen bonding in two-dimensional crystal engineering. ChemistryOpen 2020, 9 (2), 225– 241,  DOI: 10.1002/open.201900337
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    Halogen Bonding in Two-Dimensional Crystal Engineering
    Teyssandier, Joan; Mali, Kunal S.; De Feyter, Steven
    ChemistryOpen (2020), 9 (2), 225-241CODEN: CHOPCK; ISSN:2191-1363. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. Halogen bonds, which provide an intermol. interaction with moderate strength and high directionality, have emerged as a promising tool in the repertoire of non-covalent interactions. In this review, we provide a survey of the literature where halogen bonding was used for the fabrication of supramol. networks on solid surfaces. The definitions of, and the distinction between halogen bonding and halogen-halogen interactions are provided. Self-assembled networks formed at the soln./solid interface and at the vacuum-solid interface, stabilized in part by halogen bonding, are discussed. Besides the broad classification based on the interface at which the systems are studied, the systems are categorized further as those sustained by halogen-halogen and halogen-heteroatom contacts.
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    Kampes, R.; Zechel, S.; Hager, M. D.; Schubert, U. S. Halogen bonding in polymer science: towards new smart materials. Chem. Sci. 2021, 12 (27), 9275– 9286,  DOI: 10.1039/D1SC02608A
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    Halogen bonding in polymer science: towards new smart materials
    Kampes, Robin; Zechel, Stefan; Hager, Martin D.; Schubert, Ulrich S.
    Chemical Science (2021), 12 (27), 9275-9286CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
    A review. The halogen bond is a special non-covalent interaction, which can represent a powerful tool in supramol. chem. Although the halogen bond offers several advantages compared to the related hydrogen bond, it is currently still underrepresented in polymer science. The structural related hydrogen bonding assumes a leading position in polymer materials contg. supramol. interactions, clearly indicating the high potential of using halogen bonding for the design of polymeric materials. The current developments regarding halogen bonding contg. polymers include self-assembly, photo-responsive materials, self-healing materials and others. These aspects are highlighted in the present perspective. Furthermore, a perspective on the future of this rising young research field is provided.
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    Metrangolo, P.; Canil, L.; Abate, A.; Terraneo, G.; Cavallo, G. Halogen bonding in perovskite solar cells: a new tool for improving solar energy conversion. Angew. Chem., Int. Ed. 2022, 61 (11), e202114793  DOI: 10.1002/anie.202114793
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    Halogen Bonding in Perovskite Solar Cells: A New Tool for Improving Solar Energy Conversion
    Metrangolo, Pierangelo; Canil, Laura; Abate, Antonio; Terraneo, Giancarlo; Cavallo, Gabriella
    Angewandte Chemie, International Edition (2022), 61 (11), e202114793CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. Hybrid org.-inorg. halide perovskites (HOIHPs) have recently emerged as a flourishing area of research. Their easy and low-cost prodn. and their unique optoelectronic properties make them promising materials for many applications. In particular, HOIHPs hold great potential for next-generation solar cells. However, their practical implementation is still hindered by their poor stability in air and moisture, which is responsible for their short lifetime. Optimizing the chem. compn. of materials and exploiting non-covalent interactions for interfacial and defects engineering, as well as defect passivation, are efficient routes towards enhancing the overall efficiency and stability of perovskite solar cells (PSCs). Due to the rich halogen chem. of HOIHPs, exploiting halogen bonding, in particular, may pave the way towards the development of highly stable PSCs. Improved crystn. and stability, redn. of the surface trap states, and the possibility of forming ordered structures have already been preliminarily demonstrated.
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    Xu, Y.; Hao, A.; Xing, P. X··· X Halogen Bond-Induced Supramolecular Helices. Angew. Chem., Int. Ed. 2022, 61 (2), e202113786  DOI: 10.1002/anie.202113786
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    Semenov, A. V.; Baykov, S. V.; Soldatova, N. S.; Geyl, K. K.; Ivanov, D. M.; Frontera, A.; Boyarskiy, V. P.; Postnikov, P. S.; Kukushkin, V. Y. Noncovalent Chelation by Halogen Bonding in the Design of Metal-Containing Arrays: Assembly of Double σ-Hole Donating Halolium with CuI-Containing O, O-Donors. Inorg. Chem. 2023, 62 (15), 6128– 6137,  DOI: 10.1021/acs.inorgchem.3c00229
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    Wang, D.; Wang, Z.; Liu, W.; Arramel; Zhong, S.; Feng, Y. P.; Loh, K. P.; Wee, A. T. S. Real-Space Investigation of the Multiple Halogen Bonds by Ultrahigh-Resolution Scanning Probe Microscopy. Small 2022, 18 (28), 2202368,  DOI: 10.1002/smll.202202368
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    Peyrot, D.; Silly, F. Toward Two-Dimensional Tessellation through Halogen Bonding between Molecules and On-Surface-Synthesized Covalent Multimers. Int. J. Mol. Sci. 2023, 24 (14), 11291,  DOI: 10.3390/ijms241411291
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    Piquero-Zulaica, I.; Lobo-Checa, J.; Sadeghi, A.; El-Fattah, Z. M. A.; Mitsui, C.; Okamoto, T.; Pawlak, R.; Meier, T.; Arnau, A.; Ortega, J. E. Precise engineering of quantum dot array coupling through their barrier widths. Nat. Commun. 2017, 8 (1), 787,  DOI: 10.1038/s41467-017-00872-2
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    Precise engineering of quantum dot array coupling through their barrier widths
    Piquero-Zulaica Ignacio; Arnau Andres; Ortega J Enrique; Lobo-Checa Jorge; Lobo-Checa Jorge; Sadeghi Ali; El-Fattah Zakaria M Abd; Mitsui Chikahiko; Okamoto Toshihiro; Takeya Jun; Okamoto Toshihiro; Kawai Shigeki; Pawlak Remy; Meier Tobias; Goedecker Stefan; Meyer Ernst; Kawai Shigeki; Arnau Andres; Ortega J Enrique; Arnau Andres; Ortega J Enrique; Kawai Shigeki
    Nature communications (2017), 8 (1), 787 ISSN:.
    Quantum dots are known to confine electrons within their structure. Whenever they periodically aggregate into arrays and cooperative interactions arise, novel quantum properties suitable for technological applications show up. Control over the potential barriers existing between neighboring quantum dots is therefore essential to alter their mutual crosstalk. Here we show that precise engineering of the barrier width can be experimentally achieved on surfaces by a single atom substitution in a haloaromatic compound, which in turn tunes the confinement properties through the degree of quantum dot intercoupling. We achieved this by generating self-assembled molecular nanoporous networks that confine the two-dimensional electron gas present at the surface. Indeed, these extended arrays form up on bulk surface and thin silver films alike, maintaining their overall interdot coupling. These findings pave the way to reach full control over two-dimensional electron gases by means of self-assembled molecular networks.Arrays of quantum dots can exhibit a variety of quantum properties, being sensitive to their spacing. Here, the authors fine tune interdot coupling using hexagonal molecular networks in which the dots are separated by single or double haloaromatic compounds, structurally identical but for a single atom.
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    Lawrence, J.; Sosso, G. C.; Đorđević, L.; Pinfold, H.; Bonifazi, D.; Costantini, G. Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding. Nat. Commun. 2020, 11 (1), 2103,  DOI: 10.1038/s41467-020-15898-2
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    Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding
    Lawrence, James; Sosso, Gabriele C.; Djordjevic, Luka; Pinfold, Harry; Bonifazi, Davide; Costantini, Giovanni
    Nature Communications (2020), 11 (1), 2103CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
    Scanning tunnelling microscopy (STM) is commonly used to identify on-surface mol. self-assembled structures. However, its limited ability to reveal only the overall shape of mols. and their relative positions is not always enough to fully solve a supramol. structure. Here, we analyze the assembly of a brominated polycyclic arom. mol. on Au(111) and demonstrate that std. STM measurements cannot conclusively establish the nature of the intermol. interactions. By performing high-resoln. STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, detg. that halogen bonding governs the assemblies. This is supported by d. functional theory calcns. that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron d. topol. anal. that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramol. structures, and we predict its increasing use in mol. nanoscience at surfaces.
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    Pham, T. A.; Song, F.; Nguyen, M.-T.; Stöhr, M. Self-assembly of pyrene derivatives on Au (111): substituent effects on intermolecular interactions. Chem. Commun. 2014, 50 (91), 14089– 14092,  DOI: 10.1039/C4CC02753A
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    Gutzler, R.; Ivasenko, O.; Fu, C.; Brusso, J. L.; Rosei, F.; Perepichka, D. F. Halogen bonds as stabilizing interactions in a chiral self-assembled molecular monolayer. Chem. Commun. 2011, 47 (33), 9453– 9455,  DOI: 10.1039/c1cc13114a
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    Xing, L.; Jiang, W.; Huang, Z.; Liu, J.; Song, H.; Zhao, W.; Dai, J.; Zhu, H.; Wang, Z.; Weiss, P. S. Steering two-dimensional porous networks with σ-hole interactions of Br··· S and Br··· Br. Chem. Mater. 2019, 31 (8), 3041– 3048,  DOI: 10.1021/acs.chemmater.9b01126
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    Aakeroy, C. B.; Bryce, D. L.; Desiraju, G. R.; Frontera, A.; Legon, A. C.; Nicotra, F.; Rissanen, K.; Scheiner, S.; Terraneo, G.; Metrangolo, P. Definition of the chalcogen bond (IUPAC Recommendations 2019). Pure Appl. Chem. 2019, 91 (11), 1889– 1892,  DOI: 10.1515/pac-2018-0713
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    Definition of the chalcogen bond (IUPAC Recommendations 2019)
    Aakeroy, Christer B.; Bryce, David L.; Desiraju, Gautam R.; Frontera, Antonio; Legon, Anthony C.; Nicotra, Francesco; Rissanen, Kari; Scheiner, Steve; Terraneo, Giancarlo; Metrangolo, Pierangelo; Resnati, Giuseppe
    Pure and Applied Chemistry (2019), 91 (11), 1889-1892CODEN: PACHAS; ISSN:0033-4545. (Walter de Gruyter, Inc.)
    This recommendation proposes a definition for the term "chalcogen bond"; it is recommended the term is used to designate the specific subset of inter- and intramol. interactions formed by chalcogen atoms wherein the Group 16 element is the electrophilic site.
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    Biot, N.; Bonifazi, D. Chalcogen-bond driven molecular recognition at work. Coord. Chem. Rev. 2020, 413, 213243,  DOI: 10.1016/j.ccr.2020.213243
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    Chalcogen-bond driven molecular recognition at work
    Biot, Nicolas; Bonifazi, Davide
    Coordination Chemistry Reviews (2020), 413 (), 213243CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
    A review. Out of the supramol. toolbox, Secondary Bonding Interactions (SBIs) have attracted in the last decades the attention of the chem. community as novel non-covalent interactions of choice for a large no. of chem. systems. Amongst all SBIs, halogen-bonding (XBIs) and chalcogen-bonding (EBIs) interactions are certainly the most important. However, the use of EBIs have received marginal consideration if compared to that of XBIs. By sieving the most significant examples, this review focuses on the theor. and exptl. studies carried out with EBIs in functional systems. In a systematic way the reader is guided through the most recent and representative examples in which chemists have rationally designed mol. modules that, through EBIs, trigger the initiation of chem. reactions, mol. recognition events in solns. and at the solid state to produce self-assembled and self-organised functional materials at different length scales. The study and understanding of the fundamental geometrical and phys. parameters ruling EBIs is at its infancy, and it still needs to establish those principles to rationally design and program synthons that, undergoing mol. recognition through EBIs, allow the development of new tailored materials for applications in the field of optoelectronic, sensing, catalysis, and drug discovery.
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    De Silva, V.; Magueres, P. L.; Averkiev, B. B.; Aakeröy, C. B. Competition between chalcogen and halogen bonding assessed through isostructural species. Acta Crystallogr., Sect. C: Struct. Chem. 2022, 78 (12), 716– 721,  DOI: 10.1107/S205322962201052X
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    Torubaev, Y. V.; Rozhkov, A. V.; Skabitsky, I. V.; Gomila, R. M.; Frontera, A.; Kukushkin, V. Y. Heterovalent chalcogen bonding: supramolecular assembly driven by the occurrence of a tellurium (ii)··· Ch (i)(Ch= S, Se, Te) linkage. Inorg. Chem. Front. 2022, 9 (21), 5635– 5644,  DOI: 10.1039/D2QI01420C
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    Ishigaki, Y.; Asai, K.; Jacquot de Rouville, H. P.; Shimajiri, T.; Hu, J.; Heitz, V.; Suzuki, T. Solid-State Assembly by Chelating Chalcogen Bonding in Quinodimethane Tetraesters Fused with a Chalcogenadiazole. ChemPlusChem. 2022, 87 (4), e202200075  DOI: 10.1002/cplu.202200075
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    Romito, D.; Ho, P. C.; Vargas-Baca, I.; Bonifazi, D. Supramolecular Chemistry via Chalcogen Bonding Interactions. In Chalcogen Chemistry: Fundamentals and Applications; The Royal Society of Chemistry, 2023; pp 494– 528.
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    Ho, P. C.; Wang, J. Z.; Meloni, F.; Vargas-Baca, I. Chalcogen bonding in materials chemistry. Coord. Chem. Rev. 2020, 422, 213464,  DOI: 10.1016/j.ccr.2020.213464
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    Chalcogen bonding in materials chemistry
    Ho, Peter C.; Wang, Jin Z.; Meloni, Francesca; Vargas-Baca, Ignacio
    Coordination Chemistry Reviews (2020), 422 (), 213464CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
    A review. This review examines recent literature in search for evidence of the influence that chalcogen bonding has on the structure and properties of functional materials. Key examples from research on charge transfer salts, neutral heterocyclic free radicals, and paramagnetic coordination compds. are highlighted as intermol. interactions are crit. to properties such as cond. and magnetic response. Other cases reviewed include the influence of chalcogen bonding on optical properties such as the electronic absorption spectra and the nonlinear optical response of non-centrosym. crystal structures. There is also evidence that this type of interaction between mols. translates into macroscopic mech. properties such as the bulk modulus.
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    Romito, D.; Fresta, E.; Cavinato, L. M.; Kählig, H.; Amenitsch, H.; Caputo, L.; Chen, Y.; Samorì, P.; Charlier, J. C.; Costa, R. D.; Bonifazi, D. Supramolecular Chalcogen-Bonded Semiconducting Nanoribbons at Work in Lighting Devices. Angew. Chem., Int. Ed. 2022, 61 (38), e202202137  DOI: 10.1002/anie.202202137
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    Cameron, J.; Kanibolotsky, A. L.; Skabara, P. J. Lest we Forget-the Importance of Heteroatom Interactions in Heterocyclic Conjugated Systems, from Synthetic Metals to Organic Semiconductors. Adv. Mater. 2024, 36, 2302259,  DOI: 10.1002/adma.202302259
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    Ren, B.; Lu, Y.; Wang, R.; Liu, H. First-principles study of chalcogen-bonded self-assembly structures on silicene: Some insight into the fabrication of molecular architectures on surfaces through chalcogen bonding. Chem. Phys. 2023, 565, 111763,  DOI: 10.1016/j.chemphys.2022.111763
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    Selective assembly on a surface of supramolecular aggregates with controlled size and shape
    Yokoyanna, Takashi; Yokoyama, Shilyoshi; Kamikado, Tashiya; Okuno, Yoshishige; Mashiko, Shinro
    Nature (London, United Kingdom) (2001), 413 (6856), 619-621CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    The realization of mol.-based miniature devices with advanced functions requires the development of new and efficient approaches for combining mol. building blocks into desired functional structures, ideally with these structures supported on suitable substrates. Supramol. aggregation occurs spontaneously and can lead to controlled structures if selective and directional noncovalent interactions are exploited. But such selective supramol. assembly has yielded almost exclusively crystals or dissolved structures; the self-assembly of adsorbed mols. into larger structures, in contrast, has not yet been directed by controlling selective intermol. interactions. Here the authors report the formation of surface-supported supramol. structures whose size and aggregation pattern are rationally controlled by tuning the noncovalent interactions between individual adsorbed mols. Using low-temp. scanning tunnelling microscopy, substituted porphyrin mols. adsorbed on a Au surface form monomers, trimers, tetramers or extended wire-like structures. Each structure corresponds in a predictable fashion to the geometric and chem. nature of the porphyrin substituents that mediate the interactions between individual adsorbed mols. Findings suggest that careful placement of functional groups that are able to participate in directed non-covalent interactions will allow the rational design and construction of a wide range of supramol. architectures adsorbed to surfaces.
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    Wu, T.; Xue, N.; Wang, Z.; Li, J.; Li, Y.; Huang, W.; Shen, Q.; Hou, S.; Wang, Y. Surface self-assembly involving the interaction between S and N atoms. Chem. Commun. 2021, 57, 1328– 1331,  DOI: 10.1039/D0CC07931F
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    Cozzolino, A. F.; Dimopoulos-Italiano, G.; Lee, L. M.; Vargas-Baca, I. Chalcogen-Nitrogen Secondary Bonding Interactions in the Gas Phase - Spectrometric Detection of Ionized Benzo-2,1,3-telluradiazole Dimers. Eur. J. Inorg. Chem. 2013, 2013, 2751– 2756,  DOI: 10.1002/ejic.201201439
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    Risto, M.; Reed, R. W.; Robertson, C. M.; Oilunkaniemi, R.; Laitinen, R. S.; Oakley, R. T. Self-association of the N-methyl benzotellurodiazolylium cation: implications for the generation of super-heavy atom radicals. Chem. Commun. 2008, 3278– 3280,  DOI: 10.1039/b803159b
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    Self-association of the N-methyl benzotellurodiazolylium cation: implications for the generation of super-heavy atom radicals
    Risto, Maarit; Reed, Robert W.; Robertson, Craig M.; Oilunkaniemi, Raija; Laitinen, Risto S.; Oakley, Richard T.
    Chemical Communications (Cambridge, United Kingdom) (2008), (28), 3278-3280CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    The N-Me benzotellurodiazolylium cation self-assocs. in the solid state via short (2.471(3) Å) 4-center Te···N' intermol. contacts; electrochem. data and the results of DFT calcns. suggest that the dimers persist in soln.
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    Biot, N.; Bonifazi, D. Programming Recognition Arrays through Double Chalcogen-Bonding Interactions. Chem. Eur. J. 2018, 24 (21), 5439– 5443,  DOI: 10.1002/chem.201705428
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    Programming Recognition Arrays through Double Chalcogen-Bonding Interactions
    Biot, Nicolas; Bonifazi, Davide
    Chemistry - A European Journal (2018), 24 (21), 5439-5443CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    In this work, we have programmed and synthesized a recognition motif constructed around a chalcogenazolo-pyridine scaffold (CGP) that, through the formation of frontal double chalcogen-bonding interactions, assocs. into dimeric EX-type complexes. The reliability of the double chalcogen-bonding interaction has been shown at the solid-state by X-ray anal., depicting the strongest recognition persistence for a Te-congener. The high recognition fidelity, chem. and thermal stability and easy derivatization at the 2-position makes CGP a convenient motif for constructing supramol. architectures through programmed chalcogen-bonding interactions.
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    Romito, D.; Biot, N.; Babudri, F.; Bonifazi, D. Non-covalent bridging of bithiophenes through chalcogen bonding grips. New J. Chem. 2020, 44 (17), 6732– 6738,  DOI: 10.1039/C9NJ06202E
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    Biot, N.; Bonifazi, D. Concurring Chalcogen-and Halogen-Bonding Interactions in Supramolecular Polymers for Crystal Engineering Applications. Chem. Eur. J. 2020, 26 (13), 2904– 2913,  DOI: 10.1002/chem.201904762
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    Romito, D.; Bonifazi, D. Engineering Te-Containing Recognition Modules for Chalcogen Bonding: Towards Supramolecular Polymeric Materials. Helv. Chim. Acta 2023, 106 (2), e202200159  DOI: 10.1002/hlca.202200159
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    Chivers, T.; Laitinen, R. S. Tellurium: a maverick among the chalcogens. Chem. Soc. Rev. 2015, 44 (7), 1725– 1739,  DOI: 10.1039/C4CS00434E
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    Tellurium: a maverick among the chalcogens
    Chivers, Tristram; Laitinen, Risto S.
    Chemical Society Reviews (2015), 44 (7), 1725-1739CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    The scant attention paid to tellurium in both inorg. and org. chem. textbooks may reflect, in part, the very low natural abundance of the element. Such treatments commonly imply that the structures and reactivities of tellurium compds. can be extrapolated from the behavior of their lighter chalcogen analogs (sulfur and selenium). In fact, recent findings and well-established observations clearly illustrate that this assumption is not valid. The emerging importance of the unique properties of tellurium compds. is apparent from the variety of their known and potential applications in both inorg. and org. chem., as well as materials science. With ref. to selected contemporary examples, this Tutorial Review examines the fundamental concepts that are essential for an understanding of the unique features of tellurium chem. with an emphasis on hypervalency, three-center bonding, secondary bonding interactions, σ and π-bond energies (multiply bonded compds.), and Lewis acid behavior.
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    Michalczyk, M.; Malik, M.; Zierkiewicz, W.; Scheiner, S. Experimental and theoretical studies of dimers stabilized by two chalcogen bonds in the presence of a N··· N pnicogen bond. J. Phys. Chem. A 2021, 125 (2), 657– 668,  DOI: 10.1021/acs.jpca.0c10814
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    Scheiner, S. Principles guiding the square bonding motif containing a pair of chalcogen bonds between chalcogenadiazoles. J. Phys. Chem. A 2022, 126 (7), 1194– 1203,  DOI: 10.1021/acs.jpca.1c10818
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    Tsuzuki, S.; Sato, N. Origin of Attraction in Chalgogen-Nitrogen Interaction of 1, 2, 5-Chalcogenadiazole Dimers. J. Phys. Chem. B 2013, 117 (22), 6849– 6855,  DOI: 10.1021/jp403200j
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    Origin of Attraction in Chalcogen-Nitrogen Interaction of 1,2,5-Chalcogenadiazole Dimers
    Tsuzuki, Seiji; Sato, Naoki
    Journal of Physical Chemistry B (2013), 117 (22), 6849-6855CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    Intermol. interaction in the 1,2,5-chalcogenadiazole dimers was studied by ab initio MO calcns. Estd. CCSD(T) interaction energies for the thia-, selena- and tellura-diazole dimers are -3.14, -5.29, and -12.42 kcal/mol, resp. The electrostatic and dispersion interactions are the major sources of the attraction in the dimers, although it was claimed that the orbital mixing (charge-transfer interaction) was the most prominent contribution to the stabilization. The induction (induced polarization) interaction also contributes largely to the attraction in the telluradiazole dimer. The large electrostatic and induction interactions are responsible for the strong attraction in the telluradiazole dimer. The short-range (orbital-orbital) interaction (sum of the exchange-repulsion and charge-transfer interactions) is repulsive. The directionality of the interactions increases in order of S < Se < Te. The electrostatic interaction is mainly responsible for the directionality. The strong directionality suggests that the chalcogen-nitrogen interaction plays important roles in controlling the orientation of mols. in those org. crystals. The nature of the chalcogen-nitrogen interaction in the chalcogenadiazole dimers is similar to that of the halogen bond, which is an electrostatically driven noncovalent interaction.
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    Haberhauer, G.; Gleiter, R. The Nature of Strong Chalcogen Bonds Involving Chalcogen-Containing Heterocycles. Angew. Chem., Int. Ed. 2020, 59 (47), 21236– 21243,  DOI: 10.1002/anie.202010309
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    The Nature of Strong Chalcogen Bonds Involving Chalcogen-Containing Heterocycles
    Haberhauer, Gebhard; Gleiter, Rolf
    Angewandte Chemie, International Edition (2020), 59 (47), 21236-21243CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Chalcogen bonds are σ hole interactions and have been used in recent years as an alternative to hydrogen bonds. In general, the electrostatic potential at the chalcogen atom and orbital delocalization effects are made responsible for the orientation of the chalcogen bond. Here, we were able to show by means of SAPT calcns. that neither the induction (orbital delocalization effects) nor the electrostatic term is causing the spatial orientation of strong chalcogen bonds in tellurium-contg. aroms. Instead, steric interactions (Pauli repulsion) are responsible for the orientation. Against chem. intuition the dispersion energies of the examd. tellurium-contg. aroms. are far less important for the net attractive forces compared to the energies in the corresponding sulfur and selenium compds. Our results underline the importance of often overlooked steric interactions (Pauli repulsion) in conformational control of σ hole interactions.
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    Johnson, E. R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A. J.; Yang, W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132 (18), 6498– 6506,  DOI: 10.1021/ja100936w
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    Revealing Noncovalent Interactions
    Johnson, Erin R.; Keinan, Shahar; Mori-Sanchez, Paula; Contreras-Garcia, Julia; Cohen, Aron J.; Yang, Weitao
    Journal of the American Chemical Society (2010), 132 (18), 6498-6506CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Mol. structure does not easily identify the intricate noncovalent interactions that govern many areas of biol. and chem., including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron d. and its derivs. Our approach reveals the underlying chem. that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small mols., mol. complexes, and solids. Most importantly, the method, requiring only knowledge of the at. coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
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    Cioslowski, J. A Theory of Molecules: Atoms In Molecules. A Quantum Theory. Science 1991, 252 (5012), 1566– 1567,  DOI: 10.1126/science.252.5012.1566-b
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    Garrett, G. E.; Gibson, G. L.; Straus, R. N.; Seferos, D. S.; Taylor, M. S. Chalcogen bonding in solution: interactions of benzotelluradiazoles with anionic and uncharged Lewis bases. J. Am. Chem. Soc. 2015, 137 (12), 4126– 4133,  DOI: 10.1021/ja512183e
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    Chalcogen Bonding in Solution: Interactions of Benzotelluradiazoles with Anionic and Uncharged Lewis Bases
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  • Abstract

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    Figure 1

    Figure 1. Schematic representations of the first examples of noncovalent molecular self-assembly at surfaces, respectively driven by (A) hydrogen bonds, (48) (B) metal coordination bonds, (49) (C) dipole–dipole interactions, (50) (D) halogen bonds, (35) and (E) ChBIs investigated in this work.

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    Figure 2

    Figure 2. (A) STM image of (CGP-Te)2 dimers on Au(111). The herringbone reconstruction of the Au substrate is also visible. In the rectangles, the 3-fold equivalent dimer orientations are highlighted. Tunneling current (It) = 300 pA; tunneling bias (Vt) = 1.000 V; T = 11 K. The top-right-corner inset shows two enantiomers; It = 250 pA; Vt = 0.500 V. (B) Experimental (It = 300 pA; Vt= 0.630 V; T = 11 K) and (C) simulated (Vt = 0.630 V) STM image of an individual dimer. In the simulated image, the chemical structure of the monomer is also overlaid to display the strong Te-centered signal. (D) STM image of self-assembled (CGP-Se)2 dimers on Au(111). It = 300 pA; Vt = 0.800 V; T = 8.5 K. (E) STM image of an individual dimer. It = 150 pA; Vt = 0.100 V; T = 8.5 K. (F) STM image of the reference tellurazole molecules deposited on Au(111). Kinetic aggregates of various shapes and sizes can be observed. It = 400 pA; Vt = 1.000 V; T = 11 K. (G) Detail of a molecular assembly. It = 400 pA; Vt = 1.000 V; T = 11 K. Scale bars: 5 nm in (A), (D), and (F); 0.5 nm in (B), (C), (E), and (G); and 2 nm in the inset of (A).

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    Figure 3

    Figure 3. From top to bottom: BRSTM image (constant height, Vt = 5 mV, T = 8.7 K) and DFT relaxed geometrical model of the individual (CGP-Te)2 and (CGP-Se)2 dimers.

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    Figure 4

    Figure 4. DFT analysis of ChBIs in a (CGP-Te)2 dimer. (A, B) Gas phase and adsorption geometries (side view). The tilt angle of the chalcogenazole moiety with respect to the pyrene unit is shown. (C, D) Electrostatic potential (in au) superimposed on a charge density isosurface (ρ = 0.025 au). Atomic charges Q are reported for Te and N. (E, F) Molecular graph showing bond paths (dotted lines), bond critical points in red, and ring critical points in green. For clarity, bond paths between the dimer and substrate are not shown, except for Te···Au and N···Au. (G, H) Reduced density gradient (on the 0.5 au isosurface) showing the noncovalent ChBIs; blue and red regions indicate attractive and repulsive interactions, respectively; the dashed circles highlight the attractive interaction at the bond critical point between Te and N atoms.

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    4. 4
      Cui, D.; Perepichka, D. F.; MacLeod, J. M.; Rosei, F. Surface-confined single-layer covalent organic frameworks: design, synthesis and application. Chem. Soc. Rev. 2020, 49 (7), 2020,  DOI: 10.1039/C9CS00456D
      4
      Surface-confined single-layer covalent organic frameworks: design, synthesis and application
      Cui, Daling; Perepichka, Dmitrii F.; MacLeod, Jennifer M.; Rosei, Federico
      Chemical Society Reviews (2020), 49 (7), 2020-2038CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      A review. Two-dimensional (2D) nanomaterials, such as graphene and single layer covalent org. frameworks (sCOFs) are being widely studied due to their unusual structure/property relationships. sCOFs typically feature at. thickness, intrinsic nanoscale porosity and a cryst. lattice. Compared to other org. 2D materials, sCOFs exhibit major advantages including topol. designation and constitutional tunability. This review describes the state of the art of surface-confined sCOFs, emphasizing reticular design, synthesis approaches, and key challenges related to improving quality and exploring applications.
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    5. 5
      Ariga, K.; Yamauchi, Y. Nanoarchitectonics from atom to life. Chem. Asian J. 2020, 15 (6), 718– 728,  DOI: 10.1002/asia.202000106
      There is no corresponding record for this reference.
    6. 6
      Ariga, K.; Jia, X.; Song, J.; Hill, J. P.; Leong, D. T.; Jia, Y.; Li, J. Nanoarchitectonics beyond self-assembly: challenges to create bio-like hierarchic organization. Angew. Chem., Int. Ed. 2020, 59 (36), 15424– 15446,  DOI: 10.1002/anie.202000802
      6
      Nanoarchitectonics beyond Self-Assembly: Challenges to Create Bio-Like Hierarchic Organization
      Ariga, Katsuhiko; Jia, Xiaofang; Song, Jingwen; Hill, Jonathan P.; Leong, David Tai; Jia, Yi; Li, Junbai
      Angewandte Chemie, International Edition (2020), 59 (36), 15424-15446CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. Incorporation of non-equil. actions in the sequence of self-assembly processes would be an effective means to establish bio-like high functionality hierarchical assemblies. As a novel methodol. beyond self-assembly, nanoarchitectonics, which has as its aim the fabrication of functional materials systems from nanoscopic units through the methodol. fusion of nanotechnol. with other scientific disciplines including org. synthesis, supramol. chem., microfabrication, and bio-process, has been applied to this strategy. The application of non-equil. factors to conventional self-assembly processes is discussed on the basis of examples of directed assembly, Langmuir-Blodgett assembly, and layer-by-layer assembly. In particular, examples of the fabrication of hierarchical functional structures using bio-active components such as proteins or by the combination of bio-components and two-dimensional nanomaterials, are described. Methodologies described in this review article highlight possible approaches using the nanoarchitectonics concept beyond self-assembly for creation of bio-like higher functionalities and hierarchical structural organization.
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    7. 7
      Bai, L.; Wang, N.; Li, Y. Controlled Growth and Self-Assembly of Multiscale Organic Semiconductor. Adv. Mater. 2022, 34 (22), 2102811,  DOI: 10.1002/adma.202270168
      There is no corresponding record for this reference.
    8. 8
      Zhang, S.; Chen, C.; Li, J.; Ma, C.; Li, X.; Ma, W.; Zhang, M.; Cheng, F.; Deng, K.; Zeng, Q. The self-assembly and pyridine regulation of a hydrogen-bonded dimeric building block formed by a low-symmetric aromatic carboxylic acid. Nanoscale 2022, 14 (6), 2419– 2426,  DOI: 10.1039/D1NR07840B
      There is no corresponding record for this reference.
    9. 9
      Barragán, A.; Lois, S.; Sarasola, A.; Vitali, L. Empowering non-covalent hydrogen, halogen, and [S-N] 2 bonds in synergistic molecular assemblies on Au (111). Nanoscale 2022, 14 (48), 17895– 17899,  DOI: 10.1039/D2NR05984C
      There is no corresponding record for this reference.
    10. 10
      Lei, P.; Luo, W.; Tu, B.; Xiao, X.; Fang, Q.; Wang, C.; Zeng, Q. Minor adjustments in the chemical structures of pyridine derivatives induced different co-assemblies by O-H··· N hydrogen bonds. Chem. Commun. 2022, 58 (71), 9914– 9917,  DOI: 10.1039/D2CC03859E
      There is no corresponding record for this reference.
    11. 11
      Tao, J.; Xiao, Y.; Sun, L.; Liu, J.; Zeng, Q.; Xu, H. Synthesis, optical properties and self-assemblies of three novel asymmetrical perylene diimides modified with functional hydrogen bonding groups at bay positions. New J. Chem. 2022, 46 (36), 17235– 17243,  DOI: 10.1039/D2NJ03624J
      There is no corresponding record for this reference.
    12. 12
      Xie, R.; Zeng, X.; Jiang, Z.-H.; Hu, Y.; Lee, S.-L. STM Study of the Self-Assembly of Biphenyl-3, 3′, 5, 5′-Tetracarboxylic Acid and Its Mixing Behavior with Coronene at the Liquid-Solid Interface. Langmuir 2023, 39 (10), 3637– 3644,  DOI: 10.1021/acs.langmuir.2c03199
      There is no corresponding record for this reference.
    13. 13
      Vijayaraghavan, S.; Ecija, D.; Auwärter, W.; Joshi, S.; Seufert, K.; Drach, M.; Nieckarz, D.; Szabelski, P.; Aurisicchio, C.; Bonifazi, D. Supramolecular Assembly of Interfacial Nanoporous Networks with Simultaneous Expression of Metal-Organic and Organic-Bonding Motifs. Chem. Eur. J. 2013, 19 (42), 14143– 14150,  DOI: 10.1002/chem.201301852
      There is no corresponding record for this reference.
    14. 14
      Sun, Q.; Cai, L.; Ma, H.; Yuan, C.; Xu, W. On-surface construction of a metal-organic Sierpiński triangle. Chem. Commun. 2015, 51 (75), 14164– 14166,  DOI: 10.1039/C5CC05554G
      14
      On-surface construction of a metal-organic Sierpi´nski triangle
      Sun, Qiang; Cai, Liangliang; Ma, Honghong; Yuan, Chunxue; Xu, Wei
      Chemical Communications (Cambridge, United Kingdom) (2015), 51 (75), 14164-14166CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      Through a careful design of the mol. precursor the authors have successfully constructed the metal-org. Sierpi´nski triangles on Au(111) via on-surface coordination chem., which is demonstrated by the interplay of high-resoln. STM imaging and DFT calcns. The coordination Sierpi´nski triangles show high stabilities as evidenced by room temp. STM imaging, and could withstand a thermal treatment up to 450 K.
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    15. 15
      Geng, Y.-f.; Li, P.; Li, J.-z.; Zhang, X.-m.; Zeng, Q.-d.; Wang, C. STM probing the supramolecular coordination chemistry on solid surface: Structure, dynamic, and reactivity. Coord. Chem. Rev. 2017, 337, 145– 177,  DOI: 10.1016/j.ccr.2017.01.014
      15
      STM probing the supramolecular coordination chemistry on solid surface: Structure, dynamic, and reactivity
      Geng, Yan-fang; Li, Ping; Li, Ji-zhen; Zhang, Xue-mei; Zeng, Qing-dao; Wang, Chen
      Coordination Chemistry Reviews (2017), 337 (), 145-177CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
      A review. Supramol. coordination chem. is currently a very popular topic in metalorg. chem. and has a very large impact on a broad field of applications. More importantly, the invention of STM has opened new doorways to study these concepts on surfaces. This review summarizes the recent progress on surface-confined metallosupramol. engineering based on the supramol. coordination chem., with the aid of STM. At the beginning, a discussion of metalloids, alkali metals, and alk. earth metal-based metallosupramol. engineering is conducted. Next, transition metal-based coordination chem. on surfaces is discussed. Then, polygonal, double- and triple-decker structures based on rare-earth-metal coordination chem. are presented. Based on these supramol. structures, the dynamics of coordination as well as the formed supramols. are discussed. In the end, the coordination chem., including stability of coordination bonds, org. mols., and gas mol. adsorption is described. Throughout this review, the coordination structures, dynamics and reactivity were emphasized, which are important current and future research themes.
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    16. 16
      Sun, X.; Yao, X.; Lafolet, F. d. r.; Lemercier, G.; Lacroix, J.-C. One-Dimensional Double Wires and Two-Dimensional Mobile Grids: Cobalt/Bipyridine Coordination Networks at the Solid/Liquid Interface. J. Phys. Chem. Lett. 2019, 10 (15), 4164– 4169,  DOI: 10.1021/acs.jpclett.9b01292
      16
      One-Dimensional Double Wires and Two-Dimensional Mobile Grids: Cobalt/Bipyridine Coordination Networks at the Solid/Liquid Interface
      Sun, Xiaonan; Yao, Xinlei; Lafolet, Frederic; Lemercier, Gilles; Lacroix, Jean-Christophe
      Journal of Physical Chemistry Letters (2019), 10 (15), 4164-4169CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
      Various architectures have been generated and obsd. by STM at a solid/liq. interface resulting from an in situ chem. reaction between the bipyridine terminal groups of a ditopic ligand and Co(II) ions. Large monodomains of one-dimensional (1D) double wires are formed by Co(II)/ligand coordination, with polymer lengths as long as 150 nm. The polymers are organized as parallel wires 8 nm apart, and the voids between wires are occupied by solvent mols. Two-dimensional (2D) grids, showing high surface mobility, coexist with the wires. The wires are formed from linear chain motifs where each cobalt center is bonded to two bipyridines. 2D grids are generated from a bifurcation node where one cobalt bonds to three bipyridines. Surface reconstruction of the grids and of the 1D wires was obsd. under the STM tip. As an exciting result, anal. of these movements strongly indicates surface reactions at the solid/liq. interface.
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    17. 17
      Moreno, D.; Santos, J.; Parreiras, S. O.; Martín-Fuentes, C.; Lauwaet, K.; Urgel, J. I.; Miranda, R.; Martín, N.; Gallego, J. M.; Écija, D. Stoichiometry-Directed Two-Level Hierarchical Growth of Lanthanide-Based Supramolecular Nanoarchitectures. Chem. Eur. J. 2023, 29, e202300461  DOI: 10.1002/chem.202300461
      There is no corresponding record for this reference.
    18. 18
      Wintjes, N.; Hornung, J.; Lobo-Checa, J.; Voigt, T.; Samuely, T.; Thilgen, C.; Stöhr, M.; Diederich, F.; Jung, T. A. Supramolecular synthons on surfaces: Controlling dimensionality and periodicity of tetraarylporphyrin assemblies by the interplay of cyano and alkoxy substituents. Chem. Eur. J. 2008, 14 (19), 5794– 5802,  DOI: 10.1002/chem.200800746
      There is no corresponding record for this reference.
    19. 19
      Stöhr, M.; Boz, S.; Schär, M.; Nguyen, M. T.; Pignedoli, C. A.; Passerone, D.; Schweizer, W. B.; Thilgen, C.; Jung, T. A.; Diederich, F. Self-Assembly and Two-Dimensional Spontaneous Resolution of Cyano-Functionalized [7] Helicenes on Cu (111). Angew. Chem., Int. Ed. 2011, 50 (42), 9982– 9986,  DOI: 10.1002/anie.201102627
      There is no corresponding record for this reference.
    20. 20
      Alcock, N. W. Secondary bonding to nonmetallic elements. In Adv. Inorg. Chem. Radiochem.; Elsevier, 1972; Vol. 15, pp 1– 58.
      There is no corresponding record for this reference.
    21. 21
      Politzer, P.; Murray, J. S.; Clark, T. Halogen bonding and other σ-hole interactions: A perspective. Phys. Chem. Chem. Phys. 2013, 15 (27), 11178– 11189,  DOI: 10.1039/c3cp00054k
      21
      Halogen bonding and other σ-hole interactions: a perspective
      Politzer, Peter; Murray, Jane S.; Clark, Timothy
      Physical Chemistry Chemical Physics (2013), 15 (27), 11178-11189CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      A review. A σ-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV-VII and a neg. site, e.g. a lone pair of a Lewis base or an anion. It involves a region of pos. electrostatic potential, labeled a σ-hole, on the extension of one of the covalent bonds to the atom. The σ-hole is due to the anisotropy of the atom's charge distribution. Halogen bonding is a subset of σ-hole interactions. Their features and properties can be fully explained in terms of electrostatics and polarization plus dispersion. The strengths of the interactions generally correlate well with the magnitudes of the pos. and neg. electrostatic potentials of the σ-hole and the neg. site. In certain instances, however, polarizabilities must be taken into account explicitly, as the polarization of the neg. site reaches a level that can be viewed as a degree of dative sharing (coordinate covalence). In the gas phase, σ-hole interactions with neutral bases are often thermodynamically unfavorable due to the relatively large entropy loss upon complex formation.
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    22. 22
      Lim, J. Y.; Beer, P. D. Sigma-hole interactions in anion recognition. Chem. 2018, 4 (4), 731– 783,  DOI: 10.1016/j.chempr.2018.02.022
      22
      Sigma-Hole Interactions in Anion Recognition
      Lim, Jason Y. C.; Beer, Paul D.
      Chem (2018), 4 (4), 731-783CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)
      A review. Sigma (σ)-holes are electron-deficient regions that arise from the anisotropic distribution of electron d. on the atom of group 14 (tetrels), 15 (pnictogens), 16 (chalcogens), and 17 (halogens) elements when covalently bonded to electron-withdrawing groups. Named after the donor atom's group, the σ-hole interactions, halogen bonding, and chalcogen bonding with anionic species have found ground-breaking applications in anion supramol. chem. within the last decade. In this review, we feature key recent discoveries and advances across the whole range of σ-hole interactions for anion recognition, from the familiar halogen bonding to the almost unknown pnictogen and tetrel bonding. In particular, the novel anion recognition properties and applications that result from the unique aspects of each σ-hole interaction, together with detailed design considerations of anion-binding receptor motifs, are highlighted.
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    23. 23
      Mallada, B.; Gallardo, A.; Lamanec, M.; De La Torre, B.; Špirko, V.; Hobza, P.; Jelinek, P. Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy. Science 2021, 374 (6569), 863– 867,  DOI: 10.1126/science.abk1479
      23
      Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy
      Mallada, B.; Gallardo, A.; Lamanec, M.; de la Torre, B.; Spirko, V.; Hobza, P.; Jelinek, P.
      Science (Washington, DC, United States) (2021), 374 (6569), 863-867CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
      An anisotropic charge distribution on individual atoms, such as σ-holes, may strongly affect the material and structural properties of systems. However, the spatial resoln. of such anisotropic charge distributions on an atom represents a long-standing exptl. challenge. In particular, the existence of the σ-hole on halogen atoms has been demonstrated only indirectly through the detn. of the crystal structures of org. mols. contg. halogens or with theor. calcns., consequently calling for its direct exptl. visualization. We show that Kelvin probe force microscopy with a properly functionalized probe can image the anisotropic charge of the σ-hole and the quadrupolar charge of a carbon monoxide mol. This opens a new way to characterize biol. and chem. systems in which anisotropic at. charges play a decisive role.
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    24. 24
      Pascoe, D. J.; Ling, K. B.; Cockroft, S. L. The origin of chalcogen-bonding interactions. J. Am. Chem. Soc. 2017, 139 (42), 15160– 15167,  DOI: 10.1021/jacs.7b08511
      24
      The Origin of Chalcogen-Bonding Interactions
      Pascoe, Dominic J.; Ling, Kenneth B.; Cockroft, Scott L.
      Journal of the American Chemical Society (2017), 139 (42), 15160-15167CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Favorable mol. interactions between group 16 elements have been implicated in catalysis, biol. processes, and materials and medicinal chem. Such interactions have since become known as chalcogen bonds by analogy to hydrogen and halogen bonds. Although the prevalence and applications of chalcogen-bonding interactions continues to develop, debate still surrounds the energetic significance and physicochem. origins of this class of σ-hole interaction. Here, synthetic mol. balances were used to perform a quant. exptl. investigation of chalcogen-bonding interactions. Over 160 exptl. conformational free energies were measured in 13 different solvents to examine the energetics of O···S, O···Se, S···S, O···HC, and S···HC contacts and the assocd. substituent and solvent effects. The strongest chalcogen-bonding interactions were found to be at least as strong as conventional H-bonds, but unlike H-bonds, surprisingly independent of the solvent. The independence of the conformational free energies on solvent polarity, polarizability, and H-bonding characteristics showed that electrostatic, solvophobic, and van der Waals dispersion forces did not account for the obsd. exptl. trends. Instead, a quant. relationship between the exptl. conformational free energies and computed MO energies was consistent with the chalcogen-bonding interactions being dominated by n → σ* orbital delocalization between a lone pair (n) of a (thio)amide donor and the antibonding σ* orbital of an acceptor thiophene or selenophene. Interestingly, stabilization was manifested through the same acceptor MO irresp. of whether a direct chalcogen···chalcogen or chalcogen···H-C contact was made. Our results underline the importance of often-overlooked orbital delocalization effects in conformational control and mol. recognition phenomena.
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    25. 25
      Teyssandier, J.; Mali, K. S.; De Feyter, S. Halogen bonding in two-dimensional crystal engineering. ChemistryOpen 2020, 9 (2), 225– 241,  DOI: 10.1002/open.201900337
      25
      Halogen Bonding in Two-Dimensional Crystal Engineering
      Teyssandier, Joan; Mali, Kunal S.; De Feyter, Steven
      ChemistryOpen (2020), 9 (2), 225-241CODEN: CHOPCK; ISSN:2191-1363. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. Halogen bonds, which provide an intermol. interaction with moderate strength and high directionality, have emerged as a promising tool in the repertoire of non-covalent interactions. In this review, we provide a survey of the literature where halogen bonding was used for the fabrication of supramol. networks on solid surfaces. The definitions of, and the distinction between halogen bonding and halogen-halogen interactions are provided. Self-assembled networks formed at the soln./solid interface and at the vacuum-solid interface, stabilized in part by halogen bonding, are discussed. Besides the broad classification based on the interface at which the systems are studied, the systems are categorized further as those sustained by halogen-halogen and halogen-heteroatom contacts.
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    26. 26
      Kampes, R.; Zechel, S.; Hager, M. D.; Schubert, U. S. Halogen bonding in polymer science: towards new smart materials. Chem. Sci. 2021, 12 (27), 9275– 9286,  DOI: 10.1039/D1SC02608A
      26
      Halogen bonding in polymer science: towards new smart materials
      Kampes, Robin; Zechel, Stefan; Hager, Martin D.; Schubert, Ulrich S.
      Chemical Science (2021), 12 (27), 9275-9286CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
      A review. The halogen bond is a special non-covalent interaction, which can represent a powerful tool in supramol. chem. Although the halogen bond offers several advantages compared to the related hydrogen bond, it is currently still underrepresented in polymer science. The structural related hydrogen bonding assumes a leading position in polymer materials contg. supramol. interactions, clearly indicating the high potential of using halogen bonding for the design of polymeric materials. The current developments regarding halogen bonding contg. polymers include self-assembly, photo-responsive materials, self-healing materials and others. These aspects are highlighted in the present perspective. Furthermore, a perspective on the future of this rising young research field is provided.
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    27. 27
      Metrangolo, P.; Canil, L.; Abate, A.; Terraneo, G.; Cavallo, G. Halogen bonding in perovskite solar cells: a new tool for improving solar energy conversion. Angew. Chem., Int. Ed. 2022, 61 (11), e202114793  DOI: 10.1002/anie.202114793
      27
      Halogen Bonding in Perovskite Solar Cells: A New Tool for Improving Solar Energy Conversion
      Metrangolo, Pierangelo; Canil, Laura; Abate, Antonio; Terraneo, Giancarlo; Cavallo, Gabriella
      Angewandte Chemie, International Edition (2022), 61 (11), e202114793CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. Hybrid org.-inorg. halide perovskites (HOIHPs) have recently emerged as a flourishing area of research. Their easy and low-cost prodn. and their unique optoelectronic properties make them promising materials for many applications. In particular, HOIHPs hold great potential for next-generation solar cells. However, their practical implementation is still hindered by their poor stability in air and moisture, which is responsible for their short lifetime. Optimizing the chem. compn. of materials and exploiting non-covalent interactions for interfacial and defects engineering, as well as defect passivation, are efficient routes towards enhancing the overall efficiency and stability of perovskite solar cells (PSCs). Due to the rich halogen chem. of HOIHPs, exploiting halogen bonding, in particular, may pave the way towards the development of highly stable PSCs. Improved crystn. and stability, redn. of the surface trap states, and the possibility of forming ordered structures have already been preliminarily demonstrated.
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    28. 28
      Xu, Y.; Hao, A.; Xing, P. X··· X Halogen Bond-Induced Supramolecular Helices. Angew. Chem., Int. Ed. 2022, 61 (2), e202113786  DOI: 10.1002/anie.202113786
      There is no corresponding record for this reference.
    29. 29
      Semenov, A. V.; Baykov, S. V.; Soldatova, N. S.; Geyl, K. K.; Ivanov, D. M.; Frontera, A.; Boyarskiy, V. P.; Postnikov, P. S.; Kukushkin, V. Y. Noncovalent Chelation by Halogen Bonding in the Design of Metal-Containing Arrays: Assembly of Double σ-Hole Donating Halolium with CuI-Containing O, O-Donors. Inorg. Chem. 2023, 62 (15), 6128– 6137,  DOI: 10.1021/acs.inorgchem.3c00229
      There is no corresponding record for this reference.
    30. 30
      Wang, D.; Wang, Z.; Liu, W.; Arramel; Zhong, S.; Feng, Y. P.; Loh, K. P.; Wee, A. T. S. Real-Space Investigation of the Multiple Halogen Bonds by Ultrahigh-Resolution Scanning Probe Microscopy. Small 2022, 18 (28), 2202368,  DOI: 10.1002/smll.202202368
      There is no corresponding record for this reference.
    31. 31
      Peyrot, D.; Silly, F. Toward Two-Dimensional Tessellation through Halogen Bonding between Molecules and On-Surface-Synthesized Covalent Multimers. Int. J. Mol. Sci. 2023, 24 (14), 11291,  DOI: 10.3390/ijms241411291
      There is no corresponding record for this reference.
    32. 32
      Piquero-Zulaica, I.; Lobo-Checa, J.; Sadeghi, A.; El-Fattah, Z. M. A.; Mitsui, C.; Okamoto, T.; Pawlak, R.; Meier, T.; Arnau, A.; Ortega, J. E. Precise engineering of quantum dot array coupling through their barrier widths. Nat. Commun. 2017, 8 (1), 787,  DOI: 10.1038/s41467-017-00872-2
      32
      Precise engineering of quantum dot array coupling through their barrier widths
      Piquero-Zulaica Ignacio; Arnau Andres; Ortega J Enrique; Lobo-Checa Jorge; Lobo-Checa Jorge; Sadeghi Ali; El-Fattah Zakaria M Abd; Mitsui Chikahiko; Okamoto Toshihiro; Takeya Jun; Okamoto Toshihiro; Kawai Shigeki; Pawlak Remy; Meier Tobias; Goedecker Stefan; Meyer Ernst; Kawai Shigeki; Arnau Andres; Ortega J Enrique; Arnau Andres; Ortega J Enrique; Kawai Shigeki
      Nature communications (2017), 8 (1), 787 ISSN:.
      Quantum dots are known to confine electrons within their structure. Whenever they periodically aggregate into arrays and cooperative interactions arise, novel quantum properties suitable for technological applications show up. Control over the potential barriers existing between neighboring quantum dots is therefore essential to alter their mutual crosstalk. Here we show that precise engineering of the barrier width can be experimentally achieved on surfaces by a single atom substitution in a haloaromatic compound, which in turn tunes the confinement properties through the degree of quantum dot intercoupling. We achieved this by generating self-assembled molecular nanoporous networks that confine the two-dimensional electron gas present at the surface. Indeed, these extended arrays form up on bulk surface and thin silver films alike, maintaining their overall interdot coupling. These findings pave the way to reach full control over two-dimensional electron gases by means of self-assembled molecular networks.Arrays of quantum dots can exhibit a variety of quantum properties, being sensitive to their spacing. Here, the authors fine tune interdot coupling using hexagonal molecular networks in which the dots are separated by single or double haloaromatic compounds, structurally identical but for a single atom.
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    33. 33
      Lawrence, J.; Sosso, G. C.; Đorđević, L.; Pinfold, H.; Bonifazi, D.; Costantini, G. Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding. Nat. Commun. 2020, 11 (1), 2103,  DOI: 10.1038/s41467-020-15898-2
      33
      Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding
      Lawrence, James; Sosso, Gabriele C.; Djordjevic, Luka; Pinfold, Harry; Bonifazi, Davide; Costantini, Giovanni
      Nature Communications (2020), 11 (1), 2103CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
      Scanning tunnelling microscopy (STM) is commonly used to identify on-surface mol. self-assembled structures. However, its limited ability to reveal only the overall shape of mols. and their relative positions is not always enough to fully solve a supramol. structure. Here, we analyze the assembly of a brominated polycyclic arom. mol. on Au(111) and demonstrate that std. STM measurements cannot conclusively establish the nature of the intermol. interactions. By performing high-resoln. STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, detg. that halogen bonding governs the assemblies. This is supported by d. functional theory calcns. that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron d. topol. anal. that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramol. structures, and we predict its increasing use in mol. nanoscience at surfaces.
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    34. 34
      Pham, T. A.; Song, F.; Nguyen, M.-T.; Stöhr, M. Self-assembly of pyrene derivatives on Au (111): substituent effects on intermolecular interactions. Chem. Commun. 2014, 50 (91), 14089– 14092,  DOI: 10.1039/C4CC02753A
      There is no corresponding record for this reference.
    35. 35
      Gutzler, R.; Ivasenko, O.; Fu, C.; Brusso, J. L.; Rosei, F.; Perepichka, D. F. Halogen bonds as stabilizing interactions in a chiral self-assembled molecular monolayer. Chem. Commun. 2011, 47 (33), 9453– 9455,  DOI: 10.1039/c1cc13114a
      There is no corresponding record for this reference.
    36. 36
      Xing, L.; Jiang, W.; Huang, Z.; Liu, J.; Song, H.; Zhao, W.; Dai, J.; Zhu, H.; Wang, Z.; Weiss, P. S. Steering two-dimensional porous networks with σ-hole interactions of Br··· S and Br··· Br. Chem. Mater. 2019, 31 (8), 3041– 3048,  DOI: 10.1021/acs.chemmater.9b01126
      There is no corresponding record for this reference.
    37. 37
      Aakeroy, C. B.; Bryce, D. L.; Desiraju, G. R.; Frontera, A.; Legon, A. C.; Nicotra, F.; Rissanen, K.; Scheiner, S.; Terraneo, G.; Metrangolo, P. Definition of the chalcogen bond (IUPAC Recommendations 2019). Pure Appl. Chem. 2019, 91 (11), 1889– 1892,  DOI: 10.1515/pac-2018-0713
      37
      Definition of the chalcogen bond (IUPAC Recommendations 2019)
      Aakeroy, Christer B.; Bryce, David L.; Desiraju, Gautam R.; Frontera, Antonio; Legon, Anthony C.; Nicotra, Francesco; Rissanen, Kari; Scheiner, Steve; Terraneo, Giancarlo; Metrangolo, Pierangelo; Resnati, Giuseppe
      Pure and Applied Chemistry (2019), 91 (11), 1889-1892CODEN: PACHAS; ISSN:0033-4545. (Walter de Gruyter, Inc.)
      This recommendation proposes a definition for the term "chalcogen bond"; it is recommended the term is used to designate the specific subset of inter- and intramol. interactions formed by chalcogen atoms wherein the Group 16 element is the electrophilic site.
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    38. 38
      Biot, N.; Bonifazi, D. Chalcogen-bond driven molecular recognition at work. Coord. Chem. Rev. 2020, 413, 213243,  DOI: 10.1016/j.ccr.2020.213243
      38
      Chalcogen-bond driven molecular recognition at work
      Biot, Nicolas; Bonifazi, Davide
      Coordination Chemistry Reviews (2020), 413 (), 213243CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
      A review. Out of the supramol. toolbox, Secondary Bonding Interactions (SBIs) have attracted in the last decades the attention of the chem. community as novel non-covalent interactions of choice for a large no. of chem. systems. Amongst all SBIs, halogen-bonding (XBIs) and chalcogen-bonding (EBIs) interactions are certainly the most important. However, the use of EBIs have received marginal consideration if compared to that of XBIs. By sieving the most significant examples, this review focuses on the theor. and exptl. studies carried out with EBIs in functional systems. In a systematic way the reader is guided through the most recent and representative examples in which chemists have rationally designed mol. modules that, through EBIs, trigger the initiation of chem. reactions, mol. recognition events in solns. and at the solid state to produce self-assembled and self-organised functional materials at different length scales. The study and understanding of the fundamental geometrical and phys. parameters ruling EBIs is at its infancy, and it still needs to establish those principles to rationally design and program synthons that, undergoing mol. recognition through EBIs, allow the development of new tailored materials for applications in the field of optoelectronic, sensing, catalysis, and drug discovery.
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    39. 39
      De Silva, V.; Magueres, P. L.; Averkiev, B. B.; Aakeröy, C. B. Competition between chalcogen and halogen bonding assessed through isostructural species. Acta Crystallogr., Sect. C: Struct. Chem. 2022, 78 (12), 716– 721,  DOI: 10.1107/S205322962201052X
      There is no corresponding record for this reference.
    40. 40
      Torubaev, Y. V.; Rozhkov, A. V.; Skabitsky, I. V.; Gomila, R. M.; Frontera, A.; Kukushkin, V. Y. Heterovalent chalcogen bonding: supramolecular assembly driven by the occurrence of a tellurium (ii)··· Ch (i)(Ch= S, Se, Te) linkage. Inorg. Chem. Front. 2022, 9 (21), 5635– 5644,  DOI: 10.1039/D2QI01420C
      There is no corresponding record for this reference.
    41. 41
      Ishigaki, Y.; Asai, K.; Jacquot de Rouville, H. P.; Shimajiri, T.; Hu, J.; Heitz, V.; Suzuki, T. Solid-State Assembly by Chelating Chalcogen Bonding in Quinodimethane Tetraesters Fused with a Chalcogenadiazole. ChemPlusChem. 2022, 87 (4), e202200075  DOI: 10.1002/cplu.202200075
      There is no corresponding record for this reference.
    42. 42
      Romito, D.; Ho, P. C.; Vargas-Baca, I.; Bonifazi, D. Supramolecular Chemistry via Chalcogen Bonding Interactions. In Chalcogen Chemistry: Fundamentals and Applications; The Royal Society of Chemistry, 2023; pp 494– 528.
      There is no corresponding record for this reference.
    43. 43
      Ho, P. C.; Wang, J. Z.; Meloni, F.; Vargas-Baca, I. Chalcogen bonding in materials chemistry. Coord. Chem. Rev. 2020, 422, 213464,  DOI: 10.1016/j.ccr.2020.213464
      43
      Chalcogen bonding in materials chemistry
      Ho, Peter C.; Wang, Jin Z.; Meloni, Francesca; Vargas-Baca, Ignacio
      Coordination Chemistry Reviews (2020), 422 (), 213464CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
      A review. This review examines recent literature in search for evidence of the influence that chalcogen bonding has on the structure and properties of functional materials. Key examples from research on charge transfer salts, neutral heterocyclic free radicals, and paramagnetic coordination compds. are highlighted as intermol. interactions are crit. to properties such as cond. and magnetic response. Other cases reviewed include the influence of chalcogen bonding on optical properties such as the electronic absorption spectra and the nonlinear optical response of non-centrosym. crystal structures. There is also evidence that this type of interaction between mols. translates into macroscopic mech. properties such as the bulk modulus.
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    44. 44
      Romito, D.; Fresta, E.; Cavinato, L. M.; Kählig, H.; Amenitsch, H.; Caputo, L.; Chen, Y.; Samorì, P.; Charlier, J. C.; Costa, R. D.; Bonifazi, D. Supramolecular Chalcogen-Bonded Semiconducting Nanoribbons at Work in Lighting Devices. Angew. Chem., Int. Ed. 2022, 61 (38), e202202137  DOI: 10.1002/anie.202202137
      There is no corresponding record for this reference.
    45. 45
      Cameron, J.; Kanibolotsky, A. L.; Skabara, P. J. Lest we Forget-the Importance of Heteroatom Interactions in Heterocyclic Conjugated Systems, from Synthetic Metals to Organic Semiconductors. Adv. Mater. 2024, 36, 2302259,  DOI: 10.1002/adma.202302259
      There is no corresponding record for this reference.
    46. 46
      Ren, B.; Lu, Y.; Wang, R.; Liu, H. First-principles study of chalcogen-bonded self-assembly structures on silicene: Some insight into the fabrication of molecular architectures on surfaces through chalcogen bonding. Chem. Phys. 2023, 565, 111763,  DOI: 10.1016/j.chemphys.2022.111763
      There is no corresponding record for this reference.
    47. 47
      Wang, H.; Li, B.; Wang, X.; Yin, F.; Wei, Q.; Wang, X.; Ni, Y.; Wang, H. First-principles study of square chalcogen bond interactions and its adsorption behavior on silver surface. Phys. Chem. Chem. Phys. 2023, 25 (15), 10836– 10844,  DOI: 10.1039/D2CP05825A
      There is no corresponding record for this reference.
    48. 48
      Yang, W.; Chai, X.; Chi, L.; Liu, X.; Cao, Y.; Lu, R.; Jiang, Y.; Tang, X.; Fuchs, H.; Li, T. From achiral molecular components to chiral supermolecules and supercoil self-assembly. Chem. Eur. J. 1999, 5 (4), 1144– 1149,  DOI: 10.1002/(SICI)1521-3765(19990401)5:4<1144::AID-CHEM1144>3.0.CO;2-K
      There is no corresponding record for this reference.
    49. 49
      Semenov, A.; Spatz, J. P.; Möller, M.; Lehn, J. M.; Sell, B.; Schubert, D.; Weidl, C. H.; Schubert, U. S. Controlled arrangement of supramolecular metal coordination arrays on surfaces. Angew. Chem., Int. Ed. 1999, 38 (17), 2547– 2550,  DOI: 10.1002/(SICI)1521-3773(19990903)38:17<2547::AID-ANIE2547>3.0.CO;2-M
      There is no corresponding record for this reference.
    50. 50
      Yokoyama, T.; Yokoyama, S.; Kamikado, T.; Okuno, Y.; Mashiko, S. Selective assembly on a surface of supramolecular aggregates with controlled size and shape. Nature 2001, 413 (6856), 619– 621,  DOI: 10.1038/35098059
      50
      Selective assembly on a surface of supramolecular aggregates with controlled size and shape
      Yokoyanna, Takashi; Yokoyama, Shilyoshi; Kamikado, Tashiya; Okuno, Yoshishige; Mashiko, Shinro
      Nature (London, United Kingdom) (2001), 413 (6856), 619-621CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
      The realization of mol.-based miniature devices with advanced functions requires the development of new and efficient approaches for combining mol. building blocks into desired functional structures, ideally with these structures supported on suitable substrates. Supramol. aggregation occurs spontaneously and can lead to controlled structures if selective and directional noncovalent interactions are exploited. But such selective supramol. assembly has yielded almost exclusively crystals or dissolved structures; the self-assembly of adsorbed mols. into larger structures, in contrast, has not yet been directed by controlling selective intermol. interactions. Here the authors report the formation of surface-supported supramol. structures whose size and aggregation pattern are rationally controlled by tuning the noncovalent interactions between individual adsorbed mols. Using low-temp. scanning tunnelling microscopy, substituted porphyrin mols. adsorbed on a Au surface form monomers, trimers, tetramers or extended wire-like structures. Each structure corresponds in a predictable fashion to the geometric and chem. nature of the porphyrin substituents that mediate the interactions between individual adsorbed mols. Findings suggest that careful placement of functional groups that are able to participate in directed non-covalent interactions will allow the rational design and construction of a wide range of supramol. architectures adsorbed to surfaces.
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    51. 51
      Wu, T.; Xue, N.; Wang, Z.; Li, J.; Li, Y.; Huang, W.; Shen, Q.; Hou, S.; Wang, Y. Surface self-assembly involving the interaction between S and N atoms. Chem. Commun. 2021, 57, 1328– 1331,  DOI: 10.1039/D0CC07931F
      There is no corresponding record for this reference.
    52. 52
      Cozzolino, A. F.; Dimopoulos-Italiano, G.; Lee, L. M.; Vargas-Baca, I. Chalcogen-Nitrogen Secondary Bonding Interactions in the Gas Phase - Spectrometric Detection of Ionized Benzo-2,1,3-telluradiazole Dimers. Eur. J. Inorg. Chem. 2013, 2013, 2751– 2756,  DOI: 10.1002/ejic.201201439
      There is no corresponding record for this reference.
    53. 53
      Risto, M.; Reed, R. W.; Robertson, C. M.; Oilunkaniemi, R.; Laitinen, R. S.; Oakley, R. T. Self-association of the N-methyl benzotellurodiazolylium cation: implications for the generation of super-heavy atom radicals. Chem. Commun. 2008, 3278– 3280,  DOI: 10.1039/b803159b
      53
      Self-association of the N-methyl benzotellurodiazolylium cation: implications for the generation of super-heavy atom radicals
      Risto, Maarit; Reed, Robert W.; Robertson, Craig M.; Oilunkaniemi, Raija; Laitinen, Risto S.; Oakley, Richard T.
      Chemical Communications (Cambridge, United Kingdom) (2008), (28), 3278-3280CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      The N-Me benzotellurodiazolylium cation self-assocs. in the solid state via short (2.471(3) Å) 4-center Te···N' intermol. contacts; electrochem. data and the results of DFT calcns. suggest that the dimers persist in soln.
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    54. 54
      Biot, N.; Bonifazi, D. Programming Recognition Arrays through Double Chalcogen-Bonding Interactions. Chem. Eur. J. 2018, 24 (21), 5439– 5443,  DOI: 10.1002/chem.201705428
      54
      Programming Recognition Arrays through Double Chalcogen-Bonding Interactions
      Biot, Nicolas; Bonifazi, Davide
      Chemistry - A European Journal (2018), 24 (21), 5439-5443CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
      In this work, we have programmed and synthesized a recognition motif constructed around a chalcogenazolo-pyridine scaffold (CGP) that, through the formation of frontal double chalcogen-bonding interactions, assocs. into dimeric EX-type complexes. The reliability of the double chalcogen-bonding interaction has been shown at the solid-state by X-ray anal., depicting the strongest recognition persistence for a Te-congener. The high recognition fidelity, chem. and thermal stability and easy derivatization at the 2-position makes CGP a convenient motif for constructing supramol. architectures through programmed chalcogen-bonding interactions.
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    55. 55
      Romito, D.; Biot, N.; Babudri, F.; Bonifazi, D. Non-covalent bridging of bithiophenes through chalcogen bonding grips. New J. Chem. 2020, 44 (17), 6732– 6738,  DOI: 10.1039/C9NJ06202E
      There is no corresponding record for this reference.
    56. 56
      Biot, N.; Bonifazi, D. Concurring Chalcogen-and Halogen-Bonding Interactions in Supramolecular Polymers for Crystal Engineering Applications. Chem. Eur. J. 2020, 26 (13), 2904– 2913,  DOI: 10.1002/chem.201904762
      There is no corresponding record for this reference.
    57. 57
      Romito, D.; Bonifazi, D. Engineering Te-Containing Recognition Modules for Chalcogen Bonding: Towards Supramolecular Polymeric Materials. Helv. Chim. Acta 2023, 106 (2), e202200159  DOI: 10.1002/hlca.202200159
      There is no corresponding record for this reference.
    58. 58
      Chivers, T.; Laitinen, R. S. Tellurium: a maverick among the chalcogens. Chem. Soc. Rev. 2015, 44 (7), 1725– 1739,  DOI: 10.1039/C4CS00434E
      58
      Tellurium: a maverick among the chalcogens
      Chivers, Tristram; Laitinen, Risto S.
      Chemical Society Reviews (2015), 44 (7), 1725-1739CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      The scant attention paid to tellurium in both inorg. and org. chem. textbooks may reflect, in part, the very low natural abundance of the element. Such treatments commonly imply that the structures and reactivities of tellurium compds. can be extrapolated from the behavior of their lighter chalcogen analogs (sulfur and selenium). In fact, recent findings and well-established observations clearly illustrate that this assumption is not valid. The emerging importance of the unique properties of tellurium compds. is apparent from the variety of their known and potential applications in both inorg. and org. chem., as well as materials science. With ref. to selected contemporary examples, this Tutorial Review examines the fundamental concepts that are essential for an understanding of the unique features of tellurium chem. with an emphasis on hypervalency, three-center bonding, secondary bonding interactions, σ and π-bond energies (multiply bonded compds.), and Lewis acid behavior.
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    59. 59
      Michalczyk, M.; Malik, M.; Zierkiewicz, W.; Scheiner, S. Experimental and theoretical studies of dimers stabilized by two chalcogen bonds in the presence of a N··· N pnicogen bond. J. Phys. Chem. A 2021, 125 (2), 657– 668,  DOI: 10.1021/acs.jpca.0c10814
      There is no corresponding record for this reference.
    60. 60
      Scheiner, S. Principles guiding the square bonding motif containing a pair of chalcogen bonds between chalcogenadiazoles. J. Phys. Chem. A 2022, 126 (7), 1194– 1203,  DOI: 10.1021/acs.jpca.1c10818
      There is no corresponding record for this reference.
    61. 61
      Tsuzuki, S.; Sato, N. Origin of Attraction in Chalgogen-Nitrogen Interaction of 1, 2, 5-Chalcogenadiazole Dimers. J. Phys. Chem. B 2013, 117 (22), 6849– 6855,  DOI: 10.1021/jp403200j
      61
      Origin of Attraction in Chalcogen-Nitrogen Interaction of 1,2,5-Chalcogenadiazole Dimers
      Tsuzuki, Seiji; Sato, Naoki
      Journal of Physical Chemistry B (2013), 117 (22), 6849-6855CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      Intermol. interaction in the 1,2,5-chalcogenadiazole dimers was studied by ab initio MO calcns. Estd. CCSD(T) interaction energies for the thia-, selena- and tellura-diazole dimers are -3.14, -5.29, and -12.42 kcal/mol, resp. The electrostatic and dispersion interactions are the major sources of the attraction in the dimers, although it was claimed that the orbital mixing (charge-transfer interaction) was the most prominent contribution to the stabilization. The induction (induced polarization) interaction also contributes largely to the attraction in the telluradiazole dimer. The large electrostatic and induction interactions are responsible for the strong attraction in the telluradiazole dimer. The short-range (orbital-orbital) interaction (sum of the exchange-repulsion and charge-transfer interactions) is repulsive. The directionality of the interactions increases in order of S < Se < Te. The electrostatic interaction is mainly responsible for the directionality. The strong directionality suggests that the chalcogen-nitrogen interaction plays important roles in controlling the orientation of mols. in those org. crystals. The nature of the chalcogen-nitrogen interaction in the chalcogenadiazole dimers is similar to that of the halogen bond, which is an electrostatically driven noncovalent interaction.
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    62. 62
      Haberhauer, G.; Gleiter, R. The Nature of Strong Chalcogen Bonds Involving Chalcogen-Containing Heterocycles. Angew. Chem., Int. Ed. 2020, 59 (47), 21236– 21243,  DOI: 10.1002/anie.202010309
      62
      The Nature of Strong Chalcogen Bonds Involving Chalcogen-Containing Heterocycles
      Haberhauer, Gebhard; Gleiter, Rolf
      Angewandte Chemie, International Edition (2020), 59 (47), 21236-21243CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Chalcogen bonds are σ hole interactions and have been used in recent years as an alternative to hydrogen bonds. In general, the electrostatic potential at the chalcogen atom and orbital delocalization effects are made responsible for the orientation of the chalcogen bond. Here, we were able to show by means of SAPT calcns. that neither the induction (orbital delocalization effects) nor the electrostatic term is causing the spatial orientation of strong chalcogen bonds in tellurium-contg. aroms. Instead, steric interactions (Pauli repulsion) are responsible for the orientation. Against chem. intuition the dispersion energies of the examd. tellurium-contg. aroms. are far less important for the net attractive forces compared to the energies in the corresponding sulfur and selenium compds. Our results underline the importance of often overlooked steric interactions (Pauli repulsion) in conformational control of σ hole interactions.
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    63. 63
      Johnson, E. R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A. J.; Yang, W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132 (18), 6498– 6506,  DOI: 10.1021/ja100936w
      63
      Revealing Noncovalent Interactions
      Johnson, Erin R.; Keinan, Shahar; Mori-Sanchez, Paula; Contreras-Garcia, Julia; Cohen, Aron J.; Yang, Weitao
      Journal of the American Chemical Society (2010), 132 (18), 6498-6506CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Mol. structure does not easily identify the intricate noncovalent interactions that govern many areas of biol. and chem., including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron d. and its derivs. Our approach reveals the underlying chem. that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small mols., mol. complexes, and solids. Most importantly, the method, requiring only knowledge of the at. coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
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    64. 64
      Cioslowski, J. A Theory of Molecules: Atoms In Molecules. A Quantum Theory. Science 1991, 252 (5012), 1566– 1567,  DOI: 10.1126/science.252.5012.1566-b
      There is no corresponding record for this reference.
    65. 65
      Garrett, G. E.; Gibson, G. L.; Straus, R. N.; Seferos, D. S.; Taylor, M. S. Chalcogen bonding in solution: interactions of benzotelluradiazoles with anionic and uncharged Lewis bases. J. Am. Chem. Soc. 2015, 137 (12), 4126– 4133,  DOI: 10.1021/ja512183e
      65
      Chalcogen Bonding in Solution: Interactions of Benzotelluradiazoles with Anionic and Uncharged Lewis Bases
      Garrett, Graham E.; Gibson, Gregory L.; Straus, Rita N.; Seferos, Dwight S.; Taylor, Mark S.
      Journal of the American Chemical Society (2015), 137 (12), 4126-4133CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Chalcogen bonding is the noncovalent interaction between an electron-deficient, covalently bonded chalcogen (Te, Se, S) and a Lewis base. Although substantial evidence supports the existence of chalcogen bonding in the solid state, quant. data regarding the strengths of the interactions in the soln. phase are lacking. Herein, detns. of the assocn. consts. of benzotelluradiazoles with a variety of Lewis bases (Cl-, Br-, I-, NO3- and quinuclidine, in org. solvent) are described. The participation of the benzotelluradiazoles in chalcogen bonding interactions was probed by UV-vis, 1H and 19F NMR spectroscopy as well as nano-ESI mass spectrometry. Trends in the free energy of chalcogen bonds upon variation of the donor, acceptor and solvent are evident from these data, including a linear free energy relationship between chalcogen bond donor ability and calcd. electrostatic potential at the tellurium center. Calcns. using the dispersion-cor. B97-D3 functional were found to give good agreement with the exptl. free energies of chalcogen bonding.
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      Nečas, D.; Klapetek, P. Gwyddion: an open-source software for SPM data analysis. Open Physics 2012, 10 (1), 181– 188,  DOI: 10.2478/s11534-011-0096-2
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      Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G. L.; Cococcioni, M.; Dabo, I. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys.: Condens. Matter 2009, 21 (39), 395502,  DOI: 10.1088/0953-8984/21/39/395502
      67
      QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials
      Giannozzi Paolo; Baroni Stefano; Bonini Nicola; Calandra Matteo; Car Roberto; Cavazzoni Carlo; Ceresoli Davide; Chiarotti Guido L; Cococcioni Matteo; Dabo Ismaila; Dal Corso Andrea; de Gironcoli Stefano; Fabris Stefano; Fratesi Guido; Gebauer Ralph; Gerstmann Uwe; Gougoussis Christos; Kokalj Anton; Lazzeri Michele; Martin-Samos Layla; Marzari Nicola; Mauri Francesco; Mazzarello Riccardo; Paolini Stefano; Pasquarello Alfredo; Paulatto Lorenzo; Sbraccia Carlo; Scandolo Sandro; Sclauzero Gabriele; Seitsonen Ari P; Smogunov Alexander; Umari Paolo; Wentzcovitch Renata M
      Journal of physics. Condensed matter : an Institute of Physics journal (2009), 21 (39), 395502 ISSN:.
      QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.
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      Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996, 77 (18), 3865– 3868,  DOI: 10.1103/PhysRevLett.77.3865
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      Generalized gradient approximation made simple
      Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
      Physical Review Letters (1996), 77 (18), 3865-3868CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
      Generalized gradient approxns. (GGA's) for the exchange-correlation energy improve upon the local spin d. (LSD) description of atoms, mols., and solids. We present a simple derivation of a simple GGA, in which all parameters (other than those in LSD) are fundamental consts. Only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked. Improvements over PW91 include an accurate description of the linear response of the uniform electron gas, correct behavior under uniform scaling, and a smoother potential.
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      Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. 2011, 32 (7), 1456– 1465,  DOI: 10.1002/jcc.21759
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      Effect of the damping function in dispersion corrected density functional theory
      Grimme, Stefan; Ehrlich, Stephan; Goerigk, Lars
      Journal of Computational Chemistry (2011), 32 (7), 1456-1465CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      It is shown by an extensive benchmark on mol. energy data that the math. form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a std. "zero-damping" formula and rational damping to finite values for small interat. distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coeffs. is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interat. forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramol. dispersion in four representative mol. structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermol. distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of cor. GGAs for non-covalent interactions. According to the thermodn. benchmarks BJ-damping is more accurate esp. for medium-range electron correlation problems and only small and practically insignificant double-counting effects are obsd. It seems to provide a phys. correct short-range behavior of correlation/dispersion even with unmodified std. functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying d. functional. © 2011 Wiley Periodicals, Inc.; J. Comput. Chem., 2011.
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      Marzari, N.; Vanderbilt, D.; De Vita, A.; Payne, M. Thermal contraction and disordering of the Al (110) surface. Phys. Rev. Lett. 1999, 82 (16), 3296– 3299,  DOI: 10.1103/PhysRevLett.82.3296
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      Thermal Contraction and Disordering of the Al(110) Surface
      Marzari, Nicola; Vanderbilt, David; De Vita, Alessandro; Payne, M. C.
      Physical Review Letters (1999), 82 (16), 3296-3299CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
      Al(110) has been studied for temps. up to 900 K via ensemble d.-functional mol. dynamics. The strong anharmonicity displayed by this surface results in a neg. coeff. of thermal expansion, where the first interlayer distance decreases with increasing temp. Very shallow channels of oscillation for the second-layer atoms in the direction perpendicular to the surface support this anomalous contraction, and provide a novel mechanism for the formation of adatom-vacancy pairs, preliminary to the disordering and premelting transition. Such characteristic behavior originates in the free-electron-gas bonding at a loosely packed surface.
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      Johnson, E. R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A. J.; Yang, W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132 (18), 6498– 6506,  DOI: 10.1021/ja100936w
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      Revealing Noncovalent Interactions
      Johnson, Erin R.; Keinan, Shahar; Mori-Sanchez, Paula; Contreras-Garcia, Julia; Cohen, Aron J.; Yang, Weitao
      Journal of the American Chemical Society (2010), 132 (18), 6498-6506CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Mol. structure does not easily identify the intricate noncovalent interactions that govern many areas of biol. and chem., including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron d. and its derivs. Our approach reveals the underlying chem. that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small mols., mol. complexes, and solids. Most importantly, the method, requiring only knowledge of the at. coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
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    72. 72
      Otero-de-la-Roza, A.; Johnson, E. R.; Luaña, V. Critic2: A program for real-space analysis of quantum chemical interactions in solids. Comput. Phys. Commun. 2014, 185 (3), 1007– 1018,  DOI: 10.1016/j.cpc.2013.10.026
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      Critic2: A program for real-space analysis of quantum chemical interactions in solids
      Otero-de-la-Roza, A.; Johnson, Erin R.; Luana, Victor
      Computer Physics Communications (2014), 185 (3), 1007-1018CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier B.V.)
      We present critic2, a program for the anal. of quantum-mech. at. and mol. interactions in periodic solids. This code, a greatly improved version of the previous critic program (Otero-de-la Roza et al., 2009), can: (i) find crit. points of the electron d. and related scalar fields such as the electron localization function (ELF), Laplacian, ... (ii) integrate at. properties in the framework of Bader's Atoms-in-Mols. theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, at. basins, ... and (v) perform transformations between file formats describing scalar fields and crystal structures. Critic2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. Critic2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License.
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      Momma, K.; Izumi, F. VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data. J. Appl. Crystallogr. 2011, 44 (6), 1272– 1276,  DOI: 10.1107/S0021889811038970
      73
      VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data
      Momma, Koichi; Izumi, Fujio
      Journal of Applied Crystallography (2011), 44 (6), 1272-1276CODEN: JACGAR; ISSN:0021-8898. (International Union of Crystallography)
      VESTA is a 3D visualization system for crystallog. studies and electronic state calcns. It was upgraded to the latest version, VESTA 3, implementing new features including drawing the external morphpol. of crysals; superimposing multiple structural models, volumetric data and crystal faces; calcn. of electron and nuclear densities from structure parameters; calcn. of Patterson functions from the structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels, detn. of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex mols. and cage-like structures; undo and redo is graphical user interface operations; and significant performance improvements in rendering isosurfaces and calcg. slices.
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    74. 74
      Tersoff, J.; Hamann, D. R. Theory of the scanning tunneling microscope. Phys. Rev. B 1985, 31 (2), 805– 813,  DOI: 10.1103/PhysRevB.31.805
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      Theory of the scanning tunneling microscope
      Tersoff, J.; Hamann, D. R.
      Physical Review B: Condensed Matter and Materials Physics (1985), 31 (2), 805-13CODEN: PRBMDO; ISSN:0163-1829.
      A theory is given for tunneling between a real surface and a model probe tip, applicable to the recently developed "scanning tunneling microscope". The tunneling current is proportional to the local d. of states of the surface, at the position of the tip. The theory is applied to the 2 × 1 and 3 × 1 reconstructions of Au(110); results for the resp. corrugation amplitudes and for the gap distance agree with exptl. results of Binnig et al. (1983) if a 9-Å tip radius is assumed. In addn., a convenient approx. calculational method based on atom superposition is tested; it agrees with the self-consistent calcn. and with expt. for Au(110). This method is used to test the structure sensitivity of the microscope. For the Au(110) measurements the exptl. "image" is relatively insensitive to the positions of atoms beyond the 1st at. layer. Finally, tunneling to semiconductor surfaces is considered. Calcns. for GaAs(110) illustrate interesting qual. differences from tunneling to metal surfaces.
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      Fonseca Guerra, C.; Handgraaf, J. W.; Baerends, E. J.; Bickelhaupt, F. M. Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. J. Comput. Chem. 2004, 25 (2), 189– 210,  DOI: 10.1002/jcc.10351
      75
      Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis
      Fonseca Guerra Celia; Handgraaf Jan-Willem; Baerends Evert Jan; Bickelhaupt F Matthias
      Journal of computational chemistry (2004), 25 (2), 189-210 ISSN:0192-8651.
      We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to bond formation by spatial integration of the deformation density over the atomic Voronoi cell. We compare our method to the well-known Mulliken, Hirshfeld, Bader, and Weinhold [Natural Population Analysis (NPA)] charges for a variety of biological, organic, and inorganic molecules. The Mulliken charges are (again) shown to be useless due to heavy basis set dependency, and the Bader charges (and often also the NPA charges) are not realistic, yielding too extreme values that suggest much ionic character even in the case of covalent bonds. The Hirshfeld and VDD charges, which prove to be numerically very similar, are to be recommended because they yield chemically meaningful charges. We stress the need to use spatial integration over an atomic domain to get rid of basis set dependency, and the need to integrate the deformation density in order to obtain a realistic picture of the charge rearrangement upon bonding. An asset of the VDD charges is the transparency of the approach owing to the simple geometric partitioning of space. The deformation density based charges prove to conform to chemical experience.
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