A computational study to determine the role of σ-hole in Br/OH substituted nido-carborane and its binding capabilities

A detailed investigation of the σ-hole on the halogen atom present in the nido-heteroboranes is made by employing quantum mechanical methods. The bromide and the hydroxyl groups are incorporated in the exo-substituents of the nido-boranes. The potential of the bromide σ-hole was compared to that of electrostatic potential of hydroxyl group counterpart. The presence of a carbon atom vertex, in a different position of a system, influences the σ-hole and hence its binding abilities. Bromide substituted nido-carboranes have less potential and hence weaker binding ability compared to their closo-counterparts. Binding affinity with aliphatic is found to be more compared to that of aromatic system. The presence of solvent dampened the electrostatic interactions. Apart from the neutral system, the binding capabilities of charged nido-heteroboranes were also studied. The results of this study will be further useful for several applications viz., crystal engineering, drug designing (Pharmaceuticals), medicine, material science, energy storage devices, etc.

Chalcogen and Hydrogen Bond Team up in Driving Anion⋅⋅⋅Anion Self-Assembly

H-selenite anions (HSeO3 - ) form in the solid unprecedented anionic supramolecular chains wherein single units are assembled via alternating short Se⋅⋅⋅O and H⋅⋅⋅O contacts. Crystallographic analyses and computational studies (the quantum theory of "atoms-in-molecules", QTAIM, and the noncovalent interaction plot, NCIPlot) consistently prove the attractive nature of these chalcogen bonds (ChBs) and hydrogen honds (HBs), the Janus-type character of HSeO3 - anions which act as both donors and acceptors of ChB and HB, and the possible stability of anion dimers in solution. The effectiveness of the ChBs herein described may lead to consider the HSeO3 - moiety as a new entry in the toolbox of crystal engineering based on ChB.

Search for Osme Bonds with π Systems as Electron Donors

The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO4 (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C2H2, C2H4, C6H6, C4H5N, C4H4O, and C4H4S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, and those involving more extensive π-systems within the aromatic rings form stronger bonds than do the smaller ethylene and acetylene. Extensive analysis questions the existence of a true Osme bond, as the bonding chiefly involves interactions with the three O atoms of MO4 that lie closest to the π-system, via π(C-C)→σ*(M-O) transfers. These interactions are supplemented by back donation from M-O bonds to the π*(CC) antibonding orbitals of the π-systems. Dispersion makes a large contribution to these interactions, higher than electrostatics and much greater than induction.

The Tetrel Bonds of Hypervalent Halogen Compounds

The tetrel bond between PhXF2Y(TF3) (T = C and Si; X = Cl, Br, and I; Y = F and Cl) and the electron donor MCN (M = Li and Na) was investigated at the M06-2X/aug-cc-pVDZ level of theory. As the electronegativity of the halogen atom X increases, the strength of the tetrel bond also increases, but as the electronegativity of the halogen atom Y increases, the strength of the tetrel bond decreases. The magnitude of the interaction energy in most -CF3 complexes was found to be less than 10 kcal/mol, but to exceed 11 kcal/mol for PhClF2Cl(CF3)⋯NCNa. The tetrel bond is greatly enhanced when the -SiF3 group interacts with LiCN or NaCN, with the largest interaction energy approaching 100 kcal/mol and displaying a covalent Si⋯N interaction. Along with this enhancement, the Si⋯N distance was found to be less than the X-Si bond length, the -SiF3 group to be closer to the N atom, and in most -SiF3 systems, the X-Si-F angle to be less than 90°; the -SiF3 group therefore undergoes inversion and complete transfer in some systems.

Chalcogen Bonding Catalysis: Tellurium, the Last Frontier?

Chalcogen bonding (ChB) is the non-covalent interaction occurring between chalcogen atoms as Lewis acid sites and atoms or groups of atoms able to behave as Lewis bases through their lone pair or π electrons. Analogously to its sister halogen bonding, the high directionality of this interaction was implemented for precise structural organizations in the solid state and in solution. Regarding catalysis, ChB is now accepted as a new mode of activation as demonstrated by the increased number of examples in the last five years. In the family of ChB catalysts, those based on tellurium rapidly appeared to overcome their lighter sulfur and selenium counterparts. In this review, we highlight the Lewis acid properties of tellurium-based derivatives in solution and summarize the start-of-the-art of their applications in catalysis.

The effect of various partial atomic charges on the bulk and liquid/vacuum interface properties of iodobenzene derivatives at their melting points

In this work, various atomic charge schemes including natural bond orbital (NBO), electrostatic potential based (CHELPG), and σ-hole model charges were applied in the OPLS-AA force field to investigate their effects on the thermophysical and structural properties of iodobenzene and its derivatives. Molecular dynamics simulations presented in this work show that the studied structural and thermophysical properties are in good agreement with experiments when the CHELPG charge was coupled with the OPLS-AA force field. Also, the arrangement of iodobenzene derivatives in the liquid phase was investigated via combined radial/angular distribution functions (CDFs) analyses and halogen-bonding theory. The most probable orientation of iodobenzene derivatives at the liquid/vacuum interface was assigned by atom density profile and bivariate orientational distribution maps. For all studied iodobenzene derivatives, benzene rings are oriented such that the iodine atoms tend toward the vacuum phase.

Experimental and Theoretical Evidence of a Pb⋅⋅⋅Pb Ditetrel Bond Without a σ-Hole

The crystal structure of a newly synthesized compound, [PbL(Ac)]₂ , (where L=2 (amino(pyrazin-2-yl) methylene) hydrazinecarbothioamide, Ac=acetate anion) exhibits a close contact between pairs of Pb atoms, suggesting a ditetrel bond, in addition to two Pb⋅⋅⋅O tetrel bonds, and two C-H⋅⋅⋅O H-bonds. The presence of this ditetrel bond as an attractive component is confirmed by various quantum chemical methods. This novelty of this particular bond is its existence even in the absence of a σ-hole on the Pb atom, which is typically considered a prerequisite for a bond of this type. From a wider perspective, a survey of the Cambridge Structural Database suggests this bond may be more common than was hitherto thought, with 44 examples of Pb⋅⋅⋅Pb contacts amongst a total number of 219 examples of T⋅⋅⋅T interactions in general (T=Si, Ge, Sn, Pb).

Type I-IV Halogen⋯Halogen Interactions: A Comparative Theoretical Study in Halobenzene⋯Halobenzene Homodimers

In the current study, unexplored type IV halogen⋯halogen interaction was thoroughly elucidated, for the first time, and compared to the well-established types I−III interactions by means of the second-order Møller−Plesset (MP2) method. For this aim, the halobenzene⋯halobenzene homodimers (where halogen = Cl, Br, and I) were designed into four different types, parodying the considered interactions. From the energetic perspective, the preference of scouted homodimers was ascribed to type II interactions (i.e., highest binding energy), whereas the lowest binding energies were discerned in type III interactions. Generally, binding energies of the studied interactions were observed to decline with the decrease in the σ-hole size in the order, C6H5I⋯IC6H5 > C6H5Br⋯BrC6H5 > C6H5Cl⋯ClC6H5 homodimers and the reverse was noticed in the case of type IV interactions. Such peculiar observations were relevant to the ample contributions of negative-belt⋯negative-belt interactions within the C6H5Cl⋯ClC6H5 homodimer. Further, type IV torsional trans → cis interconversion of C6H5X⋯XC6H5 homodimers was investigated to quantify the π⋯π contributions into the total binding energies. Evidently, the energetic features illustrated the amelioration of the considered homodimers (i.e., more negative binding energy) along the prolonged scope of torsional trans → cis interconversion. In turn, these findings outlined the efficiency of the cis configuration over the trans analog. Generally, symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) demonstrated the predominance of all the scouted homodimers by the dispersion forces. The obtained results would be beneficial for the omnipresent studies relevant to the applications of halogen bonds in the fields of materials science and crystal engineering.

Simulating chalcogen bonding using molecular mechanics: a pseudoatom approach to model ebselen

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19; however, efforts to model ebselen in silico have been hampered by the lack of an efficient and accurate method to assess its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to simulate the σ-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach is justified using an energy decomposition analysis of a number of density functional theory–optimized structures, which shows that the σ-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting molecular dynamics simulations on a number of simple complexes, as well as the clinically relevant enzyme SOD1 (superoxide dismutase), which is known to bind to ebselen.

Graphical Abstract

Influence of Substituents in the Benzene Ring on the Halogen Bond of Iodobenzene with Ammonia

The effects on the CI··N halogen bond between iodobenzene and NH3 of placing various substituents on the phenyl ring are monitored by quantum calculations. Substituents R = N(CH3)2, NH2, CH3, OCH3, COCH3, Cl, F, COH, CN, and NO2 were each placed ortho, meta, and para to the I. The depth of the σ-hole on I is deepened as R became more electron-withdrawing which is reflected in a strengthening of the halogen bond, which varied between 3.3 and 5.5 kcal/mol. In most cases, the ortho placement yields the largest perturbation, followed by meta and then para, but this trend is not universal. Parallel to these substituent effects is a progressive lengthening of the covalent C-I bond. Formation of the halogen bond reduces the NMR chemical shielding of all three nuclei directly involved in the C-I··N interaction. The deshielding of the electron donor N is most closely correlated with the strength of the bond, as is the coupling constant between I and N, so both have potential use as spectroscopic measures of halogen bond strength.

Three types of noncovalent interactions studied between pyrazine and XF

Three types noncovalent interactions (type I, II and III) between pyrazine (C₄H₄N₂) and XF (X = F, Cl, Br, and I) have been discovered at the MP2/aug-cc-pVTZ level. TypeI is σ-hole interaction between the positive site on the halogen X of XF and the negative site on one of the pyrazine nitrogens. Type II is counterintuitive σ-hole interaction driven by polarization between the positive site on the halogen X of XF and a portion of the pyrazine ring. Type III is an interaction between the lateral regions of the halogen X of XF and the position of the pyrazine ring. Through comparing the calculated interaction energy, we can know that the type II and type III interactions are weaker than the corresponding type I interactions, and type III interactions are weaker than the corresponding type II interactions in C₄H₄N₂-XF complexes. SAPT analysis shows that the electrostatic energy are the major source of the attraction for the type I (σ-hole) interactions while the type III interactions are mainly dispersion energy. For the type II (counterintuitive σ-hole) interactions in C₄H₄N₂-XF (X = F and Cl) complexes, electrostatic energy are the major source of the attraction, while in C₄H₄N₂-XF (X = Br and I) complexes, the electrostatic term, induction and dispersion play equally important role in the total attractive interaction. NBO analysis, AIM theory, and conceptual DFT are also being utilized.

"Anti-electrostatic" Halogen Bonding between Ions of Like Charge

Halogen bonding occurs between molecules featuring Lewis acidic halogen substituents and Lewis bases. It is often rationalized as a predominantly electrostatic interaction and thus interactions between ions of like charge (e. g., of anionic halogen bond donors with halides) seem counter-intuitive. Herein, we provide an overview on such complexes. First, theoretical studies are described and their findings are compared. Next, experimental evidences are presented in the form of crystal structure database analyses, recent examples of strong "anti-electrostatic" halogen bonding in crystals, and the observation of such interactions also in solution. We then compare these complexes to select examples of "counter-intuitive" adducts formed by other interactions, like hydrogen bonding. Finally, we comment on key differences between charge-transfer and electrostatic polarization.

Anion⋅⋅⋅Anion Interactions Involving σ-Holes of Perrhenate, Pertechnetate and Permanganate Anions

In this communication experimental and theoretical results are reported affording strong evidence that interactions between electron rich atoms and the metal of tetroxide anions of group 7 elements are a new case of attractive and σ‐hole interactions. Single crystal X‐ray analyses, molecular electrostatic potentials, quantum theory of atoms‐in‐molecules, and noncovalent interaction plot analyses show that in crystalline permanganate and perrhenate salts the metal in Mn/ReO₄⁻ anion can act as electron acceptors, the oxygen of another Mn/ReO₄⁻ anion can act as the donor and supramolecular anionic dimers or polymers are formed. The name matere bond (MaB) is proposed to categorize these noncovalent interactions and to differentiate them from the classical metal‐ligand coordination bond.

A-X⋯σ Interactions-Halogen Bonds with σ-Electrons as the Lewis Base Centre

CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F₂, Cl₂, Br₂ and I₂ molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds.

Concerning the Role of σ-Hole in Non-Covalent Interactions: Insights from the Study of the Complexes of ArBeO with Simple Ligands

The structure, stability, and bonding character of some exemplary LAr and L-ArBeO (L = He, Ne, Ar, N₂, CO, F₂, Cl₂, ClF, HF, HCl, NH₃) were investigated by MP2 and coupled-cluster calculations, and by symmetry-adapted perturbation theory. The nature of the stabilizing interactions was also assayed by the method recently proposed by the authors to classify the chemical bonds in noble-gas compounds. The comparative analysis of the LAr and L-ArBeO unraveled geometric and bonding effects peculiarly related to the σ-hole at the Ar atom of ArBeO, including the major stabilizing/destabilizing role of the electrostatic interactionensuing from the negative/positive molecular electrostatic potential of L at the contact zone with ArBeO. The role of the inductive and dispersive components was also assayed, making it possible to discern the factors governing the transition from the (mainly) dispersive domain of the LAr, to the σ-hole domain of the L-ArBeO. Our conclusions could be valid for various types of non-covalent interactions, especially those involving σ-holes of respectable strength such as those occurring in ArBeO.

The Balance between Hydrogen Bonds, Halogen Bonds, and Chalcogen Bonds in the Crystal Structures of a Series of 1,3,4-Chalcogenadiazoles

In order to explore how specific atom-to-atom replacements change the electrostatic potentials on 1,3,4-chalcogenadiazole derivatives, and to deliberately alter the balance between intermolecular interactions, four target molecules were synthesized and characterized. DFT calculations indicated that the atom-to-atom substitution of Br with I, and S with Se enhanced the σ-hole potentials, thus increasing the structure directing ability of halogen bonds and chalcogen bonds as compared to intermolecular hydrogen bonding. The delicate balance between these intermolecular forces was further underlined by the formation of two polymorphs of 5-(4-iodophenyl)-1,3,4-thiadiazol-2-amine; Form I displayed all three interactions while Form II only showed hydrogen and chalcogen bonding. The results emphasize that the deliberate alterations of the electrostatic potential on polarizable atoms can cause specific and deliberate changes to the main synthons and subsequent assemblies in the structures of this family of compounds.

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN^- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.

Comparison of Bifurcated Halogen with Hydrogen Bonds

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.

Halogen bonding interactions in the XC5H4N···YCF3 (X = CH3, H, Cl, CN, NO2; Y = Cl, Br, I) complexes

The noncovalent interactions between the σ-hole region outside the halogen atom and the nitrogen atom of pyridine and its para-substituted derivatives are the focus of this work. Based on the analyses of the electrostatic potentials, YCF₃ (Y = Cl, Br, I) act as halogen bond donors, XC₅H₄N (X = CH₃, H, Cl, CN, NO₂) act as halogen bond acceptors, and the binary halogen-bonded complexes XC₅H₄N···YCF₃ have been designed and investigated by B3LYP-D3/aug-cc-pVDZ calculations together with the aug-cc-pVDZ-PP basis set for iodine. When the halogen bond acceptor remains unchanged, the interactions between C₅H₅N and YCF₃ (Y = Cl, Br, I) increase with the order of Y = Cl, Br, and I. When the halogen donor ICF₃ is fixed, the halogen bonding interactions decrease along the sequence of X = CH₃, H, Cl, CN, NO₂. Therefore, the halogen bond of the CH₃C₅H₄N···ICF₃ complex is the strongest. The interactions between Lewis acid YCF₃ (Y = Cl, Br, I) and pyridine and para-substituted pyridine are closed-shell and noncovalent interactions. On the one hand, when the halogen bond acceptor XC₅H₄N is fixed, with the increase of halogen atomic number, the strength of halogen bond increases; on the other hand, when the halogen bond donor ICF₃ is fixed, as the electron-withdrawing ability of the electron-withdrawing group (X) increases, the halogen bond gradually weakens.

Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4'-Bipyridine Derivatives

Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader-Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4'-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C-Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (V_S) and by comparing and dissecting in atomic/atomic group contributions the V_S maxima (V_S,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.

Computational study of the substituent effect of halogenated fused-ring heteroaromatics on halogen bonding

Halogen bonding (XB) has been applied in many fields from crystal engineering to medicinal chemistry. Compared with the well-studied XB of simple halogenated aromatics, little research has been done on the XB of halogenated fused-ring heteroaromatics, a prevalent substructure in organic compounds. With 1H-pyrrolo[3,2-b]pyridines (PPs) as examples of novel fused-ring heteroaromatics with hydrogen bond donor and acceptor and XB donor, the XB formed by the halogenated heteroaromatics was explored in this study. With 4 different substituents, viz., -CH₃, -NH₂, -F, and -CONH₂, at different positions, 339 derivatives of brominated PP (Br-PP) were designed for calculating their electrostatic potential of the σ-hole of the halogen atom (V_S,max) and binding energy with ammonia as XB acceptor (E_int) at M06-2X/6-311++G(d,p) level by PCM model in dichloromethane. The calculated V_S,max values ranging from -1.3 to 35.1 kcal/mol and the calculated E_int ranging from -0.82 to -2.37 kcal/mol demonstrated that the XB is complicated and highly tunable. Noticeably, the electron-withdrawing substituents, especially at ortho-position, do not always increase the values of V_S,max, while the electron-donating substituents do not always decrease V_S,max. Similar results were observed from the calculation on 339 iodinated PPs at M06-2X/6-311++G(d,p) level. The complexity of the XB formed by the halogenated fused ring heteroaromatics indicated a great potential of tuning its strength by different substituents at different positions and revealed a necessity of quantum chemistry calculation for predicting the XB.Graphical abstract.

Chimeric supramolecular synthons in Ph2Te2(I2)Se

Iodination of Ph₂Te₂Se by molecular iodine is directed towards the Te atom and yields {diiodo[(phenyltellanyl)selanyl]-λ⁴-tellanyl}benzene, PhTeSeTeI₂Ph or C₁₂H₁₀I₂SeTe₂. The molecule can be considered as a chimera of PhTeSeR, PhTeSeTePh and R'TeI₂Ph fragments. The crystal structure features a complex interplay of the supramolecular synthons Te...π(Ph), Se...Te and I...Te, combining molecules into a three-dimensional framework. Their combination affords long-range supramolecular synthons which are fused in a way resembling the mythological chimera and could be defined as chimeric supramolecular synthons. The energies of the intermolecular interactions have also been calculated and analyzed.

Chiral Chalcogen Bond Donors Based on the 4,4'-Bipyridine Scaffold

Organocatalysis through chalcogen bonding (ChB) is in its infancy, as its proof-of-principle was only reported in 2016. Herein, we report the design and synthesis of new chiral ChB donors, as well as the catalytic activity evaluation of the 5,5′-dibromo-2,2′-dichloro-3-((perfluorophenyl)selanyl)-4,4′-bipyridine as organocatalyst. The latter is based on the use of two electron-withdrawing groups, a pentafluorophenyl ring and a tetrahalo-4,4′-bipyridine skeleton, as substituents at the selenium center. Atropisomery of the tetrahalo-4,4′-bipyridine motif provides a chiral environment to these new ChB donors. Their synthesis was achieved through either selective lithium exchange and trapping or a site-selective copper-mediated reaction. Pure enantiomers of the 3-selanyl-4,4′-bipyridine were obtained by high performance liquid chromatography enantioseparation on specific chiral stationary phase, and their absolute configuration was assigned by comparison of the measured and calculated electronic circular dichroism spectra. The capability of the selenium compound to participate in σ-hole-based interactions in solution was studied by ¹⁹F NMR. Even if no asymmetric induction has been observed so far, the new selenium motif proved to be catalytically active in the reduction of 2-phenylquinoline by Hantzsch ester.

Noncovalent Complexes of the Noble-Gas Atoms: Analyzing the Transition from Physical to Chemical Interactions

The bonding character of the noncovalent complexes of the noble-gas (Ng) atoms ranges from nearly purely dispersive contacts to interactions featuring appreciable contributions of induction and charge transfer. In this study, we discuss a new quantitative index that seems peculiarly informative about these diverse bonding situations. This index was termed as the degree of polarization (DoP) of Ng, as it measures, in essence, the Ng polarization promoted by the binding partner. The definition of the DoP(Ng) relies on the analysis of the local electron energy density H(r), and its physical meaning was best appreciated by studying also the charge-displacement function and the molecular electrostatic potential of the investigated benchmark species, that include nearly 60 Ngs complexes of different bonding character. The DoP(Ng) appears of general applicability, and is also positively correlated with other bonding character indices. © 2019 Wiley Periodicals, Inc.

Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design

Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.

A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context

We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.

Dual Geometry Schemes in Tetrel Bonds: Complexes between TF₄ (T = Si, Ge, Sn) and Pyridine Derivatives

When an N-base approaches the tetrel atom of TF₄ (T = Si, Ge, Sn) the latter molecule deforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situate itself at either an axial or equatorial position, leading to two different equilibrium geometries. The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol, which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform the tetrahedral monomer into the equatorial structure is much higher than the equivalent deformation energy in the axial dimer. When these two opposite trends are combined, it is the axial geometry which is somewhat more stable than the equatorial, yielding binding energies in the 8–34 kcal/mol range. There is a clear trend of increasing interaction energy as the tetrel atom grows larger: Si < Ge < Sn, a pattern which is accentuated for the binding energies.

On the Power of Geometry over Tetrel Bonds

Tetrel bonds are noncovalent interactions formed by tetrel atoms (as σ-hole carriers) with a Lewis base. Here, we present a computational and molecular orbital study on the effect of the geometry of the substituents around the tetrel atom on the σ-hole and on the binding strengths. We show that changing the angles between substituents can dramatically increase bond strength. In addition, our findings suggest that the established Sn > Ge > Si order of binding strength can be changed in sufficiently distorted molecules due to the enhancement of the charge transfer component, making silicon the strongest tetrel donor.

Strong Tetrel Bonds: Theoretical Aspects and Experimental Evidence

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

Digging the Sigma-Hole of Organoantimony Lewis Acids by Oxidation

The development of group 15 Lewis acids is an area of active investigation that has led to numerous advances in anion sensing and catalysis. While phosphorus has drawn considerable attention, emerging research shows that organoantimony(III) reagents may also act as potent Lewis acids. Comparison of the properties of SbPh₃ , Sb(C₆ F₅ )₃ , and SbAr^F ₃ with those of their tetrachlorocatecholate analogues SbPh₃ Cat, Sb(C₆ F₅ )₃ Cat, and SbAr^F ₃ Cat (Cat=o-O₂ C₆ Cl₄ , Ar^F =3,5-(CF₃ )₂ C₆ H₃ ) demonstrates that the Lewis acidity of electron deficient organoantimony(III) reagents can be readily enhanced by oxidation to the +V state-as verified by binding studies, organic reaction catalysis, and computational studies. The results are rationalized by explaining that oxidation of the antimony center leads to a lowering of the accepting σ* orbital and a deeper carving of the associated σ-hole.

Selective non-enzymatic total bilirubin detection in serum using europium complexes with different β-diketone-derived ligands as luminescence probes

Three europium(III) complexes, Eu(ectfd)₃ (Hectfd = 1-(9-ethyl-9H-carbazol-7-yl)-4,4,4-trifluorobutane-1,3-dione), Eu(tta)₃ (Htta = 4,4,4-trifluoro-1-(thiophen-2-yl)-butane-1,3-dione), and Eu(dbt)₃ (Hdbt = 2-(4',4',4'-trifluoro-1',3'-dioxobutyl)dibenzothiophene), were synthesized and employed to detect total bilirubin (BR) in blood-serum samples. UV-visible absorption and fluorescence (FL) spectroscopies were used to evaluate the selectivity of each europium (III) fluorescence probe to BR, which was shown to remarkably reduce the luminescence intensities of the europium(III) complexes at a wavelength of 612 nm. The luminescence intensity of each complex is linearly related to BR concentration. Eu(tta)₃ was shown to be the more-appropriate fluorescence probe for the sensitive and reliable detection of total BR in blood serum samples than either Eu(ectfd)₃ or Eu(dbt)₃. This observation can be ascribed to special σ-hole bonding between Htta and BR. In addition, the optimal pH test conditions for the detection of BR in human serum by the Eu(tta)₃ probe were determined. Sensitivity was shown to be dramatically affected by the pH of the medium. The experimental results reveal that pH 7.5 is optimal for this probe, which coincides with the pH of human serum. Furthermore, BR detection using the Eu(tta)₃ luminescence probe is simple, practical, and relatively free of interference from coexisting substances; it has a minimum detection limit (DL) of 68 nM and is a potential candidate for the routine assessment of total BR in serum samples. Graphical Abstract ᅟ.

Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations

A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the Protein Data Bank (PDB). We have found that a large fraction (23 %) of complexes with a S/Se-containing ligand feature close S/Se⋅⋅⋅O/N/S contacts. Eleven non-redundant representative potential S/Se⋅⋅⋅O chalcogen-bond motifs were selected and truncated to model systems and seven more model systems were prepared by S-to-Se substitution. These systems were then subjected to analysis by quantum chemical (QM) methods-electrostatic potential, geometry optimisation or interaction energy calculations, including solvent effects. The QM calculations indicate that chalcogen bonding does indeed play a dominant role in stabilising some of the interaction motifs studied. We thus advocate further exploration of chalcogen bonding with the aim of potential future use in structure-based drug design.

Synthesis and Characterization of Nonclassical Interhalides Based on Bromine Monochloride

Due to a more distinct σ-hole, BrCl is able to form stronger halogen bonds than those in polyhalogen anions based on Cl₂ and Br₂ . This stabilization allows the crystallographic characterization of a variety of new polyinterhalides, in which chloride functions as the central ion as shown by the molecular structures of [AsPh₄ ][Cl(BrCl)₃ ] and [CCl(NMe₂ )₂ ][Cl(BrCl)₅ ]. Furthermore, the solid-state structure of an octahedrally coordinated nonclassical interhalide is reported for the first time. The tridecainterhalide monoanion [Cl(BrCl)₆ ]^- consists of a central chloride ion, which is coordinated by six BrCl molecules in a slightly distorted octahedral structure. All new compounds were characterized by single-crystal X-ray diffraction (XRD), NMR and Raman spectroscopy, as well as quantum-chemical calculations.

Tetrel Bonds with π-Electrons Acting as Lewis Bases-Theoretical Results and Experimental Evidences

MP2/aug-cc-pVTZ calculations were carried out for the ZFH₃-B complexes (Z = C, Si, Ge, Sn and Pb; B = C₂H₂, C₂H₄, C₆H₆ and C₅H₅⁻; relativistic effects were taken into account for Ge, Sn and Pb elements). These calculations are supported by other approaches; the decomposition of the energy of interaction, Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) method. The results show that tetrel bonds with π-electrons as Lewis bases are classified as Z···C links between single centers (C is an atom of the π-electron system) or as Z···π interactions where F‒Z bond is directed to the mid-point (or nearly so) of the CC bond of the Lewis base. The analogous systems with Z···C/π interactions were found in the Cambridge Structural Database (CSD). It was found that the strength of interaction increases with the increase of the atomic number of the tetrel element and that for heavier tetrel elements the ZFH₃ tetrahedral structure is more deformed towards the structure with the planar ZH₃ fragment. The results of calculations show that the tetrel bond is sometimes accompanied by the Z-H···C hydrogen bond or even sometimes the ZFH₃-B complexes are linked only by the hydrogen bond interaction.

Structural Examination of Halogen-Bonded Co-Crystals of Tritopic Acceptors

A series of tritopic N-heterocyclic compounds containing electrostatically and geometrically equivalent binding sites were synthesized and subjected to systematic co-crystallizations with selected perfluoroiodoarenes in order to map out their structural landscapes. More than 70% of the attempted reactions produced a co-crystal as indicated by IR spectroscopy. Four new crystal structures are reported and in all of them, at least one potential binding site on the acceptor is left vacant. The absence of halogen bonds to all sites can be ascribed primarily due to deactivation of the σ-hole on the iodo-arene donors and partially due to steric hindrance. The tritopic acceptors containing 5,6-dimethylbenzimidazole derivatives yield discrete tetrameric aggregates in the solid state, whereas the pyrazole and imidazole analogues assemble into halogen-bonded 1-D chains.

Discovering protein-ligand chalcogen bonding in the protein data bank using endocyclic sulfur-containing heterocycles as ligand search subsets

The chalcogen bond, the noncovalent, electrostatic attraction between covalently bonded atoms in group 16 and Lewis bases, is present in protein-ligand interactions based on X-ray structures deposited in the Protein Data Bank (PDB). Discovering protein-ligand chalcogen bonding in the PDB employed a strategy that focused on searching the database for protein complexes of five-membered, heterocyclic ligands containing endocyclic sulfur with endo electron-withdrawing groups (isothiazoles; thiazoles; 1,2,3-, 1,2.4-, 1,2,5-, 1,3,4-thiadiazoles) and thiophenes with exo electron-withdrawing groups, e.g., 2-chloro, 2-bromo, 2-amino, 2-alkylthio. Out of 930 ligands investigated, 33 or 3.5% have protein-ligand S---O interactions of which 31 are chalcogen bonds and two appear to be S---HO hydrogen bonds. The bond angles for some of the chalcogen bonds found in the PDB are less than 90°, and an electrostatic model is proposed to explain this phenomenon.

The enhancing effect of a cation-π interaction on the cooperativity of halogen bonds: A computational study

In this work, we investigate the effect of a cation-π interaction on the cooperativity of X⋯N halogen bonds in PhX⋯NCX⋯NH₃ complexes, where Ph=phenyl and X=Cl, Br, I. Molecular geometries and interaction energies of the resulting complexes are studied at the MP2/aug-cc-pVDZ(-PP) computational level. The mechanism of the cooperativity between halogen bonds is analyzed using parameters derived from the noncovalent index, quantum theory of atoms in molecules and natural bond orbital methodologies. It is found that the divalent cations (Be²⁺, Mg²⁺) have a larger influence on the cooperativity of halogen bonds than monovalent ones (Li⁺, Na⁺). The formation of a cation-π interaction leads to strengthening of the halogen bonds, hence increases their cooperativity.