Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry

Intermolecular interaction potential maps from energy decomposition for interpreting reactivity and intermolecular interactions

The electrostatic potential (ESP) has been widely used to visualize electrostatic interactions about a molecule. However, electrostatic effects are often insufficient for capturing the entirety of an interaction or a reaction of interest. In this investigation, intermolecular interaction potential maps (IMIPs), constructed from the potentials derived from energy decomposition analysis (EDA) using density functional theory, were developed and applied to provide unique insight into molecular interactions and reactivity. To this end, rather than constructing a potential map from probe point charge interactions, IMIPs were constructed from probe interactions with small molecular fragments, including CH3+, CH3-, benzene, and atomic probes including alkali metals, transition metals, and halides. The interaction potentials are further decomposed producing IMIPs for each interaction component using EDA (electrostatic, orbital, steric, etc.). The IMIPs are applied to the study of various interactions including cation-π and anion-π interactions, electrophilic and nucleophilic aromatic substitution, Lewis acid activation, π-stacking, endohedral fullerenes, and select organometallics which reveal fundamental insight into the positional preferences and physical origins of the interactions that otherwise would be difficult to uncover through other surface analyses.

Effect of weak intermolecular interactions on the ionization of benzene derivatives dimers

The interactions between π-systems in dimers of aromatic molecules lead to particularly stable conformations within the relative orientations of the monomers. Extensive research has been conducted on the properties of these complexes in the neutral state. However, in recent decades, there has been a significant surge in applications harnessing these structures for electrical purposes. Therefore, this study places particular emphasis on a deeper understanding of the redox properties of these compounds and how to modify them. To achieve this, we have focused on modeling the effect of a wide range of functional groups on the redox properties of benzene derivatives, observing a correlation between these properties and the change in the molecular dipole moment. Then, we investigated the effect of π-stacking interactions on these properties in dimers formed by either identical or different monomers. In both cases, there is an enhancement of the reducing character of the systems due to these interactions. Upon oxidation, the charge is distributed proportionally to the redox potential of each monomer. Therefore, if there is heterogeneity in these potentials, the properties of the complete cationic system will be influenced by the monomer with a greater tendency to undergo oxidation. The considered models serve as an excellent example for studying the behavior of nucleobases in DNA or aromatic amino acids, among others.

Growth mechanism of aromatic prebiotic molecules: insights from different processes of ion-molecule reactions in benzonitrile-ammonia and benzonitrile-methylamine clusters

Benzonitrile (BN, C6H5CN) has been detected in the cold molecular cloud Taurus molecular cloud-1 (TMC-1) in 2018, which is suggested to be a precursor in the formation of more complex nitrogen-containing aromatic interstellar compounds. In this study, we utilized mass-selected infrared (IR) photodissociation spectroscopy and quantum chemical calculations to investigate the structures and gaseous ion-molecule reactions of benzonitrile-ammonia (BN-NH3) and benzonitrile-methylamine (BN-MA) clusters. The spectral observations indicate that the cyclic hydrogen bonding structure predominates in both neutral clusters. After VUV (118 nm) single-photon ionization, a new C-N covalent bond formed between BN and NH3 in the (BN-NH3)+ cluster. However, proton sharing constitutes the primary structure of the (BN-MA)+ cluster. The two nitrogen-containing interstellar molecules react with BN to yield distinct products due to difference in charge distribution and molecular polarity in the ionized clusters. The reactions of BN with other molecules contribute to our understanding of the growth mechanisms of complex interstellar molecules.

Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size

We have reported in the last years the strong effect that Be- and Mg-containing Lewis acids have on the intrinsic properties of typical bases, which become acids upon complexation. In an effort to investigate these changes when the Be and Mg derivatives form clusters of increasing size, we have examined the behavior of the (MX2)n (M = Be, Mg; X = H, F; n = 1, 2, 3) clusters when they interact with ammonia, methanimine, hydrogen cyanide and pyridine, and with their corresponding deprotonated forms. The complexes obtained at the M06-2X/aug-cc-pVTZ level were analyzed using the MBIE energy decomposition formalism, in parallel with QTAIM, ELF, NCIPLOT and AdNDP analyses of their electron density. For n = 1 the interaction enthalpy for the different families of monomers, Be (Mg) hydrides and Be (Mg) fluorides, follows the same trend as the intrinsic basicity of the base that interacts with them. This interaction is greatly reinforced after the deprotonation of the base, resulting in a significant enhancement of the intrinsic acidity of the corresponding MX2-Base complex. For (MX2)2 clusters a further reinforcement of the interaction with the base is observed, this reinforcement being again larger for the deprotonated complexes. However, the concomitant increase of their intrinsic acidity is one order of magnitude larger for hydrides than for fluorides. Unexpectedly, the cyclic conformers (MX2)3, which are more unstable than the linear ones, become the global minima after association with the base and the same is true for the deprotonated complex. Accordingly, a further increase of the intrinsic acidity of the (MX2)3-Base complexes with respect to the (MX2)2-Base ones is observed. This effect is maximum for (MgF2)3 clusters, to the point that the (MgF2)3-Base complexes become more acidic than nitric acid, the extreme case being the cluster (MgF2)3-NCH, whose acidity is higher than that of perchloric acid.

Onset of Nitriles Hydration with an Environmentally Benign Catalyst: in-Water versus on-Water Conditions

The reaction yield of nitriles hydration using a catalyst depends on the aqueous medium. Using ab initio molecular dynamics, we probed whether "in-water" (in bulk medium) or "on-water" (at the interface with vacuum) conditions can change the onset of the reaction. Investigating a hydrogen-bond mediated mechanism, the lifetimes of the intermolecular interaction between benzonitrile and choline in the two protocols were compared, and the diffusion of the hydroxide anion around the cyano group was discussed.

Electronic substituent effect on the conformation of a phenylalanine-incorporated cyclic peptide

The Phe-incorporated cyclic peptide [cyclo(-Phe1-oxazoline2-d-Val3-thiazole4-Ile5-oxazoline6-d-Val7-thiazole8-)] is in a conformational equilibrium between square and folded forms in solution. In the folded form, a CH⋯π interaction between the Phe1 aromatic ring and the Oxz2 methyl group is observed. We endeavored to control the local conformation and thus modulate the CH⋯π interaction and flexibility of the Phe1 side chain by controlling the electronic substituent effects at the 4-position of the aromatic ring of the Phe1 residue. The effect of the 4-substituent on the global conformation was indicated by the linear relationship between the conformational free energies (ΔGo) determined through NMR-based quantification and the Hammett constants (σ). Electron-donating substituents, which had relatively strong CH⋯π interactions, promoted peptide folding by restraining the loss in entropy. Local control by the 4-substituent effects suggested that the Phe side chain exerts an entropic influence on the folding of these cyclic peptides.

Sheltering Mono-P-Ligated Metal Complexes in Porous Polystyrene Monolith: Effect of Aryl Pendant Stabilizers on Catalytic Durability

Metal centers that can generate coordinatively unsaturated metals in accessible and stable states have been developed using synthetic polymers with sophisticated ligand and scaffold designs, which required synthetic efforts. Herein, we report a simple and direct strategy for producing polymer-supported phosphine-metal complexes, which stabilizes mono-P-ligated metals by modulating the electronic properties of the aryl pendant groups in the polymer platform. A three-fold vinylated PPh3 was copolymerized with a styrene derivative and a cross-linker to produce a porous polystyrene-phosphine hybrid monolith. Based on the Hammett substituent constants, the electronic properties of styrene derivatives were modulated and incorporated into the polystyrene backbone to stabilize the mono-P-ligated Pd complex via Pd-arene interactions. Through NMR, TEM, and comparative catalytic studies, the polystyrene-phosphine hybrid, which induces selective mono-P-ligation and moderate Pd-arene interactions, demonstrated high catalytic durability for the cross-coupling of chloroarenes under continuous-flow conditions.

Harnessing the cation-π interactions of metalated gold monolayer-protected clusters to detect aromatic volatile organic compounds

The strong, non-covalent interactions between π-systems and cations have been the focus of numerous studies on biomolecule structure and catalysis. These interactions, however, have yet to be explored as a sensing mechanism for detecting trace levels of volatile organic compounds (VOCs). In this article, we provide evidence that cation-π interactions can be used to elicit sensitive and selective chemiresistor responses to aromatic VOCs. The chemiresistors are fitted with carboxylate-linked alkali metals bound to the surface of gold monolayer-protected clusters formulated on microfabricated interdigitated electrodes. Sensor responses to aromatic and non-aromatic VOCs are consistent with a model for cation-π interactions arising from association of electron-rich aromatic π-systems to metal ions with the relative strength of attraction following the order K⁺ > Na⁺ > Li⁺. The results point toward cation-π interactions as a promising research avenue to explore for developing aromatic VOC-selective sensors.

Bonding and 13 C-NMR properties of coinage metal tris(ethylene) and tris(norbornene) complexes: Evaluation of the role of relativistic effects from DFT calculations

The π-complexes of cationic coinage metal ions (Cu(I), Ag(I), Au(I)) provide useful experimental support for understanding fundamental characteristics of bonding and ¹³ C-NMR patterns of the group 11 triad. Here, we account for the role of relativistic effects on olefin-coinage metal ion interaction for cationic, homoleptic tris-ethylene, and tris-norbornene complexes, [M(η² -C₂ H₄ )₃ ]⁺ and [M(η² -C₇ H₁₀ )₃ ]⁺ (M = Cu, Ag, Au), as representative case of studies. The M-(CC) bond strength in the cationic, tris-ethylene complexes is affected sizably for Au and to a lesser extent for Ag and Cu (48.6%, 16.7%, and 4.3%, respectively), owing to the influence on the different stabilizing terms accounting for the interaction energy in the formation of coinage metal cation-π complexes. The bonding elements provided by olefin → M σ-donation and olefin ← M π-backbonding are consequently affected, leading to a lesser covalent interaction going down in the triad if the relativistic effects are ignored. Analysis of the ¹³ C-NMR tensors provides further understanding of the observed experimental values, where the degree of backbonding charge donation to π₂ *-olefin orbital is the main influence on the observed high-field shifts in comparison to the free olefin. This donation is larger for ethylene complexes and lower for norbornene counterparts. However, the bonding energy in the later complexes is slightly stabilized given by the enhancement in the electrostatic character of the interaction. Thus, the theoretical evaluation of metal-alkene bonds, and other metal-bonding situations, benefits from the incorporation of relativistic effects even in lighter counterparts, which have an increasing role going down in the group.

Electrostatic penetration effects stand at the heart of aromatic π interactions

The nature of the interaction in benzene-containing dimers has been analysed by means of Symmetry Adapted Perturbation Theory (SAPT). The total interaction energy and the preference for the dimers to adopt slipped structures are, apparently, consequence of the balance between repulsion and dispersion. However, our results indicate that this only holds when trends are analysed using fixed intermolecular distances. Employing the most favourable separations between rings it turns out that the changes on the total interaction energy are mostly controlled by electrostatics, while repulsion and dispersion cancel each other to a great extent. Most of the electrostatic contribution is accounted for by electrostatic penetration, so a description based on multipoles should not be employed to rationalise the interaction in benzene-containing dimers. The changes on the interaction energy in benzene-containing dimers are steered by electrostatic penetration which, though often overlooked, plays an essential role for the description of aromatic π interactions.

Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds

Composites of carbon nanotubes (CNTs) and lignin are promising and potentially cheap precursors of-to this day-expensive carbon fibers. Since the control of the CNT-lignin interface is crucial to maximize fiber performance, it is imperative to understand the fundamental noncovalent interactions between lignin and CNT. In the present study a density functional theory study is conducted to investigate the fundamental noncovalent interaction strength between metallic (n, n) single-walled CNT (SWCNT) and simple lignin model molecules. In particular, the respective adsorption energies are used to gauge the strength of interaction classes (ππ interaction, CHπ hydrogen bonding and OH-related hydrogen bonding. From the data, substituent-dependent interaction trends as well as class- and curvature-dependent interaction trends are derived. Overall, we find that most of the interaction strength trends appear to be strongly influenced by geometry: flat orientation of the test molecules relative to the (n, n) SWCNT surface and small (n, n) SWCNT curvature-that is, large diameter enhances the CHπ and ππ interactions.

Alkaline Stability Evaluation of Polymerizable Hexyl-Tethered Ammonium Cations

One of the important challenges in designing robust alkaline anion exchange membranes is the difficulty associated with the chemical stability of covalently bound cationic units. Here, a systematic study exploring alkaline stabilities of polymerizable hexyltrimethylammonium cations is presented, where the hexyl chain is linked to a phenyl ring through a direct carbon-carbon, phenyl ether, or benzyl ether functionality. For this work, small molecule model compounds, styrenic monomer analogs, and their homopolymers are synthesized. Alkaline stabilities of the small molecule cations and their homopolymers are compared to alkaline stability of benzyltrimethylammonium (BTMA) cation and its homopolymer poly(BTMA), respectively. All the hexyl-tethered cations and their homopolymers are significantly more stable under strongly alkaline conditions (2 m KOD at 80 °C). Moreover, ether-linked cations show comparable stability to the direct carbon-carbon linked cation. Via ¹ H NMR analyses, possible degradation mechanisms are investigated for each small molecule cation. Findings of this study strongly suggest that the alkaline stability is dictated by the steric hindrance around the β-hydrogen. This study expands beyond the limits of general knowledge on alkaline stability of alkyl-tethered ammonium cations via the Hofmann elimination route, highlights important design parameters for stable ammonium cations, and demonstrates accessible directly polymerizable alkaline stable ammonium cations.

Insight into the protein salting-in mechanism of arginine, magnesium chloride and ethylene glycol: Solvent interaction with aromatic solutes

Key factors in the salting-in effects on proteins of additives are their interactions with aromatic groups. We studied the interaction of four aromatic solutes, benzyl alcohol (BA), phenol, 4-hydroxybenzyl alcohol (4-HBA) and methyl gallate (MG), with different salting-in additives, arginine hydrochloride (ArgHCl), magnesium chloride (MgCl₂), ethylene glycol (EG), and guanidine hydrochloride (GdnHCl) using solubility measurements. We used sodium chloride (NaCl) as a control. MgCl₂ decreased the solubility of the four aromatic solutes with weak solute dependence. In contrast, ArgHCl, GdnHCl, and EG increased the solubility of four aromatic solutes with a similar solute dependence. Their salting-in effects were weaker on BA and 4-HBA and stronger on phenol and MG. These results indicate that attached groups alter the aromatic properties, affecting the interactions between the benzene ring and these three additives. More importantly, the observed results demonstrate that the salting-in mechanism is different between MgCl₂, EG and ArgHCl, which should play a role in their effects on protein solubility.

A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions

DNA can assume various structures as a result of interactions at atomic and molecular levels (e.g., hydrogen bonds, π–π stacking interactions, and electrostatic potentials), so understanding of the consequences of these interactions could guide development of ways to produce elaborate programmable DNA for applications in bio- and nanotechnology. We conducted advanced ab initio calculations to investigate nucleobase model structures by componentizing their donor-acceptor interactions. By unifying computational conditions, we compared the independent interactions of DNA duplexes, triplexes, and quadruplexes, which led us to evaluate a stability trend among Watson–Crick and Hoogsteen base pairing, stacking, and even ion binding. For a realistic solution-like environment, the influence of water molecules was carefully considered, and the potassium-ion preference of G-quadruplex was first analyzed at an ab initio level by considering both base-base and ion-water interactions. We devised new structure factors including hydrogen bond length, glycosidic vector angle, and twist angle, which were highly effective for comparison between computationally-predicted and experimentally-determined structures; we clarified the function of phosphate backbone during nucleobase ordering. The simulated tendency of net interaction energies agreed well with that of real world, and this agreement validates the potential of ab initio study to guide programming of complicated DNA constructs.

Discovery of a potent, highly selective, and orally bioavailable inhibitor of CDK8 through a structure-based optimisation

CDK8 is deregulated in multiple types of human cancer and is viewed as a therapeutic target for the treatment of the disease. Accordingly, the search for small-molecule inhibitors of CDK8 is being intensified. Capitalising on our initial discovery of AU1-100, a potent CDK8 inhibitor yet with a limited degree of kinase selectivity, a structure-based optimisation was carried out, with a series of new multi-substituted pyridines rationally designed, chemically prepared and biologically evaluated. Such endeavour has culminated in the identification of 42, a more potent CDK8 inhibitor with superior kinomic selectivity and oral bioavailability. The mechanism underlying the anti-proliferative effect of 42 on MV4-11 cells was studied, revealing that the compound arrested the G1 cell cycle and triggered apoptosis. The low risk of hepato- and cardio-toxicity of 42 was estimated. These findings merit further investigation of 42 as a targeted cancer therapeutic.

The effect of cation-π interactions on the stability and electronic properties of anticancer drug Altretamine: a theoretical study

The present work utilizes density functional theory (DFT) calculations to study the influence of cation-π interactions on the electronic properties of the complexes formed by Altretamine [2,4,6-tris(dimethylamino)-1,3,5-triazine], an anticancer drug, with mono- and divalent (Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺ and Ca²⁺) metal cations. The structures were optimized with the M06-2X method and the 6-311++G(d,p) basis set in the gas phase and in solution. The theory of `Atoms in Molecules' (AIM) was applied to study the nature of the interactions by calculating the electron density ρ(r) and its Laplacian at the bond critical points. The charge-transfer process during complexation was evaluated using natural bond orbital (NBO) analysis. The results of DFT calculations demonstrate that the strongest/weakest interactions belong to Be²⁺/K⁺ complexes. There are good correlations between the achieved densities and the amounts of charge transfer with the interaction energies. Finally, the stability and reactivity of the cation-π interactions can be determined by quantum chemical computation based on the molecular orbital (MO) theory.

The relative position of π-π interacting rings notably changes the nature of the substituent effect

The substituent effect in monosubstituted benzene dimers mostly follows changes on electrostatics mainly controlled by the direct interaction of the substituent and the other phenyl ring, whereas the contribution from the interacting rings is smaller. As the substituent is located further away the two contributions become of similar magnitude, so the global result is a combination of both effects. These trends are confirmed in larger systems containing a contact between phenyl rings; at closer distances the interaction of the substituent and the other ring clearly dominates over changes associated with the substituted ring, but as the substituent is located further away its contribution decreases and the contribution from the ring becomes more relevant. Care should be taken in larger systems because the observed energy change can also be affected by interactions with other regions of the molecule not directly involved in the π-π interaction.

Understanding the Reactivity and Selectivity of Fluxional Chiral DMAP-Catalyzed Kinetic Resolutions of Axially Chiral Biaryls

Fluxional chiral DMAP-catalyzed kinetic resolutions of axially chiral biaryls were examined using density functional theory. Computational analyses lead to a revised understanding of this reaction in which the interplay of numerous non-covalent interactions control the conformation and flexibility of the active catalyst, the preferred mechanism, and the stereoselectivity. Notably, while the DMAP catalyst itself is confirmed to be highly fluxional, electrostatically driven π⋅⋅⋅π⁺ interactions render the active, acylated form of the catalyst highly rigid, explaining its pronounced stereoselectivity.

Intermolecular distance measurement with TNT suppressor on the M13 bacteriophage-based Förster resonance energy transfer system

An M13 bacteriophage-based Förster resonance energy transfer (FRET) system is developed to estimate intermolecular distance at the nanoscale using a complex of CdSSe/ZnS nanocrystal quantum dots, genetically engineered M13 bacteriophages labeled with fluorescein isothiocyanate and trinitrotoluene (TNT) as an inhibitor. In the absence of trinitrotoluene, it is observed that a significant spectral shift from blue to green occur, which represents efficient energy transfer through dipole-dipole coupling between donor and acceptor, or FRET-on mode. On the other hand, in the presence of trinitrotoluene, the energy transfer is suppressed, since the donor-to-acceptor intermolecular distance is detuned by the specific capturing of TNT by the M13 bacteriophage, denoted as FRET-off mode. These noble features are confirmed by changes in the fluorescence intensity and the fluorescence decay curve. TNT addition to our system results in reducing the total energy transfer efficiency considerably from 16.1% to 7.6% compared to that in the non-TNT condition, while the exciton decay rate is significantly enhanced. In particular, we confirm that the energy transfer efficiency satisfies the original intermolecular distance dependence of FRET. The relative donor-to-acceptor distance is changed from 70.03 Å to 80.61 Å by inclusion of TNT.

Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.

Tuning Stacking Interactions between Asp-Arg Salt Bridges and Heterocyclic Drug Fragments

Stacking interactions can play an integral role in the strength and selectivity of protein-drug binding and are of particular interest given the ubiquity and variety of heterocyclic fragments in drugs. In addition to traditional stacking interactions between aromatic rings, stacking interactions involving heterocyclic drug fragments and protein salt bridges have also been observed. These "salt-bridge stacking interactions" can be quite strong but are not well understood. We studied stacked dimers of the acetate···guanidinium ion pair with a diverse set of 63 heterocycles using robust ab initio methods. The computed interaction energies span more than 10 kcal mol^-1, indicating the sensitivity of these salt-bridge stacking interactions to heterocycle features. Trends in both the strength and preferred geometry of these interactions can be understood through analyses of the electrostatic potentials and electric fields above the heterocycles. We have developed new heterocycle descriptors that quantify these effects and used them to create robust predictors of the strength of salt-bridge stacking interactions both in the gas phase and a protein-like dielectric environment. These predictive tools, combined with a set of qualitative guidelines, should facilitate the choice of heterocycles that maximize salt-bridge stacking interactions in drug binding sites.

Büchi's model based analysis of local anesthetic action in procaine hydrochloride: Vibrational spectroscopic approach

The drug action of ester type local anesthetic (LA) procaine hydrochloride (PRC HCl) is activated by blocking Na⁺ ion flow when it binds to the ion channel in the ligand gated sodium ion channel protein. Büchi's model, explains binding action of ester type LA drug with receptor in terms of charge transfer, dipole-dipole, hydrogen bonding and van der Waals interactions through lipophilic, ester and hydrophilic moieties. The present work investigates molecular structural and vibrational spectral features of para amino benzoate group, ester part and tertiary amino group respectively belonging to lipophilic, ester and hydrophilic moieties, accountable for the binding of drug to sodium channel. The electron transport mechanism through the ring responsible for structural deviation from benzenoid to quinonoid form and consequent dipolar nature of carbonyl group have been investigated, based on the analysis of XRD, DFT computed molecular structure, 8a ring mode and NBO charges. The characteristic UV absorption peaks and vibrational marker bands of LA drugs have been identified and the charge transfer interaction responsible for lipophilic binding has been investigated. The blocking of Na⁺ in the ion channel has been probed using attractive and repulsive energy profile. The molecular polarizability has been computed to substantiate the correlation between the structure activity relationship of LA drug molecule and molecular polarizability. The low toxicity of PRC HCl was evaluated using in vitro cytotoxicity study, confirming it as a potential short acting local anesthetic.

Topology and Electronic Density Driven Generation of Alkali Cation Complexes

The formation and characterization of K⁺ and Cs⁺ complexes originating from the cooperativity of three non-covalent interactions is explored. The tridimensional preorganization of the naphthothiophene platform displays a favorable well-defined bay region combining a π fragment and a carbonyl moiety flanking a central sulfur atom. A joint theoretical and experimental infrared multiple photon dissociation (IRMPD) study allowed deciphering the key contribution of the orthogonal phenyl fragment to the elaboration of alkali metal complexes. In combination with S and CO interactions, the π-cation interaction significantly enhances the binding energies of naphthothiophene derivatives.

Substituent effect of the stacking interaction between carbon monoxide and benzene

Noncovalent interactions (NCIs) between carbon monoxide and substituted benzene were investigated at the M06-2X/6-311++G(d,p) level. rThe results of interaction energy analysis indicated different effects for the electron-donating (-NH₂, -OH, -CH₃) and electron-withdrawing (-F, -CN, -NO₂) groups on the CO⋯PhX complex. Atoms in molecules analysis confirmed the NCIs between CO and PhX. NCI analysis revealed that these interactions belong to van der Waals interactions. The electron density shift of the complexes was investigated with electron density difference analysis. Ternary CO⋯PhX⋯Bz complexes were designed to study the interplay between CO⋯π and π⋯π stacking interactions.

Interactions of Substituted Nitroaromatics with Model Graphene Systems: Applicability of Hammett Substituent Constants To Predict Binding Energies

Applicability of Hammett parameters (σ m and σ p ) was tested in extended π-systems in gas phase. Three different model graphene systems, viz. 5,5-graphene (GR), 3-B-5,5-graphene (3BGR), and 3-N-5,5-graphene (3NGR), were designed as extended π-systems, and interactions of various nitrobenzene derivatives (mainly m- and p-substituted together with some multiple substitutions) on such platforms were monitored using density functional theory (M06/cc-pVDZ, M06/cc-pVTZ, M06/sp-aug-cc-pVTZ) and Møller-Plesset second-order perturbation (MP2/cc-pV-DZ) theory. Offset face to face (OSFF) stackings were found to be the favored orientations, and reasonable correlations were found between binding energies (ΔE B) and the ∑|σ m | values of the substituted nitrobenzenes. It was proposed previously that |σ m | contains information about the substituents' polarizability and controls electrostatic and dispersion interactions. The combination of ∑|σ m | and molar refractivity (as ∑M r) or change in polarizability (Δα: with respect to benzene) of nitrobenzene derivatives generated statistically significant correlation with respect to ΔE B, thereby supporting the hypothesis related to the validity of |σ m | correlations. The |σ p | parameters also maintain similar correlations for the various p-substituted nitrobenzene derivatives together with several multiply-substituted nitrobenzene derivatives. The correlation properties in such cases are similar to the |σ m | cases, and the energy partition analysis for both the situations reveled importance of electrostatic and dispersion contributions in such interactions. The applicability of Hammett parameters was observed previously on the restricted parallel face to face orientation of benzene···substituted benzene systems, and the present results show that such an idea could be used to predict ΔE B values in OSFF orientations, if the scaffolds are designed in such a way that substituted benzene systems cannot escape their π-clouds.

Stacking Interactions of Heterocyclic Drug Fragments with Protein Amide Backbones

Stacking interactions can be important enthalpic contributors to drug binding. Among the less well-studied stacking interactions are those occurring between an arene and the π-face of an amide group. Given the ubiquity of heterocycles in drugs, combined with the abundance of amides in the protein backbone, optimizing these noncovalent interactions can provide a potential route to enhanced drug binding. Previously, Diederich et al. (ChemMedChem 2013, 8, 397-404) studied stacked dimers of a model amide with a set of 18 heterocycles, showing that computed interaction energies correlate with the dipole moments of the heterocycles and providing guidelines for the optimization of these interactions. We considered stacked dimers of the same model amide with a larger set of 28 heterocycles common in pharmaceuticals, by using more robust ab initio methods. While the overall trends in these new data corroborate many of the results of Diederich et al., these data provide a more refined view of the nature of amide stacking interactions. We present a robust scoring function for amide stacking interaction energies based on the molecular dipole moment and strength of the electric field above the arene.

Cation-π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine

The interactions of neutral aromatic ligands with cationic arginine, histidine and lysine amino acid residues have been studied with ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of X-ray structures.

We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pK_a. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol^–1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings.

Inverting Steric Effects: Using "Attractive" Noncovalent Interactions To Direct Silver-Catalyzed Nitrene Transfer

Nitrene transfer (NT) reactions represent powerful and direct methods to convert C-H bonds into amine groups that are prevalent in many commodity chemicals and pharmaceuticals. The importance of the C-N bond has stimulated the development of numerous transition-metal complexes to effect chemo-, regio-, and diastereoselective NT. An ongoing challenge is to understand how subtle interactions between catalyst and substrate influence the site-selectivity of the C-H amination event. In this work, we explore the underlying reasons why Ag(tpa)OTf (tpa = tris(pyridylmethyl)amine) prefers to activate α-conjugated C-H bonds over 3° alkyl C(sp3)-H bonds and apply these insights to reaction optimization and catalyst design. Experimental results suggest possible roles of noncovalent interactions (NCIs) in directing the NT; computational studies support the involvement of π···π and Ag···π interactions between catalyst and substrate, primarily by lowering the energy of the directed transition state and reaction conformers. A simple Hess's law relationship can be employed to predict selectivities for new substrates containing competing NCIs. The insights presented herein are poised to inspire the design of other catalyst-controlled C-H functionalization reactions.

Competitive/co-operative interactions in acid base sandwich: role of cation vs. substituents

The cation-π interaction can be envisaged as a lewis acid base interaction, and it is in line with Pearson's acid base concept. The critical examination of interactions between the π-acids (alkali metal cations - Li⁺, Na⁺ and alkaline earth metal cations Mg²⁺, Ca²⁺) on one face and tripodal Cr(CO)₃ moiety on the other π face of substituted arenes demonstrates the role of cation and substitutents in manipulating the interactions between them. The interaction of the two π acids on both faces of arene is not expectedly additive, rather it shows either depreciation of interaction energy revealing the competition of acids toward the base or enhancement of interaction energy denoting a cooperative effect. Among the metal cations under study, Mg²⁺ shows a cooperative gesture. Although the substituents play a meek role, they unfailingly exert their electronic effects and are amply documented by excellent correlation of various parameters with the Hammett constant σ_m. The elusive switching of λ_max from the UV to IR region on binding Mg²⁺ with substituted arene-Cr(CO)₃ complex is a characteristic clue that TDDFT can help design the ionic sensors for Mg²⁺ cations.

Exploiting non-covalent π interactions for catalyst design

Molecular recognition, binding and catalysis are often mediated by non-covalent interactions involving aromatic functional groups. Although the relative complexity of these so-called π interactions has made them challenging to study, theory and modelling have now reached the stage at which we can explain their physical origins and obtain reliable insight into their effects on molecular binding and chemical transformations. This offers opportunities for the rational manipulation of these complex non-covalent interactions and their direct incorporation into the design of small-molecule catalysts and enzymes.

New insights about the hydrogen bonds formed between acetylene and hydrogen fluoride: π⋯H, C⋯H and F⋯H

A theoretical study of hydrogen bond strength and bond properties in the C₂H₂⋯(HF)-T, C₂H₂⋯2(HF)-T, C₂H₂⋯2(HF), C₂H₂⋯3(HF) and C₂H₂⋯4(HF) complexes was carried out at the B3LYP/6-311++G(d,p) theory level. In these systems, a strength competition between the π⋯H and C⋯H interactions was examined. Specifically the F⋯H hydrogen bond, its properties were studied through a comparison between the hydrogen fluoride and the higher-order complexes (trimer, tetramer and pentamer). Regarding the electronic properties, the hydrogen bond strength could not be determined by the supermolecule approach. Thus, the hydrogen bond energies were computed via NBO calculations. Additionally to NBO, the ChelpG charge calculations were used to interpret the intermolecular charge transfer. The QTAIM integrations were useful to predict the covalent character of the π⋯H, C⋯H and F⋯H hydrogen bonds. Moreover, values of hybrid orbitals (s and p) and atomic radii were also determined in order to justify the red shifts in the stretch frequencies of the HF bonds.

Stacked homodimers of substituted contorted hexabenzocoronenes and their complexes with C60 fullerene

Computations show that the tendency of contorted hexabenzocoronene (c-HBC) to form either homodimers or complexes with C₆₀ can be tuned by changing the curvature of the c-HBC via the addition of substituents.

Synergy between experimental and computational studies of aromatic stacking interactions

Aromatic stacking interactions are one of the most common types of non-covalent interactions. However, their fundamental origins and the ability to accurately predict their stability trends are still an active area of research. The study of aromatic stacking interactions has been particularly challenging. The interaction involves a delicate balance of multiple forces, and the aromatic surfaces can readily adopt different interaction geometries. Thus, the collaborative efforts of theoretical and experimental researchers have been essential to understand and build more accurate predictive models of aromatic stacking interactions.

The Cation-π Interaction in Small-Molecule Catalysis

Catalysis by small molecules (≤1000 Da, 10(-9)  m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.

Palladium-Catalyzed Enantioselective Redox-Relay Heck Arylation of 1,1-Disubstituted Homoallylic Alcohols

An enantioselective redox-relay oxidative Heck arylation of 1,1-disubstituted alkenes to construct β-stereocenters was developed using a new pyridyl-oxazoline ligand. Various 1,2-diaryl carbonyl compounds were readily obtained in moderate yield and good to excellent enantioselectivity. Additionally, analysis of the reaction outcomes using multidimensional correlations revealed that enantioselectivity is tied to specific electronic features of the 1,1-disubstituted alkenol and the extent of polarizability of the ligand.