Hydrogen Bonding: A Coulombic σ-Hole Interaction

Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr)

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

Probing intramolecular interactions using molecular electrostatic potentials: changing electron density contours to unveil both attractive and repulsive interactions

We focus on intramolecular interactions, using the electrostatic potential plotted on iso-density surfaces to lead the way. We show that plotting the electrostatic potential on varying iso-density envelopes much closer to the nuclei than the commonly used 0.001 a.u. contour can reveal the driving forces for such interactions, whether they be stabilizing or destabilizing. Our approach involves optimizing the structures of molecules exhibiting intramolecular interactions and then finding the contour of the electronic density which allows the interacting atoms to be separated; we call this the nearly-touching contour. The electrostatic potential allows then to identify the intramolecular interactions as either attractive or repulsive. The discussed 1,5- and 1,6-intramolecular interactions in o-bromophenol and o-nitrophenol are attractive, while the interactions between terminal methyl hydrogens in diethyl disulfides (as shown recently) and those between the closest hydrogens in planar biphenyl and phenanthrene are clearly repulsive in nature. For the attractive 1,4-interactions in trinitromethane and chlorotrinitromethane, and the 1,3-S⋯N and the 1,4-Si⋯N interactions in the ClH2Si(CH2)nNH2 series, the lack of (3,-1) bond critical points has often been cited as reason to not identify such interactions as attractive in nature. Here, by looking at the nearly-touching contours we see that bond critical points are neither necessary nor sufficient for attractive interactions, as others have pointed out, and in some instances also pointing to repulsive interactions, as the examples of planar biphenyl and phenanthrene discussed in this work show.

Revealing the contradiction between DLVO/XDLVO theory and membrane fouling propensity for oil-in-water emulsion separation

Oil fouling is the crucial issue for the separation of oil-in-water emulsion by membrane technology. The latest research found that the membrane fouling rate was opposite to the widely used theoretical prediction by Derjaguin-Landau-Verwey-Overbeek (DLVO) or extended DLVO (XDLVO) theory. To interpret the contradiction, the molecular dynamics was adopted to explore the molecular behavior of oil and emulsifier (Tween 80) at membrane interface with the assistance of DLVO/XDLVO theory and membrane fouling models. The decreased flux attenuation and fitting of fouling models proved that the existence of Tween 80 effectively alleviated membrane fouling. Conversely, DLVO/XDLVO theory predicted that the membrane fouling should be exacerbated with the increase of Tween 80 concentration in O/W emulsion. This contradiction originated from the different interaction energy between oil/Tween 80 molecules and polyether sulfone (PES) membrane. The favorable free energy of Tween 80 was resulted from the sulfuryl groups in PES and hydrogen bonds (O-H…O) formation further strengthened the interaction. Therefore, Tween 80 could preferentially adsorb on membrane surface and form an isolation layer by demulsification and steric hindrance and resist the aggregation of oil, which effectively alleviated membrane fouling. This study provided a new insight in the interpretation of interaction in O/W emulsion.

Intramolecular Repulsion Visible Through the Electrostatic Potential in Disulfides: Analysis via Varying Iso-density Envelopes

For a series of diethyl disulfide conformations, the nearly touching contours of the electrostatic potential plotted on iso-density molecular surfaces allow the assessment of intramolecular repulsion. The electrostatic potential is plotted on varying iso-density envelopes to find the nearly touching contours for which (a) the surface electrostatic potential does not show overlap between atoms or functional groups and (b) the typical features are visible (σ-hole, lone pair, hydrogen VS,max). When these nearly touching contours X are closer to the nuclei, the more electron density is excluded from the iso-density envelopes and the smaller are the volumes corresponding to these envelopes. Both the contours X and the corresponding volumes are found to correlate with relative conformational energy, reflecting the degree of intramolecular repulsion present in the various diethyl disulfides. Quantitative estimates of intramolecular repulsion can be made based on relationships between the nearly touching contour X vs relative energy and volume (of the nearly touching contour X) vs relative energy, obtained for series of diethyl disulfide conformers. These relations were used to analyze intramolecular repulsion in a set of disulfides broader than diethyl disulfide conformers. We have shown that the approach of varying electronic density contours can be used in the study of repulsive intramolecular interactions, hereby extending earlier work involving attractive intermolecular interactions.

Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter?

Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.

Valence Bond Theory Allows a Generalized Description of Hydrogen Bonding

This paper describes the nature of the hydrogen bond (HB), B:---H-A, using valence bond theory (VBT). Our analysis shows that the most important HB interactions are polarization and charge transfer, and their corresponding sum displays a pattern that is identical for a variety of energy decomposition analysis (EDA) methods. Furthermore, the sum terms obtained with the different EDA methods correlate linearly with the corresponding VB quantities. The VBT analysis demonstrates that the total covalent-ionic resonance energy (RECS) of the HB portion (B---H in B:---H-A) correlates linearly with the dissociation energy of the HB, ΔEdiss. In principle, therefore, RECS(HB) can be determined by experiment. The VBT wavefunction reveals that the contributions of ionic structures to the HB increase the positive charge on the hydrogen of the corresponding external/free O-H bonds in, for example, the water dimer compared with a free water molecule. This increases the electric field of the external O-H bonds of water clusters and contributes to bringing about catalysis of reactions by water droplets and in water-hydrophobic interfaces.

Molecular Modelling of Polychlorinated Dibenzo-p-Dioxins Non-Covalent Interactions with β and γ-Cyclodextrins

Polychlorinated dibenzo-p-dioxins (PCDD) are persistent organic pollutants which result as byproducts in industrial or combustion processes and induce toxicity in both wildlife and humans. In this study, all seven PCDD, tetrachlorinated dibenzo-p-dioxins (TCDD), pentachlorinated dibenzo-p-dioxins (P5CDD), hexachlorinated dibenzo-p-dioxins (H6CDD), heptachlorinated dibenzo-p-dioxins (H7CDD), and octachlorinated dibenzo-p-dioxins (OCDD) were studied in interaction with two cyclodextrins, β-CD and γ-CD, resulting in a total of 40 host-guest complexes. The flexibility of the cyclodextrins was given by the number of glucose units, and the placement of the chlorine groups on the dioxins structure accounted for the different complex formed. Various geometries of interaction obtained by guided docking were studied, and the complexation and binding energy were calculated in the frame of MM+ and OPLS force fields. The results show that the recognition of the PCDD pollutants by the CD may be possible through the formation of PCDD:CD inclusion complexes. This recognition is based on the formation of Coulombic interactions between the chlorine atom of the PCDD and the primary and secondary hydroxyl groups of the CD and van der Waals interaction of the CD hydrophobic cavity with PCDD aromatic structures. Both MM+ and OPLS calculus resulted in close values for the complexation and binding energies. Molecular mechanics calculations offer a proper insight into the molecular recognition process between the PCDD compounds and CD molecules, proved by a good description of the C-H···O bonds formed between the guest and host molecules. It was shown for the first time that CD may efficiently trap PCCDs, opening the way for their tremendous potential use in environmental remediation.

Supramolecular Organization in Salts of Riluzole with Dihydroxybenzoic Acids—The Key Role of the Mutual Arrangement of OH Groups

Intermolecular interactions, in particular hydrogen bonds, play a key role in crystal engineering. The ability to form hydrogen bonds of various types and strengths causes competition between supramolecular synthons in pharmaceutical multicomponent crystals. In this work, we investigate the influence of positional isomerism on the packing arrangements and the network of hydrogen bonds in multicomponent crystals of the drug riluzole with hydroxyl derivatives of salicylic acid. The supramolecular organization of the riluzole salt containing 2,6-dihydroxybenzoic acid differs from that of the solid forms with 2,4- and 2,5-dihydroxybenzoic acids. Because the second OH group is not at position 6 in the latter crystals, intermolecular charge-assisted hydrogen bonds are formed. According to periodic DFT calculations, the enthalpy of these H-bonds exceeds 30 kJ·mol−1. The positional isomerism appears to have little effect on the enthalpy of the primary supramolecular synthon (65–70 kJ·mol−1), but it does result in the formation of a two-dimensional network of hydrogen bonds and an increase in the overall lattice energy. According to the results of the present study, 2,6-dihydroxybenzoic acid can be treated as a promising counterion for the design of pharmaceutical multicomponent crystals.

Virtual Screening, Structural Analysis, and Formation Thermodynamics of Carbamazepine Cocrystals

In this study, the existing set of carbamazepine (CBZ) cocrystals was extended through the successful combination of the drug with the positional isomers of acetamidobenzoic acid. The structural and energetic features of the CBZ cocrystals with 3- and 4-acetamidobenzoic acids were elucidated via single-crystal X-ray diffraction followed by QTAIMC analysis. The ability of three fundamentally different virtual screening methods to predict the correct cocrystallization outcome for CBZ was assessed based on the new experimental results obtained in this study and data available in the literature. It was found that the hydrogen bond propensity model performed the worst in distinguishing positive and negative results of CBZ cocrystallization experiments with 87 coformers, attaining an accuracy value lower than random guessing. The method that utilizes molecular electrostatic potential maps and the machine learning approach named CCGNet exhibited comparable results in terms of prediction metrics, albeit the latter resulted in superior specificity and overall accuracy while requiring no time-consuming DFT computations. In addition, formation thermodynamic parameters for the newly obtained CBZ cocrystals with 3- and 4-acetamidobenzoic acids were evaluated using temperature dependences of the cocrystallization Gibbs energy. The cocrystallization reactions between CBZ and the selected coformers were found to be enthalpy-driven, with entropy terms being statistically different from zero. The observed difference in dissolution behavior of the cocrystals in aqueous media was thought to be caused by variations in their thermodynamic stability.

Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms-in-Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode-mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal-like structures makes them interesting for potential hydrogen storage applications.

The Importance of Electrostatics and Polarization for Noncovalent Interactions: Ionic Hydrogen Bonds vs Ionic Halogen Bonds

A series of 26 hydrogen-bonded complexes between Br⁻ and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6–311 + G(2df,2p) level of theory. Analysis using a model in which Br⁻ is replaced by a point charge shows that the interaction energy (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}$$\end{document}ΔEInt) of the complexes is accurately reproduced by the scaled interaction energy with the point charge (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}^{PC}$$\end{document}ΔEIntPC).This is demonstrated by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}=0.86{\Delta E}_{Int}^{PC}$$\end{document}ΔEInt=0.86ΔEIntPC with a correlation coefficient, R² =0.999. The only outlier is (Br-H-Br)⁻, which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}^{PC}$$\end{document}ΔEIntPC can be divided rigorously into an electrostatic contribution (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{ES}^{PC}$$\end{document}ΔEESPC) and a polarization contribution (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Pol}^{PC}$$\end{document}ΔEPolPC).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol⁻¹, whereas the latter varies between -1.6 and -11.5 kcal mol⁻¹. Compared to our previous study of halogen-bonded (XB) complexes between Br⁻ and C–Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br⁻···HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\Delta E}_{Int}$$\end{document}ΔEInt at short distances in this complex to a large extent can be attributed to charge penetration.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

The proton and the lithium cation linked with π-electron and σ-electron systems: are such interactions beyond or within the definition of hydrogen/lithium bond?

MP2/aug-cc-pVTZ calculations were performed on systems containing the proton or the lithium cation located between two π-electron systems or between π-electron and σ-electron units. The proton or the lithium cation attached to the acetylene or its derivative may be treated as the Lewis acid unit while the remaining part of the complex, the π-electron species or the dihydrogen, act as the Lewis base through their π-electrons or σ-electrons, respectively. The complexes analysed here are linked by the π∙∙∙H + /Li + ∙∙∙π and π∙∙∙H + /Li + ∙∙∙σ interactions. It is discussed whether these interactions are classified as hydrogen and lithium bonds. Therefore, different definitions of the latter interactions are presented. The Electron Localization Function (ELF) and the Natural Bond Orbital (NBO) approaches were applied to analyse the above-mentioned complexes. The unique properties of interactions with the proton and with the lithium cation that occur in complexes analysed here are described.

Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study

Rings are one of the major scaffold components of drugs in medicinal chemistry, due to their unique electronic distribution, scaffold rigidity, and three-dimensionality while lipophilicity is considered as a vital parameter of rings that can influence the reactivity, metabolic stability, and toxicity. We have analyzed the electronic features, hydration patterns, solvation effect and lipophilicity data for 51 most widely used ring systems in drugs. Molecular electrostatic potential (MESP) topology analysis has been used to assess the electronic distribution in rings which provided an easy interpretation of the most suitable hydration patterns of the ring with H₂ O molecule. Further, the global minimum of ring…H₂ O complex has been utilized to predict lipophilicity (logP) with the incorporation of implicit solvation effect. Classification of ring systems based on their molecular weight into four categories, viz. small ring 'sr', medium ring 'mr', large ring 'lr' and extra large ring 'xlr' systems has led to the finding of strong correlations between logP and hydration energy with R = 0.942, 0.933, 0.968 and 0.933, respectively. The micro solvation model is found to be useful for locating the hydrophobic-hydrophilic border for each category of rings in terms of hydration energy whereas the implicit solvation model used for two solvents, n-octanol and water on the most stable hydrated structure led to a global correlation between logP and solvation energy ratio. This correlation predicts a limiting logP value -7.03 for the most hydrophilic ring system and also suggests a clear partitioning of the ring molecules into hydrophobic and hydrophilic classes. The MESP topology-guided approach to understand the electronic features and hydration patterns of rings in drugs lead to powerful predictions on their lipophilicity behavior.

Yet another perspective on hole interactions

Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.

Can Counter-Intuitive Halogen Bonding Be Coulombic?

We use the term "counter-intuitive" to describe an intermolecular interaction in which the electrostatic potentials of the interacting regions of the ground-state molecules have the same sign, both positive or both negative. In the present work, we consider counter-intuitive halogen bonding with nitrogen bases, in which both the halogen σ-hole and the nitrogen lone pair have negative potentials on their molecular surfaces. We show that these interactions can be treated as Coulombic despite the apparent repulsion between the ground-state molecules, provided that both electrostatics and polarization are explicitly taken into account. We demonstrate first that the energies of 20 counter-intuitive interactions with four nitrogen bases can be expressed very well in terms of just two molecular properties: the electrostatic potential of the halogen σ-hole and the average polarizability of the nitrogen base. Then we show that the same two properties can also represent the energies of an expanded data base that includes the 20 counter-intuitive plus an additional 20 weak and moderately-strong intuitive halogen bonding interactions (in which the σ-hole potentials are now positive).

Novel cocrystals of the potent 1,2,4-thiadiazole-based neuroprotector with carboxylic acids: virtual screening, crystal structures and solubility performance

Five new multicomponent solid forms of the biologically active 1,2,4-thiadiazole derivative (TDZH) with dicarboxylic and hydroxybenzoic acids have been discovered by combined virtual/experimental cocrystal screening.

Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations.

Interaction and Polarization Energy Relationships in σ-Hole and π-Hole Bonding

We demonstrate that a wide range of σ- and π-hole interaction energies can be related to (a) the electrostatic potentials and electric fields of the σ- and π-hole molecules at the approximate positions of the negative sites and (b) the electrostatic potentials and polarizabilities of the latter. This is consistent with the Coulombic nature of these interactions, which should be understood to include both electrostatics and polarization. The energies associated with polarization were estimated and were shown to overall be greater for the stronger interactions; no new factors need be introduced to account for these. All of the interactions can be treated in the same manner.

Identification of a previously unreported co-crystal form of acetazolamide: a combination of multiple experimental and virtual screening methods

In this work, we demonstrate an approach of trying multiple methods in a more comprehensive search for co-crystals of acetazolamide.