Resonance Assisted Chalcogen Bonding as a New Synthon in the Design of Dyes

Intramolecular chalcogen bonding in arylhydrazones of sulfamethizole is strengthened by conjugation in the π-system of a noncovalent five-membered ring. The S⋅⋅⋅O distance in the sulfamethizole moiety of these compounds ranges from 2.698(3) to 2.806(15) Å, which indicates its strong dependence on the attached arylhydrazone fragments. Information on the nature of the intramolecular chalcogen bond was afforded by DFT calculations.     

Creating σ‐Holes through the Formation of Beryllium Bonds

Through the use of ab initio theoretical models based on MP2/aug‐cc‐pVDZ‐optimized geometries and CCSD(T)/aug‐cc‐pVTZ and CCSD(T)/aug‐c‐pVDZ total energies, it has been shown that the significant electron density rearrangements that follow the formation of a beryllium bond may lead to the appearance of a σ‐hole in systems that previously do not exhibit this feature, such as CH₃OF, NO₂F, NO₃F, and other fluorine‐containing systems. The creation of the σ‐hole is another manifestation of the bond activation–reinforcement (BAR) rule. The appearance of a σ‐hole on the F atoms of CH₃OF is due to the enhancement of the electronegativity of the O atom that participates in the beryllium bond. This atom recovers part of the charge transferred to Be by polarizing the valence density of the F into the bonding region. An analysis of the electron density shows that indeed this bond becomes reinforced, but the F atom becomes more electron deficient with the appearance of the σ‐hole. Importantly, similar effects are also observed even when the atom participating in the beryllium bond is not directly attached to the F atom, as in NO₂F, NO₃F, or NCF. Hence, whereas the isolated CH₃OF, NO₂F, and NO₃F are unable to yield F ??? Base halogen bonds, their complexes with BeX₂ derivatives are able to yield such bonds. Significant cooperative effects between the new halogen bond and the beryllium bond reinforce the strength of both noncovalent interactions.     

Simultaneous Aromatic–Beryllium Bonds and Aromatic–Anion Interactions: Naphthalene and Pyrene as Models of Fullerenes,Carbon Single‐Walled Nanotubes,and Graphene

The possibility of forming stable BeR₂:ArH:Y^? (R=H, F, Cl; ArH=naphthalene, pyrene; Y=Cl, Br) ternary complexes in which the beryllium compounds and anions are located on the opposite sides of an extended aromatic system is explored by means of MP2/aug‐cc‐pVDZ ab initio calculations. Comparison of the electron‐density distribution of these ternary complexes with the corresponding BeR₂:ArH and ArH:Y^? binary complexes reveals the existence of significant cooperativity between the two noncovalent interactions in the triads. The energetic effects of this cooperativity are quantified by evaluation of the three‐body interaction energy Δ³E in the framework of the many‐body interaction‐energy (MBIE) approach. Although an essential component of the interaction energies is electrostatic and is well reflected in the changes in the molecular electrostatic potential of the aromatic system on complexation, strong polarization effects, in particular for the BeR₂:ArH interactions, also play a significant role. The charge transfers associated with these polarization effects are responsible for significant distortion of both the BeR₂ and the aromatic moieties. The former are systematically bent in all the complexes, and the latter are curved to a degree that depends on the nature of the R substituents of the BeR₂ subunit.     

Cooperative and Diminutive Effects of Pnicogen Bonds and Cation–π Interactions

The interplay between pnicogen bonds and cation–π interactions has been investigated at the MP2/aug‐cc‐pVDZ level. Interesting cooperative and diminutive effects are observed when pnicogen bonds and cation–π interactions coexist in the same complex. These effects have been analyzed in terms of the structural, energetic, and charge‐transfer properties of the complexes. The variations in electron density at critical points of the intermolecular bond have been used to analyze bond strengthening or weakening. The nature of the interactions and the mechanisms of cooperative and diminutive effects have been studied by means of symmetry‐adapted perturbation theory and molecular electrostatic potentials.     

Intermolecular Weak Interactions in HTeXH Dimers (X=O,S, Se,Te): Hydrogen Bonds,Chalcogen–Chalcogen Contacts and Chiral Discrimination

A theoretical study of the HTeXH (X=O, S, Se and Te) monomers and homodimers was carried out by means of second‐order Møller‐Plesset perturbation theory (MP2) computational methods. In the case of monomers, the isomerization energy from HTeXH to H₂Te=X and H₂X=Te (X=O, S, Se, and Te) and the rotational transition‐state barriers were obtained. Due to the chiral nature of these compounds, homo and heterochiral dimers were found. The electron density of the complexes was characterized with the atoms‐in‐molecules (AIM) methodology, finding a large variety of interactions. The charge transfer within the dimers was analyzed by means of natural bond orbitals (NBO). The density functional theory‐symmetry adapted perturbation theory (DFT‐SAPT) method was used to compute the components of the interaction energies. Hydrogen bonds and chalcogen–chalcogen interactions were characterized and their influence analyzed concerning the stability and chiral discrimination of the dimers.     

Dissecting Noncovalent Interactions in Carboxyl-Functionalized Ionic Liquids Exhibiting Double and Single Hydrogens Bonds Between Ions of Like Charge

We show that the carboxyl-functionalized ionic liquid 1-(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC-CH₂-py][NTf₂] exhibits three types of hydrogen bonding: the expected single hydrogen bonds between cation and anion, and, surprisingly, single and double hydrogen bonds between the cations, despite the repulsive Coulomb forces between the ions of like charge. Combining X-ray crystallography, differential scanning calorimetry, IR spectroscopy, thermodynamic methods and DFT calculations allows the analysis and characterization of all types of hydrogen bonding present in the solid, liquid and gaseous states of the ionic liquid (IL). We find doubly hydrogen bonded cationic dimers (c⁺=c⁺) in the crystalline phase. With increasing temperature, this binding motif opens in the liquid and is replaced by (c⁺−c⁺−a⁻ species, with a remaining single cationic hydrogen bond and an additional hydrogen bond between cation and anion. We provide clear evidence that the IL evaporates as hydrogen-bonded ion pairs (c⁺−a⁻) into the gas phase. The measured transition enthalpies allow the noncovalent interactions to be dissected and the hydrogen bond strength between ions of like charge to be determined.     

Theoretical Study on Cooperativity Effects between Anion–π and Halogen‐Bonding Interactions

This article analyzes the interplay between lone pair–π (lp–π) or anion–π interactions and halogen‐bonding interactions. Interesting cooperativity effects are observed when lp/anion–π and halogen‐bonding interactions coexist in the same complex, and they are found even in systems in which the distance between the anion and halogen‐bond donor molecule is longer than 9 Å. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods. Bader′s theory of “atoms in molecules” is used to characterize the interactions and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The physical nature of the interactions and cooperativity effects are studied by means of molecular interaction potential with polarization partition scheme. By taking advantage of all aforementioned computational methods, the present study examines how these interactions mutually influence each other. Additionally, experimental evidence for such interactions is obtained from the Cambridge Structural Database (CSD).     

Hydrogen‐Bond Cooperativity in Formamide2–Water: A Model for Water‐Mediated Interactions

The rotational spectrum of formamide₂–H₂O formed in a supersonic jet has been characterized by Fourier‐transform microwave spectroscopy. This adduct provides a simple model of water‐mediated interaction involving the amide linkages, as occur in protein folding or amide‐association processes, showing the interplay between self‐association and solvation. Mono‐substituted ¹³C, ¹⁵N, ¹⁸O, and ²H isotopologues have been observed and their data used to investigate the structure. The adduct forms an almost planar three‐body sequential cycle. The two formamide molecules link on one side through an N?H???O hydrogen bond and on the other side through a water‐mediated interaction with the formation of C=O???H?O and O???H?N hydrogen bonds. The analysis of the quadrupole coupling effects of two ¹⁴N‐nuclei reveals the subtle inductive forces associated to cooperative hydrogen bonding. These forces are involved in the changes in the C=O and C?N bond lengths with respect to pure formamide.     

Contributions of Various Noncovalent Bonds to the Interaction between an Amide and S‐Containing Molecules

N‐Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH₃SH, CH₃SCH₃, and CH₃SSCH₃ as models of S‐containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH???O, NH???S, CH???O, CH???S, SH???π, and CH???π H‐bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H‐bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the global minimum, charge‐transfer‐type noncovalent bonds play only a supporting role. The majority of dimers are bound by a collection of several of these attractive interactions. The SH???O and NH???S H‐bonds are of comparable strength, followed by CH???O and CH???S.     

Methyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines

Lysine methylation can modify noncovalent interactions by altering lysine's hydrophobicity as well as its electronic structure. Although the ramifications of the former are documented, the effects of the latter remain largely unknown. Understanding the electronic structure is important for determining how biological methylation modulates protein−protein binding, and the impact of artificial methylation experiments in which methylated lysines are used as spectroscopic probes and protein crystallization facilitators. The benchmarked first-principles calculations undertaken here reveal that methyl-induced polarization weakens the electrostatic attraction of amines with protein functional groups – salt bridges, hydrogen bonds and cation-π interactions weaken by as much as 10.3, 7.9 and 3.5 kT, respectively. Multipole analysis shows that weakened electrostatics is due to the altered inductive effects, which overcome increased attraction from methyl-enhanced polarizability and dispersion. Due to their fundamental nature, these effects are expected to be present in many cases. A survey of methylated lysines in protein structures reveals several cases in which methyl-induced polarization is the primary driver of altered noncovalent interactions; in these cases, destabilizations are found to be in the 0.6–4.7 kT range. The clearest case of where methyl-induced polarization plays a dominant role in regulating biological function is that of the PHD1-PHD2 domain, which recognizes lysine-methylated states on histones. These results broaden our understanding of how methylation modulates noncovalent interactions.     

Double Chalcogen Bonds: Crystal Engineering Stratagems via Diffraction and Multinuclear Solid-State Magnetic Resonance Spectroscopy

Group 16 chalcogens potentially provide Lewis-acidic σ-holes, which are able to form attractive supramolecular interactions with electron rich partners through chalcogen bonds. Here, a multifaceted experimental and computational study of a large series of novel chalcogen-bonded cocrystals, prepared using the principles of crystal engineering, is presented. Single-crystal X-ray diffraction studies reveal that dicyanoselenadiazole and dicyanotelluradiazole derivatives work as promising supramolecular synthons with the ability to form double chalcogen bonds with a wide range of electron donors including halides and oxygen- and nitrogen-containing heterocycles. Extensive ⁷⁷Se and ¹²⁵Te solid-state nuclear magnetic resonance spectroscopic investigations of cocrystals establish correlations between the NMR parameters of selenium and tellurium and the local chalcogen bonding geometry. The relationships between the electronic environment of the chalcogen bond and the ⁷⁷Se and ¹²⁵Te chemical shift tensors were elucidated through a natural localized molecular orbital density functional theory analysis. This systematic study of chalcogen-bond-based crystal engineering lays the foundations for the preparation of the various multicomponent systems and establishes solid-state NMR protocols to detect these interactions in powdered materials.     

A Combined Experimental/Quantum-Chemical Study of Tetrel,Pnictogen, and Chalcogen Bonds of Linear Triatomic Molecules

Linear triatomic molecules (CO₂, N₂O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO₂ and OCS) or pnictogen (N₂O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency to form end-on chalcogen bonds. Comparison of the IR spectra of the complexes with the corresponding monomers in cryogenic solutions in liquid argon enables to determine the stoichiometry and the nature of the complexes. In the present cases, perpendicular tetrel and pnictogen 1:1 complexes are identified mainly on the basis of the lifting of the degenerate ν 2 bending mode with the appearance of both a blue and a red shift. Van ′t Hoff plots of equilibrium constants as a function of temperature lead to complexation enthalpies that, when converted to complexation energies, form the first series of experimental complexation energies on sp¹ tetrel bonds in the literature, directly comparable to quantum-chemically obtained values. Their order of magnitude corresponds with what can be expected on the basis of experimental work on halogen and chalcogen bonds and previous computational work on tetrel bonds. Both the order of magnitude and sequence are in fair agreement with both CCSD(T) and DFA calculations, certainly when taking into account the small differences in complexation energies of the different complexes (often not more than a few kJ mol⁻¹) and the experimental error. It should, however, be noted that the OCS chalcogen complexes are not identified experimentally, most probably owing to entropic effects. For a given Lewis base, the stability sequence of the complexes is first successfully interpreted via a classical electrostatic quadrupole–dipole moment model, highlighting the importance of the magnitude and sign of the quadrupole moment of the Lewis acid. This approach is validated by a subsequent analysis of the molecular electrostatic potential, scrutinizing the σ and π holes, as well as the evolution in preference for chalcogen versus tetrel bonds when passing to “higher” chalcogens in agreement with the evolution of the quadrupole moment. The energy decomposition analysis gives further support to the importance/dominance of electrostatic effects, as it turns out to be the largest attractive term in all cases considered, followed by the orbital interaction and the dispersion term. The natural orbitals for chemical valence highlight the sequence of charge transfer in the orbital interaction term, which is dominated by an electron-donating effect of the N or O lone-pair(s) of the base to the central atom of the triatomics, with its value being lower than in the case of comparable halogen bonding situations. The effect is appreciably larger for TMA, in line with its much higher basicity than DME, explaining the comparable complexation energies for DME and TMA despite the much larger dipole moment for DME.     

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds,Interactions, and Bond/Line Paths

Currently, bonding analysis of molecules based on the Quantum Theory of Atoms in Molecules (QTAIM) is popular; however, “misinterpretations” of the QTAIM analysis are also very frequent. In this contribution the chemical relevance of the bond path as one of the key topological entities emerging from the QTAIM’s topological analysis of the one‐electron density is reconsidered. The role of nuclear vibrations on the topological analysis is investigated demonstrating that the bond paths are not indicators of chemical bonds. Also, it is argued that the detection of the bond paths is not necessary for the “interaction” to be present between two atoms in a molecule. The conceptual disentanglement of chemical bonds/interactions from the bonds paths, which are alternatively termed “line paths” in this contribution, dismisses many superficial inconsistencies. Such inconsistencies emerge from the presence/absence of the line paths in places of a molecule in which chemical intuition or alternative bonding analysis does not support the presence/absence of a chemical bond. Moreover, computational QTAIM studies have been performed on some “problematic” molecules, which were considered previously by other authors, and the role of nuclear vibrations on presence/absence of the line paths is studied demonstrating that a bonding pattern consistent with other theoretical schemes appears after a careful QTAIM analysis and a new “interpretation” of data is performed.     

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding

The hierarchical self‐assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide‐based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error‐check and error‐correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed.     

Extraordinary Modulation of Disulfide Redox‐Responsiveness by Cooperativity of Twin‐Disulfide Bonds

Disulfide bonds have frequently been incorporated into synthetic materials to promote sensitivity of the systems towards different redox environments. Although many strategies have been developed to rationally tune the stability of disulfide linkers, methods to tune their responsiveness towards different redox environments remain elusive. In this work we have developed and explored a disulfide linker bearing two independent disulfide bonds, referred to as a twin‐disulfide linker. We have demonstrated that the twin‐disulfide linker displays an ultrahigh stability at lower concentrations of reducing agent or in weakly reducing environments without a significant compromise in the sensitivity of its response to highly reducing environments such as cytoplasm, a feature that is in remarkable contrast to the traditional single disulfide bonds. Such an extraordinary responsiveness arises from the cooperativity of the twin‐disulfide bonds, which should be of particular interest for applications such as controlled drug delivery and sensing, because relatively large differences in disulfide stability in different redox environments is desired in these applications.     

Control over the Self‐Assembly Modes of PtII Complexes by Alkyl Chain Variation: From Slipped to Parallel π‐Stacks

We report the self‐assembly of a new family of hydrophobic, bis(pyridyl) Pt^II complexes featuring an extended oligophenyleneethynylene‐derived π‐surface appended with six long (dodecyloxy ( 2 )) or short (methoxy ( 3 )) side groups. Complex 2 , containing dodecyloxy chains, forms fibrous assemblies with a slipped arrangement of the monomer units (d_Pt???Pt≈14 Å) in both nonpolar solvents and the solid state. Dispersion‐corrected PM6 calculations suggest that this organization is driven by cooperative π–π, C?H???Cl and π–Pt interactions, which is supported by EXAFS and 2D NMR spectroscopic analysis. In contrast, nearly parallel π‐stacks (d_Pt???Pt≈4.4 Å) stabilized by multiple π–π and C?H???Cl contacts are obtained in the crystalline state for 3 lacking long side chains, as shown by X‐ray analysis and PM6 calculations. Our results reveal not only the key role of alkyl chain length in controlling self‐assembly modes but also show the relevance of Pt‐bound chlorine ligands as new supramolecular synthons.